Morfometría, Morphometrics - aragosaurus.com · TD1. Procustes analisis: ... APS program CP...
49
Morfometría, Morphometrics • Postgrado en Geología • Asignatura de Master Metodología y técnicas de campo y laboratorio en investigación paleontológica 60331 • José Ignacio Canudo y Gloria Cuenca-Bescós
Transcript of Morfometría, Morphometrics - aragosaurus.com · TD1. Procustes analisis: ... APS program CP...
Morfometriacutea Morphometrics
bull Postgrado en Geologiacutea
bull Asignatura de Master Metodologiacutea y teacutecnicas de campo y laboratorio en investigacioacuten paleontoloacutegica 60331
bull Joseacute Ignacio Canudo y Gloria Cuenca-Bescoacutes
Introduccioacuten a la Morfometriacutea
geomeacutetrica en Paleontologia
bull Profesores Joseacute Ignacio Canudo y Gloria
Cuenca-Bescoacutes
bull Web wwwaragosauruscomdocenciamaster
iquestQue es la morfometriacutea
bull La morfometriacutea es el estudio de la
variacioacuten de forma en covariacioacuten con
otras variables (Bookstein 1991 Dryden
and Mardia 1998 Adams et 04) como la
filogenia paleogeografiacutea biomecaacutenica
bull Es el estudio del cambio de forma con el
crecimiento o alometriacutea (Jolicoeur 1963
Adams et 04v) o con la evolucioacuten en una
liacutenea filogeneacutetica
iquestQue es morfometriacutea
bull Gingerich Ph 1990 Prediction of body size in mammalian species from long bone lengths and diameters Contributions from the Museum of Paleontolgoy University of Michigan 28
Utilizoacute la foacutermula Y = axb (donde x es la variable independiente la masa corporal e y es la variable dependiente la longitud o el diaacutemetro de un hueso largo)
bull Dean C Adams F James Rohlf and Dennis E Slice 2004 Geometric Morphometrics Ten Years of Progress Following the lsquoRevolutionrsquo Italian Journal of Zoology along with papers by the participants of the workshop held in Rome in January 2002 J Zool 71 5-16
Morfometriacutea La medida de la forma
iquestqueacute es la forma en biologiacutea bull Expresioacuten de los genes fenotipo
bull Expresioacuten de la adaptacioacuten y la historia filogeneacutetica adaptacioacuten ecoloacutegico-evolutiva
Lobo placentado
-Tarsos maacutes largos
-Funciones
trituradoras y cortantes
en distintas piezas
dentales
-Angulo de apertura de
boca menor
Lobo marsupial o
Tilacino
-Tarsos cortos
-Funcioacuten trituradora y
cortante en los
mismos molares
-Angulo de apertura
de boca mayor
-Mandiacutebula Proceso
angular acusado y
curvado hacia el lado
interno
Los dientes de los
mamiacuteferos los
arvicoacutelidos
bull Cuenca Bescoacutes et al 1995
Estiramos lat
La forma en postcraneal el feacutemur de los
sauroacutepodos
bull Canudo y Cuenca Bescoacutes 2004
iquestCoacutemo y por queacute estudiamos la
forma
Orientacioacuten y funciones de los
dientes
bull Arrancar
bull Retener
bull Peinar y
cuidar el
pelo
bull Descortezar
bull roer
bull Cortar
bull Moler
Toma de medidas
W
L
iquestCoacutemo estudiamos la forma
httplifebiosunysbedumorphindexhtml
Adquisicioacuten de los datos
bull Calibre
bull Datos tomados con otras herramientas y volcados a una hoja de caacutelculo (Excel Pasthellip)
bull Imaacutegenes yo datos a partir de la literatura
bull Imaacutegenes tomadas con caacutemara digital
bull Imaacutegenes tomadas desde un microscopio o lupa binocular
Espeacutecimen Longitud (mm)
1a 33
1b 45
1c 29
Landmarks digitalizados con tpsDig2
httplifebiosunysbedumorphindexhtml
Tps digit program
Free at Suny
httplifebiosunysbedumorph
Dientes complejos Arvicolinae
Iberon 25 Landmarks
1
2
4
3
5
6
7
8 9
1011
12
14
15
16
17
18
19
20
21
22
23
24
13
1
2
3
4
5
6
7
89
10
11
12
131415
16
17
18
19
20
21
22
23
24
25
25
archivo 25 iberomys landmarks
Some extreme morphologies
Allophaiomys pliocaenicus Pirro
Nord
Early Pleistocene Italy Iberomys cabrerae
Extant Spain
Allophaiomys lavocati
Sima del Elefante
Atapuerca
Early Pleistocene (older
than the Italian species
Spain
AllophLavF
N3_1r
Early
Pleistocen
e of
Granada
similar to
Atapuerca
LM =17-14 of Iberon LM =15-14 of Iberon LM =15-14 of Iberon
Landmarks de 90 especiacutemenes de
Microtus agrestis
Landmarks de 90 especiacutemenes de
Microtus agrestis
Data 90 Specimens 22 Points 2 Dimensions
All specimen superimposed by GLS method
Sum of Squared Deviations = 1101217
The groups limit is after the specimen 0
PCS and scores computed
Percentages of variance for the 8 first PCS
61395977 61395977
8155754 69551731
4681460 74233190
3352225 77585415
2619139 80204554
2500418 82704973
2235576 84940549
1789387 86729936
Multivariate regression coefficients (normalized) with 3 PCS
PCS 1 0998142
PCS 2 -0057223
PCS 3 -0020926
Regression statistic for 3 components
Rsup2= 0227471 F= 8244611 with 3 and 86 DF plt 0000070
Plot de 90 especiacutemenes de
Microtus agrestis
Distribucioacuten estratigraacutefica de los roedores del cuaternario de Gran Dolina Atapuerca Burgos
0 m
Allo
ph
aio
mys
Mim
om
ys
Ibe
rom
ys
Terr
ico
la
Ste
no
cra
niu
s
Arv
ico
la
Mic
rom
ys
Hy
str
ix
Ca
sto
r
Ma
rmo
ta
Plio
mys
Mic
rotu
s
Allo
cri
cetu
s
Ap
od
em
us
Elio
mys
TD7
TD8
TD10
TD11
TD6
TD5
TD34
TD2
TD1
Procustes analisis APS
bull Procuste fue un ladroacuten que bien descuartizaba o bien estiraba a sus viacutectimas para ajustarlas al tamantildeo de su cama de ahiacute viene la frase hecha de ldquola cama Procusterdquo que se aplica sobre todo en poliacutetica la censura o para prestaciones puacuteblicas en las que es el usuario el que debe adaptarse y no al reveacuteshellip
bull The APS package
bull The shape analysis softwares APS ApsDigit and ApsUtil are written in English and always free for the students Aps combines Procuste superposition and statistical calculations ApsDigit is used locate landmarks on digital images (JPEG Bitmap tiff GIF) ApsUtil is used to handle files (Selection of points individuals change of classification)
bull httpwwwprocustecom
APS
APS est un logiciel danalyse quantitative de la
variabiliteacute morphologique des formes vivantes La
meacutethode utiliseacutee est la superposition procruste
geacuteneacuteraliseacutee
Destineacute aux biologistes et aux cliniciens APS prend en
charge les aspects matheacutematiques et statistiques de
lanalyse de forme Lanalyse se fait en 2 temps
1 Une superposition procruste de lensemble des
speacutecimens
2 Une analyse statistique qui visualise et teste la covariance
entre dune part la conformation et dautre part un facteur
biologique comme la taille lappartenance agrave groupe la
preacutesence ou non dune pathologie
Il est conccedilu pour eacutetudier un ou deux groupes
APS Digitalizar landmarks
DigitX is designed to digitize landmarks on Jpeg or Bitmap picture
middot Select the total number of landmarks to digitize with the second
Combo-Box of the toolbar
middot Select a picture in the graphic file selector on the left
middot Click on to load the link file (optional)
middot Click on to load the consensus file (optional)
middot Digitize landmarks using the left button of the mouse
middot To cancel last landmark position by a click on undo arrow
middot When all landmarks are digitized save the file by a click on save file
APS Crear archivo
Getting started with ApsUtil
ApsUtil create a data file (dat) with specimen ordered by
addition of smaller data files Input and output files are to
APS data format with an header line (number of specimens
number
of landmarks number of dimensions) followed by landmarks
coordinates
NEW button clear all previous data and begin a new data file
ADD button add a file containing one or many specimen
MIX button add a new file to a previous one by mixing the
two file
This ordering of specimen is required before to compute
shape differences
When file is saved specimens are ordered like
specimen 1 of the 1st file
specimen 1 of the 2nd file
specimen 2 of the 1st file
APS analisis
bull New features of Version 241
bull A single specimen or all a sample can be superimposed on any reloaded
bull specimen as consensus (File -gt Reload -gt Consensus)
bull Shape vectors (eg discriminant vectors computed with other software)
bull can be reloaded for visualization (File -gt Reload -gt Pcs)
bull The shape vector must be of norm 1
bull Projections of specimens on shape vectors are automatically computed
Otros
elementos del
esqueleto
A Antarctosaurus wichmannianus B
Saltasaurus loricatus C Neuquensaurus
australis D Neuquensaurus robustus E
Lirainosaurus astibiae F Ampelosaurus atacis
G Magyarosaurus dacus H Magyarosaurus
dacus Jianu I Alamosaurus sanjuanensis J
Aegyptosaurus baharijiensis K
Opisthocoelicaudia skarzynskii
Canudo amp Cuenca Bescos 2004
wwwaragosauruscom
Aegyptosaurus Alamosaurus
Imaacutegenes literatura
Fotos ejemplares
Hacer un poliacutegono con los landmarks
Guardar la misma posicioacuten (en una liacutenea basal por ej)
APS digit
APS util
APS program CP
Opisthocoelicaudia
Resultados
APS Fecha Thu 21 Sep 2006 213918
+0200 [210906 213918 CEST]
De Info Procuste
ltinfoprocustecomgt
Para cuencagunizares
Asunto Re analyse de forme chez
les arvicolides
Cabeceras Mostrar todas las
cabeceras
Chegravere collegravegue
Voici le lien pour teacuteleacutecharger le le
setup dinstallation des 3
logiciels APS ApsDigit et ApsUtil
httpwwwprocustecomprogramsset
up_aps_allexe
Noubliez pas de citer APS dans vos
publications
Bien cordialement
Xavier Penin
Paacuteginas web recomendadas
bull httplifebiosunysbedumorph la mejor paacutegina de
morfometriacutea geomeacutetrica Contiene un listado con todos los
programas de morfometriacutea Universidad de Stony Brook NY
bull httpwwwmorphometricsorgindexhtml es la paacutegina en la
que se mantiene la lista de email morphmet Es la base de la
organizacioacuten de la morfometriacutea en Suny
bull httpwwwflywingsorgukindexhtm iquestporqueacute hay variacioacuten
morfoloacutegica Universidad de Manchester UK
bull httpwwwprocustecomindexhtml anaacutelisis de la forma con
Procruste Aps Xavier Penin Universidad de Paris V
bull Shapehellipy otros ver la paacutegina de Suny
Las ldquoseries TPSrdquo Thin-plate spline
(laacuteminas finas de grosor uniforme)
tpsDIG2
Data acquisition
bull Digitize landmarks amp outlines from image files scanner or video Windows TpsDig is a Windows (95 through XP) program for digitizing landmarks and outlines for geometric morphometric analyses Includes simple image enhancement operations scale factors image brightness profile and support for AVI and MOV files Output is in the TPS file format used by the tps series of programs The TPS file includes the name of the image file for each specimen so that landmarks can always be visualized on the image Since output files are ASCII they can be converted to formats for other software Users should note that the tpsUtil program is useful for both the preparation of the input files to tpsDig as well as for some useful conversions afterwards The program also computes areas of enclosed regions perimeters and linear distances The tpsDig2 link at the left is for the new 205 version
bull Execute the downloaded file to install the program By F James Rohlf
Las ldquoseries TPSrdquo
ordenar los archivos digitalizados
TPS util
bull tps file utility program Windows At present it can randomly scramble the order of specimens in a tps file to minimize bias in digitizing landmark locations restore the original order (eg before statistical analyses are performed) create an empty TPS file from a directory with image files add keywords and values to the variables field of a TPS file combine TPS files into a single TPS file deletereorder landmarks remove outlines from a TPS file and convert TPS and NTS files to NTS M or CSV files It can also split an NTS file into several matrices Graphic editors are included for drawing link and sliders files Unbending a deformed specimen Converting outline and curves points to landmarks
bull Other operations can be added - let me know what you need Execute the TPSUTILW32EXE file to install the program By F James Rohlf Version 138
tpsTree
bull Fit and visualize thin-plate splines on trees Windows Performs a least-squares orthogonal generalized Procrustes analysis to obtain a reference and then estimates the splines for each group (internal node) on a tree Both ultrametric (eg WPGMA and UPGMA trees) and additive trees (using squared change parsimony to estimate the shapes of the HTUs) are supported The estimated shapes can be visualized with estimated images in the background (see the tpsSuper program) The file expands into a Windows setup program and associated files By F James Rohlf Version 118 File containing HTU coordinates and HTU images to demo that feature The older and more limited 16 bit Windows version is still available
tpsRegr
bull Multivariate multiple regression of shape onto independent variables Windows performs a multivariate multiple regression of shape (as captured by partial warp scores and the uniform shape component) onto one or more independent variables By appropriate setting up of independent variables this program can perform various types of MANOVA and MANCOVA Can be used to study allometry By F James Rohlf Version 131
tpsSplin
bull Thin-plate spline Windows Program to
compare pairs of specimens by displaying
a Darcy Thompson style transformation
grid based on a thin-plate spline Several
options are given for sliding
semilandmarks The tpssplnwexe file
expands into a Windows setup program
that will be run automatically By F James
Rohlf Version 120
tpsRelw el anaacutelisis de la
deformacioacuten relativa bull Relative warps analysis Windows Performs a
relative warp (deformacioacuten) analysis This corresponds to a principal components analysis of variation in a sample (relative to bending energy if the alpha parameter is not equal to zero) Displays a plot of relative warp scores and a visualization window that displays the estimated shape for arbitrary points in the ordination Also displays partial warp scores and their visualizations Allows fitting of semilandmark points along curves Version 144 By F James Rohlf
tpsPLS
bull Partial least-squares analysis for shapes Windows Used to explore the covariance between a set of variables and variation in shape or between two shapes It performs a two-block partial least-squares analysis It differs from regression in that both variables and shape are considered equally (one is not considered to be a set of independent variables measured without error) Its use is described in Rohlf and Corti (2000 Systematic Biology 49740-753) By F James Rohlf Version 118
tpsSmall
bull Test for small variation in shape Windows Use to test whether the variation in shape among a set of specimens is too large and thus statistical methods based on the tangent space approximation (eg thin-plate spline methods) cannot be used The program can process both 2D and 3D data files Output files include consensus and aligned specimens By F James Rohlf Version 120
tpsPower
bull Estimate statistical power for comparing shapes Windows Program for estimating statistical power for comparing the mean shapes of two populations Provides methods based on several different approaches Can be used for planning morphometric studies as well as to compare power using different approaches Version 104 By F James Rohlf
Morpheus et al bull Morpheus et al is a software package that will provide a
comprehensive cross-platform environment for morphometric data analysis It is available in graphical and command-line versions for a number of operating systems (see below) More information about new features and previous changes can be found in the release notes
httplifebiosunysbedumorphmorpheus
Multivariate analysis
bull PAST is a free easy-to-use data analysis package aimed at paleontology Windows 95+ Multivariate statistical methods include Principal Components (with Minimal Spanning Tree) Principal Coordinates (ten distance measures) Non-metric Multidimensional Scaling (ten distance measures) Detrended Correspondence Analysis Cluster analysis (three algorithms 11 distance measures) k-means clustering seriation discriminant analysis one-way MANOVA Hotellings t-squared Boxs M Canonical Variates Analysis Also includes Fourier shape analysis thin-plate splines parsimony and time series analysis among others Oslashyvind Hammer University of Oslo
Analysis of outlines
bull Shape Elliptic Fourier WINDOWS Extracts the contour shape from a full color bitmap image delineates the contour shape with the elliptic Fourier descriptors and performs a principal component analysis for summarizing the shape information By Hiroyoshi Iwata For more information see Shape home page tutorial or manual
bull Iwata H and Y Ukai (2002) SHAPE A computer program package for quantitative evaluation of biological shapes based on elliptic Fourier descriptors Journal of Heredity 93 384-385
Eigenshape analysis
bull httpwwwnhmacukhosted_sitespaleonetftpftphtml
bull This archive contains a series of programs designed to perform an eigenshape analysis on xy coordinate data from object outlines Routines include xy -gt phi() transformation phi() -gt xy transformation eigenshape analysis and projection of objects into the eigenshape space Two completely worked example analyses and a users guide are also provided El autor es Norman McLeod del BMNH de Londres
Graphical representation of the four-step morphometric protocol A Quantify raw data
(landmarks recorded on body of cichlid fish) B Remove non-shape variation (landmarks of 412
specimens before and after GPA) C statistical analysis (CVA) and graphical presentation of
results Deformation grids for mean specimen for (right) Eretmodus cyanostictus and (left)
Spathodus erythrodon (magnified by 3X to emphasize shape differences) Data from Ruumlber and
Adams 2001 En Adams Rolhf Slice 2002
Introduccioacuten a la Morfometriacutea
geomeacutetrica en Paleontologia
bull Profesores Joseacute Ignacio Canudo y Gloria
Cuenca-Bescoacutes
bull Web wwwaragosauruscomdocenciamaster
iquestQue es la morfometriacutea
bull La morfometriacutea es el estudio de la
variacioacuten de forma en covariacioacuten con
otras variables (Bookstein 1991 Dryden
and Mardia 1998 Adams et 04) como la
filogenia paleogeografiacutea biomecaacutenica
bull Es el estudio del cambio de forma con el
crecimiento o alometriacutea (Jolicoeur 1963
Adams et 04v) o con la evolucioacuten en una
liacutenea filogeneacutetica
iquestQue es morfometriacutea
bull Gingerich Ph 1990 Prediction of body size in mammalian species from long bone lengths and diameters Contributions from the Museum of Paleontolgoy University of Michigan 28
Utilizoacute la foacutermula Y = axb (donde x es la variable independiente la masa corporal e y es la variable dependiente la longitud o el diaacutemetro de un hueso largo)
bull Dean C Adams F James Rohlf and Dennis E Slice 2004 Geometric Morphometrics Ten Years of Progress Following the lsquoRevolutionrsquo Italian Journal of Zoology along with papers by the participants of the workshop held in Rome in January 2002 J Zool 71 5-16
Morfometriacutea La medida de la forma
iquestqueacute es la forma en biologiacutea bull Expresioacuten de los genes fenotipo
bull Expresioacuten de la adaptacioacuten y la historia filogeneacutetica adaptacioacuten ecoloacutegico-evolutiva
Lobo placentado
-Tarsos maacutes largos
-Funciones
trituradoras y cortantes
en distintas piezas
dentales
-Angulo de apertura de
boca menor
Lobo marsupial o
Tilacino
-Tarsos cortos
-Funcioacuten trituradora y
cortante en los
mismos molares
-Angulo de apertura
de boca mayor
-Mandiacutebula Proceso
angular acusado y
curvado hacia el lado
interno
Los dientes de los
mamiacuteferos los
arvicoacutelidos
bull Cuenca Bescoacutes et al 1995
Estiramos lat
La forma en postcraneal el feacutemur de los
sauroacutepodos
bull Canudo y Cuenca Bescoacutes 2004
iquestCoacutemo y por queacute estudiamos la
forma
Orientacioacuten y funciones de los
dientes
bull Arrancar
bull Retener
bull Peinar y
cuidar el
pelo
bull Descortezar
bull roer
bull Cortar
bull Moler
Toma de medidas
W
L
iquestCoacutemo estudiamos la forma
httplifebiosunysbedumorphindexhtml
Adquisicioacuten de los datos
bull Calibre
bull Datos tomados con otras herramientas y volcados a una hoja de caacutelculo (Excel Pasthellip)
bull Imaacutegenes yo datos a partir de la literatura
bull Imaacutegenes tomadas con caacutemara digital
bull Imaacutegenes tomadas desde un microscopio o lupa binocular
Espeacutecimen Longitud (mm)
1a 33
1b 45
1c 29
Landmarks digitalizados con tpsDig2
httplifebiosunysbedumorphindexhtml
Tps digit program
Free at Suny
httplifebiosunysbedumorph
Dientes complejos Arvicolinae
Iberon 25 Landmarks
1
2
4
3
5
6
7
8 9
1011
12
14
15
16
17
18
19
20
21
22
23
24
13
1
2
3
4
5
6
7
89
10
11
12
131415
16
17
18
19
20
21
22
23
24
25
25
archivo 25 iberomys landmarks
Some extreme morphologies
Allophaiomys pliocaenicus Pirro
Nord
Early Pleistocene Italy Iberomys cabrerae
Extant Spain
Allophaiomys lavocati
Sima del Elefante
Atapuerca
Early Pleistocene (older
than the Italian species
Spain
AllophLavF
N3_1r
Early
Pleistocen
e of
Granada
similar to
Atapuerca
LM =17-14 of Iberon LM =15-14 of Iberon LM =15-14 of Iberon
Landmarks de 90 especiacutemenes de
Microtus agrestis
Landmarks de 90 especiacutemenes de
Microtus agrestis
Data 90 Specimens 22 Points 2 Dimensions
All specimen superimposed by GLS method
Sum of Squared Deviations = 1101217
The groups limit is after the specimen 0
PCS and scores computed
Percentages of variance for the 8 first PCS
61395977 61395977
8155754 69551731
4681460 74233190
3352225 77585415
2619139 80204554
2500418 82704973
2235576 84940549
1789387 86729936
Multivariate regression coefficients (normalized) with 3 PCS
PCS 1 0998142
PCS 2 -0057223
PCS 3 -0020926
Regression statistic for 3 components
Rsup2= 0227471 F= 8244611 with 3 and 86 DF plt 0000070
Plot de 90 especiacutemenes de
Microtus agrestis
Distribucioacuten estratigraacutefica de los roedores del cuaternario de Gran Dolina Atapuerca Burgos
0 m
Allo
ph
aio
mys
Mim
om
ys
Ibe
rom
ys
Terr
ico
la
Ste
no
cra
niu
s
Arv
ico
la
Mic
rom
ys
Hy
str
ix
Ca
sto
r
Ma
rmo
ta
Plio
mys
Mic
rotu
s
Allo
cri
cetu
s
Ap
od
em
us
Elio
mys
TD7
TD8
TD10
TD11
TD6
TD5
TD34
TD2
TD1
Procustes analisis APS
bull Procuste fue un ladroacuten que bien descuartizaba o bien estiraba a sus viacutectimas para ajustarlas al tamantildeo de su cama de ahiacute viene la frase hecha de ldquola cama Procusterdquo que se aplica sobre todo en poliacutetica la censura o para prestaciones puacuteblicas en las que es el usuario el que debe adaptarse y no al reveacuteshellip
bull The APS package
bull The shape analysis softwares APS ApsDigit and ApsUtil are written in English and always free for the students Aps combines Procuste superposition and statistical calculations ApsDigit is used locate landmarks on digital images (JPEG Bitmap tiff GIF) ApsUtil is used to handle files (Selection of points individuals change of classification)
bull httpwwwprocustecom
APS
APS est un logiciel danalyse quantitative de la
variabiliteacute morphologique des formes vivantes La
meacutethode utiliseacutee est la superposition procruste
geacuteneacuteraliseacutee
Destineacute aux biologistes et aux cliniciens APS prend en
charge les aspects matheacutematiques et statistiques de
lanalyse de forme Lanalyse se fait en 2 temps
1 Une superposition procruste de lensemble des
speacutecimens
2 Une analyse statistique qui visualise et teste la covariance
entre dune part la conformation et dautre part un facteur
biologique comme la taille lappartenance agrave groupe la
preacutesence ou non dune pathologie
Il est conccedilu pour eacutetudier un ou deux groupes
APS Digitalizar landmarks
DigitX is designed to digitize landmarks on Jpeg or Bitmap picture
middot Select the total number of landmarks to digitize with the second
Combo-Box of the toolbar
middot Select a picture in the graphic file selector on the left
middot Click on to load the link file (optional)
middot Click on to load the consensus file (optional)
middot Digitize landmarks using the left button of the mouse
middot To cancel last landmark position by a click on undo arrow
middot When all landmarks are digitized save the file by a click on save file
APS Crear archivo
Getting started with ApsUtil
ApsUtil create a data file (dat) with specimen ordered by
addition of smaller data files Input and output files are to
APS data format with an header line (number of specimens
number
of landmarks number of dimensions) followed by landmarks
coordinates
NEW button clear all previous data and begin a new data file
ADD button add a file containing one or many specimen
MIX button add a new file to a previous one by mixing the
two file
This ordering of specimen is required before to compute
shape differences
When file is saved specimens are ordered like
specimen 1 of the 1st file
specimen 1 of the 2nd file
specimen 2 of the 1st file
APS analisis
bull New features of Version 241
bull A single specimen or all a sample can be superimposed on any reloaded
bull specimen as consensus (File -gt Reload -gt Consensus)
bull Shape vectors (eg discriminant vectors computed with other software)
bull can be reloaded for visualization (File -gt Reload -gt Pcs)
bull The shape vector must be of norm 1
bull Projections of specimens on shape vectors are automatically computed
Otros
elementos del
esqueleto
A Antarctosaurus wichmannianus B
Saltasaurus loricatus C Neuquensaurus
australis D Neuquensaurus robustus E
Lirainosaurus astibiae F Ampelosaurus atacis
G Magyarosaurus dacus H Magyarosaurus
dacus Jianu I Alamosaurus sanjuanensis J
Aegyptosaurus baharijiensis K
Opisthocoelicaudia skarzynskii
Canudo amp Cuenca Bescos 2004
wwwaragosauruscom
Aegyptosaurus Alamosaurus
Imaacutegenes literatura
Fotos ejemplares
Hacer un poliacutegono con los landmarks
Guardar la misma posicioacuten (en una liacutenea basal por ej)
APS digit
APS util
APS program CP
Opisthocoelicaudia
Resultados
APS Fecha Thu 21 Sep 2006 213918
+0200 [210906 213918 CEST]
De Info Procuste
ltinfoprocustecomgt
Para cuencagunizares
Asunto Re analyse de forme chez
les arvicolides
Cabeceras Mostrar todas las
cabeceras
Chegravere collegravegue
Voici le lien pour teacuteleacutecharger le le
setup dinstallation des 3
logiciels APS ApsDigit et ApsUtil
httpwwwprocustecomprogramsset
up_aps_allexe
Noubliez pas de citer APS dans vos
publications
Bien cordialement
Xavier Penin
Paacuteginas web recomendadas
bull httplifebiosunysbedumorph la mejor paacutegina de
morfometriacutea geomeacutetrica Contiene un listado con todos los
programas de morfometriacutea Universidad de Stony Brook NY
bull httpwwwmorphometricsorgindexhtml es la paacutegina en la
que se mantiene la lista de email morphmet Es la base de la
organizacioacuten de la morfometriacutea en Suny
bull httpwwwflywingsorgukindexhtm iquestporqueacute hay variacioacuten
morfoloacutegica Universidad de Manchester UK
bull httpwwwprocustecomindexhtml anaacutelisis de la forma con
Procruste Aps Xavier Penin Universidad de Paris V
bull Shapehellipy otros ver la paacutegina de Suny
Las ldquoseries TPSrdquo Thin-plate spline
(laacuteminas finas de grosor uniforme)
tpsDIG2
Data acquisition
bull Digitize landmarks amp outlines from image files scanner or video Windows TpsDig is a Windows (95 through XP) program for digitizing landmarks and outlines for geometric morphometric analyses Includes simple image enhancement operations scale factors image brightness profile and support for AVI and MOV files Output is in the TPS file format used by the tps series of programs The TPS file includes the name of the image file for each specimen so that landmarks can always be visualized on the image Since output files are ASCII they can be converted to formats for other software Users should note that the tpsUtil program is useful for both the preparation of the input files to tpsDig as well as for some useful conversions afterwards The program also computes areas of enclosed regions perimeters and linear distances The tpsDig2 link at the left is for the new 205 version
bull Execute the downloaded file to install the program By F James Rohlf
Las ldquoseries TPSrdquo
ordenar los archivos digitalizados
TPS util
bull tps file utility program Windows At present it can randomly scramble the order of specimens in a tps file to minimize bias in digitizing landmark locations restore the original order (eg before statistical analyses are performed) create an empty TPS file from a directory with image files add keywords and values to the variables field of a TPS file combine TPS files into a single TPS file deletereorder landmarks remove outlines from a TPS file and convert TPS and NTS files to NTS M or CSV files It can also split an NTS file into several matrices Graphic editors are included for drawing link and sliders files Unbending a deformed specimen Converting outline and curves points to landmarks
bull Other operations can be added - let me know what you need Execute the TPSUTILW32EXE file to install the program By F James Rohlf Version 138
tpsTree
bull Fit and visualize thin-plate splines on trees Windows Performs a least-squares orthogonal generalized Procrustes analysis to obtain a reference and then estimates the splines for each group (internal node) on a tree Both ultrametric (eg WPGMA and UPGMA trees) and additive trees (using squared change parsimony to estimate the shapes of the HTUs) are supported The estimated shapes can be visualized with estimated images in the background (see the tpsSuper program) The file expands into a Windows setup program and associated files By F James Rohlf Version 118 File containing HTU coordinates and HTU images to demo that feature The older and more limited 16 bit Windows version is still available
tpsRegr
bull Multivariate multiple regression of shape onto independent variables Windows performs a multivariate multiple regression of shape (as captured by partial warp scores and the uniform shape component) onto one or more independent variables By appropriate setting up of independent variables this program can perform various types of MANOVA and MANCOVA Can be used to study allometry By F James Rohlf Version 131
tpsSplin
bull Thin-plate spline Windows Program to
compare pairs of specimens by displaying
a Darcy Thompson style transformation
grid based on a thin-plate spline Several
options are given for sliding
semilandmarks The tpssplnwexe file
expands into a Windows setup program
that will be run automatically By F James
Rohlf Version 120
tpsRelw el anaacutelisis de la
deformacioacuten relativa bull Relative warps analysis Windows Performs a
relative warp (deformacioacuten) analysis This corresponds to a principal components analysis of variation in a sample (relative to bending energy if the alpha parameter is not equal to zero) Displays a plot of relative warp scores and a visualization window that displays the estimated shape for arbitrary points in the ordination Also displays partial warp scores and their visualizations Allows fitting of semilandmark points along curves Version 144 By F James Rohlf
tpsPLS
bull Partial least-squares analysis for shapes Windows Used to explore the covariance between a set of variables and variation in shape or between two shapes It performs a two-block partial least-squares analysis It differs from regression in that both variables and shape are considered equally (one is not considered to be a set of independent variables measured without error) Its use is described in Rohlf and Corti (2000 Systematic Biology 49740-753) By F James Rohlf Version 118
tpsSmall
bull Test for small variation in shape Windows Use to test whether the variation in shape among a set of specimens is too large and thus statistical methods based on the tangent space approximation (eg thin-plate spline methods) cannot be used The program can process both 2D and 3D data files Output files include consensus and aligned specimens By F James Rohlf Version 120
tpsPower
bull Estimate statistical power for comparing shapes Windows Program for estimating statistical power for comparing the mean shapes of two populations Provides methods based on several different approaches Can be used for planning morphometric studies as well as to compare power using different approaches Version 104 By F James Rohlf
Morpheus et al bull Morpheus et al is a software package that will provide a
comprehensive cross-platform environment for morphometric data analysis It is available in graphical and command-line versions for a number of operating systems (see below) More information about new features and previous changes can be found in the release notes
httplifebiosunysbedumorphmorpheus
Multivariate analysis
bull PAST is a free easy-to-use data analysis package aimed at paleontology Windows 95+ Multivariate statistical methods include Principal Components (with Minimal Spanning Tree) Principal Coordinates (ten distance measures) Non-metric Multidimensional Scaling (ten distance measures) Detrended Correspondence Analysis Cluster analysis (three algorithms 11 distance measures) k-means clustering seriation discriminant analysis one-way MANOVA Hotellings t-squared Boxs M Canonical Variates Analysis Also includes Fourier shape analysis thin-plate splines parsimony and time series analysis among others Oslashyvind Hammer University of Oslo
Analysis of outlines
bull Shape Elliptic Fourier WINDOWS Extracts the contour shape from a full color bitmap image delineates the contour shape with the elliptic Fourier descriptors and performs a principal component analysis for summarizing the shape information By Hiroyoshi Iwata For more information see Shape home page tutorial or manual
bull Iwata H and Y Ukai (2002) SHAPE A computer program package for quantitative evaluation of biological shapes based on elliptic Fourier descriptors Journal of Heredity 93 384-385
Eigenshape analysis
bull httpwwwnhmacukhosted_sitespaleonetftpftphtml
bull This archive contains a series of programs designed to perform an eigenshape analysis on xy coordinate data from object outlines Routines include xy -gt phi() transformation phi() -gt xy transformation eigenshape analysis and projection of objects into the eigenshape space Two completely worked example analyses and a users guide are also provided El autor es Norman McLeod del BMNH de Londres
Graphical representation of the four-step morphometric protocol A Quantify raw data
(landmarks recorded on body of cichlid fish) B Remove non-shape variation (landmarks of 412
specimens before and after GPA) C statistical analysis (CVA) and graphical presentation of
results Deformation grids for mean specimen for (right) Eretmodus cyanostictus and (left)
Spathodus erythrodon (magnified by 3X to emphasize shape differences) Data from Ruumlber and
Adams 2001 En Adams Rolhf Slice 2002
iquestQue es la morfometriacutea
bull La morfometriacutea es el estudio de la
variacioacuten de forma en covariacioacuten con
otras variables (Bookstein 1991 Dryden
and Mardia 1998 Adams et 04) como la
filogenia paleogeografiacutea biomecaacutenica
bull Es el estudio del cambio de forma con el
crecimiento o alometriacutea (Jolicoeur 1963
Adams et 04v) o con la evolucioacuten en una
liacutenea filogeneacutetica
iquestQue es morfometriacutea
bull Gingerich Ph 1990 Prediction of body size in mammalian species from long bone lengths and diameters Contributions from the Museum of Paleontolgoy University of Michigan 28
Utilizoacute la foacutermula Y = axb (donde x es la variable independiente la masa corporal e y es la variable dependiente la longitud o el diaacutemetro de un hueso largo)
bull Dean C Adams F James Rohlf and Dennis E Slice 2004 Geometric Morphometrics Ten Years of Progress Following the lsquoRevolutionrsquo Italian Journal of Zoology along with papers by the participants of the workshop held in Rome in January 2002 J Zool 71 5-16
Morfometriacutea La medida de la forma
iquestqueacute es la forma en biologiacutea bull Expresioacuten de los genes fenotipo
bull Expresioacuten de la adaptacioacuten y la historia filogeneacutetica adaptacioacuten ecoloacutegico-evolutiva
Lobo placentado
-Tarsos maacutes largos
-Funciones
trituradoras y cortantes
en distintas piezas
dentales
-Angulo de apertura de
boca menor
Lobo marsupial o
Tilacino
-Tarsos cortos
-Funcioacuten trituradora y
cortante en los
mismos molares
-Angulo de apertura
de boca mayor
-Mandiacutebula Proceso
angular acusado y
curvado hacia el lado
interno
Los dientes de los
mamiacuteferos los
arvicoacutelidos
bull Cuenca Bescoacutes et al 1995
Estiramos lat
La forma en postcraneal el feacutemur de los
sauroacutepodos
bull Canudo y Cuenca Bescoacutes 2004
iquestCoacutemo y por queacute estudiamos la
forma
Orientacioacuten y funciones de los
dientes
bull Arrancar
bull Retener
bull Peinar y
cuidar el
pelo
bull Descortezar
bull roer
bull Cortar
bull Moler
Toma de medidas
W
L
iquestCoacutemo estudiamos la forma
httplifebiosunysbedumorphindexhtml
Adquisicioacuten de los datos
bull Calibre
bull Datos tomados con otras herramientas y volcados a una hoja de caacutelculo (Excel Pasthellip)
bull Imaacutegenes yo datos a partir de la literatura
bull Imaacutegenes tomadas con caacutemara digital
bull Imaacutegenes tomadas desde un microscopio o lupa binocular
Espeacutecimen Longitud (mm)
1a 33
1b 45
1c 29
Landmarks digitalizados con tpsDig2
httplifebiosunysbedumorphindexhtml
Tps digit program
Free at Suny
httplifebiosunysbedumorph
Dientes complejos Arvicolinae
Iberon 25 Landmarks
1
2
4
3
5
6
7
8 9
1011
12
14
15
16
17
18
19
20
21
22
23
24
13
1
2
3
4
5
6
7
89
10
11
12
131415
16
17
18
19
20
21
22
23
24
25
25
archivo 25 iberomys landmarks
Some extreme morphologies
Allophaiomys pliocaenicus Pirro
Nord
Early Pleistocene Italy Iberomys cabrerae
Extant Spain
Allophaiomys lavocati
Sima del Elefante
Atapuerca
Early Pleistocene (older
than the Italian species
Spain
AllophLavF
N3_1r
Early
Pleistocen
e of
Granada
similar to
Atapuerca
LM =17-14 of Iberon LM =15-14 of Iberon LM =15-14 of Iberon
Landmarks de 90 especiacutemenes de
Microtus agrestis
Landmarks de 90 especiacutemenes de
Microtus agrestis
Data 90 Specimens 22 Points 2 Dimensions
All specimen superimposed by GLS method
Sum of Squared Deviations = 1101217
The groups limit is after the specimen 0
PCS and scores computed
Percentages of variance for the 8 first PCS
61395977 61395977
8155754 69551731
4681460 74233190
3352225 77585415
2619139 80204554
2500418 82704973
2235576 84940549
1789387 86729936
Multivariate regression coefficients (normalized) with 3 PCS
PCS 1 0998142
PCS 2 -0057223
PCS 3 -0020926
Regression statistic for 3 components
Rsup2= 0227471 F= 8244611 with 3 and 86 DF plt 0000070
Plot de 90 especiacutemenes de
Microtus agrestis
Distribucioacuten estratigraacutefica de los roedores del cuaternario de Gran Dolina Atapuerca Burgos
0 m
Allo
ph
aio
mys
Mim
om
ys
Ibe
rom
ys
Terr
ico
la
Ste
no
cra
niu
s
Arv
ico
la
Mic
rom
ys
Hy
str
ix
Ca
sto
r
Ma
rmo
ta
Plio
mys
Mic
rotu
s
Allo
cri
cetu
s
Ap
od
em
us
Elio
mys
TD7
TD8
TD10
TD11
TD6
TD5
TD34
TD2
TD1
Procustes analisis APS
bull Procuste fue un ladroacuten que bien descuartizaba o bien estiraba a sus viacutectimas para ajustarlas al tamantildeo de su cama de ahiacute viene la frase hecha de ldquola cama Procusterdquo que se aplica sobre todo en poliacutetica la censura o para prestaciones puacuteblicas en las que es el usuario el que debe adaptarse y no al reveacuteshellip
bull The APS package
bull The shape analysis softwares APS ApsDigit and ApsUtil are written in English and always free for the students Aps combines Procuste superposition and statistical calculations ApsDigit is used locate landmarks on digital images (JPEG Bitmap tiff GIF) ApsUtil is used to handle files (Selection of points individuals change of classification)
bull httpwwwprocustecom
APS
APS est un logiciel danalyse quantitative de la
variabiliteacute morphologique des formes vivantes La
meacutethode utiliseacutee est la superposition procruste
geacuteneacuteraliseacutee
Destineacute aux biologistes et aux cliniciens APS prend en
charge les aspects matheacutematiques et statistiques de
lanalyse de forme Lanalyse se fait en 2 temps
1 Une superposition procruste de lensemble des
speacutecimens
2 Une analyse statistique qui visualise et teste la covariance
entre dune part la conformation et dautre part un facteur
biologique comme la taille lappartenance agrave groupe la
preacutesence ou non dune pathologie
Il est conccedilu pour eacutetudier un ou deux groupes
APS Digitalizar landmarks
DigitX is designed to digitize landmarks on Jpeg or Bitmap picture
middot Select the total number of landmarks to digitize with the second
Combo-Box of the toolbar
middot Select a picture in the graphic file selector on the left
middot Click on to load the link file (optional)
middot Click on to load the consensus file (optional)
middot Digitize landmarks using the left button of the mouse
middot To cancel last landmark position by a click on undo arrow
middot When all landmarks are digitized save the file by a click on save file
APS Crear archivo
Getting started with ApsUtil
ApsUtil create a data file (dat) with specimen ordered by
addition of smaller data files Input and output files are to
APS data format with an header line (number of specimens
number
of landmarks number of dimensions) followed by landmarks
coordinates
NEW button clear all previous data and begin a new data file
ADD button add a file containing one or many specimen
MIX button add a new file to a previous one by mixing the
two file
This ordering of specimen is required before to compute
shape differences
When file is saved specimens are ordered like
specimen 1 of the 1st file
specimen 1 of the 2nd file
specimen 2 of the 1st file
APS analisis
bull New features of Version 241
bull A single specimen or all a sample can be superimposed on any reloaded
bull specimen as consensus (File -gt Reload -gt Consensus)
bull Shape vectors (eg discriminant vectors computed with other software)
bull can be reloaded for visualization (File -gt Reload -gt Pcs)
bull The shape vector must be of norm 1
bull Projections of specimens on shape vectors are automatically computed
Otros
elementos del
esqueleto
A Antarctosaurus wichmannianus B
Saltasaurus loricatus C Neuquensaurus
australis D Neuquensaurus robustus E
Lirainosaurus astibiae F Ampelosaurus atacis
G Magyarosaurus dacus H Magyarosaurus
dacus Jianu I Alamosaurus sanjuanensis J
Aegyptosaurus baharijiensis K
Opisthocoelicaudia skarzynskii
Canudo amp Cuenca Bescos 2004
wwwaragosauruscom
Aegyptosaurus Alamosaurus
Imaacutegenes literatura
Fotos ejemplares
Hacer un poliacutegono con los landmarks
Guardar la misma posicioacuten (en una liacutenea basal por ej)
APS digit
APS util
APS program CP
Opisthocoelicaudia
Resultados
APS Fecha Thu 21 Sep 2006 213918
+0200 [210906 213918 CEST]
De Info Procuste
ltinfoprocustecomgt
Para cuencagunizares
Asunto Re analyse de forme chez
les arvicolides
Cabeceras Mostrar todas las
cabeceras
Chegravere collegravegue
Voici le lien pour teacuteleacutecharger le le
setup dinstallation des 3
logiciels APS ApsDigit et ApsUtil
httpwwwprocustecomprogramsset
up_aps_allexe
Noubliez pas de citer APS dans vos
publications
Bien cordialement
Xavier Penin
Paacuteginas web recomendadas
bull httplifebiosunysbedumorph la mejor paacutegina de
morfometriacutea geomeacutetrica Contiene un listado con todos los
programas de morfometriacutea Universidad de Stony Brook NY
bull httpwwwmorphometricsorgindexhtml es la paacutegina en la
que se mantiene la lista de email morphmet Es la base de la
organizacioacuten de la morfometriacutea en Suny
bull httpwwwflywingsorgukindexhtm iquestporqueacute hay variacioacuten
morfoloacutegica Universidad de Manchester UK
bull httpwwwprocustecomindexhtml anaacutelisis de la forma con
Procruste Aps Xavier Penin Universidad de Paris V
bull Shapehellipy otros ver la paacutegina de Suny
Las ldquoseries TPSrdquo Thin-plate spline
(laacuteminas finas de grosor uniforme)
tpsDIG2
Data acquisition
bull Digitize landmarks amp outlines from image files scanner or video Windows TpsDig is a Windows (95 through XP) program for digitizing landmarks and outlines for geometric morphometric analyses Includes simple image enhancement operations scale factors image brightness profile and support for AVI and MOV files Output is in the TPS file format used by the tps series of programs The TPS file includes the name of the image file for each specimen so that landmarks can always be visualized on the image Since output files are ASCII they can be converted to formats for other software Users should note that the tpsUtil program is useful for both the preparation of the input files to tpsDig as well as for some useful conversions afterwards The program also computes areas of enclosed regions perimeters and linear distances The tpsDig2 link at the left is for the new 205 version
bull Execute the downloaded file to install the program By F James Rohlf
Las ldquoseries TPSrdquo
ordenar los archivos digitalizados
TPS util
bull tps file utility program Windows At present it can randomly scramble the order of specimens in a tps file to minimize bias in digitizing landmark locations restore the original order (eg before statistical analyses are performed) create an empty TPS file from a directory with image files add keywords and values to the variables field of a TPS file combine TPS files into a single TPS file deletereorder landmarks remove outlines from a TPS file and convert TPS and NTS files to NTS M or CSV files It can also split an NTS file into several matrices Graphic editors are included for drawing link and sliders files Unbending a deformed specimen Converting outline and curves points to landmarks
bull Other operations can be added - let me know what you need Execute the TPSUTILW32EXE file to install the program By F James Rohlf Version 138
tpsTree
bull Fit and visualize thin-plate splines on trees Windows Performs a least-squares orthogonal generalized Procrustes analysis to obtain a reference and then estimates the splines for each group (internal node) on a tree Both ultrametric (eg WPGMA and UPGMA trees) and additive trees (using squared change parsimony to estimate the shapes of the HTUs) are supported The estimated shapes can be visualized with estimated images in the background (see the tpsSuper program) The file expands into a Windows setup program and associated files By F James Rohlf Version 118 File containing HTU coordinates and HTU images to demo that feature The older and more limited 16 bit Windows version is still available
tpsRegr
bull Multivariate multiple regression of shape onto independent variables Windows performs a multivariate multiple regression of shape (as captured by partial warp scores and the uniform shape component) onto one or more independent variables By appropriate setting up of independent variables this program can perform various types of MANOVA and MANCOVA Can be used to study allometry By F James Rohlf Version 131
tpsSplin
bull Thin-plate spline Windows Program to
compare pairs of specimens by displaying
a Darcy Thompson style transformation
grid based on a thin-plate spline Several
options are given for sliding
semilandmarks The tpssplnwexe file
expands into a Windows setup program
that will be run automatically By F James
Rohlf Version 120
tpsRelw el anaacutelisis de la
deformacioacuten relativa bull Relative warps analysis Windows Performs a
relative warp (deformacioacuten) analysis This corresponds to a principal components analysis of variation in a sample (relative to bending energy if the alpha parameter is not equal to zero) Displays a plot of relative warp scores and a visualization window that displays the estimated shape for arbitrary points in the ordination Also displays partial warp scores and their visualizations Allows fitting of semilandmark points along curves Version 144 By F James Rohlf
tpsPLS
bull Partial least-squares analysis for shapes Windows Used to explore the covariance between a set of variables and variation in shape or between two shapes It performs a two-block partial least-squares analysis It differs from regression in that both variables and shape are considered equally (one is not considered to be a set of independent variables measured without error) Its use is described in Rohlf and Corti (2000 Systematic Biology 49740-753) By F James Rohlf Version 118
tpsSmall
bull Test for small variation in shape Windows Use to test whether the variation in shape among a set of specimens is too large and thus statistical methods based on the tangent space approximation (eg thin-plate spline methods) cannot be used The program can process both 2D and 3D data files Output files include consensus and aligned specimens By F James Rohlf Version 120
tpsPower
bull Estimate statistical power for comparing shapes Windows Program for estimating statistical power for comparing the mean shapes of two populations Provides methods based on several different approaches Can be used for planning morphometric studies as well as to compare power using different approaches Version 104 By F James Rohlf
Morpheus et al bull Morpheus et al is a software package that will provide a
comprehensive cross-platform environment for morphometric data analysis It is available in graphical and command-line versions for a number of operating systems (see below) More information about new features and previous changes can be found in the release notes
httplifebiosunysbedumorphmorpheus
Multivariate analysis
bull PAST is a free easy-to-use data analysis package aimed at paleontology Windows 95+ Multivariate statistical methods include Principal Components (with Minimal Spanning Tree) Principal Coordinates (ten distance measures) Non-metric Multidimensional Scaling (ten distance measures) Detrended Correspondence Analysis Cluster analysis (three algorithms 11 distance measures) k-means clustering seriation discriminant analysis one-way MANOVA Hotellings t-squared Boxs M Canonical Variates Analysis Also includes Fourier shape analysis thin-plate splines parsimony and time series analysis among others Oslashyvind Hammer University of Oslo
Analysis of outlines
bull Shape Elliptic Fourier WINDOWS Extracts the contour shape from a full color bitmap image delineates the contour shape with the elliptic Fourier descriptors and performs a principal component analysis for summarizing the shape information By Hiroyoshi Iwata For more information see Shape home page tutorial or manual
bull Iwata H and Y Ukai (2002) SHAPE A computer program package for quantitative evaluation of biological shapes based on elliptic Fourier descriptors Journal of Heredity 93 384-385
Eigenshape analysis
bull httpwwwnhmacukhosted_sitespaleonetftpftphtml
bull This archive contains a series of programs designed to perform an eigenshape analysis on xy coordinate data from object outlines Routines include xy -gt phi() transformation phi() -gt xy transformation eigenshape analysis and projection of objects into the eigenshape space Two completely worked example analyses and a users guide are also provided El autor es Norman McLeod del BMNH de Londres
Graphical representation of the four-step morphometric protocol A Quantify raw data
(landmarks recorded on body of cichlid fish) B Remove non-shape variation (landmarks of 412
specimens before and after GPA) C statistical analysis (CVA) and graphical presentation of
results Deformation grids for mean specimen for (right) Eretmodus cyanostictus and (left)
Spathodus erythrodon (magnified by 3X to emphasize shape differences) Data from Ruumlber and
Adams 2001 En Adams Rolhf Slice 2002
iquestQue es morfometriacutea
bull Gingerich Ph 1990 Prediction of body size in mammalian species from long bone lengths and diameters Contributions from the Museum of Paleontolgoy University of Michigan 28
Utilizoacute la foacutermula Y = axb (donde x es la variable independiente la masa corporal e y es la variable dependiente la longitud o el diaacutemetro de un hueso largo)
bull Dean C Adams F James Rohlf and Dennis E Slice 2004 Geometric Morphometrics Ten Years of Progress Following the lsquoRevolutionrsquo Italian Journal of Zoology along with papers by the participants of the workshop held in Rome in January 2002 J Zool 71 5-16
Morfometriacutea La medida de la forma
iquestqueacute es la forma en biologiacutea bull Expresioacuten de los genes fenotipo
bull Expresioacuten de la adaptacioacuten y la historia filogeneacutetica adaptacioacuten ecoloacutegico-evolutiva
Lobo placentado
-Tarsos maacutes largos
-Funciones
trituradoras y cortantes
en distintas piezas
dentales
-Angulo de apertura de
boca menor
Lobo marsupial o
Tilacino
-Tarsos cortos
-Funcioacuten trituradora y
cortante en los
mismos molares
-Angulo de apertura
de boca mayor
-Mandiacutebula Proceso
angular acusado y
curvado hacia el lado
interno
Los dientes de los
mamiacuteferos los
arvicoacutelidos
bull Cuenca Bescoacutes et al 1995
Estiramos lat
La forma en postcraneal el feacutemur de los
sauroacutepodos
bull Canudo y Cuenca Bescoacutes 2004
iquestCoacutemo y por queacute estudiamos la
forma
Orientacioacuten y funciones de los
dientes
bull Arrancar
bull Retener
bull Peinar y
cuidar el
pelo
bull Descortezar
bull roer
bull Cortar
bull Moler
Toma de medidas
W
L
iquestCoacutemo estudiamos la forma
httplifebiosunysbedumorphindexhtml
Adquisicioacuten de los datos
bull Calibre
bull Datos tomados con otras herramientas y volcados a una hoja de caacutelculo (Excel Pasthellip)
bull Imaacutegenes yo datos a partir de la literatura
bull Imaacutegenes tomadas con caacutemara digital
bull Imaacutegenes tomadas desde un microscopio o lupa binocular
Espeacutecimen Longitud (mm)
1a 33
1b 45
1c 29
Landmarks digitalizados con tpsDig2
httplifebiosunysbedumorphindexhtml
Tps digit program
Free at Suny
httplifebiosunysbedumorph
Dientes complejos Arvicolinae
Iberon 25 Landmarks
1
2
4
3
5
6
7
8 9
1011
12
14
15
16
17
18
19
20
21
22
23
24
13
1
2
3
4
5
6
7
89
10
11
12
131415
16
17
18
19
20
21
22
23
24
25
25
archivo 25 iberomys landmarks
Some extreme morphologies
Allophaiomys pliocaenicus Pirro
Nord
Early Pleistocene Italy Iberomys cabrerae
Extant Spain
Allophaiomys lavocati
Sima del Elefante
Atapuerca
Early Pleistocene (older
than the Italian species
Spain
AllophLavF
N3_1r
Early
Pleistocen
e of
Granada
similar to
Atapuerca
LM =17-14 of Iberon LM =15-14 of Iberon LM =15-14 of Iberon
Landmarks de 90 especiacutemenes de
Microtus agrestis
Landmarks de 90 especiacutemenes de
Microtus agrestis
Data 90 Specimens 22 Points 2 Dimensions
All specimen superimposed by GLS method
Sum of Squared Deviations = 1101217
The groups limit is after the specimen 0
PCS and scores computed
Percentages of variance for the 8 first PCS
61395977 61395977
8155754 69551731
4681460 74233190
3352225 77585415
2619139 80204554
2500418 82704973
2235576 84940549
1789387 86729936
Multivariate regression coefficients (normalized) with 3 PCS
PCS 1 0998142
PCS 2 -0057223
PCS 3 -0020926
Regression statistic for 3 components
Rsup2= 0227471 F= 8244611 with 3 and 86 DF plt 0000070
Plot de 90 especiacutemenes de
Microtus agrestis
Distribucioacuten estratigraacutefica de los roedores del cuaternario de Gran Dolina Atapuerca Burgos
0 m
Allo
ph
aio
mys
Mim
om
ys
Ibe
rom
ys
Terr
ico
la
Ste
no
cra
niu
s
Arv
ico
la
Mic
rom
ys
Hy
str
ix
Ca
sto
r
Ma
rmo
ta
Plio
mys
Mic
rotu
s
Allo
cri
cetu
s
Ap
od
em
us
Elio
mys
TD7
TD8
TD10
TD11
TD6
TD5
TD34
TD2
TD1
Procustes analisis APS
bull Procuste fue un ladroacuten que bien descuartizaba o bien estiraba a sus viacutectimas para ajustarlas al tamantildeo de su cama de ahiacute viene la frase hecha de ldquola cama Procusterdquo que se aplica sobre todo en poliacutetica la censura o para prestaciones puacuteblicas en las que es el usuario el que debe adaptarse y no al reveacuteshellip
bull The APS package
bull The shape analysis softwares APS ApsDigit and ApsUtil are written in English and always free for the students Aps combines Procuste superposition and statistical calculations ApsDigit is used locate landmarks on digital images (JPEG Bitmap tiff GIF) ApsUtil is used to handle files (Selection of points individuals change of classification)
bull httpwwwprocustecom
APS
APS est un logiciel danalyse quantitative de la
variabiliteacute morphologique des formes vivantes La
meacutethode utiliseacutee est la superposition procruste
geacuteneacuteraliseacutee
Destineacute aux biologistes et aux cliniciens APS prend en
charge les aspects matheacutematiques et statistiques de
lanalyse de forme Lanalyse se fait en 2 temps
1 Une superposition procruste de lensemble des
speacutecimens
2 Une analyse statistique qui visualise et teste la covariance
entre dune part la conformation et dautre part un facteur
biologique comme la taille lappartenance agrave groupe la
preacutesence ou non dune pathologie
Il est conccedilu pour eacutetudier un ou deux groupes
APS Digitalizar landmarks
DigitX is designed to digitize landmarks on Jpeg or Bitmap picture
middot Select the total number of landmarks to digitize with the second
Combo-Box of the toolbar
middot Select a picture in the graphic file selector on the left
middot Click on to load the link file (optional)
middot Click on to load the consensus file (optional)
middot Digitize landmarks using the left button of the mouse
middot To cancel last landmark position by a click on undo arrow
middot When all landmarks are digitized save the file by a click on save file
APS Crear archivo
Getting started with ApsUtil
ApsUtil create a data file (dat) with specimen ordered by
addition of smaller data files Input and output files are to
APS data format with an header line (number of specimens
number
of landmarks number of dimensions) followed by landmarks
coordinates
NEW button clear all previous data and begin a new data file
ADD button add a file containing one or many specimen
MIX button add a new file to a previous one by mixing the
two file
This ordering of specimen is required before to compute
shape differences
When file is saved specimens are ordered like
specimen 1 of the 1st file
specimen 1 of the 2nd file
specimen 2 of the 1st file
APS analisis
bull New features of Version 241
bull A single specimen or all a sample can be superimposed on any reloaded
bull specimen as consensus (File -gt Reload -gt Consensus)
bull Shape vectors (eg discriminant vectors computed with other software)
bull can be reloaded for visualization (File -gt Reload -gt Pcs)
bull The shape vector must be of norm 1
bull Projections of specimens on shape vectors are automatically computed
Otros
elementos del
esqueleto
A Antarctosaurus wichmannianus B
Saltasaurus loricatus C Neuquensaurus
australis D Neuquensaurus robustus E
Lirainosaurus astibiae F Ampelosaurus atacis
G Magyarosaurus dacus H Magyarosaurus
dacus Jianu I Alamosaurus sanjuanensis J
Aegyptosaurus baharijiensis K
Opisthocoelicaudia skarzynskii
Canudo amp Cuenca Bescos 2004
wwwaragosauruscom
Aegyptosaurus Alamosaurus
Imaacutegenes literatura
Fotos ejemplares
Hacer un poliacutegono con los landmarks
Guardar la misma posicioacuten (en una liacutenea basal por ej)
APS digit
APS util
APS program CP
Opisthocoelicaudia
Resultados
APS Fecha Thu 21 Sep 2006 213918
+0200 [210906 213918 CEST]
De Info Procuste
ltinfoprocustecomgt
Para cuencagunizares
Asunto Re analyse de forme chez
les arvicolides
Cabeceras Mostrar todas las
cabeceras
Chegravere collegravegue
Voici le lien pour teacuteleacutecharger le le
setup dinstallation des 3
logiciels APS ApsDigit et ApsUtil
httpwwwprocustecomprogramsset
up_aps_allexe
Noubliez pas de citer APS dans vos
publications
Bien cordialement
Xavier Penin
Paacuteginas web recomendadas
bull httplifebiosunysbedumorph la mejor paacutegina de
morfometriacutea geomeacutetrica Contiene un listado con todos los
programas de morfometriacutea Universidad de Stony Brook NY
bull httpwwwmorphometricsorgindexhtml es la paacutegina en la
que se mantiene la lista de email morphmet Es la base de la
organizacioacuten de la morfometriacutea en Suny
bull httpwwwflywingsorgukindexhtm iquestporqueacute hay variacioacuten
morfoloacutegica Universidad de Manchester UK
bull httpwwwprocustecomindexhtml anaacutelisis de la forma con
Procruste Aps Xavier Penin Universidad de Paris V
bull Shapehellipy otros ver la paacutegina de Suny
Las ldquoseries TPSrdquo Thin-plate spline
(laacuteminas finas de grosor uniforme)
tpsDIG2
Data acquisition
bull Digitize landmarks amp outlines from image files scanner or video Windows TpsDig is a Windows (95 through XP) program for digitizing landmarks and outlines for geometric morphometric analyses Includes simple image enhancement operations scale factors image brightness profile and support for AVI and MOV files Output is in the TPS file format used by the tps series of programs The TPS file includes the name of the image file for each specimen so that landmarks can always be visualized on the image Since output files are ASCII they can be converted to formats for other software Users should note that the tpsUtil program is useful for both the preparation of the input files to tpsDig as well as for some useful conversions afterwards The program also computes areas of enclosed regions perimeters and linear distances The tpsDig2 link at the left is for the new 205 version
bull Execute the downloaded file to install the program By F James Rohlf
Las ldquoseries TPSrdquo
ordenar los archivos digitalizados
TPS util
bull tps file utility program Windows At present it can randomly scramble the order of specimens in a tps file to minimize bias in digitizing landmark locations restore the original order (eg before statistical analyses are performed) create an empty TPS file from a directory with image files add keywords and values to the variables field of a TPS file combine TPS files into a single TPS file deletereorder landmarks remove outlines from a TPS file and convert TPS and NTS files to NTS M or CSV files It can also split an NTS file into several matrices Graphic editors are included for drawing link and sliders files Unbending a deformed specimen Converting outline and curves points to landmarks
bull Other operations can be added - let me know what you need Execute the TPSUTILW32EXE file to install the program By F James Rohlf Version 138
tpsTree
bull Fit and visualize thin-plate splines on trees Windows Performs a least-squares orthogonal generalized Procrustes analysis to obtain a reference and then estimates the splines for each group (internal node) on a tree Both ultrametric (eg WPGMA and UPGMA trees) and additive trees (using squared change parsimony to estimate the shapes of the HTUs) are supported The estimated shapes can be visualized with estimated images in the background (see the tpsSuper program) The file expands into a Windows setup program and associated files By F James Rohlf Version 118 File containing HTU coordinates and HTU images to demo that feature The older and more limited 16 bit Windows version is still available
tpsRegr
bull Multivariate multiple regression of shape onto independent variables Windows performs a multivariate multiple regression of shape (as captured by partial warp scores and the uniform shape component) onto one or more independent variables By appropriate setting up of independent variables this program can perform various types of MANOVA and MANCOVA Can be used to study allometry By F James Rohlf Version 131
tpsSplin
bull Thin-plate spline Windows Program to
compare pairs of specimens by displaying
a Darcy Thompson style transformation
grid based on a thin-plate spline Several
options are given for sliding
semilandmarks The tpssplnwexe file
expands into a Windows setup program
that will be run automatically By F James
Rohlf Version 120
tpsRelw el anaacutelisis de la
deformacioacuten relativa bull Relative warps analysis Windows Performs a
relative warp (deformacioacuten) analysis This corresponds to a principal components analysis of variation in a sample (relative to bending energy if the alpha parameter is not equal to zero) Displays a plot of relative warp scores and a visualization window that displays the estimated shape for arbitrary points in the ordination Also displays partial warp scores and their visualizations Allows fitting of semilandmark points along curves Version 144 By F James Rohlf
tpsPLS
bull Partial least-squares analysis for shapes Windows Used to explore the covariance between a set of variables and variation in shape or between two shapes It performs a two-block partial least-squares analysis It differs from regression in that both variables and shape are considered equally (one is not considered to be a set of independent variables measured without error) Its use is described in Rohlf and Corti (2000 Systematic Biology 49740-753) By F James Rohlf Version 118
tpsSmall
bull Test for small variation in shape Windows Use to test whether the variation in shape among a set of specimens is too large and thus statistical methods based on the tangent space approximation (eg thin-plate spline methods) cannot be used The program can process both 2D and 3D data files Output files include consensus and aligned specimens By F James Rohlf Version 120
tpsPower
bull Estimate statistical power for comparing shapes Windows Program for estimating statistical power for comparing the mean shapes of two populations Provides methods based on several different approaches Can be used for planning morphometric studies as well as to compare power using different approaches Version 104 By F James Rohlf
Morpheus et al bull Morpheus et al is a software package that will provide a
comprehensive cross-platform environment for morphometric data analysis It is available in graphical and command-line versions for a number of operating systems (see below) More information about new features and previous changes can be found in the release notes
httplifebiosunysbedumorphmorpheus
Multivariate analysis
bull PAST is a free easy-to-use data analysis package aimed at paleontology Windows 95+ Multivariate statistical methods include Principal Components (with Minimal Spanning Tree) Principal Coordinates (ten distance measures) Non-metric Multidimensional Scaling (ten distance measures) Detrended Correspondence Analysis Cluster analysis (three algorithms 11 distance measures) k-means clustering seriation discriminant analysis one-way MANOVA Hotellings t-squared Boxs M Canonical Variates Analysis Also includes Fourier shape analysis thin-plate splines parsimony and time series analysis among others Oslashyvind Hammer University of Oslo
Analysis of outlines
bull Shape Elliptic Fourier WINDOWS Extracts the contour shape from a full color bitmap image delineates the contour shape with the elliptic Fourier descriptors and performs a principal component analysis for summarizing the shape information By Hiroyoshi Iwata For more information see Shape home page tutorial or manual
bull Iwata H and Y Ukai (2002) SHAPE A computer program package for quantitative evaluation of biological shapes based on elliptic Fourier descriptors Journal of Heredity 93 384-385
Eigenshape analysis
bull httpwwwnhmacukhosted_sitespaleonetftpftphtml
bull This archive contains a series of programs designed to perform an eigenshape analysis on xy coordinate data from object outlines Routines include xy -gt phi() transformation phi() -gt xy transformation eigenshape analysis and projection of objects into the eigenshape space Two completely worked example analyses and a users guide are also provided El autor es Norman McLeod del BMNH de Londres
Graphical representation of the four-step morphometric protocol A Quantify raw data
(landmarks recorded on body of cichlid fish) B Remove non-shape variation (landmarks of 412
specimens before and after GPA) C statistical analysis (CVA) and graphical presentation of
results Deformation grids for mean specimen for (right) Eretmodus cyanostictus and (left)
Spathodus erythrodon (magnified by 3X to emphasize shape differences) Data from Ruumlber and
Adams 2001 En Adams Rolhf Slice 2002
Morfometriacutea La medida de la forma
iquestqueacute es la forma en biologiacutea bull Expresioacuten de los genes fenotipo
bull Expresioacuten de la adaptacioacuten y la historia filogeneacutetica adaptacioacuten ecoloacutegico-evolutiva
Lobo placentado
-Tarsos maacutes largos
-Funciones
trituradoras y cortantes
en distintas piezas
dentales
-Angulo de apertura de
boca menor
Lobo marsupial o
Tilacino
-Tarsos cortos
-Funcioacuten trituradora y
cortante en los
mismos molares
-Angulo de apertura
de boca mayor
-Mandiacutebula Proceso
angular acusado y
curvado hacia el lado
interno
Los dientes de los
mamiacuteferos los
arvicoacutelidos
bull Cuenca Bescoacutes et al 1995
Estiramos lat
La forma en postcraneal el feacutemur de los
sauroacutepodos
bull Canudo y Cuenca Bescoacutes 2004
iquestCoacutemo y por queacute estudiamos la
forma
Orientacioacuten y funciones de los
dientes
bull Arrancar
bull Retener
bull Peinar y
cuidar el
pelo
bull Descortezar
bull roer
bull Cortar
bull Moler
Toma de medidas
W
L
iquestCoacutemo estudiamos la forma
httplifebiosunysbedumorphindexhtml
Adquisicioacuten de los datos
bull Calibre
bull Datos tomados con otras herramientas y volcados a una hoja de caacutelculo (Excel Pasthellip)
bull Imaacutegenes yo datos a partir de la literatura
bull Imaacutegenes tomadas con caacutemara digital
bull Imaacutegenes tomadas desde un microscopio o lupa binocular
Espeacutecimen Longitud (mm)
1a 33
1b 45
1c 29
Landmarks digitalizados con tpsDig2
httplifebiosunysbedumorphindexhtml
Tps digit program
Free at Suny
httplifebiosunysbedumorph
Dientes complejos Arvicolinae
Iberon 25 Landmarks
1
2
4
3
5
6
7
8 9
1011
12
14
15
16
17
18
19
20
21
22
23
24
13
1
2
3
4
5
6
7
89
10
11
12
131415
16
17
18
19
20
21
22
23
24
25
25
archivo 25 iberomys landmarks
Some extreme morphologies
Allophaiomys pliocaenicus Pirro
Nord
Early Pleistocene Italy Iberomys cabrerae
Extant Spain
Allophaiomys lavocati
Sima del Elefante
Atapuerca
Early Pleistocene (older
than the Italian species
Spain
AllophLavF
N3_1r
Early
Pleistocen
e of
Granada
similar to
Atapuerca
LM =17-14 of Iberon LM =15-14 of Iberon LM =15-14 of Iberon
Landmarks de 90 especiacutemenes de
Microtus agrestis
Landmarks de 90 especiacutemenes de
Microtus agrestis
Data 90 Specimens 22 Points 2 Dimensions
All specimen superimposed by GLS method
Sum of Squared Deviations = 1101217
The groups limit is after the specimen 0
PCS and scores computed
Percentages of variance for the 8 first PCS
61395977 61395977
8155754 69551731
4681460 74233190
3352225 77585415
2619139 80204554
2500418 82704973
2235576 84940549
1789387 86729936
Multivariate regression coefficients (normalized) with 3 PCS
PCS 1 0998142
PCS 2 -0057223
PCS 3 -0020926
Regression statistic for 3 components
Rsup2= 0227471 F= 8244611 with 3 and 86 DF plt 0000070
Plot de 90 especiacutemenes de
Microtus agrestis
Distribucioacuten estratigraacutefica de los roedores del cuaternario de Gran Dolina Atapuerca Burgos
0 m
Allo
ph
aio
mys
Mim
om
ys
Ibe
rom
ys
Terr
ico
la
Ste
no
cra
niu
s
Arv
ico
la
Mic
rom
ys
Hy
str
ix
Ca
sto
r
Ma
rmo
ta
Plio
mys
Mic
rotu
s
Allo
cri
cetu
s
Ap
od
em
us
Elio
mys
TD7
TD8
TD10
TD11
TD6
TD5
TD34
TD2
TD1
Procustes analisis APS
bull Procuste fue un ladroacuten que bien descuartizaba o bien estiraba a sus viacutectimas para ajustarlas al tamantildeo de su cama de ahiacute viene la frase hecha de ldquola cama Procusterdquo que se aplica sobre todo en poliacutetica la censura o para prestaciones puacuteblicas en las que es el usuario el que debe adaptarse y no al reveacuteshellip
bull The APS package
bull The shape analysis softwares APS ApsDigit and ApsUtil are written in English and always free for the students Aps combines Procuste superposition and statistical calculations ApsDigit is used locate landmarks on digital images (JPEG Bitmap tiff GIF) ApsUtil is used to handle files (Selection of points individuals change of classification)
bull httpwwwprocustecom
APS
APS est un logiciel danalyse quantitative de la
variabiliteacute morphologique des formes vivantes La
meacutethode utiliseacutee est la superposition procruste
geacuteneacuteraliseacutee
Destineacute aux biologistes et aux cliniciens APS prend en
charge les aspects matheacutematiques et statistiques de
lanalyse de forme Lanalyse se fait en 2 temps
1 Une superposition procruste de lensemble des
speacutecimens
2 Une analyse statistique qui visualise et teste la covariance
entre dune part la conformation et dautre part un facteur
biologique comme la taille lappartenance agrave groupe la
preacutesence ou non dune pathologie
Il est conccedilu pour eacutetudier un ou deux groupes
APS Digitalizar landmarks
DigitX is designed to digitize landmarks on Jpeg or Bitmap picture
middot Select the total number of landmarks to digitize with the second
Combo-Box of the toolbar
middot Select a picture in the graphic file selector on the left
middot Click on to load the link file (optional)
middot Click on to load the consensus file (optional)
middot Digitize landmarks using the left button of the mouse
middot To cancel last landmark position by a click on undo arrow
middot When all landmarks are digitized save the file by a click on save file
APS Crear archivo
Getting started with ApsUtil
ApsUtil create a data file (dat) with specimen ordered by
addition of smaller data files Input and output files are to
APS data format with an header line (number of specimens
number
of landmarks number of dimensions) followed by landmarks
coordinates
NEW button clear all previous data and begin a new data file
ADD button add a file containing one or many specimen
MIX button add a new file to a previous one by mixing the
two file
This ordering of specimen is required before to compute
shape differences
When file is saved specimens are ordered like
specimen 1 of the 1st file
specimen 1 of the 2nd file
specimen 2 of the 1st file
APS analisis
bull New features of Version 241
bull A single specimen or all a sample can be superimposed on any reloaded
bull specimen as consensus (File -gt Reload -gt Consensus)
bull Shape vectors (eg discriminant vectors computed with other software)
bull can be reloaded for visualization (File -gt Reload -gt Pcs)
bull The shape vector must be of norm 1
bull Projections of specimens on shape vectors are automatically computed
Otros
elementos del
esqueleto
A Antarctosaurus wichmannianus B
Saltasaurus loricatus C Neuquensaurus
australis D Neuquensaurus robustus E
Lirainosaurus astibiae F Ampelosaurus atacis
G Magyarosaurus dacus H Magyarosaurus
dacus Jianu I Alamosaurus sanjuanensis J
Aegyptosaurus baharijiensis K
Opisthocoelicaudia skarzynskii
Canudo amp Cuenca Bescos 2004
wwwaragosauruscom
Aegyptosaurus Alamosaurus
Imaacutegenes literatura
Fotos ejemplares
Hacer un poliacutegono con los landmarks
Guardar la misma posicioacuten (en una liacutenea basal por ej)
APS digit
APS util
APS program CP
Opisthocoelicaudia
Resultados
APS Fecha Thu 21 Sep 2006 213918
+0200 [210906 213918 CEST]
De Info Procuste
ltinfoprocustecomgt
Para cuencagunizares
Asunto Re analyse de forme chez
les arvicolides
Cabeceras Mostrar todas las
cabeceras
Chegravere collegravegue
Voici le lien pour teacuteleacutecharger le le
setup dinstallation des 3
logiciels APS ApsDigit et ApsUtil
httpwwwprocustecomprogramsset
up_aps_allexe
Noubliez pas de citer APS dans vos
publications
Bien cordialement
Xavier Penin
Paacuteginas web recomendadas
bull httplifebiosunysbedumorph la mejor paacutegina de
morfometriacutea geomeacutetrica Contiene un listado con todos los
programas de morfometriacutea Universidad de Stony Brook NY
bull httpwwwmorphometricsorgindexhtml es la paacutegina en la
que se mantiene la lista de email morphmet Es la base de la
organizacioacuten de la morfometriacutea en Suny
bull httpwwwflywingsorgukindexhtm iquestporqueacute hay variacioacuten
morfoloacutegica Universidad de Manchester UK
bull httpwwwprocustecomindexhtml anaacutelisis de la forma con
Procruste Aps Xavier Penin Universidad de Paris V
bull Shapehellipy otros ver la paacutegina de Suny
Las ldquoseries TPSrdquo Thin-plate spline
(laacuteminas finas de grosor uniforme)
tpsDIG2
Data acquisition
bull Digitize landmarks amp outlines from image files scanner or video Windows TpsDig is a Windows (95 through XP) program for digitizing landmarks and outlines for geometric morphometric analyses Includes simple image enhancement operations scale factors image brightness profile and support for AVI and MOV files Output is in the TPS file format used by the tps series of programs The TPS file includes the name of the image file for each specimen so that landmarks can always be visualized on the image Since output files are ASCII they can be converted to formats for other software Users should note that the tpsUtil program is useful for both the preparation of the input files to tpsDig as well as for some useful conversions afterwards The program also computes areas of enclosed regions perimeters and linear distances The tpsDig2 link at the left is for the new 205 version
bull Execute the downloaded file to install the program By F James Rohlf
Las ldquoseries TPSrdquo
ordenar los archivos digitalizados
TPS util
bull tps file utility program Windows At present it can randomly scramble the order of specimens in a tps file to minimize bias in digitizing landmark locations restore the original order (eg before statistical analyses are performed) create an empty TPS file from a directory with image files add keywords and values to the variables field of a TPS file combine TPS files into a single TPS file deletereorder landmarks remove outlines from a TPS file and convert TPS and NTS files to NTS M or CSV files It can also split an NTS file into several matrices Graphic editors are included for drawing link and sliders files Unbending a deformed specimen Converting outline and curves points to landmarks
bull Other operations can be added - let me know what you need Execute the TPSUTILW32EXE file to install the program By F James Rohlf Version 138
tpsTree
bull Fit and visualize thin-plate splines on trees Windows Performs a least-squares orthogonal generalized Procrustes analysis to obtain a reference and then estimates the splines for each group (internal node) on a tree Both ultrametric (eg WPGMA and UPGMA trees) and additive trees (using squared change parsimony to estimate the shapes of the HTUs) are supported The estimated shapes can be visualized with estimated images in the background (see the tpsSuper program) The file expands into a Windows setup program and associated files By F James Rohlf Version 118 File containing HTU coordinates and HTU images to demo that feature The older and more limited 16 bit Windows version is still available
tpsRegr
bull Multivariate multiple regression of shape onto independent variables Windows performs a multivariate multiple regression of shape (as captured by partial warp scores and the uniform shape component) onto one or more independent variables By appropriate setting up of independent variables this program can perform various types of MANOVA and MANCOVA Can be used to study allometry By F James Rohlf Version 131
tpsSplin
bull Thin-plate spline Windows Program to
compare pairs of specimens by displaying
a Darcy Thompson style transformation
grid based on a thin-plate spline Several
options are given for sliding
semilandmarks The tpssplnwexe file
expands into a Windows setup program
that will be run automatically By F James
Rohlf Version 120
tpsRelw el anaacutelisis de la
deformacioacuten relativa bull Relative warps analysis Windows Performs a
relative warp (deformacioacuten) analysis This corresponds to a principal components analysis of variation in a sample (relative to bending energy if the alpha parameter is not equal to zero) Displays a plot of relative warp scores and a visualization window that displays the estimated shape for arbitrary points in the ordination Also displays partial warp scores and their visualizations Allows fitting of semilandmark points along curves Version 144 By F James Rohlf
tpsPLS
bull Partial least-squares analysis for shapes Windows Used to explore the covariance between a set of variables and variation in shape or between two shapes It performs a two-block partial least-squares analysis It differs from regression in that both variables and shape are considered equally (one is not considered to be a set of independent variables measured without error) Its use is described in Rohlf and Corti (2000 Systematic Biology 49740-753) By F James Rohlf Version 118
tpsSmall
bull Test for small variation in shape Windows Use to test whether the variation in shape among a set of specimens is too large and thus statistical methods based on the tangent space approximation (eg thin-plate spline methods) cannot be used The program can process both 2D and 3D data files Output files include consensus and aligned specimens By F James Rohlf Version 120
tpsPower
bull Estimate statistical power for comparing shapes Windows Program for estimating statistical power for comparing the mean shapes of two populations Provides methods based on several different approaches Can be used for planning morphometric studies as well as to compare power using different approaches Version 104 By F James Rohlf
Morpheus et al bull Morpheus et al is a software package that will provide a
comprehensive cross-platform environment for morphometric data analysis It is available in graphical and command-line versions for a number of operating systems (see below) More information about new features and previous changes can be found in the release notes
httplifebiosunysbedumorphmorpheus
Multivariate analysis
bull PAST is a free easy-to-use data analysis package aimed at paleontology Windows 95+ Multivariate statistical methods include Principal Components (with Minimal Spanning Tree) Principal Coordinates (ten distance measures) Non-metric Multidimensional Scaling (ten distance measures) Detrended Correspondence Analysis Cluster analysis (three algorithms 11 distance measures) k-means clustering seriation discriminant analysis one-way MANOVA Hotellings t-squared Boxs M Canonical Variates Analysis Also includes Fourier shape analysis thin-plate splines parsimony and time series analysis among others Oslashyvind Hammer University of Oslo
Analysis of outlines
bull Shape Elliptic Fourier WINDOWS Extracts the contour shape from a full color bitmap image delineates the contour shape with the elliptic Fourier descriptors and performs a principal component analysis for summarizing the shape information By Hiroyoshi Iwata For more information see Shape home page tutorial or manual
bull Iwata H and Y Ukai (2002) SHAPE A computer program package for quantitative evaluation of biological shapes based on elliptic Fourier descriptors Journal of Heredity 93 384-385
Eigenshape analysis
bull httpwwwnhmacukhosted_sitespaleonetftpftphtml
bull This archive contains a series of programs designed to perform an eigenshape analysis on xy coordinate data from object outlines Routines include xy -gt phi() transformation phi() -gt xy transformation eigenshape analysis and projection of objects into the eigenshape space Two completely worked example analyses and a users guide are also provided El autor es Norman McLeod del BMNH de Londres
Graphical representation of the four-step morphometric protocol A Quantify raw data
(landmarks recorded on body of cichlid fish) B Remove non-shape variation (landmarks of 412
specimens before and after GPA) C statistical analysis (CVA) and graphical presentation of
results Deformation grids for mean specimen for (right) Eretmodus cyanostictus and (left)
Spathodus erythrodon (magnified by 3X to emphasize shape differences) Data from Ruumlber and
Adams 2001 En Adams Rolhf Slice 2002
iquestqueacute es la forma en biologiacutea bull Expresioacuten de los genes fenotipo
bull Expresioacuten de la adaptacioacuten y la historia filogeneacutetica adaptacioacuten ecoloacutegico-evolutiva
Lobo placentado
-Tarsos maacutes largos
-Funciones
trituradoras y cortantes
en distintas piezas
dentales
-Angulo de apertura de
boca menor
Lobo marsupial o
Tilacino
-Tarsos cortos
-Funcioacuten trituradora y
cortante en los
mismos molares
-Angulo de apertura
de boca mayor
-Mandiacutebula Proceso
angular acusado y
curvado hacia el lado
interno
Los dientes de los
mamiacuteferos los
arvicoacutelidos
bull Cuenca Bescoacutes et al 1995
Estiramos lat
La forma en postcraneal el feacutemur de los
sauroacutepodos
bull Canudo y Cuenca Bescoacutes 2004
iquestCoacutemo y por queacute estudiamos la
forma
Orientacioacuten y funciones de los
dientes
bull Arrancar
bull Retener
bull Peinar y
cuidar el
pelo
bull Descortezar
bull roer
bull Cortar
bull Moler
Toma de medidas
W
L
iquestCoacutemo estudiamos la forma
httplifebiosunysbedumorphindexhtml
Adquisicioacuten de los datos
bull Calibre
bull Datos tomados con otras herramientas y volcados a una hoja de caacutelculo (Excel Pasthellip)
bull Imaacutegenes yo datos a partir de la literatura
bull Imaacutegenes tomadas con caacutemara digital
bull Imaacutegenes tomadas desde un microscopio o lupa binocular
Espeacutecimen Longitud (mm)
1a 33
1b 45
1c 29
Landmarks digitalizados con tpsDig2
httplifebiosunysbedumorphindexhtml
Tps digit program
Free at Suny
httplifebiosunysbedumorph
Dientes complejos Arvicolinae
Iberon 25 Landmarks
1
2
4
3
5
6
7
8 9
1011
12
14
15
16
17
18
19
20
21
22
23
24
13
1
2
3
4
5
6
7
89
10
11
12
131415
16
17
18
19
20
21
22
23
24
25
25
archivo 25 iberomys landmarks
Some extreme morphologies
Allophaiomys pliocaenicus Pirro
Nord
Early Pleistocene Italy Iberomys cabrerae
Extant Spain
Allophaiomys lavocati
Sima del Elefante
Atapuerca
Early Pleistocene (older
than the Italian species
Spain
AllophLavF
N3_1r
Early
Pleistocen
e of
Granada
similar to
Atapuerca
LM =17-14 of Iberon LM =15-14 of Iberon LM =15-14 of Iberon
Landmarks de 90 especiacutemenes de
Microtus agrestis
Landmarks de 90 especiacutemenes de
Microtus agrestis
Data 90 Specimens 22 Points 2 Dimensions
All specimen superimposed by GLS method
Sum of Squared Deviations = 1101217
The groups limit is after the specimen 0
PCS and scores computed
Percentages of variance for the 8 first PCS
61395977 61395977
8155754 69551731
4681460 74233190
3352225 77585415
2619139 80204554
2500418 82704973
2235576 84940549
1789387 86729936
Multivariate regression coefficients (normalized) with 3 PCS
PCS 1 0998142
PCS 2 -0057223
PCS 3 -0020926
Regression statistic for 3 components
Rsup2= 0227471 F= 8244611 with 3 and 86 DF plt 0000070
Plot de 90 especiacutemenes de
Microtus agrestis
Distribucioacuten estratigraacutefica de los roedores del cuaternario de Gran Dolina Atapuerca Burgos
0 m
Allo
ph
aio
mys
Mim
om
ys
Ibe
rom
ys
Terr
ico
la
Ste
no
cra
niu
s
Arv
ico
la
Mic
rom
ys
Hy
str
ix
Ca
sto
r
Ma
rmo
ta
Plio
mys
Mic
rotu
s
Allo
cri
cetu
s
Ap
od
em
us
Elio
mys
TD7
TD8
TD10
TD11
TD6
TD5
TD34
TD2
TD1
Procustes analisis APS
bull Procuste fue un ladroacuten que bien descuartizaba o bien estiraba a sus viacutectimas para ajustarlas al tamantildeo de su cama de ahiacute viene la frase hecha de ldquola cama Procusterdquo que se aplica sobre todo en poliacutetica la censura o para prestaciones puacuteblicas en las que es el usuario el que debe adaptarse y no al reveacuteshellip
bull The APS package
bull The shape analysis softwares APS ApsDigit and ApsUtil are written in English and always free for the students Aps combines Procuste superposition and statistical calculations ApsDigit is used locate landmarks on digital images (JPEG Bitmap tiff GIF) ApsUtil is used to handle files (Selection of points individuals change of classification)
bull httpwwwprocustecom
APS
APS est un logiciel danalyse quantitative de la
variabiliteacute morphologique des formes vivantes La
meacutethode utiliseacutee est la superposition procruste
geacuteneacuteraliseacutee
Destineacute aux biologistes et aux cliniciens APS prend en
charge les aspects matheacutematiques et statistiques de
lanalyse de forme Lanalyse se fait en 2 temps
1 Une superposition procruste de lensemble des
speacutecimens
2 Une analyse statistique qui visualise et teste la covariance
entre dune part la conformation et dautre part un facteur
biologique comme la taille lappartenance agrave groupe la
preacutesence ou non dune pathologie
Il est conccedilu pour eacutetudier un ou deux groupes
APS Digitalizar landmarks
DigitX is designed to digitize landmarks on Jpeg or Bitmap picture
middot Select the total number of landmarks to digitize with the second
Combo-Box of the toolbar
middot Select a picture in the graphic file selector on the left
middot Click on to load the link file (optional)
middot Click on to load the consensus file (optional)
middot Digitize landmarks using the left button of the mouse
middot To cancel last landmark position by a click on undo arrow
middot When all landmarks are digitized save the file by a click on save file
APS Crear archivo
Getting started with ApsUtil
ApsUtil create a data file (dat) with specimen ordered by
addition of smaller data files Input and output files are to
APS data format with an header line (number of specimens
number
of landmarks number of dimensions) followed by landmarks
coordinates
NEW button clear all previous data and begin a new data file
ADD button add a file containing one or many specimen
MIX button add a new file to a previous one by mixing the
two file
This ordering of specimen is required before to compute
shape differences
When file is saved specimens are ordered like
specimen 1 of the 1st file
specimen 1 of the 2nd file
specimen 2 of the 1st file
APS analisis
bull New features of Version 241
bull A single specimen or all a sample can be superimposed on any reloaded
bull specimen as consensus (File -gt Reload -gt Consensus)
bull Shape vectors (eg discriminant vectors computed with other software)
bull can be reloaded for visualization (File -gt Reload -gt Pcs)
bull The shape vector must be of norm 1
bull Projections of specimens on shape vectors are automatically computed
Otros
elementos del
esqueleto
A Antarctosaurus wichmannianus B
Saltasaurus loricatus C Neuquensaurus
australis D Neuquensaurus robustus E
Lirainosaurus astibiae F Ampelosaurus atacis
G Magyarosaurus dacus H Magyarosaurus
dacus Jianu I Alamosaurus sanjuanensis J
Aegyptosaurus baharijiensis K
Opisthocoelicaudia skarzynskii
Canudo amp Cuenca Bescos 2004
wwwaragosauruscom
Aegyptosaurus Alamosaurus
Imaacutegenes literatura
Fotos ejemplares
Hacer un poliacutegono con los landmarks
Guardar la misma posicioacuten (en una liacutenea basal por ej)
APS digit
APS util
APS program CP
Opisthocoelicaudia
Resultados
APS Fecha Thu 21 Sep 2006 213918
+0200 [210906 213918 CEST]
De Info Procuste
ltinfoprocustecomgt
Para cuencagunizares
Asunto Re analyse de forme chez
les arvicolides
Cabeceras Mostrar todas las
cabeceras
Chegravere collegravegue
Voici le lien pour teacuteleacutecharger le le
setup dinstallation des 3
logiciels APS ApsDigit et ApsUtil
httpwwwprocustecomprogramsset
up_aps_allexe
Noubliez pas de citer APS dans vos
publications
Bien cordialement
Xavier Penin
Paacuteginas web recomendadas
bull httplifebiosunysbedumorph la mejor paacutegina de
morfometriacutea geomeacutetrica Contiene un listado con todos los
programas de morfometriacutea Universidad de Stony Brook NY
bull httpwwwmorphometricsorgindexhtml es la paacutegina en la
que se mantiene la lista de email morphmet Es la base de la
organizacioacuten de la morfometriacutea en Suny
bull httpwwwflywingsorgukindexhtm iquestporqueacute hay variacioacuten
morfoloacutegica Universidad de Manchester UK
bull httpwwwprocustecomindexhtml anaacutelisis de la forma con
Procruste Aps Xavier Penin Universidad de Paris V
bull Shapehellipy otros ver la paacutegina de Suny
Las ldquoseries TPSrdquo Thin-plate spline
(laacuteminas finas de grosor uniforme)
tpsDIG2
Data acquisition
bull Digitize landmarks amp outlines from image files scanner or video Windows TpsDig is a Windows (95 through XP) program for digitizing landmarks and outlines for geometric morphometric analyses Includes simple image enhancement operations scale factors image brightness profile and support for AVI and MOV files Output is in the TPS file format used by the tps series of programs The TPS file includes the name of the image file for each specimen so that landmarks can always be visualized on the image Since output files are ASCII they can be converted to formats for other software Users should note that the tpsUtil program is useful for both the preparation of the input files to tpsDig as well as for some useful conversions afterwards The program also computes areas of enclosed regions perimeters and linear distances The tpsDig2 link at the left is for the new 205 version
bull Execute the downloaded file to install the program By F James Rohlf
Las ldquoseries TPSrdquo
ordenar los archivos digitalizados
TPS util
bull tps file utility program Windows At present it can randomly scramble the order of specimens in a tps file to minimize bias in digitizing landmark locations restore the original order (eg before statistical analyses are performed) create an empty TPS file from a directory with image files add keywords and values to the variables field of a TPS file combine TPS files into a single TPS file deletereorder landmarks remove outlines from a TPS file and convert TPS and NTS files to NTS M or CSV files It can also split an NTS file into several matrices Graphic editors are included for drawing link and sliders files Unbending a deformed specimen Converting outline and curves points to landmarks
bull Other operations can be added - let me know what you need Execute the TPSUTILW32EXE file to install the program By F James Rohlf Version 138
tpsTree
bull Fit and visualize thin-plate splines on trees Windows Performs a least-squares orthogonal generalized Procrustes analysis to obtain a reference and then estimates the splines for each group (internal node) on a tree Both ultrametric (eg WPGMA and UPGMA trees) and additive trees (using squared change parsimony to estimate the shapes of the HTUs) are supported The estimated shapes can be visualized with estimated images in the background (see the tpsSuper program) The file expands into a Windows setup program and associated files By F James Rohlf Version 118 File containing HTU coordinates and HTU images to demo that feature The older and more limited 16 bit Windows version is still available
tpsRegr
bull Multivariate multiple regression of shape onto independent variables Windows performs a multivariate multiple regression of shape (as captured by partial warp scores and the uniform shape component) onto one or more independent variables By appropriate setting up of independent variables this program can perform various types of MANOVA and MANCOVA Can be used to study allometry By F James Rohlf Version 131
tpsSplin
bull Thin-plate spline Windows Program to
compare pairs of specimens by displaying
a Darcy Thompson style transformation
grid based on a thin-plate spline Several
options are given for sliding
semilandmarks The tpssplnwexe file
expands into a Windows setup program
that will be run automatically By F James
Rohlf Version 120
tpsRelw el anaacutelisis de la
deformacioacuten relativa bull Relative warps analysis Windows Performs a
relative warp (deformacioacuten) analysis This corresponds to a principal components analysis of variation in a sample (relative to bending energy if the alpha parameter is not equal to zero) Displays a plot of relative warp scores and a visualization window that displays the estimated shape for arbitrary points in the ordination Also displays partial warp scores and their visualizations Allows fitting of semilandmark points along curves Version 144 By F James Rohlf
tpsPLS
bull Partial least-squares analysis for shapes Windows Used to explore the covariance between a set of variables and variation in shape or between two shapes It performs a two-block partial least-squares analysis It differs from regression in that both variables and shape are considered equally (one is not considered to be a set of independent variables measured without error) Its use is described in Rohlf and Corti (2000 Systematic Biology 49740-753) By F James Rohlf Version 118
tpsSmall
bull Test for small variation in shape Windows Use to test whether the variation in shape among a set of specimens is too large and thus statistical methods based on the tangent space approximation (eg thin-plate spline methods) cannot be used The program can process both 2D and 3D data files Output files include consensus and aligned specimens By F James Rohlf Version 120
tpsPower
bull Estimate statistical power for comparing shapes Windows Program for estimating statistical power for comparing the mean shapes of two populations Provides methods based on several different approaches Can be used for planning morphometric studies as well as to compare power using different approaches Version 104 By F James Rohlf
Morpheus et al bull Morpheus et al is a software package that will provide a
comprehensive cross-platform environment for morphometric data analysis It is available in graphical and command-line versions for a number of operating systems (see below) More information about new features and previous changes can be found in the release notes
httplifebiosunysbedumorphmorpheus
Multivariate analysis
bull PAST is a free easy-to-use data analysis package aimed at paleontology Windows 95+ Multivariate statistical methods include Principal Components (with Minimal Spanning Tree) Principal Coordinates (ten distance measures) Non-metric Multidimensional Scaling (ten distance measures) Detrended Correspondence Analysis Cluster analysis (three algorithms 11 distance measures) k-means clustering seriation discriminant analysis one-way MANOVA Hotellings t-squared Boxs M Canonical Variates Analysis Also includes Fourier shape analysis thin-plate splines parsimony and time series analysis among others Oslashyvind Hammer University of Oslo
Analysis of outlines
bull Shape Elliptic Fourier WINDOWS Extracts the contour shape from a full color bitmap image delineates the contour shape with the elliptic Fourier descriptors and performs a principal component analysis for summarizing the shape information By Hiroyoshi Iwata For more information see Shape home page tutorial or manual
bull Iwata H and Y Ukai (2002) SHAPE A computer program package for quantitative evaluation of biological shapes based on elliptic Fourier descriptors Journal of Heredity 93 384-385
Eigenshape analysis
bull httpwwwnhmacukhosted_sitespaleonetftpftphtml
bull This archive contains a series of programs designed to perform an eigenshape analysis on xy coordinate data from object outlines Routines include xy -gt phi() transformation phi() -gt xy transformation eigenshape analysis and projection of objects into the eigenshape space Two completely worked example analyses and a users guide are also provided El autor es Norman McLeod del BMNH de Londres
Graphical representation of the four-step morphometric protocol A Quantify raw data
(landmarks recorded on body of cichlid fish) B Remove non-shape variation (landmarks of 412
specimens before and after GPA) C statistical analysis (CVA) and graphical presentation of
results Deformation grids for mean specimen for (right) Eretmodus cyanostictus and (left)
Spathodus erythrodon (magnified by 3X to emphasize shape differences) Data from Ruumlber and
Adams 2001 En Adams Rolhf Slice 2002
Los dientes de los
mamiacuteferos los
arvicoacutelidos
bull Cuenca Bescoacutes et al 1995
Estiramos lat
La forma en postcraneal el feacutemur de los
sauroacutepodos
bull Canudo y Cuenca Bescoacutes 2004
iquestCoacutemo y por queacute estudiamos la
forma
Orientacioacuten y funciones de los
dientes
bull Arrancar
bull Retener
bull Peinar y
cuidar el
pelo
bull Descortezar
bull roer
bull Cortar
bull Moler
Toma de medidas
W
L
iquestCoacutemo estudiamos la forma
httplifebiosunysbedumorphindexhtml
Adquisicioacuten de los datos
bull Calibre
bull Datos tomados con otras herramientas y volcados a una hoja de caacutelculo (Excel Pasthellip)
bull Imaacutegenes yo datos a partir de la literatura
bull Imaacutegenes tomadas con caacutemara digital
bull Imaacutegenes tomadas desde un microscopio o lupa binocular
Espeacutecimen Longitud (mm)
1a 33
1b 45
1c 29
Landmarks digitalizados con tpsDig2
httplifebiosunysbedumorphindexhtml
Tps digit program
Free at Suny
httplifebiosunysbedumorph
Dientes complejos Arvicolinae
Iberon 25 Landmarks
1
2
4
3
5
6
7
8 9
1011
12
14
15
16
17
18
19
20
21
22
23
24
13
1
2
3
4
5
6
7
89
10
11
12
131415
16
17
18
19
20
21
22
23
24
25
25
archivo 25 iberomys landmarks
Some extreme morphologies
Allophaiomys pliocaenicus Pirro
Nord
Early Pleistocene Italy Iberomys cabrerae
Extant Spain
Allophaiomys lavocati
Sima del Elefante
Atapuerca
Early Pleistocene (older
than the Italian species
Spain
AllophLavF
N3_1r
Early
Pleistocen
e of
Granada
similar to
Atapuerca
LM =17-14 of Iberon LM =15-14 of Iberon LM =15-14 of Iberon
Landmarks de 90 especiacutemenes de
Microtus agrestis
Landmarks de 90 especiacutemenes de
Microtus agrestis
Data 90 Specimens 22 Points 2 Dimensions
All specimen superimposed by GLS method
Sum of Squared Deviations = 1101217
The groups limit is after the specimen 0
PCS and scores computed
Percentages of variance for the 8 first PCS
61395977 61395977
8155754 69551731
4681460 74233190
3352225 77585415
2619139 80204554
2500418 82704973
2235576 84940549
1789387 86729936
Multivariate regression coefficients (normalized) with 3 PCS
PCS 1 0998142
PCS 2 -0057223
PCS 3 -0020926
Regression statistic for 3 components
Rsup2= 0227471 F= 8244611 with 3 and 86 DF plt 0000070
Plot de 90 especiacutemenes de
Microtus agrestis
Distribucioacuten estratigraacutefica de los roedores del cuaternario de Gran Dolina Atapuerca Burgos
0 m
Allo
ph
aio
mys
Mim
om
ys
Ibe
rom
ys
Terr
ico
la
Ste
no
cra
niu
s
Arv
ico
la
Mic
rom
ys
Hy
str
ix
Ca
sto
r
Ma
rmo
ta
Plio
mys
Mic
rotu
s
Allo
cri
cetu
s
Ap
od
em
us
Elio
mys
TD7
TD8
TD10
TD11
TD6
TD5
TD34
TD2
TD1
Procustes analisis APS
bull Procuste fue un ladroacuten que bien descuartizaba o bien estiraba a sus viacutectimas para ajustarlas al tamantildeo de su cama de ahiacute viene la frase hecha de ldquola cama Procusterdquo que se aplica sobre todo en poliacutetica la censura o para prestaciones puacuteblicas en las que es el usuario el que debe adaptarse y no al reveacuteshellip
bull The APS package
bull The shape analysis softwares APS ApsDigit and ApsUtil are written in English and always free for the students Aps combines Procuste superposition and statistical calculations ApsDigit is used locate landmarks on digital images (JPEG Bitmap tiff GIF) ApsUtil is used to handle files (Selection of points individuals change of classification)
bull httpwwwprocustecom
APS
APS est un logiciel danalyse quantitative de la
variabiliteacute morphologique des formes vivantes La
meacutethode utiliseacutee est la superposition procruste
geacuteneacuteraliseacutee
Destineacute aux biologistes et aux cliniciens APS prend en
charge les aspects matheacutematiques et statistiques de
lanalyse de forme Lanalyse se fait en 2 temps
1 Une superposition procruste de lensemble des
speacutecimens
2 Une analyse statistique qui visualise et teste la covariance
entre dune part la conformation et dautre part un facteur
biologique comme la taille lappartenance agrave groupe la
preacutesence ou non dune pathologie
Il est conccedilu pour eacutetudier un ou deux groupes
APS Digitalizar landmarks
DigitX is designed to digitize landmarks on Jpeg or Bitmap picture
middot Select the total number of landmarks to digitize with the second
Combo-Box of the toolbar
middot Select a picture in the graphic file selector on the left
middot Click on to load the link file (optional)
middot Click on to load the consensus file (optional)
middot Digitize landmarks using the left button of the mouse
middot To cancel last landmark position by a click on undo arrow
middot When all landmarks are digitized save the file by a click on save file
APS Crear archivo
Getting started with ApsUtil
ApsUtil create a data file (dat) with specimen ordered by
addition of smaller data files Input and output files are to
APS data format with an header line (number of specimens
number
of landmarks number of dimensions) followed by landmarks
coordinates
NEW button clear all previous data and begin a new data file
ADD button add a file containing one or many specimen
MIX button add a new file to a previous one by mixing the
two file
This ordering of specimen is required before to compute
shape differences
When file is saved specimens are ordered like
specimen 1 of the 1st file
specimen 1 of the 2nd file
specimen 2 of the 1st file
APS analisis
bull New features of Version 241
bull A single specimen or all a sample can be superimposed on any reloaded
bull specimen as consensus (File -gt Reload -gt Consensus)
bull Shape vectors (eg discriminant vectors computed with other software)
bull can be reloaded for visualization (File -gt Reload -gt Pcs)
bull The shape vector must be of norm 1
bull Projections of specimens on shape vectors are automatically computed
Otros
elementos del
esqueleto
A Antarctosaurus wichmannianus B
Saltasaurus loricatus C Neuquensaurus
australis D Neuquensaurus robustus E
Lirainosaurus astibiae F Ampelosaurus atacis
G Magyarosaurus dacus H Magyarosaurus
dacus Jianu I Alamosaurus sanjuanensis J
Aegyptosaurus baharijiensis K
Opisthocoelicaudia skarzynskii
Canudo amp Cuenca Bescos 2004
wwwaragosauruscom
Aegyptosaurus Alamosaurus
Imaacutegenes literatura
Fotos ejemplares
Hacer un poliacutegono con los landmarks
Guardar la misma posicioacuten (en una liacutenea basal por ej)
APS digit
APS util
APS program CP
Opisthocoelicaudia
Resultados
APS Fecha Thu 21 Sep 2006 213918
+0200 [210906 213918 CEST]
De Info Procuste
ltinfoprocustecomgt
Para cuencagunizares
Asunto Re analyse de forme chez
les arvicolides
Cabeceras Mostrar todas las
cabeceras
Chegravere collegravegue
Voici le lien pour teacuteleacutecharger le le
setup dinstallation des 3
logiciels APS ApsDigit et ApsUtil
httpwwwprocustecomprogramsset
up_aps_allexe
Noubliez pas de citer APS dans vos
publications
Bien cordialement
Xavier Penin
Paacuteginas web recomendadas
bull httplifebiosunysbedumorph la mejor paacutegina de
morfometriacutea geomeacutetrica Contiene un listado con todos los
programas de morfometriacutea Universidad de Stony Brook NY
bull httpwwwmorphometricsorgindexhtml es la paacutegina en la
que se mantiene la lista de email morphmet Es la base de la
organizacioacuten de la morfometriacutea en Suny
bull httpwwwflywingsorgukindexhtm iquestporqueacute hay variacioacuten
morfoloacutegica Universidad de Manchester UK
bull httpwwwprocustecomindexhtml anaacutelisis de la forma con
Procruste Aps Xavier Penin Universidad de Paris V
bull Shapehellipy otros ver la paacutegina de Suny
Las ldquoseries TPSrdquo Thin-plate spline
(laacuteminas finas de grosor uniforme)
tpsDIG2
Data acquisition
bull Digitize landmarks amp outlines from image files scanner or video Windows TpsDig is a Windows (95 through XP) program for digitizing landmarks and outlines for geometric morphometric analyses Includes simple image enhancement operations scale factors image brightness profile and support for AVI and MOV files Output is in the TPS file format used by the tps series of programs The TPS file includes the name of the image file for each specimen so that landmarks can always be visualized on the image Since output files are ASCII they can be converted to formats for other software Users should note that the tpsUtil program is useful for both the preparation of the input files to tpsDig as well as for some useful conversions afterwards The program also computes areas of enclosed regions perimeters and linear distances The tpsDig2 link at the left is for the new 205 version
bull Execute the downloaded file to install the program By F James Rohlf
Las ldquoseries TPSrdquo
ordenar los archivos digitalizados
TPS util
bull tps file utility program Windows At present it can randomly scramble the order of specimens in a tps file to minimize bias in digitizing landmark locations restore the original order (eg before statistical analyses are performed) create an empty TPS file from a directory with image files add keywords and values to the variables field of a TPS file combine TPS files into a single TPS file deletereorder landmarks remove outlines from a TPS file and convert TPS and NTS files to NTS M or CSV files It can also split an NTS file into several matrices Graphic editors are included for drawing link and sliders files Unbending a deformed specimen Converting outline and curves points to landmarks
bull Other operations can be added - let me know what you need Execute the TPSUTILW32EXE file to install the program By F James Rohlf Version 138
tpsTree
bull Fit and visualize thin-plate splines on trees Windows Performs a least-squares orthogonal generalized Procrustes analysis to obtain a reference and then estimates the splines for each group (internal node) on a tree Both ultrametric (eg WPGMA and UPGMA trees) and additive trees (using squared change parsimony to estimate the shapes of the HTUs) are supported The estimated shapes can be visualized with estimated images in the background (see the tpsSuper program) The file expands into a Windows setup program and associated files By F James Rohlf Version 118 File containing HTU coordinates and HTU images to demo that feature The older and more limited 16 bit Windows version is still available
tpsRegr
bull Multivariate multiple regression of shape onto independent variables Windows performs a multivariate multiple regression of shape (as captured by partial warp scores and the uniform shape component) onto one or more independent variables By appropriate setting up of independent variables this program can perform various types of MANOVA and MANCOVA Can be used to study allometry By F James Rohlf Version 131
tpsSplin
bull Thin-plate spline Windows Program to
compare pairs of specimens by displaying
a Darcy Thompson style transformation
grid based on a thin-plate spline Several
options are given for sliding
semilandmarks The tpssplnwexe file
expands into a Windows setup program
that will be run automatically By F James
Rohlf Version 120
tpsRelw el anaacutelisis de la
deformacioacuten relativa bull Relative warps analysis Windows Performs a
relative warp (deformacioacuten) analysis This corresponds to a principal components analysis of variation in a sample (relative to bending energy if the alpha parameter is not equal to zero) Displays a plot of relative warp scores and a visualization window that displays the estimated shape for arbitrary points in the ordination Also displays partial warp scores and their visualizations Allows fitting of semilandmark points along curves Version 144 By F James Rohlf
tpsPLS
bull Partial least-squares analysis for shapes Windows Used to explore the covariance between a set of variables and variation in shape or between two shapes It performs a two-block partial least-squares analysis It differs from regression in that both variables and shape are considered equally (one is not considered to be a set of independent variables measured without error) Its use is described in Rohlf and Corti (2000 Systematic Biology 49740-753) By F James Rohlf Version 118
tpsSmall
bull Test for small variation in shape Windows Use to test whether the variation in shape among a set of specimens is too large and thus statistical methods based on the tangent space approximation (eg thin-plate spline methods) cannot be used The program can process both 2D and 3D data files Output files include consensus and aligned specimens By F James Rohlf Version 120
tpsPower
bull Estimate statistical power for comparing shapes Windows Program for estimating statistical power for comparing the mean shapes of two populations Provides methods based on several different approaches Can be used for planning morphometric studies as well as to compare power using different approaches Version 104 By F James Rohlf
Morpheus et al bull Morpheus et al is a software package that will provide a
comprehensive cross-platform environment for morphometric data analysis It is available in graphical and command-line versions for a number of operating systems (see below) More information about new features and previous changes can be found in the release notes
httplifebiosunysbedumorphmorpheus
Multivariate analysis
bull PAST is a free easy-to-use data analysis package aimed at paleontology Windows 95+ Multivariate statistical methods include Principal Components (with Minimal Spanning Tree) Principal Coordinates (ten distance measures) Non-metric Multidimensional Scaling (ten distance measures) Detrended Correspondence Analysis Cluster analysis (three algorithms 11 distance measures) k-means clustering seriation discriminant analysis one-way MANOVA Hotellings t-squared Boxs M Canonical Variates Analysis Also includes Fourier shape analysis thin-plate splines parsimony and time series analysis among others Oslashyvind Hammer University of Oslo
Analysis of outlines
bull Shape Elliptic Fourier WINDOWS Extracts the contour shape from a full color bitmap image delineates the contour shape with the elliptic Fourier descriptors and performs a principal component analysis for summarizing the shape information By Hiroyoshi Iwata For more information see Shape home page tutorial or manual
bull Iwata H and Y Ukai (2002) SHAPE A computer program package for quantitative evaluation of biological shapes based on elliptic Fourier descriptors Journal of Heredity 93 384-385
Eigenshape analysis
bull httpwwwnhmacukhosted_sitespaleonetftpftphtml
bull This archive contains a series of programs designed to perform an eigenshape analysis on xy coordinate data from object outlines Routines include xy -gt phi() transformation phi() -gt xy transformation eigenshape analysis and projection of objects into the eigenshape space Two completely worked example analyses and a users guide are also provided El autor es Norman McLeod del BMNH de Londres
Graphical representation of the four-step morphometric protocol A Quantify raw data
(landmarks recorded on body of cichlid fish) B Remove non-shape variation (landmarks of 412
specimens before and after GPA) C statistical analysis (CVA) and graphical presentation of
results Deformation grids for mean specimen for (right) Eretmodus cyanostictus and (left)
Spathodus erythrodon (magnified by 3X to emphasize shape differences) Data from Ruumlber and
Adams 2001 En Adams Rolhf Slice 2002
La forma en postcraneal el feacutemur de los
sauroacutepodos
bull Canudo y Cuenca Bescoacutes 2004
iquestCoacutemo y por queacute estudiamos la
forma
Orientacioacuten y funciones de los
dientes
bull Arrancar
bull Retener
bull Peinar y
cuidar el
pelo
bull Descortezar
bull roer
bull Cortar
bull Moler
Toma de medidas
W
L
iquestCoacutemo estudiamos la forma
httplifebiosunysbedumorphindexhtml
Adquisicioacuten de los datos
bull Calibre
bull Datos tomados con otras herramientas y volcados a una hoja de caacutelculo (Excel Pasthellip)
bull Imaacutegenes yo datos a partir de la literatura
bull Imaacutegenes tomadas con caacutemara digital
bull Imaacutegenes tomadas desde un microscopio o lupa binocular
Espeacutecimen Longitud (mm)
1a 33
1b 45
1c 29
Landmarks digitalizados con tpsDig2
httplifebiosunysbedumorphindexhtml
Tps digit program
Free at Suny
httplifebiosunysbedumorph
Dientes complejos Arvicolinae
Iberon 25 Landmarks
1
2
4
3
5
6
7
8 9
1011
12
14
15
16
17
18
19
20
21
22
23
24
13
1
2
3
4
5
6
7
89
10
11
12
131415
16
17
18
19
20
21
22
23
24
25
25
archivo 25 iberomys landmarks
Some extreme morphologies
Allophaiomys pliocaenicus Pirro
Nord
Early Pleistocene Italy Iberomys cabrerae
Extant Spain
Allophaiomys lavocati
Sima del Elefante
Atapuerca
Early Pleistocene (older
than the Italian species
Spain
AllophLavF
N3_1r
Early
Pleistocen
e of
Granada
similar to
Atapuerca
LM =17-14 of Iberon LM =15-14 of Iberon LM =15-14 of Iberon
Landmarks de 90 especiacutemenes de
Microtus agrestis
Landmarks de 90 especiacutemenes de
Microtus agrestis
Data 90 Specimens 22 Points 2 Dimensions
All specimen superimposed by GLS method
Sum of Squared Deviations = 1101217
The groups limit is after the specimen 0
PCS and scores computed
Percentages of variance for the 8 first PCS
61395977 61395977
8155754 69551731
4681460 74233190
3352225 77585415
2619139 80204554
2500418 82704973
2235576 84940549
1789387 86729936
Multivariate regression coefficients (normalized) with 3 PCS
PCS 1 0998142
PCS 2 -0057223
PCS 3 -0020926
Regression statistic for 3 components
Rsup2= 0227471 F= 8244611 with 3 and 86 DF plt 0000070
Plot de 90 especiacutemenes de
Microtus agrestis
Distribucioacuten estratigraacutefica de los roedores del cuaternario de Gran Dolina Atapuerca Burgos
0 m
Allo
ph
aio
mys
Mim
om
ys
Ibe
rom
ys
Terr
ico
la
Ste
no
cra
niu
s
Arv
ico
la
Mic
rom
ys
Hy
str
ix
Ca
sto
r
Ma
rmo
ta
Plio
mys
Mic
rotu
s
Allo
cri
cetu
s
Ap
od
em
us
Elio
mys
TD7
TD8
TD10
TD11
TD6
TD5
TD34
TD2
TD1
Procustes analisis APS
bull Procuste fue un ladroacuten que bien descuartizaba o bien estiraba a sus viacutectimas para ajustarlas al tamantildeo de su cama de ahiacute viene la frase hecha de ldquola cama Procusterdquo que se aplica sobre todo en poliacutetica la censura o para prestaciones puacuteblicas en las que es el usuario el que debe adaptarse y no al reveacuteshellip
bull The APS package
bull The shape analysis softwares APS ApsDigit and ApsUtil are written in English and always free for the students Aps combines Procuste superposition and statistical calculations ApsDigit is used locate landmarks on digital images (JPEG Bitmap tiff GIF) ApsUtil is used to handle files (Selection of points individuals change of classification)
bull httpwwwprocustecom
APS
APS est un logiciel danalyse quantitative de la
variabiliteacute morphologique des formes vivantes La
meacutethode utiliseacutee est la superposition procruste
geacuteneacuteraliseacutee
Destineacute aux biologistes et aux cliniciens APS prend en
charge les aspects matheacutematiques et statistiques de
lanalyse de forme Lanalyse se fait en 2 temps
1 Une superposition procruste de lensemble des
speacutecimens
2 Une analyse statistique qui visualise et teste la covariance
entre dune part la conformation et dautre part un facteur
biologique comme la taille lappartenance agrave groupe la
preacutesence ou non dune pathologie
Il est conccedilu pour eacutetudier un ou deux groupes
APS Digitalizar landmarks
DigitX is designed to digitize landmarks on Jpeg or Bitmap picture
middot Select the total number of landmarks to digitize with the second
Combo-Box of the toolbar
middot Select a picture in the graphic file selector on the left
middot Click on to load the link file (optional)
middot Click on to load the consensus file (optional)
middot Digitize landmarks using the left button of the mouse
middot To cancel last landmark position by a click on undo arrow
middot When all landmarks are digitized save the file by a click on save file
APS Crear archivo
Getting started with ApsUtil
ApsUtil create a data file (dat) with specimen ordered by
addition of smaller data files Input and output files are to
APS data format with an header line (number of specimens
number
of landmarks number of dimensions) followed by landmarks
coordinates
NEW button clear all previous data and begin a new data file
ADD button add a file containing one or many specimen
MIX button add a new file to a previous one by mixing the
two file
This ordering of specimen is required before to compute
shape differences
When file is saved specimens are ordered like
specimen 1 of the 1st file
specimen 1 of the 2nd file
specimen 2 of the 1st file
APS analisis
bull New features of Version 241
bull A single specimen or all a sample can be superimposed on any reloaded
bull specimen as consensus (File -gt Reload -gt Consensus)
bull Shape vectors (eg discriminant vectors computed with other software)
bull can be reloaded for visualization (File -gt Reload -gt Pcs)
bull The shape vector must be of norm 1
bull Projections of specimens on shape vectors are automatically computed
Otros
elementos del
esqueleto
A Antarctosaurus wichmannianus B
Saltasaurus loricatus C Neuquensaurus
australis D Neuquensaurus robustus E
Lirainosaurus astibiae F Ampelosaurus atacis
G Magyarosaurus dacus H Magyarosaurus
dacus Jianu I Alamosaurus sanjuanensis J
Aegyptosaurus baharijiensis K
Opisthocoelicaudia skarzynskii
Canudo amp Cuenca Bescos 2004
wwwaragosauruscom
Aegyptosaurus Alamosaurus
Imaacutegenes literatura
Fotos ejemplares
Hacer un poliacutegono con los landmarks
Guardar la misma posicioacuten (en una liacutenea basal por ej)
APS digit
APS util
APS program CP
Opisthocoelicaudia
Resultados
APS Fecha Thu 21 Sep 2006 213918
+0200 [210906 213918 CEST]
De Info Procuste
ltinfoprocustecomgt
Para cuencagunizares
Asunto Re analyse de forme chez
les arvicolides
Cabeceras Mostrar todas las
cabeceras
Chegravere collegravegue
Voici le lien pour teacuteleacutecharger le le
setup dinstallation des 3
logiciels APS ApsDigit et ApsUtil
httpwwwprocustecomprogramsset
up_aps_allexe
Noubliez pas de citer APS dans vos
publications
Bien cordialement
Xavier Penin
Paacuteginas web recomendadas
bull httplifebiosunysbedumorph la mejor paacutegina de
morfometriacutea geomeacutetrica Contiene un listado con todos los
programas de morfometriacutea Universidad de Stony Brook NY
bull httpwwwmorphometricsorgindexhtml es la paacutegina en la
que se mantiene la lista de email morphmet Es la base de la
organizacioacuten de la morfometriacutea en Suny
bull httpwwwflywingsorgukindexhtm iquestporqueacute hay variacioacuten
morfoloacutegica Universidad de Manchester UK
bull httpwwwprocustecomindexhtml anaacutelisis de la forma con
Procruste Aps Xavier Penin Universidad de Paris V
bull Shapehellipy otros ver la paacutegina de Suny
Las ldquoseries TPSrdquo Thin-plate spline
(laacuteminas finas de grosor uniforme)
tpsDIG2
Data acquisition
bull Digitize landmarks amp outlines from image files scanner or video Windows TpsDig is a Windows (95 through XP) program for digitizing landmarks and outlines for geometric morphometric analyses Includes simple image enhancement operations scale factors image brightness profile and support for AVI and MOV files Output is in the TPS file format used by the tps series of programs The TPS file includes the name of the image file for each specimen so that landmarks can always be visualized on the image Since output files are ASCII they can be converted to formats for other software Users should note that the tpsUtil program is useful for both the preparation of the input files to tpsDig as well as for some useful conversions afterwards The program also computes areas of enclosed regions perimeters and linear distances The tpsDig2 link at the left is for the new 205 version
bull Execute the downloaded file to install the program By F James Rohlf
Las ldquoseries TPSrdquo
ordenar los archivos digitalizados
TPS util
bull tps file utility program Windows At present it can randomly scramble the order of specimens in a tps file to minimize bias in digitizing landmark locations restore the original order (eg before statistical analyses are performed) create an empty TPS file from a directory with image files add keywords and values to the variables field of a TPS file combine TPS files into a single TPS file deletereorder landmarks remove outlines from a TPS file and convert TPS and NTS files to NTS M or CSV files It can also split an NTS file into several matrices Graphic editors are included for drawing link and sliders files Unbending a deformed specimen Converting outline and curves points to landmarks
bull Other operations can be added - let me know what you need Execute the TPSUTILW32EXE file to install the program By F James Rohlf Version 138
tpsTree
bull Fit and visualize thin-plate splines on trees Windows Performs a least-squares orthogonal generalized Procrustes analysis to obtain a reference and then estimates the splines for each group (internal node) on a tree Both ultrametric (eg WPGMA and UPGMA trees) and additive trees (using squared change parsimony to estimate the shapes of the HTUs) are supported The estimated shapes can be visualized with estimated images in the background (see the tpsSuper program) The file expands into a Windows setup program and associated files By F James Rohlf Version 118 File containing HTU coordinates and HTU images to demo that feature The older and more limited 16 bit Windows version is still available
tpsRegr
bull Multivariate multiple regression of shape onto independent variables Windows performs a multivariate multiple regression of shape (as captured by partial warp scores and the uniform shape component) onto one or more independent variables By appropriate setting up of independent variables this program can perform various types of MANOVA and MANCOVA Can be used to study allometry By F James Rohlf Version 131
tpsSplin
bull Thin-plate spline Windows Program to
compare pairs of specimens by displaying
a Darcy Thompson style transformation
grid based on a thin-plate spline Several
options are given for sliding
semilandmarks The tpssplnwexe file
expands into a Windows setup program
that will be run automatically By F James
Rohlf Version 120
tpsRelw el anaacutelisis de la
deformacioacuten relativa bull Relative warps analysis Windows Performs a
relative warp (deformacioacuten) analysis This corresponds to a principal components analysis of variation in a sample (relative to bending energy if the alpha parameter is not equal to zero) Displays a plot of relative warp scores and a visualization window that displays the estimated shape for arbitrary points in the ordination Also displays partial warp scores and their visualizations Allows fitting of semilandmark points along curves Version 144 By F James Rohlf
tpsPLS
bull Partial least-squares analysis for shapes Windows Used to explore the covariance between a set of variables and variation in shape or between two shapes It performs a two-block partial least-squares analysis It differs from regression in that both variables and shape are considered equally (one is not considered to be a set of independent variables measured without error) Its use is described in Rohlf and Corti (2000 Systematic Biology 49740-753) By F James Rohlf Version 118
tpsSmall
bull Test for small variation in shape Windows Use to test whether the variation in shape among a set of specimens is too large and thus statistical methods based on the tangent space approximation (eg thin-plate spline methods) cannot be used The program can process both 2D and 3D data files Output files include consensus and aligned specimens By F James Rohlf Version 120
tpsPower
bull Estimate statistical power for comparing shapes Windows Program for estimating statistical power for comparing the mean shapes of two populations Provides methods based on several different approaches Can be used for planning morphometric studies as well as to compare power using different approaches Version 104 By F James Rohlf
Morpheus et al bull Morpheus et al is a software package that will provide a
comprehensive cross-platform environment for morphometric data analysis It is available in graphical and command-line versions for a number of operating systems (see below) More information about new features and previous changes can be found in the release notes
httplifebiosunysbedumorphmorpheus
Multivariate analysis
bull PAST is a free easy-to-use data analysis package aimed at paleontology Windows 95+ Multivariate statistical methods include Principal Components (with Minimal Spanning Tree) Principal Coordinates (ten distance measures) Non-metric Multidimensional Scaling (ten distance measures) Detrended Correspondence Analysis Cluster analysis (three algorithms 11 distance measures) k-means clustering seriation discriminant analysis one-way MANOVA Hotellings t-squared Boxs M Canonical Variates Analysis Also includes Fourier shape analysis thin-plate splines parsimony and time series analysis among others Oslashyvind Hammer University of Oslo
Analysis of outlines
bull Shape Elliptic Fourier WINDOWS Extracts the contour shape from a full color bitmap image delineates the contour shape with the elliptic Fourier descriptors and performs a principal component analysis for summarizing the shape information By Hiroyoshi Iwata For more information see Shape home page tutorial or manual
bull Iwata H and Y Ukai (2002) SHAPE A computer program package for quantitative evaluation of biological shapes based on elliptic Fourier descriptors Journal of Heredity 93 384-385
Eigenshape analysis
bull httpwwwnhmacukhosted_sitespaleonetftpftphtml
bull This archive contains a series of programs designed to perform an eigenshape analysis on xy coordinate data from object outlines Routines include xy -gt phi() transformation phi() -gt xy transformation eigenshape analysis and projection of objects into the eigenshape space Two completely worked example analyses and a users guide are also provided El autor es Norman McLeod del BMNH de Londres
Graphical representation of the four-step morphometric protocol A Quantify raw data
(landmarks recorded on body of cichlid fish) B Remove non-shape variation (landmarks of 412
specimens before and after GPA) C statistical analysis (CVA) and graphical presentation of
results Deformation grids for mean specimen for (right) Eretmodus cyanostictus and (left)
Spathodus erythrodon (magnified by 3X to emphasize shape differences) Data from Ruumlber and
Adams 2001 En Adams Rolhf Slice 2002
iquestCoacutemo y por queacute estudiamos la
forma
Orientacioacuten y funciones de los
dientes
bull Arrancar
bull Retener
bull Peinar y
cuidar el
pelo
bull Descortezar
bull roer
bull Cortar
bull Moler
Toma de medidas
W
L
iquestCoacutemo estudiamos la forma
httplifebiosunysbedumorphindexhtml
Adquisicioacuten de los datos
bull Calibre
bull Datos tomados con otras herramientas y volcados a una hoja de caacutelculo (Excel Pasthellip)
bull Imaacutegenes yo datos a partir de la literatura
bull Imaacutegenes tomadas con caacutemara digital
bull Imaacutegenes tomadas desde un microscopio o lupa binocular
Espeacutecimen Longitud (mm)
1a 33
1b 45
1c 29
Landmarks digitalizados con tpsDig2
httplifebiosunysbedumorphindexhtml
Tps digit program
Free at Suny
httplifebiosunysbedumorph
Dientes complejos Arvicolinae
Iberon 25 Landmarks
1
2
4
3
5
6
7
8 9
1011
12
14
15
16
17
18
19
20
21
22
23
24
13
1
2
3
4
5
6
7
89
10
11
12
131415
16
17
18
19
20
21
22
23
24
25
25
archivo 25 iberomys landmarks
Some extreme morphologies
Allophaiomys pliocaenicus Pirro
Nord
Early Pleistocene Italy Iberomys cabrerae
Extant Spain
Allophaiomys lavocati
Sima del Elefante
Atapuerca
Early Pleistocene (older
than the Italian species
Spain
AllophLavF
N3_1r
Early
Pleistocen
e of
Granada
similar to
Atapuerca
LM =17-14 of Iberon LM =15-14 of Iberon LM =15-14 of Iberon
Landmarks de 90 especiacutemenes de
Microtus agrestis
Landmarks de 90 especiacutemenes de
Microtus agrestis
Data 90 Specimens 22 Points 2 Dimensions
All specimen superimposed by GLS method
Sum of Squared Deviations = 1101217
The groups limit is after the specimen 0
PCS and scores computed
Percentages of variance for the 8 first PCS
61395977 61395977
8155754 69551731
4681460 74233190
3352225 77585415
2619139 80204554
2500418 82704973
2235576 84940549
1789387 86729936
Multivariate regression coefficients (normalized) with 3 PCS
PCS 1 0998142
PCS 2 -0057223
PCS 3 -0020926
Regression statistic for 3 components
Rsup2= 0227471 F= 8244611 with 3 and 86 DF plt 0000070
Plot de 90 especiacutemenes de
Microtus agrestis
Distribucioacuten estratigraacutefica de los roedores del cuaternario de Gran Dolina Atapuerca Burgos
0 m
Allo
ph
aio
mys
Mim
om
ys
Ibe
rom
ys
Terr
ico
la
Ste
no
cra
niu
s
Arv
ico
la
Mic
rom
ys
Hy
str
ix
Ca
sto
r
Ma
rmo
ta
Plio
mys
Mic
rotu
s
Allo
cri
cetu
s
Ap
od
em
us
Elio
mys
TD7
TD8
TD10
TD11
TD6
TD5
TD34
TD2
TD1
Procustes analisis APS
bull Procuste fue un ladroacuten que bien descuartizaba o bien estiraba a sus viacutectimas para ajustarlas al tamantildeo de su cama de ahiacute viene la frase hecha de ldquola cama Procusterdquo que se aplica sobre todo en poliacutetica la censura o para prestaciones puacuteblicas en las que es el usuario el que debe adaptarse y no al reveacuteshellip
bull The APS package
bull The shape analysis softwares APS ApsDigit and ApsUtil are written in English and always free for the students Aps combines Procuste superposition and statistical calculations ApsDigit is used locate landmarks on digital images (JPEG Bitmap tiff GIF) ApsUtil is used to handle files (Selection of points individuals change of classification)
bull httpwwwprocustecom
APS
APS est un logiciel danalyse quantitative de la
variabiliteacute morphologique des formes vivantes La
meacutethode utiliseacutee est la superposition procruste
geacuteneacuteraliseacutee
Destineacute aux biologistes et aux cliniciens APS prend en
charge les aspects matheacutematiques et statistiques de
lanalyse de forme Lanalyse se fait en 2 temps
1 Une superposition procruste de lensemble des
speacutecimens
2 Une analyse statistique qui visualise et teste la covariance
entre dune part la conformation et dautre part un facteur
biologique comme la taille lappartenance agrave groupe la
preacutesence ou non dune pathologie
Il est conccedilu pour eacutetudier un ou deux groupes
APS Digitalizar landmarks
DigitX is designed to digitize landmarks on Jpeg or Bitmap picture
middot Select the total number of landmarks to digitize with the second
Combo-Box of the toolbar
middot Select a picture in the graphic file selector on the left
middot Click on to load the link file (optional)
middot Click on to load the consensus file (optional)
middot Digitize landmarks using the left button of the mouse
middot To cancel last landmark position by a click on undo arrow
middot When all landmarks are digitized save the file by a click on save file
APS Crear archivo
Getting started with ApsUtil
ApsUtil create a data file (dat) with specimen ordered by
addition of smaller data files Input and output files are to
APS data format with an header line (number of specimens
number
of landmarks number of dimensions) followed by landmarks
coordinates
NEW button clear all previous data and begin a new data file
ADD button add a file containing one or many specimen
MIX button add a new file to a previous one by mixing the
two file
This ordering of specimen is required before to compute
shape differences
When file is saved specimens are ordered like
specimen 1 of the 1st file
specimen 1 of the 2nd file
specimen 2 of the 1st file
APS analisis
bull New features of Version 241
bull A single specimen or all a sample can be superimposed on any reloaded
bull specimen as consensus (File -gt Reload -gt Consensus)
bull Shape vectors (eg discriminant vectors computed with other software)
bull can be reloaded for visualization (File -gt Reload -gt Pcs)
bull The shape vector must be of norm 1
bull Projections of specimens on shape vectors are automatically computed
Otros
elementos del
esqueleto
A Antarctosaurus wichmannianus B
Saltasaurus loricatus C Neuquensaurus
australis D Neuquensaurus robustus E
Lirainosaurus astibiae F Ampelosaurus atacis
G Magyarosaurus dacus H Magyarosaurus
dacus Jianu I Alamosaurus sanjuanensis J
Aegyptosaurus baharijiensis K
Opisthocoelicaudia skarzynskii
Canudo amp Cuenca Bescos 2004
wwwaragosauruscom
Aegyptosaurus Alamosaurus
Imaacutegenes literatura
Fotos ejemplares
Hacer un poliacutegono con los landmarks
Guardar la misma posicioacuten (en una liacutenea basal por ej)
APS digit
APS util
APS program CP
Opisthocoelicaudia
Resultados
APS Fecha Thu 21 Sep 2006 213918
+0200 [210906 213918 CEST]
De Info Procuste
ltinfoprocustecomgt
Para cuencagunizares
Asunto Re analyse de forme chez
les arvicolides
Cabeceras Mostrar todas las
cabeceras
Chegravere collegravegue
Voici le lien pour teacuteleacutecharger le le
setup dinstallation des 3
logiciels APS ApsDigit et ApsUtil
httpwwwprocustecomprogramsset
up_aps_allexe
Noubliez pas de citer APS dans vos
publications
Bien cordialement
Xavier Penin
Paacuteginas web recomendadas
bull httplifebiosunysbedumorph la mejor paacutegina de
morfometriacutea geomeacutetrica Contiene un listado con todos los
programas de morfometriacutea Universidad de Stony Brook NY
bull httpwwwmorphometricsorgindexhtml es la paacutegina en la
que se mantiene la lista de email morphmet Es la base de la
organizacioacuten de la morfometriacutea en Suny
bull httpwwwflywingsorgukindexhtm iquestporqueacute hay variacioacuten
morfoloacutegica Universidad de Manchester UK
bull httpwwwprocustecomindexhtml anaacutelisis de la forma con
Procruste Aps Xavier Penin Universidad de Paris V
bull Shapehellipy otros ver la paacutegina de Suny
Las ldquoseries TPSrdquo Thin-plate spline
(laacuteminas finas de grosor uniforme)
tpsDIG2
Data acquisition
bull Digitize landmarks amp outlines from image files scanner or video Windows TpsDig is a Windows (95 through XP) program for digitizing landmarks and outlines for geometric morphometric analyses Includes simple image enhancement operations scale factors image brightness profile and support for AVI and MOV files Output is in the TPS file format used by the tps series of programs The TPS file includes the name of the image file for each specimen so that landmarks can always be visualized on the image Since output files are ASCII they can be converted to formats for other software Users should note that the tpsUtil program is useful for both the preparation of the input files to tpsDig as well as for some useful conversions afterwards The program also computes areas of enclosed regions perimeters and linear distances The tpsDig2 link at the left is for the new 205 version
bull Execute the downloaded file to install the program By F James Rohlf
Las ldquoseries TPSrdquo
ordenar los archivos digitalizados
TPS util
bull tps file utility program Windows At present it can randomly scramble the order of specimens in a tps file to minimize bias in digitizing landmark locations restore the original order (eg before statistical analyses are performed) create an empty TPS file from a directory with image files add keywords and values to the variables field of a TPS file combine TPS files into a single TPS file deletereorder landmarks remove outlines from a TPS file and convert TPS and NTS files to NTS M or CSV files It can also split an NTS file into several matrices Graphic editors are included for drawing link and sliders files Unbending a deformed specimen Converting outline and curves points to landmarks
bull Other operations can be added - let me know what you need Execute the TPSUTILW32EXE file to install the program By F James Rohlf Version 138
tpsTree
bull Fit and visualize thin-plate splines on trees Windows Performs a least-squares orthogonal generalized Procrustes analysis to obtain a reference and then estimates the splines for each group (internal node) on a tree Both ultrametric (eg WPGMA and UPGMA trees) and additive trees (using squared change parsimony to estimate the shapes of the HTUs) are supported The estimated shapes can be visualized with estimated images in the background (see the tpsSuper program) The file expands into a Windows setup program and associated files By F James Rohlf Version 118 File containing HTU coordinates and HTU images to demo that feature The older and more limited 16 bit Windows version is still available
tpsRegr
bull Multivariate multiple regression of shape onto independent variables Windows performs a multivariate multiple regression of shape (as captured by partial warp scores and the uniform shape component) onto one or more independent variables By appropriate setting up of independent variables this program can perform various types of MANOVA and MANCOVA Can be used to study allometry By F James Rohlf Version 131
tpsSplin
bull Thin-plate spline Windows Program to
compare pairs of specimens by displaying
a Darcy Thompson style transformation
grid based on a thin-plate spline Several
options are given for sliding
semilandmarks The tpssplnwexe file
expands into a Windows setup program
that will be run automatically By F James
Rohlf Version 120
tpsRelw el anaacutelisis de la
deformacioacuten relativa bull Relative warps analysis Windows Performs a
relative warp (deformacioacuten) analysis This corresponds to a principal components analysis of variation in a sample (relative to bending energy if the alpha parameter is not equal to zero) Displays a plot of relative warp scores and a visualization window that displays the estimated shape for arbitrary points in the ordination Also displays partial warp scores and their visualizations Allows fitting of semilandmark points along curves Version 144 By F James Rohlf
tpsPLS
bull Partial least-squares analysis for shapes Windows Used to explore the covariance between a set of variables and variation in shape or between two shapes It performs a two-block partial least-squares analysis It differs from regression in that both variables and shape are considered equally (one is not considered to be a set of independent variables measured without error) Its use is described in Rohlf and Corti (2000 Systematic Biology 49740-753) By F James Rohlf Version 118
tpsSmall
bull Test for small variation in shape Windows Use to test whether the variation in shape among a set of specimens is too large and thus statistical methods based on the tangent space approximation (eg thin-plate spline methods) cannot be used The program can process both 2D and 3D data files Output files include consensus and aligned specimens By F James Rohlf Version 120
tpsPower
bull Estimate statistical power for comparing shapes Windows Program for estimating statistical power for comparing the mean shapes of two populations Provides methods based on several different approaches Can be used for planning morphometric studies as well as to compare power using different approaches Version 104 By F James Rohlf
Morpheus et al bull Morpheus et al is a software package that will provide a
comprehensive cross-platform environment for morphometric data analysis It is available in graphical and command-line versions for a number of operating systems (see below) More information about new features and previous changes can be found in the release notes
httplifebiosunysbedumorphmorpheus
Multivariate analysis
bull PAST is a free easy-to-use data analysis package aimed at paleontology Windows 95+ Multivariate statistical methods include Principal Components (with Minimal Spanning Tree) Principal Coordinates (ten distance measures) Non-metric Multidimensional Scaling (ten distance measures) Detrended Correspondence Analysis Cluster analysis (three algorithms 11 distance measures) k-means clustering seriation discriminant analysis one-way MANOVA Hotellings t-squared Boxs M Canonical Variates Analysis Also includes Fourier shape analysis thin-plate splines parsimony and time series analysis among others Oslashyvind Hammer University of Oslo
Analysis of outlines
bull Shape Elliptic Fourier WINDOWS Extracts the contour shape from a full color bitmap image delineates the contour shape with the elliptic Fourier descriptors and performs a principal component analysis for summarizing the shape information By Hiroyoshi Iwata For more information see Shape home page tutorial or manual
bull Iwata H and Y Ukai (2002) SHAPE A computer program package for quantitative evaluation of biological shapes based on elliptic Fourier descriptors Journal of Heredity 93 384-385
Eigenshape analysis
bull httpwwwnhmacukhosted_sitespaleonetftpftphtml
bull This archive contains a series of programs designed to perform an eigenshape analysis on xy coordinate data from object outlines Routines include xy -gt phi() transformation phi() -gt xy transformation eigenshape analysis and projection of objects into the eigenshape space Two completely worked example analyses and a users guide are also provided El autor es Norman McLeod del BMNH de Londres
Graphical representation of the four-step morphometric protocol A Quantify raw data
(landmarks recorded on body of cichlid fish) B Remove non-shape variation (landmarks of 412
specimens before and after GPA) C statistical analysis (CVA) and graphical presentation of
results Deformation grids for mean specimen for (right) Eretmodus cyanostictus and (left)
Spathodus erythrodon (magnified by 3X to emphasize shape differences) Data from Ruumlber and
Adams 2001 En Adams Rolhf Slice 2002
Orientacioacuten y funciones de los
dientes
bull Arrancar
bull Retener
bull Peinar y
cuidar el
pelo
bull Descortezar
bull roer
bull Cortar
bull Moler
Toma de medidas
W
L
iquestCoacutemo estudiamos la forma
httplifebiosunysbedumorphindexhtml
Adquisicioacuten de los datos
bull Calibre
bull Datos tomados con otras herramientas y volcados a una hoja de caacutelculo (Excel Pasthellip)
bull Imaacutegenes yo datos a partir de la literatura
bull Imaacutegenes tomadas con caacutemara digital
bull Imaacutegenes tomadas desde un microscopio o lupa binocular
Espeacutecimen Longitud (mm)
1a 33
1b 45
1c 29
Landmarks digitalizados con tpsDig2
httplifebiosunysbedumorphindexhtml
Tps digit program
Free at Suny
httplifebiosunysbedumorph
Dientes complejos Arvicolinae
Iberon 25 Landmarks
1
2
4
3
5
6
7
8 9
1011
12
14
15
16
17
18
19
20
21
22
23
24
13
1
2
3
4
5
6
7
89
10
11
12
131415
16
17
18
19
20
21
22
23
24
25
25
archivo 25 iberomys landmarks
Some extreme morphologies
Allophaiomys pliocaenicus Pirro
Nord
Early Pleistocene Italy Iberomys cabrerae
Extant Spain
Allophaiomys lavocati
Sima del Elefante
Atapuerca
Early Pleistocene (older
than the Italian species
Spain
AllophLavF
N3_1r
Early
Pleistocen
e of
Granada
similar to
Atapuerca
LM =17-14 of Iberon LM =15-14 of Iberon LM =15-14 of Iberon
Landmarks de 90 especiacutemenes de
Microtus agrestis
Landmarks de 90 especiacutemenes de
Microtus agrestis
Data 90 Specimens 22 Points 2 Dimensions
All specimen superimposed by GLS method
Sum of Squared Deviations = 1101217
The groups limit is after the specimen 0
PCS and scores computed
Percentages of variance for the 8 first PCS
61395977 61395977
8155754 69551731
4681460 74233190
3352225 77585415
2619139 80204554
2500418 82704973
2235576 84940549
1789387 86729936
Multivariate regression coefficients (normalized) with 3 PCS
PCS 1 0998142
PCS 2 -0057223
PCS 3 -0020926
Regression statistic for 3 components
Rsup2= 0227471 F= 8244611 with 3 and 86 DF plt 0000070
Plot de 90 especiacutemenes de
Microtus agrestis
Distribucioacuten estratigraacutefica de los roedores del cuaternario de Gran Dolina Atapuerca Burgos
0 m
Allo
ph
aio
mys
Mim
om
ys
Ibe
rom
ys
Terr
ico
la
Ste
no
cra
niu
s
Arv
ico
la
Mic
rom
ys
Hy
str
ix
Ca
sto
r
Ma
rmo
ta
Plio
mys
Mic
rotu
s
Allo
cri
cetu
s
Ap
od
em
us
Elio
mys
TD7
TD8
TD10
TD11
TD6
TD5
TD34
TD2
TD1
Procustes analisis APS
bull Procuste fue un ladroacuten que bien descuartizaba o bien estiraba a sus viacutectimas para ajustarlas al tamantildeo de su cama de ahiacute viene la frase hecha de ldquola cama Procusterdquo que se aplica sobre todo en poliacutetica la censura o para prestaciones puacuteblicas en las que es el usuario el que debe adaptarse y no al reveacuteshellip
bull The APS package
bull The shape analysis softwares APS ApsDigit and ApsUtil are written in English and always free for the students Aps combines Procuste superposition and statistical calculations ApsDigit is used locate landmarks on digital images (JPEG Bitmap tiff GIF) ApsUtil is used to handle files (Selection of points individuals change of classification)
bull httpwwwprocustecom
APS
APS est un logiciel danalyse quantitative de la
variabiliteacute morphologique des formes vivantes La
meacutethode utiliseacutee est la superposition procruste
geacuteneacuteraliseacutee
Destineacute aux biologistes et aux cliniciens APS prend en
charge les aspects matheacutematiques et statistiques de
lanalyse de forme Lanalyse se fait en 2 temps
1 Une superposition procruste de lensemble des
speacutecimens
2 Une analyse statistique qui visualise et teste la covariance
entre dune part la conformation et dautre part un facteur
biologique comme la taille lappartenance agrave groupe la
preacutesence ou non dune pathologie
Il est conccedilu pour eacutetudier un ou deux groupes
APS Digitalizar landmarks
DigitX is designed to digitize landmarks on Jpeg or Bitmap picture
middot Select the total number of landmarks to digitize with the second
Combo-Box of the toolbar
middot Select a picture in the graphic file selector on the left
middot Click on to load the link file (optional)
middot Click on to load the consensus file (optional)
middot Digitize landmarks using the left button of the mouse
middot To cancel last landmark position by a click on undo arrow
middot When all landmarks are digitized save the file by a click on save file
APS Crear archivo
Getting started with ApsUtil
ApsUtil create a data file (dat) with specimen ordered by
addition of smaller data files Input and output files are to
APS data format with an header line (number of specimens
number
of landmarks number of dimensions) followed by landmarks
coordinates
NEW button clear all previous data and begin a new data file
ADD button add a file containing one or many specimen
MIX button add a new file to a previous one by mixing the
two file
This ordering of specimen is required before to compute
shape differences
When file is saved specimens are ordered like
specimen 1 of the 1st file
specimen 1 of the 2nd file
specimen 2 of the 1st file
APS analisis
bull New features of Version 241
bull A single specimen or all a sample can be superimposed on any reloaded
bull specimen as consensus (File -gt Reload -gt Consensus)
bull Shape vectors (eg discriminant vectors computed with other software)
bull can be reloaded for visualization (File -gt Reload -gt Pcs)
bull The shape vector must be of norm 1
bull Projections of specimens on shape vectors are automatically computed
Otros
elementos del
esqueleto
A Antarctosaurus wichmannianus B
Saltasaurus loricatus C Neuquensaurus
australis D Neuquensaurus robustus E
Lirainosaurus astibiae F Ampelosaurus atacis
G Magyarosaurus dacus H Magyarosaurus
dacus Jianu I Alamosaurus sanjuanensis J
Aegyptosaurus baharijiensis K
Opisthocoelicaudia skarzynskii
Canudo amp Cuenca Bescos 2004
wwwaragosauruscom
Aegyptosaurus Alamosaurus
Imaacutegenes literatura
Fotos ejemplares
Hacer un poliacutegono con los landmarks
Guardar la misma posicioacuten (en una liacutenea basal por ej)
APS digit
APS util
APS program CP
Opisthocoelicaudia
Resultados
APS Fecha Thu 21 Sep 2006 213918
+0200 [210906 213918 CEST]
De Info Procuste
ltinfoprocustecomgt
Para cuencagunizares
Asunto Re analyse de forme chez
les arvicolides
Cabeceras Mostrar todas las
cabeceras
Chegravere collegravegue
Voici le lien pour teacuteleacutecharger le le
setup dinstallation des 3
logiciels APS ApsDigit et ApsUtil
httpwwwprocustecomprogramsset
up_aps_allexe
Noubliez pas de citer APS dans vos
publications
Bien cordialement
Xavier Penin
Paacuteginas web recomendadas
bull httplifebiosunysbedumorph la mejor paacutegina de
morfometriacutea geomeacutetrica Contiene un listado con todos los
programas de morfometriacutea Universidad de Stony Brook NY
bull httpwwwmorphometricsorgindexhtml es la paacutegina en la
que se mantiene la lista de email morphmet Es la base de la
organizacioacuten de la morfometriacutea en Suny
bull httpwwwflywingsorgukindexhtm iquestporqueacute hay variacioacuten
morfoloacutegica Universidad de Manchester UK
bull httpwwwprocustecomindexhtml anaacutelisis de la forma con
Procruste Aps Xavier Penin Universidad de Paris V
bull Shapehellipy otros ver la paacutegina de Suny
Las ldquoseries TPSrdquo Thin-plate spline
(laacuteminas finas de grosor uniforme)
tpsDIG2
Data acquisition
bull Digitize landmarks amp outlines from image files scanner or video Windows TpsDig is a Windows (95 through XP) program for digitizing landmarks and outlines for geometric morphometric analyses Includes simple image enhancement operations scale factors image brightness profile and support for AVI and MOV files Output is in the TPS file format used by the tps series of programs The TPS file includes the name of the image file for each specimen so that landmarks can always be visualized on the image Since output files are ASCII they can be converted to formats for other software Users should note that the tpsUtil program is useful for both the preparation of the input files to tpsDig as well as for some useful conversions afterwards The program also computes areas of enclosed regions perimeters and linear distances The tpsDig2 link at the left is for the new 205 version
bull Execute the downloaded file to install the program By F James Rohlf
Las ldquoseries TPSrdquo
ordenar los archivos digitalizados
TPS util
bull tps file utility program Windows At present it can randomly scramble the order of specimens in a tps file to minimize bias in digitizing landmark locations restore the original order (eg before statistical analyses are performed) create an empty TPS file from a directory with image files add keywords and values to the variables field of a TPS file combine TPS files into a single TPS file deletereorder landmarks remove outlines from a TPS file and convert TPS and NTS files to NTS M or CSV files It can also split an NTS file into several matrices Graphic editors are included for drawing link and sliders files Unbending a deformed specimen Converting outline and curves points to landmarks
bull Other operations can be added - let me know what you need Execute the TPSUTILW32EXE file to install the program By F James Rohlf Version 138
tpsTree
bull Fit and visualize thin-plate splines on trees Windows Performs a least-squares orthogonal generalized Procrustes analysis to obtain a reference and then estimates the splines for each group (internal node) on a tree Both ultrametric (eg WPGMA and UPGMA trees) and additive trees (using squared change parsimony to estimate the shapes of the HTUs) are supported The estimated shapes can be visualized with estimated images in the background (see the tpsSuper program) The file expands into a Windows setup program and associated files By F James Rohlf Version 118 File containing HTU coordinates and HTU images to demo that feature The older and more limited 16 bit Windows version is still available
tpsRegr
bull Multivariate multiple regression of shape onto independent variables Windows performs a multivariate multiple regression of shape (as captured by partial warp scores and the uniform shape component) onto one or more independent variables By appropriate setting up of independent variables this program can perform various types of MANOVA and MANCOVA Can be used to study allometry By F James Rohlf Version 131
tpsSplin
bull Thin-plate spline Windows Program to
compare pairs of specimens by displaying
a Darcy Thompson style transformation
grid based on a thin-plate spline Several
options are given for sliding
semilandmarks The tpssplnwexe file
expands into a Windows setup program
that will be run automatically By F James
Rohlf Version 120
tpsRelw el anaacutelisis de la
deformacioacuten relativa bull Relative warps analysis Windows Performs a
relative warp (deformacioacuten) analysis This corresponds to a principal components analysis of variation in a sample (relative to bending energy if the alpha parameter is not equal to zero) Displays a plot of relative warp scores and a visualization window that displays the estimated shape for arbitrary points in the ordination Also displays partial warp scores and their visualizations Allows fitting of semilandmark points along curves Version 144 By F James Rohlf
tpsPLS
bull Partial least-squares analysis for shapes Windows Used to explore the covariance between a set of variables and variation in shape or between two shapes It performs a two-block partial least-squares analysis It differs from regression in that both variables and shape are considered equally (one is not considered to be a set of independent variables measured without error) Its use is described in Rohlf and Corti (2000 Systematic Biology 49740-753) By F James Rohlf Version 118
tpsSmall
bull Test for small variation in shape Windows Use to test whether the variation in shape among a set of specimens is too large and thus statistical methods based on the tangent space approximation (eg thin-plate spline methods) cannot be used The program can process both 2D and 3D data files Output files include consensus and aligned specimens By F James Rohlf Version 120
tpsPower
bull Estimate statistical power for comparing shapes Windows Program for estimating statistical power for comparing the mean shapes of two populations Provides methods based on several different approaches Can be used for planning morphometric studies as well as to compare power using different approaches Version 104 By F James Rohlf
Morpheus et al bull Morpheus et al is a software package that will provide a
comprehensive cross-platform environment for morphometric data analysis It is available in graphical and command-line versions for a number of operating systems (see below) More information about new features and previous changes can be found in the release notes
httplifebiosunysbedumorphmorpheus
Multivariate analysis
bull PAST is a free easy-to-use data analysis package aimed at paleontology Windows 95+ Multivariate statistical methods include Principal Components (with Minimal Spanning Tree) Principal Coordinates (ten distance measures) Non-metric Multidimensional Scaling (ten distance measures) Detrended Correspondence Analysis Cluster analysis (three algorithms 11 distance measures) k-means clustering seriation discriminant analysis one-way MANOVA Hotellings t-squared Boxs M Canonical Variates Analysis Also includes Fourier shape analysis thin-plate splines parsimony and time series analysis among others Oslashyvind Hammer University of Oslo
Analysis of outlines
bull Shape Elliptic Fourier WINDOWS Extracts the contour shape from a full color bitmap image delineates the contour shape with the elliptic Fourier descriptors and performs a principal component analysis for summarizing the shape information By Hiroyoshi Iwata For more information see Shape home page tutorial or manual
bull Iwata H and Y Ukai (2002) SHAPE A computer program package for quantitative evaluation of biological shapes based on elliptic Fourier descriptors Journal of Heredity 93 384-385
Eigenshape analysis
bull httpwwwnhmacukhosted_sitespaleonetftpftphtml
bull This archive contains a series of programs designed to perform an eigenshape analysis on xy coordinate data from object outlines Routines include xy -gt phi() transformation phi() -gt xy transformation eigenshape analysis and projection of objects into the eigenshape space Two completely worked example analyses and a users guide are also provided El autor es Norman McLeod del BMNH de Londres
Graphical representation of the four-step morphometric protocol A Quantify raw data
(landmarks recorded on body of cichlid fish) B Remove non-shape variation (landmarks of 412
specimens before and after GPA) C statistical analysis (CVA) and graphical presentation of
results Deformation grids for mean specimen for (right) Eretmodus cyanostictus and (left)
Spathodus erythrodon (magnified by 3X to emphasize shape differences) Data from Ruumlber and
Adams 2001 En Adams Rolhf Slice 2002
Toma de medidas
W
L
iquestCoacutemo estudiamos la forma
httplifebiosunysbedumorphindexhtml
Adquisicioacuten de los datos
bull Calibre
bull Datos tomados con otras herramientas y volcados a una hoja de caacutelculo (Excel Pasthellip)
bull Imaacutegenes yo datos a partir de la literatura
bull Imaacutegenes tomadas con caacutemara digital
bull Imaacutegenes tomadas desde un microscopio o lupa binocular
Espeacutecimen Longitud (mm)
1a 33
1b 45
1c 29
Landmarks digitalizados con tpsDig2
httplifebiosunysbedumorphindexhtml
Tps digit program
Free at Suny
httplifebiosunysbedumorph
Dientes complejos Arvicolinae
Iberon 25 Landmarks
1
2
4
3
5
6
7
8 9
1011
12
14
15
16
17
18
19
20
21
22
23
24
13
1
2
3
4
5
6
7
89
10
11
12
131415
16
17
18
19
20
21
22
23
24
25
25
archivo 25 iberomys landmarks
Some extreme morphologies
Allophaiomys pliocaenicus Pirro
Nord
Early Pleistocene Italy Iberomys cabrerae
Extant Spain
Allophaiomys lavocati
Sima del Elefante
Atapuerca
Early Pleistocene (older
than the Italian species
Spain
AllophLavF
N3_1r
Early
Pleistocen
e of
Granada
similar to
Atapuerca
LM =17-14 of Iberon LM =15-14 of Iberon LM =15-14 of Iberon
Landmarks de 90 especiacutemenes de
Microtus agrestis
Landmarks de 90 especiacutemenes de
Microtus agrestis
Data 90 Specimens 22 Points 2 Dimensions
All specimen superimposed by GLS method
Sum of Squared Deviations = 1101217
The groups limit is after the specimen 0
PCS and scores computed
Percentages of variance for the 8 first PCS
61395977 61395977
8155754 69551731
4681460 74233190
3352225 77585415
2619139 80204554
2500418 82704973
2235576 84940549
1789387 86729936
Multivariate regression coefficients (normalized) with 3 PCS
PCS 1 0998142
PCS 2 -0057223
PCS 3 -0020926
Regression statistic for 3 components
Rsup2= 0227471 F= 8244611 with 3 and 86 DF plt 0000070
Plot de 90 especiacutemenes de
Microtus agrestis
Distribucioacuten estratigraacutefica de los roedores del cuaternario de Gran Dolina Atapuerca Burgos
0 m
Allo
ph
aio
mys
Mim
om
ys
Ibe
rom
ys
Terr
ico
la
Ste
no
cra
niu
s
Arv
ico
la
Mic
rom
ys
Hy
str
ix
Ca
sto
r
Ma
rmo
ta
Plio
mys
Mic
rotu
s
Allo
cri
cetu
s
Ap
od
em
us
Elio
mys
TD7
TD8
TD10
TD11
TD6
TD5
TD34
TD2
TD1
Procustes analisis APS
bull Procuste fue un ladroacuten que bien descuartizaba o bien estiraba a sus viacutectimas para ajustarlas al tamantildeo de su cama de ahiacute viene la frase hecha de ldquola cama Procusterdquo que se aplica sobre todo en poliacutetica la censura o para prestaciones puacuteblicas en las que es el usuario el que debe adaptarse y no al reveacuteshellip
bull The APS package
bull The shape analysis softwares APS ApsDigit and ApsUtil are written in English and always free for the students Aps combines Procuste superposition and statistical calculations ApsDigit is used locate landmarks on digital images (JPEG Bitmap tiff GIF) ApsUtil is used to handle files (Selection of points individuals change of classification)
bull httpwwwprocustecom
APS
APS est un logiciel danalyse quantitative de la
variabiliteacute morphologique des formes vivantes La
meacutethode utiliseacutee est la superposition procruste
geacuteneacuteraliseacutee
Destineacute aux biologistes et aux cliniciens APS prend en
charge les aspects matheacutematiques et statistiques de
lanalyse de forme Lanalyse se fait en 2 temps
1 Une superposition procruste de lensemble des
speacutecimens
2 Une analyse statistique qui visualise et teste la covariance
entre dune part la conformation et dautre part un facteur
biologique comme la taille lappartenance agrave groupe la
preacutesence ou non dune pathologie
Il est conccedilu pour eacutetudier un ou deux groupes
APS Digitalizar landmarks
DigitX is designed to digitize landmarks on Jpeg or Bitmap picture
middot Select the total number of landmarks to digitize with the second
Combo-Box of the toolbar
middot Select a picture in the graphic file selector on the left
middot Click on to load the link file (optional)
middot Click on to load the consensus file (optional)
middot Digitize landmarks using the left button of the mouse
middot To cancel last landmark position by a click on undo arrow
middot When all landmarks are digitized save the file by a click on save file
APS Crear archivo
Getting started with ApsUtil
ApsUtil create a data file (dat) with specimen ordered by
addition of smaller data files Input and output files are to
APS data format with an header line (number of specimens
number
of landmarks number of dimensions) followed by landmarks
coordinates
NEW button clear all previous data and begin a new data file
ADD button add a file containing one or many specimen
MIX button add a new file to a previous one by mixing the
two file
This ordering of specimen is required before to compute
shape differences
When file is saved specimens are ordered like
specimen 1 of the 1st file
specimen 1 of the 2nd file
specimen 2 of the 1st file
APS analisis
bull New features of Version 241
bull A single specimen or all a sample can be superimposed on any reloaded
bull specimen as consensus (File -gt Reload -gt Consensus)
bull Shape vectors (eg discriminant vectors computed with other software)
bull can be reloaded for visualization (File -gt Reload -gt Pcs)
bull The shape vector must be of norm 1
bull Projections of specimens on shape vectors are automatically computed
Otros
elementos del
esqueleto
A Antarctosaurus wichmannianus B
Saltasaurus loricatus C Neuquensaurus
australis D Neuquensaurus robustus E
Lirainosaurus astibiae F Ampelosaurus atacis
G Magyarosaurus dacus H Magyarosaurus
dacus Jianu I Alamosaurus sanjuanensis J
Aegyptosaurus baharijiensis K
Opisthocoelicaudia skarzynskii
Canudo amp Cuenca Bescos 2004
wwwaragosauruscom
Aegyptosaurus Alamosaurus
Imaacutegenes literatura
Fotos ejemplares
Hacer un poliacutegono con los landmarks
Guardar la misma posicioacuten (en una liacutenea basal por ej)
APS digit
APS util
APS program CP
Opisthocoelicaudia
Resultados
APS Fecha Thu 21 Sep 2006 213918
+0200 [210906 213918 CEST]
De Info Procuste
ltinfoprocustecomgt
Para cuencagunizares
Asunto Re analyse de forme chez
les arvicolides
Cabeceras Mostrar todas las
cabeceras
Chegravere collegravegue
Voici le lien pour teacuteleacutecharger le le
setup dinstallation des 3
logiciels APS ApsDigit et ApsUtil
httpwwwprocustecomprogramsset
up_aps_allexe
Noubliez pas de citer APS dans vos
publications
Bien cordialement
Xavier Penin
Paacuteginas web recomendadas
bull httplifebiosunysbedumorph la mejor paacutegina de
morfometriacutea geomeacutetrica Contiene un listado con todos los
programas de morfometriacutea Universidad de Stony Brook NY
bull httpwwwmorphometricsorgindexhtml es la paacutegina en la
que se mantiene la lista de email morphmet Es la base de la
organizacioacuten de la morfometriacutea en Suny
bull httpwwwflywingsorgukindexhtm iquestporqueacute hay variacioacuten
morfoloacutegica Universidad de Manchester UK
bull httpwwwprocustecomindexhtml anaacutelisis de la forma con
Procruste Aps Xavier Penin Universidad de Paris V
bull Shapehellipy otros ver la paacutegina de Suny
Las ldquoseries TPSrdquo Thin-plate spline
(laacuteminas finas de grosor uniforme)
tpsDIG2
Data acquisition
bull Digitize landmarks amp outlines from image files scanner or video Windows TpsDig is a Windows (95 through XP) program for digitizing landmarks and outlines for geometric morphometric analyses Includes simple image enhancement operations scale factors image brightness profile and support for AVI and MOV files Output is in the TPS file format used by the tps series of programs The TPS file includes the name of the image file for each specimen so that landmarks can always be visualized on the image Since output files are ASCII they can be converted to formats for other software Users should note that the tpsUtil program is useful for both the preparation of the input files to tpsDig as well as for some useful conversions afterwards The program also computes areas of enclosed regions perimeters and linear distances The tpsDig2 link at the left is for the new 205 version
bull Execute the downloaded file to install the program By F James Rohlf
Las ldquoseries TPSrdquo
ordenar los archivos digitalizados
TPS util
bull tps file utility program Windows At present it can randomly scramble the order of specimens in a tps file to minimize bias in digitizing landmark locations restore the original order (eg before statistical analyses are performed) create an empty TPS file from a directory with image files add keywords and values to the variables field of a TPS file combine TPS files into a single TPS file deletereorder landmarks remove outlines from a TPS file and convert TPS and NTS files to NTS M or CSV files It can also split an NTS file into several matrices Graphic editors are included for drawing link and sliders files Unbending a deformed specimen Converting outline and curves points to landmarks
bull Other operations can be added - let me know what you need Execute the TPSUTILW32EXE file to install the program By F James Rohlf Version 138
tpsTree
bull Fit and visualize thin-plate splines on trees Windows Performs a least-squares orthogonal generalized Procrustes analysis to obtain a reference and then estimates the splines for each group (internal node) on a tree Both ultrametric (eg WPGMA and UPGMA trees) and additive trees (using squared change parsimony to estimate the shapes of the HTUs) are supported The estimated shapes can be visualized with estimated images in the background (see the tpsSuper program) The file expands into a Windows setup program and associated files By F James Rohlf Version 118 File containing HTU coordinates and HTU images to demo that feature The older and more limited 16 bit Windows version is still available
tpsRegr
bull Multivariate multiple regression of shape onto independent variables Windows performs a multivariate multiple regression of shape (as captured by partial warp scores and the uniform shape component) onto one or more independent variables By appropriate setting up of independent variables this program can perform various types of MANOVA and MANCOVA Can be used to study allometry By F James Rohlf Version 131
tpsSplin
bull Thin-plate spline Windows Program to
compare pairs of specimens by displaying
a Darcy Thompson style transformation
grid based on a thin-plate spline Several
options are given for sliding
semilandmarks The tpssplnwexe file
expands into a Windows setup program
that will be run automatically By F James
Rohlf Version 120
tpsRelw el anaacutelisis de la
deformacioacuten relativa bull Relative warps analysis Windows Performs a
relative warp (deformacioacuten) analysis This corresponds to a principal components analysis of variation in a sample (relative to bending energy if the alpha parameter is not equal to zero) Displays a plot of relative warp scores and a visualization window that displays the estimated shape for arbitrary points in the ordination Also displays partial warp scores and their visualizations Allows fitting of semilandmark points along curves Version 144 By F James Rohlf
tpsPLS
bull Partial least-squares analysis for shapes Windows Used to explore the covariance between a set of variables and variation in shape or between two shapes It performs a two-block partial least-squares analysis It differs from regression in that both variables and shape are considered equally (one is not considered to be a set of independent variables measured without error) Its use is described in Rohlf and Corti (2000 Systematic Biology 49740-753) By F James Rohlf Version 118
tpsSmall
bull Test for small variation in shape Windows Use to test whether the variation in shape among a set of specimens is too large and thus statistical methods based on the tangent space approximation (eg thin-plate spline methods) cannot be used The program can process both 2D and 3D data files Output files include consensus and aligned specimens By F James Rohlf Version 120
tpsPower
bull Estimate statistical power for comparing shapes Windows Program for estimating statistical power for comparing the mean shapes of two populations Provides methods based on several different approaches Can be used for planning morphometric studies as well as to compare power using different approaches Version 104 By F James Rohlf
Morpheus et al bull Morpheus et al is a software package that will provide a
comprehensive cross-platform environment for morphometric data analysis It is available in graphical and command-line versions for a number of operating systems (see below) More information about new features and previous changes can be found in the release notes
httplifebiosunysbedumorphmorpheus
Multivariate analysis
bull PAST is a free easy-to-use data analysis package aimed at paleontology Windows 95+ Multivariate statistical methods include Principal Components (with Minimal Spanning Tree) Principal Coordinates (ten distance measures) Non-metric Multidimensional Scaling (ten distance measures) Detrended Correspondence Analysis Cluster analysis (three algorithms 11 distance measures) k-means clustering seriation discriminant analysis one-way MANOVA Hotellings t-squared Boxs M Canonical Variates Analysis Also includes Fourier shape analysis thin-plate splines parsimony and time series analysis among others Oslashyvind Hammer University of Oslo
Analysis of outlines
bull Shape Elliptic Fourier WINDOWS Extracts the contour shape from a full color bitmap image delineates the contour shape with the elliptic Fourier descriptors and performs a principal component analysis for summarizing the shape information By Hiroyoshi Iwata For more information see Shape home page tutorial or manual
bull Iwata H and Y Ukai (2002) SHAPE A computer program package for quantitative evaluation of biological shapes based on elliptic Fourier descriptors Journal of Heredity 93 384-385
Eigenshape analysis
bull httpwwwnhmacukhosted_sitespaleonetftpftphtml
bull This archive contains a series of programs designed to perform an eigenshape analysis on xy coordinate data from object outlines Routines include xy -gt phi() transformation phi() -gt xy transformation eigenshape analysis and projection of objects into the eigenshape space Two completely worked example analyses and a users guide are also provided El autor es Norman McLeod del BMNH de Londres
Graphical representation of the four-step morphometric protocol A Quantify raw data
(landmarks recorded on body of cichlid fish) B Remove non-shape variation (landmarks of 412
specimens before and after GPA) C statistical analysis (CVA) and graphical presentation of
results Deformation grids for mean specimen for (right) Eretmodus cyanostictus and (left)
Spathodus erythrodon (magnified by 3X to emphasize shape differences) Data from Ruumlber and
Adams 2001 En Adams Rolhf Slice 2002
iquestCoacutemo estudiamos la forma
httplifebiosunysbedumorphindexhtml
Adquisicioacuten de los datos
bull Calibre
bull Datos tomados con otras herramientas y volcados a una hoja de caacutelculo (Excel Pasthellip)
bull Imaacutegenes yo datos a partir de la literatura
bull Imaacutegenes tomadas con caacutemara digital
bull Imaacutegenes tomadas desde un microscopio o lupa binocular
Espeacutecimen Longitud (mm)
1a 33
1b 45
1c 29
Landmarks digitalizados con tpsDig2
httplifebiosunysbedumorphindexhtml
Tps digit program
Free at Suny
httplifebiosunysbedumorph
Dientes complejos Arvicolinae
Iberon 25 Landmarks
1
2
4
3
5
6
7
8 9
1011
12
14
15
16
17
18
19
20
21
22
23
24
13
1
2
3
4
5
6
7
89
10
11
12
131415
16
17
18
19
20
21
22
23
24
25
25
archivo 25 iberomys landmarks
Some extreme morphologies
Allophaiomys pliocaenicus Pirro
Nord
Early Pleistocene Italy Iberomys cabrerae
Extant Spain
Allophaiomys lavocati
Sima del Elefante
Atapuerca
Early Pleistocene (older
than the Italian species
Spain
AllophLavF
N3_1r
Early
Pleistocen
e of
Granada
similar to
Atapuerca
LM =17-14 of Iberon LM =15-14 of Iberon LM =15-14 of Iberon
Landmarks de 90 especiacutemenes de
Microtus agrestis
Landmarks de 90 especiacutemenes de
Microtus agrestis
Data 90 Specimens 22 Points 2 Dimensions
All specimen superimposed by GLS method
Sum of Squared Deviations = 1101217
The groups limit is after the specimen 0
PCS and scores computed
Percentages of variance for the 8 first PCS
61395977 61395977
8155754 69551731
4681460 74233190
3352225 77585415
2619139 80204554
2500418 82704973
2235576 84940549
1789387 86729936
Multivariate regression coefficients (normalized) with 3 PCS
PCS 1 0998142
PCS 2 -0057223
PCS 3 -0020926
Regression statistic for 3 components
Rsup2= 0227471 F= 8244611 with 3 and 86 DF plt 0000070
Plot de 90 especiacutemenes de
Microtus agrestis
Distribucioacuten estratigraacutefica de los roedores del cuaternario de Gran Dolina Atapuerca Burgos
0 m
Allo
ph
aio
mys
Mim
om
ys
Ibe
rom
ys
Terr
ico
la
Ste
no
cra
niu
s
Arv
ico
la
Mic
rom
ys
Hy
str
ix
Ca
sto
r
Ma
rmo
ta
Plio
mys
Mic
rotu
s
Allo
cri
cetu
s
Ap
od
em
us
Elio
mys
TD7
TD8
TD10
TD11
TD6
TD5
TD34
TD2
TD1
Procustes analisis APS
bull Procuste fue un ladroacuten que bien descuartizaba o bien estiraba a sus viacutectimas para ajustarlas al tamantildeo de su cama de ahiacute viene la frase hecha de ldquola cama Procusterdquo que se aplica sobre todo en poliacutetica la censura o para prestaciones puacuteblicas en las que es el usuario el que debe adaptarse y no al reveacuteshellip
bull The APS package
bull The shape analysis softwares APS ApsDigit and ApsUtil are written in English and always free for the students Aps combines Procuste superposition and statistical calculations ApsDigit is used locate landmarks on digital images (JPEG Bitmap tiff GIF) ApsUtil is used to handle files (Selection of points individuals change of classification)
bull httpwwwprocustecom
APS
APS est un logiciel danalyse quantitative de la
variabiliteacute morphologique des formes vivantes La
meacutethode utiliseacutee est la superposition procruste
geacuteneacuteraliseacutee
Destineacute aux biologistes et aux cliniciens APS prend en
charge les aspects matheacutematiques et statistiques de
lanalyse de forme Lanalyse se fait en 2 temps
1 Une superposition procruste de lensemble des
speacutecimens
2 Une analyse statistique qui visualise et teste la covariance
entre dune part la conformation et dautre part un facteur
biologique comme la taille lappartenance agrave groupe la
preacutesence ou non dune pathologie
Il est conccedilu pour eacutetudier un ou deux groupes
APS Digitalizar landmarks
DigitX is designed to digitize landmarks on Jpeg or Bitmap picture
middot Select the total number of landmarks to digitize with the second
Combo-Box of the toolbar
middot Select a picture in the graphic file selector on the left
middot Click on to load the link file (optional)
middot Click on to load the consensus file (optional)
middot Digitize landmarks using the left button of the mouse
middot To cancel last landmark position by a click on undo arrow
middot When all landmarks are digitized save the file by a click on save file
APS Crear archivo
Getting started with ApsUtil
ApsUtil create a data file (dat) with specimen ordered by
addition of smaller data files Input and output files are to
APS data format with an header line (number of specimens
number
of landmarks number of dimensions) followed by landmarks
coordinates
NEW button clear all previous data and begin a new data file
ADD button add a file containing one or many specimen
MIX button add a new file to a previous one by mixing the
two file
This ordering of specimen is required before to compute
shape differences
When file is saved specimens are ordered like
specimen 1 of the 1st file
specimen 1 of the 2nd file
specimen 2 of the 1st file
APS analisis
bull New features of Version 241
bull A single specimen or all a sample can be superimposed on any reloaded
bull specimen as consensus (File -gt Reload -gt Consensus)
bull Shape vectors (eg discriminant vectors computed with other software)
bull can be reloaded for visualization (File -gt Reload -gt Pcs)
bull The shape vector must be of norm 1
bull Projections of specimens on shape vectors are automatically computed
Otros
elementos del
esqueleto
A Antarctosaurus wichmannianus B
Saltasaurus loricatus C Neuquensaurus
australis D Neuquensaurus robustus E
Lirainosaurus astibiae F Ampelosaurus atacis
G Magyarosaurus dacus H Magyarosaurus
dacus Jianu I Alamosaurus sanjuanensis J
Aegyptosaurus baharijiensis K
Opisthocoelicaudia skarzynskii
Canudo amp Cuenca Bescos 2004
wwwaragosauruscom
Aegyptosaurus Alamosaurus
Imaacutegenes literatura
Fotos ejemplares
Hacer un poliacutegono con los landmarks
Guardar la misma posicioacuten (en una liacutenea basal por ej)
APS digit
APS util
APS program CP
Opisthocoelicaudia
Resultados
APS Fecha Thu 21 Sep 2006 213918
+0200 [210906 213918 CEST]
De Info Procuste
ltinfoprocustecomgt
Para cuencagunizares
Asunto Re analyse de forme chez
les arvicolides
Cabeceras Mostrar todas las
cabeceras
Chegravere collegravegue
Voici le lien pour teacuteleacutecharger le le
setup dinstallation des 3
logiciels APS ApsDigit et ApsUtil
httpwwwprocustecomprogramsset
up_aps_allexe
Noubliez pas de citer APS dans vos
publications
Bien cordialement
Xavier Penin
Paacuteginas web recomendadas
bull httplifebiosunysbedumorph la mejor paacutegina de
morfometriacutea geomeacutetrica Contiene un listado con todos los
programas de morfometriacutea Universidad de Stony Brook NY
bull httpwwwmorphometricsorgindexhtml es la paacutegina en la
que se mantiene la lista de email morphmet Es la base de la
organizacioacuten de la morfometriacutea en Suny
bull httpwwwflywingsorgukindexhtm iquestporqueacute hay variacioacuten
morfoloacutegica Universidad de Manchester UK
bull httpwwwprocustecomindexhtml anaacutelisis de la forma con
Procruste Aps Xavier Penin Universidad de Paris V
bull Shapehellipy otros ver la paacutegina de Suny
Las ldquoseries TPSrdquo Thin-plate spline
(laacuteminas finas de grosor uniforme)
tpsDIG2
Data acquisition
bull Digitize landmarks amp outlines from image files scanner or video Windows TpsDig is a Windows (95 through XP) program for digitizing landmarks and outlines for geometric morphometric analyses Includes simple image enhancement operations scale factors image brightness profile and support for AVI and MOV files Output is in the TPS file format used by the tps series of programs The TPS file includes the name of the image file for each specimen so that landmarks can always be visualized on the image Since output files are ASCII they can be converted to formats for other software Users should note that the tpsUtil program is useful for both the preparation of the input files to tpsDig as well as for some useful conversions afterwards The program also computes areas of enclosed regions perimeters and linear distances The tpsDig2 link at the left is for the new 205 version
bull Execute the downloaded file to install the program By F James Rohlf
Las ldquoseries TPSrdquo
ordenar los archivos digitalizados
TPS util
bull tps file utility program Windows At present it can randomly scramble the order of specimens in a tps file to minimize bias in digitizing landmark locations restore the original order (eg before statistical analyses are performed) create an empty TPS file from a directory with image files add keywords and values to the variables field of a TPS file combine TPS files into a single TPS file deletereorder landmarks remove outlines from a TPS file and convert TPS and NTS files to NTS M or CSV files It can also split an NTS file into several matrices Graphic editors are included for drawing link and sliders files Unbending a deformed specimen Converting outline and curves points to landmarks
bull Other operations can be added - let me know what you need Execute the TPSUTILW32EXE file to install the program By F James Rohlf Version 138
tpsTree
bull Fit and visualize thin-plate splines on trees Windows Performs a least-squares orthogonal generalized Procrustes analysis to obtain a reference and then estimates the splines for each group (internal node) on a tree Both ultrametric (eg WPGMA and UPGMA trees) and additive trees (using squared change parsimony to estimate the shapes of the HTUs) are supported The estimated shapes can be visualized with estimated images in the background (see the tpsSuper program) The file expands into a Windows setup program and associated files By F James Rohlf Version 118 File containing HTU coordinates and HTU images to demo that feature The older and more limited 16 bit Windows version is still available
tpsRegr
bull Multivariate multiple regression of shape onto independent variables Windows performs a multivariate multiple regression of shape (as captured by partial warp scores and the uniform shape component) onto one or more independent variables By appropriate setting up of independent variables this program can perform various types of MANOVA and MANCOVA Can be used to study allometry By F James Rohlf Version 131
tpsSplin
bull Thin-plate spline Windows Program to
compare pairs of specimens by displaying
a Darcy Thompson style transformation
grid based on a thin-plate spline Several
options are given for sliding
semilandmarks The tpssplnwexe file
expands into a Windows setup program
that will be run automatically By F James
Rohlf Version 120
tpsRelw el anaacutelisis de la
deformacioacuten relativa bull Relative warps analysis Windows Performs a
relative warp (deformacioacuten) analysis This corresponds to a principal components analysis of variation in a sample (relative to bending energy if the alpha parameter is not equal to zero) Displays a plot of relative warp scores and a visualization window that displays the estimated shape for arbitrary points in the ordination Also displays partial warp scores and their visualizations Allows fitting of semilandmark points along curves Version 144 By F James Rohlf
tpsPLS
bull Partial least-squares analysis for shapes Windows Used to explore the covariance between a set of variables and variation in shape or between two shapes It performs a two-block partial least-squares analysis It differs from regression in that both variables and shape are considered equally (one is not considered to be a set of independent variables measured without error) Its use is described in Rohlf and Corti (2000 Systematic Biology 49740-753) By F James Rohlf Version 118
tpsSmall
bull Test for small variation in shape Windows Use to test whether the variation in shape among a set of specimens is too large and thus statistical methods based on the tangent space approximation (eg thin-plate spline methods) cannot be used The program can process both 2D and 3D data files Output files include consensus and aligned specimens By F James Rohlf Version 120
tpsPower
bull Estimate statistical power for comparing shapes Windows Program for estimating statistical power for comparing the mean shapes of two populations Provides methods based on several different approaches Can be used for planning morphometric studies as well as to compare power using different approaches Version 104 By F James Rohlf
Morpheus et al bull Morpheus et al is a software package that will provide a
comprehensive cross-platform environment for morphometric data analysis It is available in graphical and command-line versions for a number of operating systems (see below) More information about new features and previous changes can be found in the release notes
httplifebiosunysbedumorphmorpheus
Multivariate analysis
bull PAST is a free easy-to-use data analysis package aimed at paleontology Windows 95+ Multivariate statistical methods include Principal Components (with Minimal Spanning Tree) Principal Coordinates (ten distance measures) Non-metric Multidimensional Scaling (ten distance measures) Detrended Correspondence Analysis Cluster analysis (three algorithms 11 distance measures) k-means clustering seriation discriminant analysis one-way MANOVA Hotellings t-squared Boxs M Canonical Variates Analysis Also includes Fourier shape analysis thin-plate splines parsimony and time series analysis among others Oslashyvind Hammer University of Oslo
Analysis of outlines
bull Shape Elliptic Fourier WINDOWS Extracts the contour shape from a full color bitmap image delineates the contour shape with the elliptic Fourier descriptors and performs a principal component analysis for summarizing the shape information By Hiroyoshi Iwata For more information see Shape home page tutorial or manual
bull Iwata H and Y Ukai (2002) SHAPE A computer program package for quantitative evaluation of biological shapes based on elliptic Fourier descriptors Journal of Heredity 93 384-385
Eigenshape analysis
bull httpwwwnhmacukhosted_sitespaleonetftpftphtml
bull This archive contains a series of programs designed to perform an eigenshape analysis on xy coordinate data from object outlines Routines include xy -gt phi() transformation phi() -gt xy transformation eigenshape analysis and projection of objects into the eigenshape space Two completely worked example analyses and a users guide are also provided El autor es Norman McLeod del BMNH de Londres
Graphical representation of the four-step morphometric protocol A Quantify raw data
(landmarks recorded on body of cichlid fish) B Remove non-shape variation (landmarks of 412
specimens before and after GPA) C statistical analysis (CVA) and graphical presentation of
results Deformation grids for mean specimen for (right) Eretmodus cyanostictus and (left)
Spathodus erythrodon (magnified by 3X to emphasize shape differences) Data from Ruumlber and
Adams 2001 En Adams Rolhf Slice 2002
Adquisicioacuten de los datos
bull Calibre
bull Datos tomados con otras herramientas y volcados a una hoja de caacutelculo (Excel Pasthellip)
bull Imaacutegenes yo datos a partir de la literatura
bull Imaacutegenes tomadas con caacutemara digital
bull Imaacutegenes tomadas desde un microscopio o lupa binocular
Espeacutecimen Longitud (mm)
1a 33
1b 45
1c 29
Landmarks digitalizados con tpsDig2
httplifebiosunysbedumorphindexhtml
Tps digit program
Free at Suny
httplifebiosunysbedumorph
Dientes complejos Arvicolinae
Iberon 25 Landmarks
1
2
4
3
5
6
7
8 9
1011
12
14
15
16
17
18
19
20
21
22
23
24
13
1
2
3
4
5
6
7
89
10
11
12
131415
16
17
18
19
20
21
22
23
24
25
25
archivo 25 iberomys landmarks
Some extreme morphologies
Allophaiomys pliocaenicus Pirro
Nord
Early Pleistocene Italy Iberomys cabrerae
Extant Spain
Allophaiomys lavocati
Sima del Elefante
Atapuerca
Early Pleistocene (older
than the Italian species
Spain
AllophLavF
N3_1r
Early
Pleistocen
e of
Granada
similar to
Atapuerca
LM =17-14 of Iberon LM =15-14 of Iberon LM =15-14 of Iberon
Landmarks de 90 especiacutemenes de
Microtus agrestis
Landmarks de 90 especiacutemenes de
Microtus agrestis
Data 90 Specimens 22 Points 2 Dimensions
All specimen superimposed by GLS method
Sum of Squared Deviations = 1101217
The groups limit is after the specimen 0
PCS and scores computed
Percentages of variance for the 8 first PCS
61395977 61395977
8155754 69551731
4681460 74233190
3352225 77585415
2619139 80204554
2500418 82704973
2235576 84940549
1789387 86729936
Multivariate regression coefficients (normalized) with 3 PCS
PCS 1 0998142
PCS 2 -0057223
PCS 3 -0020926
Regression statistic for 3 components
Rsup2= 0227471 F= 8244611 with 3 and 86 DF plt 0000070
Plot de 90 especiacutemenes de
Microtus agrestis
Distribucioacuten estratigraacutefica de los roedores del cuaternario de Gran Dolina Atapuerca Burgos
0 m
Allo
ph
aio
mys
Mim
om
ys
Ibe
rom
ys
Terr
ico
la
Ste
no
cra
niu
s
Arv
ico
la
Mic
rom
ys
Hy
str
ix
Ca
sto
r
Ma
rmo
ta
Plio
mys
Mic
rotu
s
Allo
cri
cetu
s
Ap
od
em
us
Elio
mys
TD7
TD8
TD10
TD11
TD6
TD5
TD34
TD2
TD1
Procustes analisis APS
bull Procuste fue un ladroacuten que bien descuartizaba o bien estiraba a sus viacutectimas para ajustarlas al tamantildeo de su cama de ahiacute viene la frase hecha de ldquola cama Procusterdquo que se aplica sobre todo en poliacutetica la censura o para prestaciones puacuteblicas en las que es el usuario el que debe adaptarse y no al reveacuteshellip
bull The APS package
bull The shape analysis softwares APS ApsDigit and ApsUtil are written in English and always free for the students Aps combines Procuste superposition and statistical calculations ApsDigit is used locate landmarks on digital images (JPEG Bitmap tiff GIF) ApsUtil is used to handle files (Selection of points individuals change of classification)
bull httpwwwprocustecom
APS
APS est un logiciel danalyse quantitative de la
variabiliteacute morphologique des formes vivantes La
meacutethode utiliseacutee est la superposition procruste
geacuteneacuteraliseacutee
Destineacute aux biologistes et aux cliniciens APS prend en
charge les aspects matheacutematiques et statistiques de
lanalyse de forme Lanalyse se fait en 2 temps
1 Une superposition procruste de lensemble des
speacutecimens
2 Une analyse statistique qui visualise et teste la covariance
entre dune part la conformation et dautre part un facteur
biologique comme la taille lappartenance agrave groupe la
preacutesence ou non dune pathologie
Il est conccedilu pour eacutetudier un ou deux groupes
APS Digitalizar landmarks
DigitX is designed to digitize landmarks on Jpeg or Bitmap picture
middot Select the total number of landmarks to digitize with the second
Combo-Box of the toolbar
middot Select a picture in the graphic file selector on the left
middot Click on to load the link file (optional)
middot Click on to load the consensus file (optional)
middot Digitize landmarks using the left button of the mouse
middot To cancel last landmark position by a click on undo arrow
middot When all landmarks are digitized save the file by a click on save file
APS Crear archivo
Getting started with ApsUtil
ApsUtil create a data file (dat) with specimen ordered by
addition of smaller data files Input and output files are to
APS data format with an header line (number of specimens
number
of landmarks number of dimensions) followed by landmarks
coordinates
NEW button clear all previous data and begin a new data file
ADD button add a file containing one or many specimen
MIX button add a new file to a previous one by mixing the
two file
This ordering of specimen is required before to compute
shape differences
When file is saved specimens are ordered like
specimen 1 of the 1st file
specimen 1 of the 2nd file
specimen 2 of the 1st file
APS analisis
bull New features of Version 241
bull A single specimen or all a sample can be superimposed on any reloaded
bull specimen as consensus (File -gt Reload -gt Consensus)
bull Shape vectors (eg discriminant vectors computed with other software)
bull can be reloaded for visualization (File -gt Reload -gt Pcs)
bull The shape vector must be of norm 1
bull Projections of specimens on shape vectors are automatically computed
Otros
elementos del
esqueleto
A Antarctosaurus wichmannianus B
Saltasaurus loricatus C Neuquensaurus
australis D Neuquensaurus robustus E
Lirainosaurus astibiae F Ampelosaurus atacis
G Magyarosaurus dacus H Magyarosaurus
dacus Jianu I Alamosaurus sanjuanensis J
Aegyptosaurus baharijiensis K
Opisthocoelicaudia skarzynskii
Canudo amp Cuenca Bescos 2004
wwwaragosauruscom
Aegyptosaurus Alamosaurus
Imaacutegenes literatura
Fotos ejemplares
Hacer un poliacutegono con los landmarks
Guardar la misma posicioacuten (en una liacutenea basal por ej)
APS digit
APS util
APS program CP
Opisthocoelicaudia
Resultados
APS Fecha Thu 21 Sep 2006 213918
+0200 [210906 213918 CEST]
De Info Procuste
ltinfoprocustecomgt
Para cuencagunizares
Asunto Re analyse de forme chez
les arvicolides
Cabeceras Mostrar todas las
cabeceras
Chegravere collegravegue
Voici le lien pour teacuteleacutecharger le le
setup dinstallation des 3
logiciels APS ApsDigit et ApsUtil
httpwwwprocustecomprogramsset
up_aps_allexe
Noubliez pas de citer APS dans vos
publications
Bien cordialement
Xavier Penin
Paacuteginas web recomendadas
bull httplifebiosunysbedumorph la mejor paacutegina de
morfometriacutea geomeacutetrica Contiene un listado con todos los
programas de morfometriacutea Universidad de Stony Brook NY
bull httpwwwmorphometricsorgindexhtml es la paacutegina en la
que se mantiene la lista de email morphmet Es la base de la
organizacioacuten de la morfometriacutea en Suny
bull httpwwwflywingsorgukindexhtm iquestporqueacute hay variacioacuten
morfoloacutegica Universidad de Manchester UK
bull httpwwwprocustecomindexhtml anaacutelisis de la forma con
Procruste Aps Xavier Penin Universidad de Paris V
bull Shapehellipy otros ver la paacutegina de Suny
Las ldquoseries TPSrdquo Thin-plate spline
(laacuteminas finas de grosor uniforme)
tpsDIG2
Data acquisition
bull Digitize landmarks amp outlines from image files scanner or video Windows TpsDig is a Windows (95 through XP) program for digitizing landmarks and outlines for geometric morphometric analyses Includes simple image enhancement operations scale factors image brightness profile and support for AVI and MOV files Output is in the TPS file format used by the tps series of programs The TPS file includes the name of the image file for each specimen so that landmarks can always be visualized on the image Since output files are ASCII they can be converted to formats for other software Users should note that the tpsUtil program is useful for both the preparation of the input files to tpsDig as well as for some useful conversions afterwards The program also computes areas of enclosed regions perimeters and linear distances The tpsDig2 link at the left is for the new 205 version
bull Execute the downloaded file to install the program By F James Rohlf
Las ldquoseries TPSrdquo
ordenar los archivos digitalizados
TPS util
bull tps file utility program Windows At present it can randomly scramble the order of specimens in a tps file to minimize bias in digitizing landmark locations restore the original order (eg before statistical analyses are performed) create an empty TPS file from a directory with image files add keywords and values to the variables field of a TPS file combine TPS files into a single TPS file deletereorder landmarks remove outlines from a TPS file and convert TPS and NTS files to NTS M or CSV files It can also split an NTS file into several matrices Graphic editors are included for drawing link and sliders files Unbending a deformed specimen Converting outline and curves points to landmarks
bull Other operations can be added - let me know what you need Execute the TPSUTILW32EXE file to install the program By F James Rohlf Version 138
tpsTree
bull Fit and visualize thin-plate splines on trees Windows Performs a least-squares orthogonal generalized Procrustes analysis to obtain a reference and then estimates the splines for each group (internal node) on a tree Both ultrametric (eg WPGMA and UPGMA trees) and additive trees (using squared change parsimony to estimate the shapes of the HTUs) are supported The estimated shapes can be visualized with estimated images in the background (see the tpsSuper program) The file expands into a Windows setup program and associated files By F James Rohlf Version 118 File containing HTU coordinates and HTU images to demo that feature The older and more limited 16 bit Windows version is still available
tpsRegr
bull Multivariate multiple regression of shape onto independent variables Windows performs a multivariate multiple regression of shape (as captured by partial warp scores and the uniform shape component) onto one or more independent variables By appropriate setting up of independent variables this program can perform various types of MANOVA and MANCOVA Can be used to study allometry By F James Rohlf Version 131
tpsSplin
bull Thin-plate spline Windows Program to
compare pairs of specimens by displaying
a Darcy Thompson style transformation
grid based on a thin-plate spline Several
options are given for sliding
semilandmarks The tpssplnwexe file
expands into a Windows setup program
that will be run automatically By F James
Rohlf Version 120
tpsRelw el anaacutelisis de la
deformacioacuten relativa bull Relative warps analysis Windows Performs a
relative warp (deformacioacuten) analysis This corresponds to a principal components analysis of variation in a sample (relative to bending energy if the alpha parameter is not equal to zero) Displays a plot of relative warp scores and a visualization window that displays the estimated shape for arbitrary points in the ordination Also displays partial warp scores and their visualizations Allows fitting of semilandmark points along curves Version 144 By F James Rohlf
tpsPLS
bull Partial least-squares analysis for shapes Windows Used to explore the covariance between a set of variables and variation in shape or between two shapes It performs a two-block partial least-squares analysis It differs from regression in that both variables and shape are considered equally (one is not considered to be a set of independent variables measured without error) Its use is described in Rohlf and Corti (2000 Systematic Biology 49740-753) By F James Rohlf Version 118
tpsSmall
bull Test for small variation in shape Windows Use to test whether the variation in shape among a set of specimens is too large and thus statistical methods based on the tangent space approximation (eg thin-plate spline methods) cannot be used The program can process both 2D and 3D data files Output files include consensus and aligned specimens By F James Rohlf Version 120
tpsPower
bull Estimate statistical power for comparing shapes Windows Program for estimating statistical power for comparing the mean shapes of two populations Provides methods based on several different approaches Can be used for planning morphometric studies as well as to compare power using different approaches Version 104 By F James Rohlf
Morpheus et al bull Morpheus et al is a software package that will provide a
comprehensive cross-platform environment for morphometric data analysis It is available in graphical and command-line versions for a number of operating systems (see below) More information about new features and previous changes can be found in the release notes
httplifebiosunysbedumorphmorpheus
Multivariate analysis
bull PAST is a free easy-to-use data analysis package aimed at paleontology Windows 95+ Multivariate statistical methods include Principal Components (with Minimal Spanning Tree) Principal Coordinates (ten distance measures) Non-metric Multidimensional Scaling (ten distance measures) Detrended Correspondence Analysis Cluster analysis (three algorithms 11 distance measures) k-means clustering seriation discriminant analysis one-way MANOVA Hotellings t-squared Boxs M Canonical Variates Analysis Also includes Fourier shape analysis thin-plate splines parsimony and time series analysis among others Oslashyvind Hammer University of Oslo
Analysis of outlines
bull Shape Elliptic Fourier WINDOWS Extracts the contour shape from a full color bitmap image delineates the contour shape with the elliptic Fourier descriptors and performs a principal component analysis for summarizing the shape information By Hiroyoshi Iwata For more information see Shape home page tutorial or manual
bull Iwata H and Y Ukai (2002) SHAPE A computer program package for quantitative evaluation of biological shapes based on elliptic Fourier descriptors Journal of Heredity 93 384-385
Eigenshape analysis
bull httpwwwnhmacukhosted_sitespaleonetftpftphtml
bull This archive contains a series of programs designed to perform an eigenshape analysis on xy coordinate data from object outlines Routines include xy -gt phi() transformation phi() -gt xy transformation eigenshape analysis and projection of objects into the eigenshape space Two completely worked example analyses and a users guide are also provided El autor es Norman McLeod del BMNH de Londres
Graphical representation of the four-step morphometric protocol A Quantify raw data
(landmarks recorded on body of cichlid fish) B Remove non-shape variation (landmarks of 412
specimens before and after GPA) C statistical analysis (CVA) and graphical presentation of
results Deformation grids for mean specimen for (right) Eretmodus cyanostictus and (left)
Spathodus erythrodon (magnified by 3X to emphasize shape differences) Data from Ruumlber and
Adams 2001 En Adams Rolhf Slice 2002
Tps digit program
Free at Suny
httplifebiosunysbedumorph
Dientes complejos Arvicolinae
Iberon 25 Landmarks
1
2
4
3
5
6
7
8 9
1011
12
14
15
16
17
18
19
20
21
22
23
24
13
1
2
3
4
5
6
7
89
10
11
12
131415
16
17
18
19
20
21
22
23
24
25
25
archivo 25 iberomys landmarks
Some extreme morphologies
Allophaiomys pliocaenicus Pirro
Nord
Early Pleistocene Italy Iberomys cabrerae
Extant Spain
Allophaiomys lavocati
Sima del Elefante
Atapuerca
Early Pleistocene (older
than the Italian species
Spain
AllophLavF
N3_1r
Early
Pleistocen
e of
Granada
similar to
Atapuerca
LM =17-14 of Iberon LM =15-14 of Iberon LM =15-14 of Iberon
Landmarks de 90 especiacutemenes de
Microtus agrestis
Landmarks de 90 especiacutemenes de
Microtus agrestis
Data 90 Specimens 22 Points 2 Dimensions
All specimen superimposed by GLS method
Sum of Squared Deviations = 1101217
The groups limit is after the specimen 0
PCS and scores computed
Percentages of variance for the 8 first PCS
61395977 61395977
8155754 69551731
4681460 74233190
3352225 77585415
2619139 80204554
2500418 82704973
2235576 84940549
1789387 86729936
Multivariate regression coefficients (normalized) with 3 PCS
PCS 1 0998142
PCS 2 -0057223
PCS 3 -0020926
Regression statistic for 3 components
Rsup2= 0227471 F= 8244611 with 3 and 86 DF plt 0000070
Plot de 90 especiacutemenes de
Microtus agrestis
Distribucioacuten estratigraacutefica de los roedores del cuaternario de Gran Dolina Atapuerca Burgos
0 m
Allo
ph
aio
mys
Mim
om
ys
Ibe
rom
ys
Terr
ico
la
Ste
no
cra
niu
s
Arv
ico
la
Mic
rom
ys
Hy
str
ix
Ca
sto
r
Ma
rmo
ta
Plio
mys
Mic
rotu
s
Allo
cri
cetu
s
Ap
od
em
us
Elio
mys
TD7
TD8
TD10
TD11
TD6
TD5
TD34
TD2
TD1
Procustes analisis APS
bull Procuste fue un ladroacuten que bien descuartizaba o bien estiraba a sus viacutectimas para ajustarlas al tamantildeo de su cama de ahiacute viene la frase hecha de ldquola cama Procusterdquo que se aplica sobre todo en poliacutetica la censura o para prestaciones puacuteblicas en las que es el usuario el que debe adaptarse y no al reveacuteshellip
bull The APS package
bull The shape analysis softwares APS ApsDigit and ApsUtil are written in English and always free for the students Aps combines Procuste superposition and statistical calculations ApsDigit is used locate landmarks on digital images (JPEG Bitmap tiff GIF) ApsUtil is used to handle files (Selection of points individuals change of classification)
bull httpwwwprocustecom
APS
APS est un logiciel danalyse quantitative de la
variabiliteacute morphologique des formes vivantes La
meacutethode utiliseacutee est la superposition procruste
geacuteneacuteraliseacutee
Destineacute aux biologistes et aux cliniciens APS prend en
charge les aspects matheacutematiques et statistiques de
lanalyse de forme Lanalyse se fait en 2 temps
1 Une superposition procruste de lensemble des
speacutecimens
2 Une analyse statistique qui visualise et teste la covariance
entre dune part la conformation et dautre part un facteur
biologique comme la taille lappartenance agrave groupe la
preacutesence ou non dune pathologie
Il est conccedilu pour eacutetudier un ou deux groupes
APS Digitalizar landmarks
DigitX is designed to digitize landmarks on Jpeg or Bitmap picture
middot Select the total number of landmarks to digitize with the second
Combo-Box of the toolbar
middot Select a picture in the graphic file selector on the left
middot Click on to load the link file (optional)
middot Click on to load the consensus file (optional)
middot Digitize landmarks using the left button of the mouse
middot To cancel last landmark position by a click on undo arrow
middot When all landmarks are digitized save the file by a click on save file
APS Crear archivo
Getting started with ApsUtil
ApsUtil create a data file (dat) with specimen ordered by
addition of smaller data files Input and output files are to
APS data format with an header line (number of specimens
number
of landmarks number of dimensions) followed by landmarks
coordinates
NEW button clear all previous data and begin a new data file
ADD button add a file containing one or many specimen
MIX button add a new file to a previous one by mixing the
two file
This ordering of specimen is required before to compute
shape differences
When file is saved specimens are ordered like
specimen 1 of the 1st file
specimen 1 of the 2nd file
specimen 2 of the 1st file
APS analisis
bull New features of Version 241
bull A single specimen or all a sample can be superimposed on any reloaded
bull specimen as consensus (File -gt Reload -gt Consensus)
bull Shape vectors (eg discriminant vectors computed with other software)
bull can be reloaded for visualization (File -gt Reload -gt Pcs)
bull The shape vector must be of norm 1
bull Projections of specimens on shape vectors are automatically computed
Otros
elementos del
esqueleto
A Antarctosaurus wichmannianus B
Saltasaurus loricatus C Neuquensaurus
australis D Neuquensaurus robustus E
Lirainosaurus astibiae F Ampelosaurus atacis
G Magyarosaurus dacus H Magyarosaurus
dacus Jianu I Alamosaurus sanjuanensis J
Aegyptosaurus baharijiensis K
Opisthocoelicaudia skarzynskii
Canudo amp Cuenca Bescos 2004
wwwaragosauruscom
Aegyptosaurus Alamosaurus
Imaacutegenes literatura
Fotos ejemplares
Hacer un poliacutegono con los landmarks
Guardar la misma posicioacuten (en una liacutenea basal por ej)
APS digit
APS util
APS program CP
Opisthocoelicaudia
Resultados
APS Fecha Thu 21 Sep 2006 213918
+0200 [210906 213918 CEST]
De Info Procuste
ltinfoprocustecomgt
Para cuencagunizares
Asunto Re analyse de forme chez
les arvicolides
Cabeceras Mostrar todas las
cabeceras
Chegravere collegravegue
Voici le lien pour teacuteleacutecharger le le
setup dinstallation des 3
logiciels APS ApsDigit et ApsUtil
httpwwwprocustecomprogramsset
up_aps_allexe
Noubliez pas de citer APS dans vos
publications
Bien cordialement
Xavier Penin
Paacuteginas web recomendadas
bull httplifebiosunysbedumorph la mejor paacutegina de
morfometriacutea geomeacutetrica Contiene un listado con todos los
programas de morfometriacutea Universidad de Stony Brook NY
bull httpwwwmorphometricsorgindexhtml es la paacutegina en la
que se mantiene la lista de email morphmet Es la base de la
organizacioacuten de la morfometriacutea en Suny
bull httpwwwflywingsorgukindexhtm iquestporqueacute hay variacioacuten
morfoloacutegica Universidad de Manchester UK
bull httpwwwprocustecomindexhtml anaacutelisis de la forma con
Procruste Aps Xavier Penin Universidad de Paris V
bull Shapehellipy otros ver la paacutegina de Suny
Las ldquoseries TPSrdquo Thin-plate spline
(laacuteminas finas de grosor uniforme)
tpsDIG2
Data acquisition
bull Digitize landmarks amp outlines from image files scanner or video Windows TpsDig is a Windows (95 through XP) program for digitizing landmarks and outlines for geometric morphometric analyses Includes simple image enhancement operations scale factors image brightness profile and support for AVI and MOV files Output is in the TPS file format used by the tps series of programs The TPS file includes the name of the image file for each specimen so that landmarks can always be visualized on the image Since output files are ASCII they can be converted to formats for other software Users should note that the tpsUtil program is useful for both the preparation of the input files to tpsDig as well as for some useful conversions afterwards The program also computes areas of enclosed regions perimeters and linear distances The tpsDig2 link at the left is for the new 205 version
bull Execute the downloaded file to install the program By F James Rohlf
Las ldquoseries TPSrdquo
ordenar los archivos digitalizados
TPS util
bull tps file utility program Windows At present it can randomly scramble the order of specimens in a tps file to minimize bias in digitizing landmark locations restore the original order (eg before statistical analyses are performed) create an empty TPS file from a directory with image files add keywords and values to the variables field of a TPS file combine TPS files into a single TPS file deletereorder landmarks remove outlines from a TPS file and convert TPS and NTS files to NTS M or CSV files It can also split an NTS file into several matrices Graphic editors are included for drawing link and sliders files Unbending a deformed specimen Converting outline and curves points to landmarks
bull Other operations can be added - let me know what you need Execute the TPSUTILW32EXE file to install the program By F James Rohlf Version 138
tpsTree
bull Fit and visualize thin-plate splines on trees Windows Performs a least-squares orthogonal generalized Procrustes analysis to obtain a reference and then estimates the splines for each group (internal node) on a tree Both ultrametric (eg WPGMA and UPGMA trees) and additive trees (using squared change parsimony to estimate the shapes of the HTUs) are supported The estimated shapes can be visualized with estimated images in the background (see the tpsSuper program) The file expands into a Windows setup program and associated files By F James Rohlf Version 118 File containing HTU coordinates and HTU images to demo that feature The older and more limited 16 bit Windows version is still available
tpsRegr
bull Multivariate multiple regression of shape onto independent variables Windows performs a multivariate multiple regression of shape (as captured by partial warp scores and the uniform shape component) onto one or more independent variables By appropriate setting up of independent variables this program can perform various types of MANOVA and MANCOVA Can be used to study allometry By F James Rohlf Version 131
tpsSplin
bull Thin-plate spline Windows Program to
compare pairs of specimens by displaying
a Darcy Thompson style transformation
grid based on a thin-plate spline Several
options are given for sliding
semilandmarks The tpssplnwexe file
expands into a Windows setup program
that will be run automatically By F James
Rohlf Version 120
tpsRelw el anaacutelisis de la
deformacioacuten relativa bull Relative warps analysis Windows Performs a
relative warp (deformacioacuten) analysis This corresponds to a principal components analysis of variation in a sample (relative to bending energy if the alpha parameter is not equal to zero) Displays a plot of relative warp scores and a visualization window that displays the estimated shape for arbitrary points in the ordination Also displays partial warp scores and their visualizations Allows fitting of semilandmark points along curves Version 144 By F James Rohlf
tpsPLS
bull Partial least-squares analysis for shapes Windows Used to explore the covariance between a set of variables and variation in shape or between two shapes It performs a two-block partial least-squares analysis It differs from regression in that both variables and shape are considered equally (one is not considered to be a set of independent variables measured without error) Its use is described in Rohlf and Corti (2000 Systematic Biology 49740-753) By F James Rohlf Version 118
tpsSmall
bull Test for small variation in shape Windows Use to test whether the variation in shape among a set of specimens is too large and thus statistical methods based on the tangent space approximation (eg thin-plate spline methods) cannot be used The program can process both 2D and 3D data files Output files include consensus and aligned specimens By F James Rohlf Version 120
tpsPower
bull Estimate statistical power for comparing shapes Windows Program for estimating statistical power for comparing the mean shapes of two populations Provides methods based on several different approaches Can be used for planning morphometric studies as well as to compare power using different approaches Version 104 By F James Rohlf
Morpheus et al bull Morpheus et al is a software package that will provide a
comprehensive cross-platform environment for morphometric data analysis It is available in graphical and command-line versions for a number of operating systems (see below) More information about new features and previous changes can be found in the release notes
httplifebiosunysbedumorphmorpheus
Multivariate analysis
bull PAST is a free easy-to-use data analysis package aimed at paleontology Windows 95+ Multivariate statistical methods include Principal Components (with Minimal Spanning Tree) Principal Coordinates (ten distance measures) Non-metric Multidimensional Scaling (ten distance measures) Detrended Correspondence Analysis Cluster analysis (three algorithms 11 distance measures) k-means clustering seriation discriminant analysis one-way MANOVA Hotellings t-squared Boxs M Canonical Variates Analysis Also includes Fourier shape analysis thin-plate splines parsimony and time series analysis among others Oslashyvind Hammer University of Oslo
Analysis of outlines
bull Shape Elliptic Fourier WINDOWS Extracts the contour shape from a full color bitmap image delineates the contour shape with the elliptic Fourier descriptors and performs a principal component analysis for summarizing the shape information By Hiroyoshi Iwata For more information see Shape home page tutorial or manual
bull Iwata H and Y Ukai (2002) SHAPE A computer program package for quantitative evaluation of biological shapes based on elliptic Fourier descriptors Journal of Heredity 93 384-385
Eigenshape analysis
bull httpwwwnhmacukhosted_sitespaleonetftpftphtml
bull This archive contains a series of programs designed to perform an eigenshape analysis on xy coordinate data from object outlines Routines include xy -gt phi() transformation phi() -gt xy transformation eigenshape analysis and projection of objects into the eigenshape space Two completely worked example analyses and a users guide are also provided El autor es Norman McLeod del BMNH de Londres
Graphical representation of the four-step morphometric protocol A Quantify raw data
(landmarks recorded on body of cichlid fish) B Remove non-shape variation (landmarks of 412
specimens before and after GPA) C statistical analysis (CVA) and graphical presentation of
results Deformation grids for mean specimen for (right) Eretmodus cyanostictus and (left)
Spathodus erythrodon (magnified by 3X to emphasize shape differences) Data from Ruumlber and
Adams 2001 En Adams Rolhf Slice 2002
Dientes complejos Arvicolinae
Iberon 25 Landmarks
1
2
4
3
5
6
7
8 9
1011
12
14
15
16
17
18
19
20
21
22
23
24
13
1
2
3
4
5
6
7
89
10
11
12
131415
16
17
18
19
20
21
22
23
24
25
25
archivo 25 iberomys landmarks
Some extreme morphologies
Allophaiomys pliocaenicus Pirro
Nord
Early Pleistocene Italy Iberomys cabrerae
Extant Spain
Allophaiomys lavocati
Sima del Elefante
Atapuerca
Early Pleistocene (older
than the Italian species
Spain
AllophLavF
N3_1r
Early
Pleistocen
e of
Granada
similar to
Atapuerca
LM =17-14 of Iberon LM =15-14 of Iberon LM =15-14 of Iberon
Landmarks de 90 especiacutemenes de
Microtus agrestis
Landmarks de 90 especiacutemenes de
Microtus agrestis
Data 90 Specimens 22 Points 2 Dimensions
All specimen superimposed by GLS method
Sum of Squared Deviations = 1101217
The groups limit is after the specimen 0
PCS and scores computed
Percentages of variance for the 8 first PCS
61395977 61395977
8155754 69551731
4681460 74233190
3352225 77585415
2619139 80204554
2500418 82704973
2235576 84940549
1789387 86729936
Multivariate regression coefficients (normalized) with 3 PCS
PCS 1 0998142
PCS 2 -0057223
PCS 3 -0020926
Regression statistic for 3 components
Rsup2= 0227471 F= 8244611 with 3 and 86 DF plt 0000070
Plot de 90 especiacutemenes de
Microtus agrestis
Distribucioacuten estratigraacutefica de los roedores del cuaternario de Gran Dolina Atapuerca Burgos
0 m
Allo
ph
aio
mys
Mim
om
ys
Ibe
rom
ys
Terr
ico
la
Ste
no
cra
niu
s
Arv
ico
la
Mic
rom
ys
Hy
str
ix
Ca
sto
r
Ma
rmo
ta
Plio
mys
Mic
rotu
s
Allo
cri
cetu
s
Ap
od
em
us
Elio
mys
TD7
TD8
TD10
TD11
TD6
TD5
TD34
TD2
TD1
Procustes analisis APS
bull Procuste fue un ladroacuten que bien descuartizaba o bien estiraba a sus viacutectimas para ajustarlas al tamantildeo de su cama de ahiacute viene la frase hecha de ldquola cama Procusterdquo que se aplica sobre todo en poliacutetica la censura o para prestaciones puacuteblicas en las que es el usuario el que debe adaptarse y no al reveacuteshellip
bull The APS package
bull The shape analysis softwares APS ApsDigit and ApsUtil are written in English and always free for the students Aps combines Procuste superposition and statistical calculations ApsDigit is used locate landmarks on digital images (JPEG Bitmap tiff GIF) ApsUtil is used to handle files (Selection of points individuals change of classification)
bull httpwwwprocustecom
APS
APS est un logiciel danalyse quantitative de la
variabiliteacute morphologique des formes vivantes La
meacutethode utiliseacutee est la superposition procruste
geacuteneacuteraliseacutee
Destineacute aux biologistes et aux cliniciens APS prend en
charge les aspects matheacutematiques et statistiques de
lanalyse de forme Lanalyse se fait en 2 temps
1 Une superposition procruste de lensemble des
speacutecimens
2 Une analyse statistique qui visualise et teste la covariance
entre dune part la conformation et dautre part un facteur
biologique comme la taille lappartenance agrave groupe la
preacutesence ou non dune pathologie
Il est conccedilu pour eacutetudier un ou deux groupes
APS Digitalizar landmarks
DigitX is designed to digitize landmarks on Jpeg or Bitmap picture
middot Select the total number of landmarks to digitize with the second
Combo-Box of the toolbar
middot Select a picture in the graphic file selector on the left
middot Click on to load the link file (optional)
middot Click on to load the consensus file (optional)
middot Digitize landmarks using the left button of the mouse
middot To cancel last landmark position by a click on undo arrow
middot When all landmarks are digitized save the file by a click on save file
APS Crear archivo
Getting started with ApsUtil
ApsUtil create a data file (dat) with specimen ordered by
addition of smaller data files Input and output files are to
APS data format with an header line (number of specimens
number
of landmarks number of dimensions) followed by landmarks
coordinates
NEW button clear all previous data and begin a new data file
ADD button add a file containing one or many specimen
MIX button add a new file to a previous one by mixing the
two file
This ordering of specimen is required before to compute
shape differences
When file is saved specimens are ordered like
specimen 1 of the 1st file
specimen 1 of the 2nd file
specimen 2 of the 1st file
APS analisis
bull New features of Version 241
bull A single specimen or all a sample can be superimposed on any reloaded
bull specimen as consensus (File -gt Reload -gt Consensus)
bull Shape vectors (eg discriminant vectors computed with other software)
bull can be reloaded for visualization (File -gt Reload -gt Pcs)
bull The shape vector must be of norm 1
bull Projections of specimens on shape vectors are automatically computed
Otros
elementos del
esqueleto
A Antarctosaurus wichmannianus B
Saltasaurus loricatus C Neuquensaurus
australis D Neuquensaurus robustus E
Lirainosaurus astibiae F Ampelosaurus atacis
G Magyarosaurus dacus H Magyarosaurus
dacus Jianu I Alamosaurus sanjuanensis J
Aegyptosaurus baharijiensis K
Opisthocoelicaudia skarzynskii
Canudo amp Cuenca Bescos 2004
wwwaragosauruscom
Aegyptosaurus Alamosaurus
Imaacutegenes literatura
Fotos ejemplares
Hacer un poliacutegono con los landmarks
Guardar la misma posicioacuten (en una liacutenea basal por ej)
APS digit
APS util
APS program CP
Opisthocoelicaudia
Resultados
APS Fecha Thu 21 Sep 2006 213918
+0200 [210906 213918 CEST]
De Info Procuste
ltinfoprocustecomgt
Para cuencagunizares
Asunto Re analyse de forme chez
les arvicolides
Cabeceras Mostrar todas las
cabeceras
Chegravere collegravegue
Voici le lien pour teacuteleacutecharger le le
setup dinstallation des 3
logiciels APS ApsDigit et ApsUtil
httpwwwprocustecomprogramsset
up_aps_allexe
Noubliez pas de citer APS dans vos
publications
Bien cordialement
Xavier Penin
Paacuteginas web recomendadas
bull httplifebiosunysbedumorph la mejor paacutegina de
morfometriacutea geomeacutetrica Contiene un listado con todos los
programas de morfometriacutea Universidad de Stony Brook NY
bull httpwwwmorphometricsorgindexhtml es la paacutegina en la
que se mantiene la lista de email morphmet Es la base de la
organizacioacuten de la morfometriacutea en Suny
bull httpwwwflywingsorgukindexhtm iquestporqueacute hay variacioacuten
morfoloacutegica Universidad de Manchester UK
bull httpwwwprocustecomindexhtml anaacutelisis de la forma con
Procruste Aps Xavier Penin Universidad de Paris V
bull Shapehellipy otros ver la paacutegina de Suny
Las ldquoseries TPSrdquo Thin-plate spline
(laacuteminas finas de grosor uniforme)
tpsDIG2
Data acquisition
bull Digitize landmarks amp outlines from image files scanner or video Windows TpsDig is a Windows (95 through XP) program for digitizing landmarks and outlines for geometric morphometric analyses Includes simple image enhancement operations scale factors image brightness profile and support for AVI and MOV files Output is in the TPS file format used by the tps series of programs The TPS file includes the name of the image file for each specimen so that landmarks can always be visualized on the image Since output files are ASCII they can be converted to formats for other software Users should note that the tpsUtil program is useful for both the preparation of the input files to tpsDig as well as for some useful conversions afterwards The program also computes areas of enclosed regions perimeters and linear distances The tpsDig2 link at the left is for the new 205 version
bull Execute the downloaded file to install the program By F James Rohlf
Las ldquoseries TPSrdquo
ordenar los archivos digitalizados
TPS util
bull tps file utility program Windows At present it can randomly scramble the order of specimens in a tps file to minimize bias in digitizing landmark locations restore the original order (eg before statistical analyses are performed) create an empty TPS file from a directory with image files add keywords and values to the variables field of a TPS file combine TPS files into a single TPS file deletereorder landmarks remove outlines from a TPS file and convert TPS and NTS files to NTS M or CSV files It can also split an NTS file into several matrices Graphic editors are included for drawing link and sliders files Unbending a deformed specimen Converting outline and curves points to landmarks
bull Other operations can be added - let me know what you need Execute the TPSUTILW32EXE file to install the program By F James Rohlf Version 138
tpsTree
bull Fit and visualize thin-plate splines on trees Windows Performs a least-squares orthogonal generalized Procrustes analysis to obtain a reference and then estimates the splines for each group (internal node) on a tree Both ultrametric (eg WPGMA and UPGMA trees) and additive trees (using squared change parsimony to estimate the shapes of the HTUs) are supported The estimated shapes can be visualized with estimated images in the background (see the tpsSuper program) The file expands into a Windows setup program and associated files By F James Rohlf Version 118 File containing HTU coordinates and HTU images to demo that feature The older and more limited 16 bit Windows version is still available
tpsRegr
bull Multivariate multiple regression of shape onto independent variables Windows performs a multivariate multiple regression of shape (as captured by partial warp scores and the uniform shape component) onto one or more independent variables By appropriate setting up of independent variables this program can perform various types of MANOVA and MANCOVA Can be used to study allometry By F James Rohlf Version 131
tpsSplin
bull Thin-plate spline Windows Program to
compare pairs of specimens by displaying
a Darcy Thompson style transformation
grid based on a thin-plate spline Several
options are given for sliding
semilandmarks The tpssplnwexe file
expands into a Windows setup program
that will be run automatically By F James
Rohlf Version 120
tpsRelw el anaacutelisis de la
deformacioacuten relativa bull Relative warps analysis Windows Performs a
relative warp (deformacioacuten) analysis This corresponds to a principal components analysis of variation in a sample (relative to bending energy if the alpha parameter is not equal to zero) Displays a plot of relative warp scores and a visualization window that displays the estimated shape for arbitrary points in the ordination Also displays partial warp scores and their visualizations Allows fitting of semilandmark points along curves Version 144 By F James Rohlf
tpsPLS
bull Partial least-squares analysis for shapes Windows Used to explore the covariance between a set of variables and variation in shape or between two shapes It performs a two-block partial least-squares analysis It differs from regression in that both variables and shape are considered equally (one is not considered to be a set of independent variables measured without error) Its use is described in Rohlf and Corti (2000 Systematic Biology 49740-753) By F James Rohlf Version 118
tpsSmall
bull Test for small variation in shape Windows Use to test whether the variation in shape among a set of specimens is too large and thus statistical methods based on the tangent space approximation (eg thin-plate spline methods) cannot be used The program can process both 2D and 3D data files Output files include consensus and aligned specimens By F James Rohlf Version 120
tpsPower
bull Estimate statistical power for comparing shapes Windows Program for estimating statistical power for comparing the mean shapes of two populations Provides methods based on several different approaches Can be used for planning morphometric studies as well as to compare power using different approaches Version 104 By F James Rohlf
Morpheus et al bull Morpheus et al is a software package that will provide a
comprehensive cross-platform environment for morphometric data analysis It is available in graphical and command-line versions for a number of operating systems (see below) More information about new features and previous changes can be found in the release notes
httplifebiosunysbedumorphmorpheus
Multivariate analysis
bull PAST is a free easy-to-use data analysis package aimed at paleontology Windows 95+ Multivariate statistical methods include Principal Components (with Minimal Spanning Tree) Principal Coordinates (ten distance measures) Non-metric Multidimensional Scaling (ten distance measures) Detrended Correspondence Analysis Cluster analysis (three algorithms 11 distance measures) k-means clustering seriation discriminant analysis one-way MANOVA Hotellings t-squared Boxs M Canonical Variates Analysis Also includes Fourier shape analysis thin-plate splines parsimony and time series analysis among others Oslashyvind Hammer University of Oslo
Analysis of outlines
bull Shape Elliptic Fourier WINDOWS Extracts the contour shape from a full color bitmap image delineates the contour shape with the elliptic Fourier descriptors and performs a principal component analysis for summarizing the shape information By Hiroyoshi Iwata For more information see Shape home page tutorial or manual
bull Iwata H and Y Ukai (2002) SHAPE A computer program package for quantitative evaluation of biological shapes based on elliptic Fourier descriptors Journal of Heredity 93 384-385
Eigenshape analysis
bull httpwwwnhmacukhosted_sitespaleonetftpftphtml
bull This archive contains a series of programs designed to perform an eigenshape analysis on xy coordinate data from object outlines Routines include xy -gt phi() transformation phi() -gt xy transformation eigenshape analysis and projection of objects into the eigenshape space Two completely worked example analyses and a users guide are also provided El autor es Norman McLeod del BMNH de Londres
Graphical representation of the four-step morphometric protocol A Quantify raw data
(landmarks recorded on body of cichlid fish) B Remove non-shape variation (landmarks of 412
specimens before and after GPA) C statistical analysis (CVA) and graphical presentation of
results Deformation grids for mean specimen for (right) Eretmodus cyanostictus and (left)
Spathodus erythrodon (magnified by 3X to emphasize shape differences) Data from Ruumlber and
Adams 2001 En Adams Rolhf Slice 2002
Iberon 25 Landmarks
1
2
4
3
5
6
7
8 9
1011
12
14
15
16
17
18
19
20
21
22
23
24
13
1
2
3
4
5
6
7
89
10
11
12
131415
16
17
18
19
20
21
22
23
24
25
25
archivo 25 iberomys landmarks
Some extreme morphologies
Allophaiomys pliocaenicus Pirro
Nord
Early Pleistocene Italy Iberomys cabrerae
Extant Spain
Allophaiomys lavocati
Sima del Elefante
Atapuerca
Early Pleistocene (older
than the Italian species
Spain
AllophLavF
N3_1r
Early
Pleistocen
e of
Granada
similar to
Atapuerca
LM =17-14 of Iberon LM =15-14 of Iberon LM =15-14 of Iberon
Landmarks de 90 especiacutemenes de
Microtus agrestis
Landmarks de 90 especiacutemenes de
Microtus agrestis
Data 90 Specimens 22 Points 2 Dimensions
All specimen superimposed by GLS method
Sum of Squared Deviations = 1101217
The groups limit is after the specimen 0
PCS and scores computed
Percentages of variance for the 8 first PCS
61395977 61395977
8155754 69551731
4681460 74233190
3352225 77585415
2619139 80204554
2500418 82704973
2235576 84940549
1789387 86729936
Multivariate regression coefficients (normalized) with 3 PCS
PCS 1 0998142
PCS 2 -0057223
PCS 3 -0020926
Regression statistic for 3 components
Rsup2= 0227471 F= 8244611 with 3 and 86 DF plt 0000070
Plot de 90 especiacutemenes de
Microtus agrestis
Distribucioacuten estratigraacutefica de los roedores del cuaternario de Gran Dolina Atapuerca Burgos
0 m
Allo
ph
aio
mys
Mim
om
ys
Ibe
rom
ys
Terr
ico
la
Ste
no
cra
niu
s
Arv
ico
la
Mic
rom
ys
Hy
str
ix
Ca
sto
r
Ma
rmo
ta
Plio
mys
Mic
rotu
s
Allo
cri
cetu
s
Ap
od
em
us
Elio
mys
TD7
TD8
TD10
TD11
TD6
TD5
TD34
TD2
TD1
Procustes analisis APS
bull Procuste fue un ladroacuten que bien descuartizaba o bien estiraba a sus viacutectimas para ajustarlas al tamantildeo de su cama de ahiacute viene la frase hecha de ldquola cama Procusterdquo que se aplica sobre todo en poliacutetica la censura o para prestaciones puacuteblicas en las que es el usuario el que debe adaptarse y no al reveacuteshellip
bull The APS package
bull The shape analysis softwares APS ApsDigit and ApsUtil are written in English and always free for the students Aps combines Procuste superposition and statistical calculations ApsDigit is used locate landmarks on digital images (JPEG Bitmap tiff GIF) ApsUtil is used to handle files (Selection of points individuals change of classification)
bull httpwwwprocustecom
APS
APS est un logiciel danalyse quantitative de la
variabiliteacute morphologique des formes vivantes La
meacutethode utiliseacutee est la superposition procruste
geacuteneacuteraliseacutee
Destineacute aux biologistes et aux cliniciens APS prend en
charge les aspects matheacutematiques et statistiques de
lanalyse de forme Lanalyse se fait en 2 temps
1 Une superposition procruste de lensemble des
speacutecimens
2 Une analyse statistique qui visualise et teste la covariance
entre dune part la conformation et dautre part un facteur
biologique comme la taille lappartenance agrave groupe la
preacutesence ou non dune pathologie
Il est conccedilu pour eacutetudier un ou deux groupes
APS Digitalizar landmarks
DigitX is designed to digitize landmarks on Jpeg or Bitmap picture
middot Select the total number of landmarks to digitize with the second
Combo-Box of the toolbar
middot Select a picture in the graphic file selector on the left
middot Click on to load the link file (optional)
middot Click on to load the consensus file (optional)
middot Digitize landmarks using the left button of the mouse
middot To cancel last landmark position by a click on undo arrow
middot When all landmarks are digitized save the file by a click on save file
APS Crear archivo
Getting started with ApsUtil
ApsUtil create a data file (dat) with specimen ordered by
addition of smaller data files Input and output files are to
APS data format with an header line (number of specimens
number
of landmarks number of dimensions) followed by landmarks
coordinates
NEW button clear all previous data and begin a new data file
ADD button add a file containing one or many specimen
MIX button add a new file to a previous one by mixing the
two file
This ordering of specimen is required before to compute
shape differences
When file is saved specimens are ordered like
specimen 1 of the 1st file
specimen 1 of the 2nd file
specimen 2 of the 1st file
APS analisis
bull New features of Version 241
bull A single specimen or all a sample can be superimposed on any reloaded
bull specimen as consensus (File -gt Reload -gt Consensus)
bull Shape vectors (eg discriminant vectors computed with other software)
bull can be reloaded for visualization (File -gt Reload -gt Pcs)
bull The shape vector must be of norm 1
bull Projections of specimens on shape vectors are automatically computed
Otros
elementos del
esqueleto
A Antarctosaurus wichmannianus B
Saltasaurus loricatus C Neuquensaurus
australis D Neuquensaurus robustus E
Lirainosaurus astibiae F Ampelosaurus atacis
G Magyarosaurus dacus H Magyarosaurus
dacus Jianu I Alamosaurus sanjuanensis J
Aegyptosaurus baharijiensis K
Opisthocoelicaudia skarzynskii
Canudo amp Cuenca Bescos 2004
wwwaragosauruscom
Aegyptosaurus Alamosaurus
Imaacutegenes literatura
Fotos ejemplares
Hacer un poliacutegono con los landmarks
Guardar la misma posicioacuten (en una liacutenea basal por ej)
APS digit
APS util
APS program CP
Opisthocoelicaudia
Resultados
APS Fecha Thu 21 Sep 2006 213918
+0200 [210906 213918 CEST]
De Info Procuste
ltinfoprocustecomgt
Para cuencagunizares
Asunto Re analyse de forme chez
les arvicolides
Cabeceras Mostrar todas las
cabeceras
Chegravere collegravegue
Voici le lien pour teacuteleacutecharger le le
setup dinstallation des 3
logiciels APS ApsDigit et ApsUtil
httpwwwprocustecomprogramsset
up_aps_allexe
Noubliez pas de citer APS dans vos
publications
Bien cordialement
Xavier Penin
Paacuteginas web recomendadas
bull httplifebiosunysbedumorph la mejor paacutegina de
morfometriacutea geomeacutetrica Contiene un listado con todos los
programas de morfometriacutea Universidad de Stony Brook NY
bull httpwwwmorphometricsorgindexhtml es la paacutegina en la
que se mantiene la lista de email morphmet Es la base de la
organizacioacuten de la morfometriacutea en Suny
bull httpwwwflywingsorgukindexhtm iquestporqueacute hay variacioacuten
morfoloacutegica Universidad de Manchester UK
bull httpwwwprocustecomindexhtml anaacutelisis de la forma con
Procruste Aps Xavier Penin Universidad de Paris V
bull Shapehellipy otros ver la paacutegina de Suny
Las ldquoseries TPSrdquo Thin-plate spline
(laacuteminas finas de grosor uniforme)
tpsDIG2
Data acquisition
bull Digitize landmarks amp outlines from image files scanner or video Windows TpsDig is a Windows (95 through XP) program for digitizing landmarks and outlines for geometric morphometric analyses Includes simple image enhancement operations scale factors image brightness profile and support for AVI and MOV files Output is in the TPS file format used by the tps series of programs The TPS file includes the name of the image file for each specimen so that landmarks can always be visualized on the image Since output files are ASCII they can be converted to formats for other software Users should note that the tpsUtil program is useful for both the preparation of the input files to tpsDig as well as for some useful conversions afterwards The program also computes areas of enclosed regions perimeters and linear distances The tpsDig2 link at the left is for the new 205 version
bull Execute the downloaded file to install the program By F James Rohlf
Las ldquoseries TPSrdquo
ordenar los archivos digitalizados
TPS util
bull tps file utility program Windows At present it can randomly scramble the order of specimens in a tps file to minimize bias in digitizing landmark locations restore the original order (eg before statistical analyses are performed) create an empty TPS file from a directory with image files add keywords and values to the variables field of a TPS file combine TPS files into a single TPS file deletereorder landmarks remove outlines from a TPS file and convert TPS and NTS files to NTS M or CSV files It can also split an NTS file into several matrices Graphic editors are included for drawing link and sliders files Unbending a deformed specimen Converting outline and curves points to landmarks
bull Other operations can be added - let me know what you need Execute the TPSUTILW32EXE file to install the program By F James Rohlf Version 138
tpsTree
bull Fit and visualize thin-plate splines on trees Windows Performs a least-squares orthogonal generalized Procrustes analysis to obtain a reference and then estimates the splines for each group (internal node) on a tree Both ultrametric (eg WPGMA and UPGMA trees) and additive trees (using squared change parsimony to estimate the shapes of the HTUs) are supported The estimated shapes can be visualized with estimated images in the background (see the tpsSuper program) The file expands into a Windows setup program and associated files By F James Rohlf Version 118 File containing HTU coordinates and HTU images to demo that feature The older and more limited 16 bit Windows version is still available
tpsRegr
bull Multivariate multiple regression of shape onto independent variables Windows performs a multivariate multiple regression of shape (as captured by partial warp scores and the uniform shape component) onto one or more independent variables By appropriate setting up of independent variables this program can perform various types of MANOVA and MANCOVA Can be used to study allometry By F James Rohlf Version 131
tpsSplin
bull Thin-plate spline Windows Program to
compare pairs of specimens by displaying
a Darcy Thompson style transformation
grid based on a thin-plate spline Several
options are given for sliding
semilandmarks The tpssplnwexe file
expands into a Windows setup program
that will be run automatically By F James
Rohlf Version 120
tpsRelw el anaacutelisis de la
deformacioacuten relativa bull Relative warps analysis Windows Performs a
relative warp (deformacioacuten) analysis This corresponds to a principal components analysis of variation in a sample (relative to bending energy if the alpha parameter is not equal to zero) Displays a plot of relative warp scores and a visualization window that displays the estimated shape for arbitrary points in the ordination Also displays partial warp scores and their visualizations Allows fitting of semilandmark points along curves Version 144 By F James Rohlf
tpsPLS
bull Partial least-squares analysis for shapes Windows Used to explore the covariance between a set of variables and variation in shape or between two shapes It performs a two-block partial least-squares analysis It differs from regression in that both variables and shape are considered equally (one is not considered to be a set of independent variables measured without error) Its use is described in Rohlf and Corti (2000 Systematic Biology 49740-753) By F James Rohlf Version 118
tpsSmall
bull Test for small variation in shape Windows Use to test whether the variation in shape among a set of specimens is too large and thus statistical methods based on the tangent space approximation (eg thin-plate spline methods) cannot be used The program can process both 2D and 3D data files Output files include consensus and aligned specimens By F James Rohlf Version 120
tpsPower
bull Estimate statistical power for comparing shapes Windows Program for estimating statistical power for comparing the mean shapes of two populations Provides methods based on several different approaches Can be used for planning morphometric studies as well as to compare power using different approaches Version 104 By F James Rohlf
Morpheus et al bull Morpheus et al is a software package that will provide a
comprehensive cross-platform environment for morphometric data analysis It is available in graphical and command-line versions for a number of operating systems (see below) More information about new features and previous changes can be found in the release notes
httplifebiosunysbedumorphmorpheus
Multivariate analysis
bull PAST is a free easy-to-use data analysis package aimed at paleontology Windows 95+ Multivariate statistical methods include Principal Components (with Minimal Spanning Tree) Principal Coordinates (ten distance measures) Non-metric Multidimensional Scaling (ten distance measures) Detrended Correspondence Analysis Cluster analysis (three algorithms 11 distance measures) k-means clustering seriation discriminant analysis one-way MANOVA Hotellings t-squared Boxs M Canonical Variates Analysis Also includes Fourier shape analysis thin-plate splines parsimony and time series analysis among others Oslashyvind Hammer University of Oslo
Analysis of outlines
bull Shape Elliptic Fourier WINDOWS Extracts the contour shape from a full color bitmap image delineates the contour shape with the elliptic Fourier descriptors and performs a principal component analysis for summarizing the shape information By Hiroyoshi Iwata For more information see Shape home page tutorial or manual
bull Iwata H and Y Ukai (2002) SHAPE A computer program package for quantitative evaluation of biological shapes based on elliptic Fourier descriptors Journal of Heredity 93 384-385
Eigenshape analysis
bull httpwwwnhmacukhosted_sitespaleonetftpftphtml
bull This archive contains a series of programs designed to perform an eigenshape analysis on xy coordinate data from object outlines Routines include xy -gt phi() transformation phi() -gt xy transformation eigenshape analysis and projection of objects into the eigenshape space Two completely worked example analyses and a users guide are also provided El autor es Norman McLeod del BMNH de Londres
Graphical representation of the four-step morphometric protocol A Quantify raw data
(landmarks recorded on body of cichlid fish) B Remove non-shape variation (landmarks of 412
specimens before and after GPA) C statistical analysis (CVA) and graphical presentation of
results Deformation grids for mean specimen for (right) Eretmodus cyanostictus and (left)
Spathodus erythrodon (magnified by 3X to emphasize shape differences) Data from Ruumlber and
Adams 2001 En Adams Rolhf Slice 2002
Some extreme morphologies
Allophaiomys pliocaenicus Pirro
Nord
Early Pleistocene Italy Iberomys cabrerae
Extant Spain
Allophaiomys lavocati
Sima del Elefante
Atapuerca
Early Pleistocene (older
than the Italian species
Spain
AllophLavF
N3_1r
Early
Pleistocen
e of
Granada
similar to
Atapuerca
LM =17-14 of Iberon LM =15-14 of Iberon LM =15-14 of Iberon
Landmarks de 90 especiacutemenes de
Microtus agrestis
Landmarks de 90 especiacutemenes de
Microtus agrestis
Data 90 Specimens 22 Points 2 Dimensions
All specimen superimposed by GLS method
Sum of Squared Deviations = 1101217
The groups limit is after the specimen 0
PCS and scores computed
Percentages of variance for the 8 first PCS
61395977 61395977
8155754 69551731
4681460 74233190
3352225 77585415
2619139 80204554
2500418 82704973
2235576 84940549
1789387 86729936
Multivariate regression coefficients (normalized) with 3 PCS
PCS 1 0998142
PCS 2 -0057223
PCS 3 -0020926
Regression statistic for 3 components
Rsup2= 0227471 F= 8244611 with 3 and 86 DF plt 0000070
Plot de 90 especiacutemenes de
Microtus agrestis
Distribucioacuten estratigraacutefica de los roedores del cuaternario de Gran Dolina Atapuerca Burgos
0 m
Allo
ph
aio
mys
Mim
om
ys
Ibe
rom
ys
Terr
ico
la
Ste
no
cra
niu
s
Arv
ico
la
Mic
rom
ys
Hy
str
ix
Ca
sto
r
Ma
rmo
ta
Plio
mys
Mic
rotu
s
Allo
cri
cetu
s
Ap
od
em
us
Elio
mys
TD7
TD8
TD10
TD11
TD6
TD5
TD34
TD2
TD1
Procustes analisis APS
bull Procuste fue un ladroacuten que bien descuartizaba o bien estiraba a sus viacutectimas para ajustarlas al tamantildeo de su cama de ahiacute viene la frase hecha de ldquola cama Procusterdquo que se aplica sobre todo en poliacutetica la censura o para prestaciones puacuteblicas en las que es el usuario el que debe adaptarse y no al reveacuteshellip
bull The APS package
bull The shape analysis softwares APS ApsDigit and ApsUtil are written in English and always free for the students Aps combines Procuste superposition and statistical calculations ApsDigit is used locate landmarks on digital images (JPEG Bitmap tiff GIF) ApsUtil is used to handle files (Selection of points individuals change of classification)
bull httpwwwprocustecom
APS
APS est un logiciel danalyse quantitative de la
variabiliteacute morphologique des formes vivantes La
meacutethode utiliseacutee est la superposition procruste
geacuteneacuteraliseacutee
Destineacute aux biologistes et aux cliniciens APS prend en
charge les aspects matheacutematiques et statistiques de
lanalyse de forme Lanalyse se fait en 2 temps
1 Une superposition procruste de lensemble des
speacutecimens
2 Une analyse statistique qui visualise et teste la covariance
entre dune part la conformation et dautre part un facteur
biologique comme la taille lappartenance agrave groupe la
preacutesence ou non dune pathologie
Il est conccedilu pour eacutetudier un ou deux groupes
APS Digitalizar landmarks
DigitX is designed to digitize landmarks on Jpeg or Bitmap picture
middot Select the total number of landmarks to digitize with the second
Combo-Box of the toolbar
middot Select a picture in the graphic file selector on the left
middot Click on to load the link file (optional)
middot Click on to load the consensus file (optional)
middot Digitize landmarks using the left button of the mouse
middot To cancel last landmark position by a click on undo arrow
middot When all landmarks are digitized save the file by a click on save file
APS Crear archivo
Getting started with ApsUtil
ApsUtil create a data file (dat) with specimen ordered by
addition of smaller data files Input and output files are to
APS data format with an header line (number of specimens
number
of landmarks number of dimensions) followed by landmarks
coordinates
NEW button clear all previous data and begin a new data file
ADD button add a file containing one or many specimen
MIX button add a new file to a previous one by mixing the
two file
This ordering of specimen is required before to compute
shape differences
When file is saved specimens are ordered like
specimen 1 of the 1st file
specimen 1 of the 2nd file
specimen 2 of the 1st file
APS analisis
bull New features of Version 241
bull A single specimen or all a sample can be superimposed on any reloaded
bull specimen as consensus (File -gt Reload -gt Consensus)
bull Shape vectors (eg discriminant vectors computed with other software)
bull can be reloaded for visualization (File -gt Reload -gt Pcs)
bull The shape vector must be of norm 1
bull Projections of specimens on shape vectors are automatically computed
Otros
elementos del
esqueleto
A Antarctosaurus wichmannianus B
Saltasaurus loricatus C Neuquensaurus
australis D Neuquensaurus robustus E
Lirainosaurus astibiae F Ampelosaurus atacis
G Magyarosaurus dacus H Magyarosaurus
dacus Jianu I Alamosaurus sanjuanensis J
Aegyptosaurus baharijiensis K
Opisthocoelicaudia skarzynskii
Canudo amp Cuenca Bescos 2004
wwwaragosauruscom
Aegyptosaurus Alamosaurus
Imaacutegenes literatura
Fotos ejemplares
Hacer un poliacutegono con los landmarks
Guardar la misma posicioacuten (en una liacutenea basal por ej)
APS digit
APS util
APS program CP
Opisthocoelicaudia
Resultados
APS Fecha Thu 21 Sep 2006 213918
+0200 [210906 213918 CEST]
De Info Procuste
ltinfoprocustecomgt
Para cuencagunizares
Asunto Re analyse de forme chez
les arvicolides
Cabeceras Mostrar todas las
cabeceras
Chegravere collegravegue
Voici le lien pour teacuteleacutecharger le le
setup dinstallation des 3
logiciels APS ApsDigit et ApsUtil
httpwwwprocustecomprogramsset
up_aps_allexe
Noubliez pas de citer APS dans vos
publications
Bien cordialement
Xavier Penin
Paacuteginas web recomendadas
bull httplifebiosunysbedumorph la mejor paacutegina de
morfometriacutea geomeacutetrica Contiene un listado con todos los
programas de morfometriacutea Universidad de Stony Brook NY
bull httpwwwmorphometricsorgindexhtml es la paacutegina en la
que se mantiene la lista de email morphmet Es la base de la
organizacioacuten de la morfometriacutea en Suny
bull httpwwwflywingsorgukindexhtm iquestporqueacute hay variacioacuten
morfoloacutegica Universidad de Manchester UK
bull httpwwwprocustecomindexhtml anaacutelisis de la forma con
Procruste Aps Xavier Penin Universidad de Paris V
bull Shapehellipy otros ver la paacutegina de Suny
Las ldquoseries TPSrdquo Thin-plate spline
(laacuteminas finas de grosor uniforme)
tpsDIG2
Data acquisition
bull Digitize landmarks amp outlines from image files scanner or video Windows TpsDig is a Windows (95 through XP) program for digitizing landmarks and outlines for geometric morphometric analyses Includes simple image enhancement operations scale factors image brightness profile and support for AVI and MOV files Output is in the TPS file format used by the tps series of programs The TPS file includes the name of the image file for each specimen so that landmarks can always be visualized on the image Since output files are ASCII they can be converted to formats for other software Users should note that the tpsUtil program is useful for both the preparation of the input files to tpsDig as well as for some useful conversions afterwards The program also computes areas of enclosed regions perimeters and linear distances The tpsDig2 link at the left is for the new 205 version
bull Execute the downloaded file to install the program By F James Rohlf
Las ldquoseries TPSrdquo
ordenar los archivos digitalizados
TPS util
bull tps file utility program Windows At present it can randomly scramble the order of specimens in a tps file to minimize bias in digitizing landmark locations restore the original order (eg before statistical analyses are performed) create an empty TPS file from a directory with image files add keywords and values to the variables field of a TPS file combine TPS files into a single TPS file deletereorder landmarks remove outlines from a TPS file and convert TPS and NTS files to NTS M or CSV files It can also split an NTS file into several matrices Graphic editors are included for drawing link and sliders files Unbending a deformed specimen Converting outline and curves points to landmarks
bull Other operations can be added - let me know what you need Execute the TPSUTILW32EXE file to install the program By F James Rohlf Version 138
tpsTree
bull Fit and visualize thin-plate splines on trees Windows Performs a least-squares orthogonal generalized Procrustes analysis to obtain a reference and then estimates the splines for each group (internal node) on a tree Both ultrametric (eg WPGMA and UPGMA trees) and additive trees (using squared change parsimony to estimate the shapes of the HTUs) are supported The estimated shapes can be visualized with estimated images in the background (see the tpsSuper program) The file expands into a Windows setup program and associated files By F James Rohlf Version 118 File containing HTU coordinates and HTU images to demo that feature The older and more limited 16 bit Windows version is still available
tpsRegr
bull Multivariate multiple regression of shape onto independent variables Windows performs a multivariate multiple regression of shape (as captured by partial warp scores and the uniform shape component) onto one or more independent variables By appropriate setting up of independent variables this program can perform various types of MANOVA and MANCOVA Can be used to study allometry By F James Rohlf Version 131
tpsSplin
bull Thin-plate spline Windows Program to
compare pairs of specimens by displaying
a Darcy Thompson style transformation
grid based on a thin-plate spline Several
options are given for sliding
semilandmarks The tpssplnwexe file
expands into a Windows setup program
that will be run automatically By F James
Rohlf Version 120
tpsRelw el anaacutelisis de la
deformacioacuten relativa bull Relative warps analysis Windows Performs a
relative warp (deformacioacuten) analysis This corresponds to a principal components analysis of variation in a sample (relative to bending energy if the alpha parameter is not equal to zero) Displays a plot of relative warp scores and a visualization window that displays the estimated shape for arbitrary points in the ordination Also displays partial warp scores and their visualizations Allows fitting of semilandmark points along curves Version 144 By F James Rohlf
tpsPLS
bull Partial least-squares analysis for shapes Windows Used to explore the covariance between a set of variables and variation in shape or between two shapes It performs a two-block partial least-squares analysis It differs from regression in that both variables and shape are considered equally (one is not considered to be a set of independent variables measured without error) Its use is described in Rohlf and Corti (2000 Systematic Biology 49740-753) By F James Rohlf Version 118
tpsSmall
bull Test for small variation in shape Windows Use to test whether the variation in shape among a set of specimens is too large and thus statistical methods based on the tangent space approximation (eg thin-plate spline methods) cannot be used The program can process both 2D and 3D data files Output files include consensus and aligned specimens By F James Rohlf Version 120
tpsPower
bull Estimate statistical power for comparing shapes Windows Program for estimating statistical power for comparing the mean shapes of two populations Provides methods based on several different approaches Can be used for planning morphometric studies as well as to compare power using different approaches Version 104 By F James Rohlf
Morpheus et al bull Morpheus et al is a software package that will provide a
comprehensive cross-platform environment for morphometric data analysis It is available in graphical and command-line versions for a number of operating systems (see below) More information about new features and previous changes can be found in the release notes
httplifebiosunysbedumorphmorpheus
Multivariate analysis
bull PAST is a free easy-to-use data analysis package aimed at paleontology Windows 95+ Multivariate statistical methods include Principal Components (with Minimal Spanning Tree) Principal Coordinates (ten distance measures) Non-metric Multidimensional Scaling (ten distance measures) Detrended Correspondence Analysis Cluster analysis (three algorithms 11 distance measures) k-means clustering seriation discriminant analysis one-way MANOVA Hotellings t-squared Boxs M Canonical Variates Analysis Also includes Fourier shape analysis thin-plate splines parsimony and time series analysis among others Oslashyvind Hammer University of Oslo
Analysis of outlines
bull Shape Elliptic Fourier WINDOWS Extracts the contour shape from a full color bitmap image delineates the contour shape with the elliptic Fourier descriptors and performs a principal component analysis for summarizing the shape information By Hiroyoshi Iwata For more information see Shape home page tutorial or manual
bull Iwata H and Y Ukai (2002) SHAPE A computer program package for quantitative evaluation of biological shapes based on elliptic Fourier descriptors Journal of Heredity 93 384-385
Eigenshape analysis
bull httpwwwnhmacukhosted_sitespaleonetftpftphtml
bull This archive contains a series of programs designed to perform an eigenshape analysis on xy coordinate data from object outlines Routines include xy -gt phi() transformation phi() -gt xy transformation eigenshape analysis and projection of objects into the eigenshape space Two completely worked example analyses and a users guide are also provided El autor es Norman McLeod del BMNH de Londres
Graphical representation of the four-step morphometric protocol A Quantify raw data
(landmarks recorded on body of cichlid fish) B Remove non-shape variation (landmarks of 412
specimens before and after GPA) C statistical analysis (CVA) and graphical presentation of
results Deformation grids for mean specimen for (right) Eretmodus cyanostictus and (left)
Spathodus erythrodon (magnified by 3X to emphasize shape differences) Data from Ruumlber and
Adams 2001 En Adams Rolhf Slice 2002
Landmarks de 90 especiacutemenes de
Microtus agrestis
Landmarks de 90 especiacutemenes de
Microtus agrestis
Data 90 Specimens 22 Points 2 Dimensions
All specimen superimposed by GLS method
Sum of Squared Deviations = 1101217
The groups limit is after the specimen 0
PCS and scores computed
Percentages of variance for the 8 first PCS
61395977 61395977
8155754 69551731
4681460 74233190
3352225 77585415
2619139 80204554
2500418 82704973
2235576 84940549
1789387 86729936
Multivariate regression coefficients (normalized) with 3 PCS
PCS 1 0998142
PCS 2 -0057223
PCS 3 -0020926
Regression statistic for 3 components
Rsup2= 0227471 F= 8244611 with 3 and 86 DF plt 0000070
Plot de 90 especiacutemenes de
Microtus agrestis
Distribucioacuten estratigraacutefica de los roedores del cuaternario de Gran Dolina Atapuerca Burgos
0 m
Allo
ph
aio
mys
Mim
om
ys
Ibe
rom
ys
Terr
ico
la
Ste
no
cra
niu
s
Arv
ico
la
Mic
rom
ys
Hy
str
ix
Ca
sto
r
Ma
rmo
ta
Plio
mys
Mic
rotu
s
Allo
cri
cetu
s
Ap
od
em
us
Elio
mys
TD7
TD8
TD10
TD11
TD6
TD5
TD34
TD2
TD1
Procustes analisis APS
bull Procuste fue un ladroacuten que bien descuartizaba o bien estiraba a sus viacutectimas para ajustarlas al tamantildeo de su cama de ahiacute viene la frase hecha de ldquola cama Procusterdquo que se aplica sobre todo en poliacutetica la censura o para prestaciones puacuteblicas en las que es el usuario el que debe adaptarse y no al reveacuteshellip
bull The APS package
bull The shape analysis softwares APS ApsDigit and ApsUtil are written in English and always free for the students Aps combines Procuste superposition and statistical calculations ApsDigit is used locate landmarks on digital images (JPEG Bitmap tiff GIF) ApsUtil is used to handle files (Selection of points individuals change of classification)
bull httpwwwprocustecom
APS
APS est un logiciel danalyse quantitative de la
variabiliteacute morphologique des formes vivantes La
meacutethode utiliseacutee est la superposition procruste
geacuteneacuteraliseacutee
Destineacute aux biologistes et aux cliniciens APS prend en
charge les aspects matheacutematiques et statistiques de
lanalyse de forme Lanalyse se fait en 2 temps
1 Une superposition procruste de lensemble des
speacutecimens
2 Une analyse statistique qui visualise et teste la covariance
entre dune part la conformation et dautre part un facteur
biologique comme la taille lappartenance agrave groupe la
preacutesence ou non dune pathologie
Il est conccedilu pour eacutetudier un ou deux groupes
APS Digitalizar landmarks
DigitX is designed to digitize landmarks on Jpeg or Bitmap picture
middot Select the total number of landmarks to digitize with the second
Combo-Box of the toolbar
middot Select a picture in the graphic file selector on the left
middot Click on to load the link file (optional)
middot Click on to load the consensus file (optional)
middot Digitize landmarks using the left button of the mouse
middot To cancel last landmark position by a click on undo arrow
middot When all landmarks are digitized save the file by a click on save file
APS Crear archivo
Getting started with ApsUtil
ApsUtil create a data file (dat) with specimen ordered by
addition of smaller data files Input and output files are to
APS data format with an header line (number of specimens
number
of landmarks number of dimensions) followed by landmarks
coordinates
NEW button clear all previous data and begin a new data file
ADD button add a file containing one or many specimen
MIX button add a new file to a previous one by mixing the
two file
This ordering of specimen is required before to compute
shape differences
When file is saved specimens are ordered like
specimen 1 of the 1st file
specimen 1 of the 2nd file
specimen 2 of the 1st file
APS analisis
bull New features of Version 241
bull A single specimen or all a sample can be superimposed on any reloaded
bull specimen as consensus (File -gt Reload -gt Consensus)
bull Shape vectors (eg discriminant vectors computed with other software)
bull can be reloaded for visualization (File -gt Reload -gt Pcs)
bull The shape vector must be of norm 1
bull Projections of specimens on shape vectors are automatically computed
Otros
elementos del
esqueleto
A Antarctosaurus wichmannianus B
Saltasaurus loricatus C Neuquensaurus
australis D Neuquensaurus robustus E
Lirainosaurus astibiae F Ampelosaurus atacis
G Magyarosaurus dacus H Magyarosaurus
dacus Jianu I Alamosaurus sanjuanensis J
Aegyptosaurus baharijiensis K
Opisthocoelicaudia skarzynskii
Canudo amp Cuenca Bescos 2004
wwwaragosauruscom
Aegyptosaurus Alamosaurus
Imaacutegenes literatura
Fotos ejemplares
Hacer un poliacutegono con los landmarks
Guardar la misma posicioacuten (en una liacutenea basal por ej)
APS digit
APS util
APS program CP
Opisthocoelicaudia
Resultados
APS Fecha Thu 21 Sep 2006 213918
+0200 [210906 213918 CEST]
De Info Procuste
ltinfoprocustecomgt
Para cuencagunizares
Asunto Re analyse de forme chez
les arvicolides
Cabeceras Mostrar todas las
cabeceras
Chegravere collegravegue
Voici le lien pour teacuteleacutecharger le le
setup dinstallation des 3
logiciels APS ApsDigit et ApsUtil
httpwwwprocustecomprogramsset
up_aps_allexe
Noubliez pas de citer APS dans vos
publications
Bien cordialement
Xavier Penin
Paacuteginas web recomendadas
bull httplifebiosunysbedumorph la mejor paacutegina de
morfometriacutea geomeacutetrica Contiene un listado con todos los
programas de morfometriacutea Universidad de Stony Brook NY
bull httpwwwmorphometricsorgindexhtml es la paacutegina en la
que se mantiene la lista de email morphmet Es la base de la
organizacioacuten de la morfometriacutea en Suny
bull httpwwwflywingsorgukindexhtm iquestporqueacute hay variacioacuten
morfoloacutegica Universidad de Manchester UK
bull httpwwwprocustecomindexhtml anaacutelisis de la forma con
Procruste Aps Xavier Penin Universidad de Paris V
bull Shapehellipy otros ver la paacutegina de Suny
Las ldquoseries TPSrdquo Thin-plate spline
(laacuteminas finas de grosor uniforme)
tpsDIG2
Data acquisition
bull Digitize landmarks amp outlines from image files scanner or video Windows TpsDig is a Windows (95 through XP) program for digitizing landmarks and outlines for geometric morphometric analyses Includes simple image enhancement operations scale factors image brightness profile and support for AVI and MOV files Output is in the TPS file format used by the tps series of programs The TPS file includes the name of the image file for each specimen so that landmarks can always be visualized on the image Since output files are ASCII they can be converted to formats for other software Users should note that the tpsUtil program is useful for both the preparation of the input files to tpsDig as well as for some useful conversions afterwards The program also computes areas of enclosed regions perimeters and linear distances The tpsDig2 link at the left is for the new 205 version
bull Execute the downloaded file to install the program By F James Rohlf
Las ldquoseries TPSrdquo
ordenar los archivos digitalizados
TPS util
bull tps file utility program Windows At present it can randomly scramble the order of specimens in a tps file to minimize bias in digitizing landmark locations restore the original order (eg before statistical analyses are performed) create an empty TPS file from a directory with image files add keywords and values to the variables field of a TPS file combine TPS files into a single TPS file deletereorder landmarks remove outlines from a TPS file and convert TPS and NTS files to NTS M or CSV files It can also split an NTS file into several matrices Graphic editors are included for drawing link and sliders files Unbending a deformed specimen Converting outline and curves points to landmarks
bull Other operations can be added - let me know what you need Execute the TPSUTILW32EXE file to install the program By F James Rohlf Version 138
tpsTree
bull Fit and visualize thin-plate splines on trees Windows Performs a least-squares orthogonal generalized Procrustes analysis to obtain a reference and then estimates the splines for each group (internal node) on a tree Both ultrametric (eg WPGMA and UPGMA trees) and additive trees (using squared change parsimony to estimate the shapes of the HTUs) are supported The estimated shapes can be visualized with estimated images in the background (see the tpsSuper program) The file expands into a Windows setup program and associated files By F James Rohlf Version 118 File containing HTU coordinates and HTU images to demo that feature The older and more limited 16 bit Windows version is still available
tpsRegr
bull Multivariate multiple regression of shape onto independent variables Windows performs a multivariate multiple regression of shape (as captured by partial warp scores and the uniform shape component) onto one or more independent variables By appropriate setting up of independent variables this program can perform various types of MANOVA and MANCOVA Can be used to study allometry By F James Rohlf Version 131
tpsSplin
bull Thin-plate spline Windows Program to
compare pairs of specimens by displaying
a Darcy Thompson style transformation
grid based on a thin-plate spline Several
options are given for sliding
semilandmarks The tpssplnwexe file
expands into a Windows setup program
that will be run automatically By F James
Rohlf Version 120
tpsRelw el anaacutelisis de la
deformacioacuten relativa bull Relative warps analysis Windows Performs a
relative warp (deformacioacuten) analysis This corresponds to a principal components analysis of variation in a sample (relative to bending energy if the alpha parameter is not equal to zero) Displays a plot of relative warp scores and a visualization window that displays the estimated shape for arbitrary points in the ordination Also displays partial warp scores and their visualizations Allows fitting of semilandmark points along curves Version 144 By F James Rohlf
tpsPLS
bull Partial least-squares analysis for shapes Windows Used to explore the covariance between a set of variables and variation in shape or between two shapes It performs a two-block partial least-squares analysis It differs from regression in that both variables and shape are considered equally (one is not considered to be a set of independent variables measured without error) Its use is described in Rohlf and Corti (2000 Systematic Biology 49740-753) By F James Rohlf Version 118
tpsSmall
bull Test for small variation in shape Windows Use to test whether the variation in shape among a set of specimens is too large and thus statistical methods based on the tangent space approximation (eg thin-plate spline methods) cannot be used The program can process both 2D and 3D data files Output files include consensus and aligned specimens By F James Rohlf Version 120
tpsPower
bull Estimate statistical power for comparing shapes Windows Program for estimating statistical power for comparing the mean shapes of two populations Provides methods based on several different approaches Can be used for planning morphometric studies as well as to compare power using different approaches Version 104 By F James Rohlf
Morpheus et al bull Morpheus et al is a software package that will provide a
comprehensive cross-platform environment for morphometric data analysis It is available in graphical and command-line versions for a number of operating systems (see below) More information about new features and previous changes can be found in the release notes
httplifebiosunysbedumorphmorpheus
Multivariate analysis
bull PAST is a free easy-to-use data analysis package aimed at paleontology Windows 95+ Multivariate statistical methods include Principal Components (with Minimal Spanning Tree) Principal Coordinates (ten distance measures) Non-metric Multidimensional Scaling (ten distance measures) Detrended Correspondence Analysis Cluster analysis (three algorithms 11 distance measures) k-means clustering seriation discriminant analysis one-way MANOVA Hotellings t-squared Boxs M Canonical Variates Analysis Also includes Fourier shape analysis thin-plate splines parsimony and time series analysis among others Oslashyvind Hammer University of Oslo
Analysis of outlines
bull Shape Elliptic Fourier WINDOWS Extracts the contour shape from a full color bitmap image delineates the contour shape with the elliptic Fourier descriptors and performs a principal component analysis for summarizing the shape information By Hiroyoshi Iwata For more information see Shape home page tutorial or manual
bull Iwata H and Y Ukai (2002) SHAPE A computer program package for quantitative evaluation of biological shapes based on elliptic Fourier descriptors Journal of Heredity 93 384-385
Eigenshape analysis
bull httpwwwnhmacukhosted_sitespaleonetftpftphtml
bull This archive contains a series of programs designed to perform an eigenshape analysis on xy coordinate data from object outlines Routines include xy -gt phi() transformation phi() -gt xy transformation eigenshape analysis and projection of objects into the eigenshape space Two completely worked example analyses and a users guide are also provided El autor es Norman McLeod del BMNH de Londres
Graphical representation of the four-step morphometric protocol A Quantify raw data
(landmarks recorded on body of cichlid fish) B Remove non-shape variation (landmarks of 412
specimens before and after GPA) C statistical analysis (CVA) and graphical presentation of
results Deformation grids for mean specimen for (right) Eretmodus cyanostictus and (left)
Spathodus erythrodon (magnified by 3X to emphasize shape differences) Data from Ruumlber and
Adams 2001 En Adams Rolhf Slice 2002
Landmarks de 90 especiacutemenes de
Microtus agrestis
Data 90 Specimens 22 Points 2 Dimensions
All specimen superimposed by GLS method
Sum of Squared Deviations = 1101217
The groups limit is after the specimen 0
PCS and scores computed
Percentages of variance for the 8 first PCS
61395977 61395977
8155754 69551731
4681460 74233190
3352225 77585415
2619139 80204554
2500418 82704973
2235576 84940549
1789387 86729936
Multivariate regression coefficients (normalized) with 3 PCS
PCS 1 0998142
PCS 2 -0057223
PCS 3 -0020926
Regression statistic for 3 components
Rsup2= 0227471 F= 8244611 with 3 and 86 DF plt 0000070
Plot de 90 especiacutemenes de
Microtus agrestis
Distribucioacuten estratigraacutefica de los roedores del cuaternario de Gran Dolina Atapuerca Burgos
0 m
Allo
ph
aio
mys
Mim
om
ys
Ibe
rom
ys
Terr
ico
la
Ste
no
cra
niu
s
Arv
ico
la
Mic
rom
ys
Hy
str
ix
Ca
sto
r
Ma
rmo
ta
Plio
mys
Mic
rotu
s
Allo
cri
cetu
s
Ap
od
em
us
Elio
mys
TD7
TD8
TD10
TD11
TD6
TD5
TD34
TD2
TD1
Procustes analisis APS
bull Procuste fue un ladroacuten que bien descuartizaba o bien estiraba a sus viacutectimas para ajustarlas al tamantildeo de su cama de ahiacute viene la frase hecha de ldquola cama Procusterdquo que se aplica sobre todo en poliacutetica la censura o para prestaciones puacuteblicas en las que es el usuario el que debe adaptarse y no al reveacuteshellip
bull The APS package
bull The shape analysis softwares APS ApsDigit and ApsUtil are written in English and always free for the students Aps combines Procuste superposition and statistical calculations ApsDigit is used locate landmarks on digital images (JPEG Bitmap tiff GIF) ApsUtil is used to handle files (Selection of points individuals change of classification)
bull httpwwwprocustecom
APS
APS est un logiciel danalyse quantitative de la
variabiliteacute morphologique des formes vivantes La
meacutethode utiliseacutee est la superposition procruste
geacuteneacuteraliseacutee
Destineacute aux biologistes et aux cliniciens APS prend en
charge les aspects matheacutematiques et statistiques de
lanalyse de forme Lanalyse se fait en 2 temps
1 Une superposition procruste de lensemble des
speacutecimens
2 Une analyse statistique qui visualise et teste la covariance
entre dune part la conformation et dautre part un facteur
biologique comme la taille lappartenance agrave groupe la
preacutesence ou non dune pathologie
Il est conccedilu pour eacutetudier un ou deux groupes
APS Digitalizar landmarks
DigitX is designed to digitize landmarks on Jpeg or Bitmap picture
middot Select the total number of landmarks to digitize with the second
Combo-Box of the toolbar
middot Select a picture in the graphic file selector on the left
middot Click on to load the link file (optional)
middot Click on to load the consensus file (optional)
middot Digitize landmarks using the left button of the mouse
middot To cancel last landmark position by a click on undo arrow
middot When all landmarks are digitized save the file by a click on save file
APS Crear archivo
Getting started with ApsUtil
ApsUtil create a data file (dat) with specimen ordered by
addition of smaller data files Input and output files are to
APS data format with an header line (number of specimens
number
of landmarks number of dimensions) followed by landmarks
coordinates
NEW button clear all previous data and begin a new data file
ADD button add a file containing one or many specimen
MIX button add a new file to a previous one by mixing the
two file
This ordering of specimen is required before to compute
shape differences
When file is saved specimens are ordered like
specimen 1 of the 1st file
specimen 1 of the 2nd file
specimen 2 of the 1st file
APS analisis
bull New features of Version 241
bull A single specimen or all a sample can be superimposed on any reloaded
bull specimen as consensus (File -gt Reload -gt Consensus)
bull Shape vectors (eg discriminant vectors computed with other software)
bull can be reloaded for visualization (File -gt Reload -gt Pcs)
bull The shape vector must be of norm 1
bull Projections of specimens on shape vectors are automatically computed
Otros
elementos del
esqueleto
A Antarctosaurus wichmannianus B
Saltasaurus loricatus C Neuquensaurus
australis D Neuquensaurus robustus E
Lirainosaurus astibiae F Ampelosaurus atacis
G Magyarosaurus dacus H Magyarosaurus
dacus Jianu I Alamosaurus sanjuanensis J
Aegyptosaurus baharijiensis K
Opisthocoelicaudia skarzynskii
Canudo amp Cuenca Bescos 2004
wwwaragosauruscom
Aegyptosaurus Alamosaurus
Imaacutegenes literatura
Fotos ejemplares
Hacer un poliacutegono con los landmarks
Guardar la misma posicioacuten (en una liacutenea basal por ej)
APS digit
APS util
APS program CP
Opisthocoelicaudia
Resultados
APS Fecha Thu 21 Sep 2006 213918
+0200 [210906 213918 CEST]
De Info Procuste
ltinfoprocustecomgt
Para cuencagunizares
Asunto Re analyse de forme chez
les arvicolides
Cabeceras Mostrar todas las
cabeceras
Chegravere collegravegue
Voici le lien pour teacuteleacutecharger le le
setup dinstallation des 3
logiciels APS ApsDigit et ApsUtil
httpwwwprocustecomprogramsset
up_aps_allexe
Noubliez pas de citer APS dans vos
publications
Bien cordialement
Xavier Penin
Paacuteginas web recomendadas
bull httplifebiosunysbedumorph la mejor paacutegina de
morfometriacutea geomeacutetrica Contiene un listado con todos los
programas de morfometriacutea Universidad de Stony Brook NY
bull httpwwwmorphometricsorgindexhtml es la paacutegina en la
que se mantiene la lista de email morphmet Es la base de la
organizacioacuten de la morfometriacutea en Suny
bull httpwwwflywingsorgukindexhtm iquestporqueacute hay variacioacuten
morfoloacutegica Universidad de Manchester UK
bull httpwwwprocustecomindexhtml anaacutelisis de la forma con
Procruste Aps Xavier Penin Universidad de Paris V
bull Shapehellipy otros ver la paacutegina de Suny
Las ldquoseries TPSrdquo Thin-plate spline
(laacuteminas finas de grosor uniforme)
tpsDIG2
Data acquisition
bull Digitize landmarks amp outlines from image files scanner or video Windows TpsDig is a Windows (95 through XP) program for digitizing landmarks and outlines for geometric morphometric analyses Includes simple image enhancement operations scale factors image brightness profile and support for AVI and MOV files Output is in the TPS file format used by the tps series of programs The TPS file includes the name of the image file for each specimen so that landmarks can always be visualized on the image Since output files are ASCII they can be converted to formats for other software Users should note that the tpsUtil program is useful for both the preparation of the input files to tpsDig as well as for some useful conversions afterwards The program also computes areas of enclosed regions perimeters and linear distances The tpsDig2 link at the left is for the new 205 version
bull Execute the downloaded file to install the program By F James Rohlf
Las ldquoseries TPSrdquo
ordenar los archivos digitalizados
TPS util
bull tps file utility program Windows At present it can randomly scramble the order of specimens in a tps file to minimize bias in digitizing landmark locations restore the original order (eg before statistical analyses are performed) create an empty TPS file from a directory with image files add keywords and values to the variables field of a TPS file combine TPS files into a single TPS file deletereorder landmarks remove outlines from a TPS file and convert TPS and NTS files to NTS M or CSV files It can also split an NTS file into several matrices Graphic editors are included for drawing link and sliders files Unbending a deformed specimen Converting outline and curves points to landmarks
bull Other operations can be added - let me know what you need Execute the TPSUTILW32EXE file to install the program By F James Rohlf Version 138
tpsTree
bull Fit and visualize thin-plate splines on trees Windows Performs a least-squares orthogonal generalized Procrustes analysis to obtain a reference and then estimates the splines for each group (internal node) on a tree Both ultrametric (eg WPGMA and UPGMA trees) and additive trees (using squared change parsimony to estimate the shapes of the HTUs) are supported The estimated shapes can be visualized with estimated images in the background (see the tpsSuper program) The file expands into a Windows setup program and associated files By F James Rohlf Version 118 File containing HTU coordinates and HTU images to demo that feature The older and more limited 16 bit Windows version is still available
tpsRegr
bull Multivariate multiple regression of shape onto independent variables Windows performs a multivariate multiple regression of shape (as captured by partial warp scores and the uniform shape component) onto one or more independent variables By appropriate setting up of independent variables this program can perform various types of MANOVA and MANCOVA Can be used to study allometry By F James Rohlf Version 131
tpsSplin
bull Thin-plate spline Windows Program to
compare pairs of specimens by displaying
a Darcy Thompson style transformation
grid based on a thin-plate spline Several
options are given for sliding
semilandmarks The tpssplnwexe file
expands into a Windows setup program
that will be run automatically By F James
Rohlf Version 120
tpsRelw el anaacutelisis de la
deformacioacuten relativa bull Relative warps analysis Windows Performs a
relative warp (deformacioacuten) analysis This corresponds to a principal components analysis of variation in a sample (relative to bending energy if the alpha parameter is not equal to zero) Displays a plot of relative warp scores and a visualization window that displays the estimated shape for arbitrary points in the ordination Also displays partial warp scores and their visualizations Allows fitting of semilandmark points along curves Version 144 By F James Rohlf
tpsPLS
bull Partial least-squares analysis for shapes Windows Used to explore the covariance between a set of variables and variation in shape or between two shapes It performs a two-block partial least-squares analysis It differs from regression in that both variables and shape are considered equally (one is not considered to be a set of independent variables measured without error) Its use is described in Rohlf and Corti (2000 Systematic Biology 49740-753) By F James Rohlf Version 118
tpsSmall
bull Test for small variation in shape Windows Use to test whether the variation in shape among a set of specimens is too large and thus statistical methods based on the tangent space approximation (eg thin-plate spline methods) cannot be used The program can process both 2D and 3D data files Output files include consensus and aligned specimens By F James Rohlf Version 120
tpsPower
bull Estimate statistical power for comparing shapes Windows Program for estimating statistical power for comparing the mean shapes of two populations Provides methods based on several different approaches Can be used for planning morphometric studies as well as to compare power using different approaches Version 104 By F James Rohlf
Morpheus et al bull Morpheus et al is a software package that will provide a
comprehensive cross-platform environment for morphometric data analysis It is available in graphical and command-line versions for a number of operating systems (see below) More information about new features and previous changes can be found in the release notes
httplifebiosunysbedumorphmorpheus
Multivariate analysis
bull PAST is a free easy-to-use data analysis package aimed at paleontology Windows 95+ Multivariate statistical methods include Principal Components (with Minimal Spanning Tree) Principal Coordinates (ten distance measures) Non-metric Multidimensional Scaling (ten distance measures) Detrended Correspondence Analysis Cluster analysis (three algorithms 11 distance measures) k-means clustering seriation discriminant analysis one-way MANOVA Hotellings t-squared Boxs M Canonical Variates Analysis Also includes Fourier shape analysis thin-plate splines parsimony and time series analysis among others Oslashyvind Hammer University of Oslo
Analysis of outlines
bull Shape Elliptic Fourier WINDOWS Extracts the contour shape from a full color bitmap image delineates the contour shape with the elliptic Fourier descriptors and performs a principal component analysis for summarizing the shape information By Hiroyoshi Iwata For more information see Shape home page tutorial or manual
bull Iwata H and Y Ukai (2002) SHAPE A computer program package for quantitative evaluation of biological shapes based on elliptic Fourier descriptors Journal of Heredity 93 384-385
Eigenshape analysis
bull httpwwwnhmacukhosted_sitespaleonetftpftphtml
bull This archive contains a series of programs designed to perform an eigenshape analysis on xy coordinate data from object outlines Routines include xy -gt phi() transformation phi() -gt xy transformation eigenshape analysis and projection of objects into the eigenshape space Two completely worked example analyses and a users guide are also provided El autor es Norman McLeod del BMNH de Londres
Graphical representation of the four-step morphometric protocol A Quantify raw data
(landmarks recorded on body of cichlid fish) B Remove non-shape variation (landmarks of 412
specimens before and after GPA) C statistical analysis (CVA) and graphical presentation of
results Deformation grids for mean specimen for (right) Eretmodus cyanostictus and (left)
Spathodus erythrodon (magnified by 3X to emphasize shape differences) Data from Ruumlber and
Adams 2001 En Adams Rolhf Slice 2002
Plot de 90 especiacutemenes de
Microtus agrestis
Distribucioacuten estratigraacutefica de los roedores del cuaternario de Gran Dolina Atapuerca Burgos
0 m
Allo
ph
aio
mys
Mim
om
ys
Ibe
rom
ys
Terr
ico
la
Ste
no
cra
niu
s
Arv
ico
la
Mic
rom
ys
Hy
str
ix
Ca
sto
r
Ma
rmo
ta
Plio
mys
Mic
rotu
s
Allo
cri
cetu
s
Ap
od
em
us
Elio
mys
TD7
TD8
TD10
TD11
TD6
TD5
TD34
TD2
TD1
Procustes analisis APS
bull Procuste fue un ladroacuten que bien descuartizaba o bien estiraba a sus viacutectimas para ajustarlas al tamantildeo de su cama de ahiacute viene la frase hecha de ldquola cama Procusterdquo que se aplica sobre todo en poliacutetica la censura o para prestaciones puacuteblicas en las que es el usuario el que debe adaptarse y no al reveacuteshellip
bull The APS package
bull The shape analysis softwares APS ApsDigit and ApsUtil are written in English and always free for the students Aps combines Procuste superposition and statistical calculations ApsDigit is used locate landmarks on digital images (JPEG Bitmap tiff GIF) ApsUtil is used to handle files (Selection of points individuals change of classification)
bull httpwwwprocustecom
APS
APS est un logiciel danalyse quantitative de la
variabiliteacute morphologique des formes vivantes La
meacutethode utiliseacutee est la superposition procruste
geacuteneacuteraliseacutee
Destineacute aux biologistes et aux cliniciens APS prend en
charge les aspects matheacutematiques et statistiques de
lanalyse de forme Lanalyse se fait en 2 temps
1 Une superposition procruste de lensemble des
speacutecimens
2 Une analyse statistique qui visualise et teste la covariance
entre dune part la conformation et dautre part un facteur
biologique comme la taille lappartenance agrave groupe la
preacutesence ou non dune pathologie
Il est conccedilu pour eacutetudier un ou deux groupes
APS Digitalizar landmarks
DigitX is designed to digitize landmarks on Jpeg or Bitmap picture
middot Select the total number of landmarks to digitize with the second
Combo-Box of the toolbar
middot Select a picture in the graphic file selector on the left
middot Click on to load the link file (optional)
middot Click on to load the consensus file (optional)
middot Digitize landmarks using the left button of the mouse
middot To cancel last landmark position by a click on undo arrow
middot When all landmarks are digitized save the file by a click on save file
APS Crear archivo
Getting started with ApsUtil
ApsUtil create a data file (dat) with specimen ordered by
addition of smaller data files Input and output files are to
APS data format with an header line (number of specimens
number
of landmarks number of dimensions) followed by landmarks
coordinates
NEW button clear all previous data and begin a new data file
ADD button add a file containing one or many specimen
MIX button add a new file to a previous one by mixing the
two file
This ordering of specimen is required before to compute
shape differences
When file is saved specimens are ordered like
specimen 1 of the 1st file
specimen 1 of the 2nd file
specimen 2 of the 1st file
APS analisis
bull New features of Version 241
bull A single specimen or all a sample can be superimposed on any reloaded
bull specimen as consensus (File -gt Reload -gt Consensus)
bull Shape vectors (eg discriminant vectors computed with other software)
bull can be reloaded for visualization (File -gt Reload -gt Pcs)
bull The shape vector must be of norm 1
bull Projections of specimens on shape vectors are automatically computed
Otros
elementos del
esqueleto
A Antarctosaurus wichmannianus B
Saltasaurus loricatus C Neuquensaurus
australis D Neuquensaurus robustus E
Lirainosaurus astibiae F Ampelosaurus atacis
G Magyarosaurus dacus H Magyarosaurus
dacus Jianu I Alamosaurus sanjuanensis J
Aegyptosaurus baharijiensis K
Opisthocoelicaudia skarzynskii
Canudo amp Cuenca Bescos 2004
wwwaragosauruscom
Aegyptosaurus Alamosaurus
Imaacutegenes literatura
Fotos ejemplares
Hacer un poliacutegono con los landmarks
Guardar la misma posicioacuten (en una liacutenea basal por ej)
APS digit
APS util
APS program CP
Opisthocoelicaudia
Resultados
APS Fecha Thu 21 Sep 2006 213918
+0200 [210906 213918 CEST]
De Info Procuste
ltinfoprocustecomgt
Para cuencagunizares
Asunto Re analyse de forme chez
les arvicolides
Cabeceras Mostrar todas las
cabeceras
Chegravere collegravegue
Voici le lien pour teacuteleacutecharger le le
setup dinstallation des 3
logiciels APS ApsDigit et ApsUtil
httpwwwprocustecomprogramsset
up_aps_allexe
Noubliez pas de citer APS dans vos
publications
Bien cordialement
Xavier Penin
Paacuteginas web recomendadas
bull httplifebiosunysbedumorph la mejor paacutegina de
morfometriacutea geomeacutetrica Contiene un listado con todos los
programas de morfometriacutea Universidad de Stony Brook NY
bull httpwwwmorphometricsorgindexhtml es la paacutegina en la
que se mantiene la lista de email morphmet Es la base de la
organizacioacuten de la morfometriacutea en Suny
bull httpwwwflywingsorgukindexhtm iquestporqueacute hay variacioacuten
morfoloacutegica Universidad de Manchester UK
bull httpwwwprocustecomindexhtml anaacutelisis de la forma con
Procruste Aps Xavier Penin Universidad de Paris V
bull Shapehellipy otros ver la paacutegina de Suny
Las ldquoseries TPSrdquo Thin-plate spline
(laacuteminas finas de grosor uniforme)
tpsDIG2
Data acquisition
bull Digitize landmarks amp outlines from image files scanner or video Windows TpsDig is a Windows (95 through XP) program for digitizing landmarks and outlines for geometric morphometric analyses Includes simple image enhancement operations scale factors image brightness profile and support for AVI and MOV files Output is in the TPS file format used by the tps series of programs The TPS file includes the name of the image file for each specimen so that landmarks can always be visualized on the image Since output files are ASCII they can be converted to formats for other software Users should note that the tpsUtil program is useful for both the preparation of the input files to tpsDig as well as for some useful conversions afterwards The program also computes areas of enclosed regions perimeters and linear distances The tpsDig2 link at the left is for the new 205 version
bull Execute the downloaded file to install the program By F James Rohlf
Las ldquoseries TPSrdquo
ordenar los archivos digitalizados
TPS util
bull tps file utility program Windows At present it can randomly scramble the order of specimens in a tps file to minimize bias in digitizing landmark locations restore the original order (eg before statistical analyses are performed) create an empty TPS file from a directory with image files add keywords and values to the variables field of a TPS file combine TPS files into a single TPS file deletereorder landmarks remove outlines from a TPS file and convert TPS and NTS files to NTS M or CSV files It can also split an NTS file into several matrices Graphic editors are included for drawing link and sliders files Unbending a deformed specimen Converting outline and curves points to landmarks
bull Other operations can be added - let me know what you need Execute the TPSUTILW32EXE file to install the program By F James Rohlf Version 138
tpsTree
bull Fit and visualize thin-plate splines on trees Windows Performs a least-squares orthogonal generalized Procrustes analysis to obtain a reference and then estimates the splines for each group (internal node) on a tree Both ultrametric (eg WPGMA and UPGMA trees) and additive trees (using squared change parsimony to estimate the shapes of the HTUs) are supported The estimated shapes can be visualized with estimated images in the background (see the tpsSuper program) The file expands into a Windows setup program and associated files By F James Rohlf Version 118 File containing HTU coordinates and HTU images to demo that feature The older and more limited 16 bit Windows version is still available
tpsRegr
bull Multivariate multiple regression of shape onto independent variables Windows performs a multivariate multiple regression of shape (as captured by partial warp scores and the uniform shape component) onto one or more independent variables By appropriate setting up of independent variables this program can perform various types of MANOVA and MANCOVA Can be used to study allometry By F James Rohlf Version 131
tpsSplin
bull Thin-plate spline Windows Program to
compare pairs of specimens by displaying
a Darcy Thompson style transformation
grid based on a thin-plate spline Several
options are given for sliding
semilandmarks The tpssplnwexe file
expands into a Windows setup program
that will be run automatically By F James
Rohlf Version 120
tpsRelw el anaacutelisis de la
deformacioacuten relativa bull Relative warps analysis Windows Performs a
relative warp (deformacioacuten) analysis This corresponds to a principal components analysis of variation in a sample (relative to bending energy if the alpha parameter is not equal to zero) Displays a plot of relative warp scores and a visualization window that displays the estimated shape for arbitrary points in the ordination Also displays partial warp scores and their visualizations Allows fitting of semilandmark points along curves Version 144 By F James Rohlf
tpsPLS
bull Partial least-squares analysis for shapes Windows Used to explore the covariance between a set of variables and variation in shape or between two shapes It performs a two-block partial least-squares analysis It differs from regression in that both variables and shape are considered equally (one is not considered to be a set of independent variables measured without error) Its use is described in Rohlf and Corti (2000 Systematic Biology 49740-753) By F James Rohlf Version 118
tpsSmall
bull Test for small variation in shape Windows Use to test whether the variation in shape among a set of specimens is too large and thus statistical methods based on the tangent space approximation (eg thin-plate spline methods) cannot be used The program can process both 2D and 3D data files Output files include consensus and aligned specimens By F James Rohlf Version 120
tpsPower
bull Estimate statistical power for comparing shapes Windows Program for estimating statistical power for comparing the mean shapes of two populations Provides methods based on several different approaches Can be used for planning morphometric studies as well as to compare power using different approaches Version 104 By F James Rohlf
Morpheus et al bull Morpheus et al is a software package that will provide a
comprehensive cross-platform environment for morphometric data analysis It is available in graphical and command-line versions for a number of operating systems (see below) More information about new features and previous changes can be found in the release notes
httplifebiosunysbedumorphmorpheus
Multivariate analysis
bull PAST is a free easy-to-use data analysis package aimed at paleontology Windows 95+ Multivariate statistical methods include Principal Components (with Minimal Spanning Tree) Principal Coordinates (ten distance measures) Non-metric Multidimensional Scaling (ten distance measures) Detrended Correspondence Analysis Cluster analysis (three algorithms 11 distance measures) k-means clustering seriation discriminant analysis one-way MANOVA Hotellings t-squared Boxs M Canonical Variates Analysis Also includes Fourier shape analysis thin-plate splines parsimony and time series analysis among others Oslashyvind Hammer University of Oslo
Analysis of outlines
bull Shape Elliptic Fourier WINDOWS Extracts the contour shape from a full color bitmap image delineates the contour shape with the elliptic Fourier descriptors and performs a principal component analysis for summarizing the shape information By Hiroyoshi Iwata For more information see Shape home page tutorial or manual
bull Iwata H and Y Ukai (2002) SHAPE A computer program package for quantitative evaluation of biological shapes based on elliptic Fourier descriptors Journal of Heredity 93 384-385
Eigenshape analysis
bull httpwwwnhmacukhosted_sitespaleonetftpftphtml
bull This archive contains a series of programs designed to perform an eigenshape analysis on xy coordinate data from object outlines Routines include xy -gt phi() transformation phi() -gt xy transformation eigenshape analysis and projection of objects into the eigenshape space Two completely worked example analyses and a users guide are also provided El autor es Norman McLeod del BMNH de Londres
Graphical representation of the four-step morphometric protocol A Quantify raw data
(landmarks recorded on body of cichlid fish) B Remove non-shape variation (landmarks of 412
specimens before and after GPA) C statistical analysis (CVA) and graphical presentation of
results Deformation grids for mean specimen for (right) Eretmodus cyanostictus and (left)
Spathodus erythrodon (magnified by 3X to emphasize shape differences) Data from Ruumlber and
Adams 2001 En Adams Rolhf Slice 2002
Distribucioacuten estratigraacutefica de los roedores del cuaternario de Gran Dolina Atapuerca Burgos
0 m
Allo
ph
aio
mys
Mim
om
ys
Ibe
rom
ys
Terr
ico
la
Ste
no
cra
niu
s
Arv
ico
la
Mic
rom
ys
Hy
str
ix
Ca
sto
r
Ma
rmo
ta
Plio
mys
Mic
rotu
s
Allo
cri
cetu
s
Ap
od
em
us
Elio
mys
TD7
TD8
TD10
TD11
TD6
TD5
TD34
TD2
TD1
Procustes analisis APS
bull Procuste fue un ladroacuten que bien descuartizaba o bien estiraba a sus viacutectimas para ajustarlas al tamantildeo de su cama de ahiacute viene la frase hecha de ldquola cama Procusterdquo que se aplica sobre todo en poliacutetica la censura o para prestaciones puacuteblicas en las que es el usuario el que debe adaptarse y no al reveacuteshellip
bull The APS package
bull The shape analysis softwares APS ApsDigit and ApsUtil are written in English and always free for the students Aps combines Procuste superposition and statistical calculations ApsDigit is used locate landmarks on digital images (JPEG Bitmap tiff GIF) ApsUtil is used to handle files (Selection of points individuals change of classification)
bull httpwwwprocustecom
APS
APS est un logiciel danalyse quantitative de la
variabiliteacute morphologique des formes vivantes La
meacutethode utiliseacutee est la superposition procruste
geacuteneacuteraliseacutee
Destineacute aux biologistes et aux cliniciens APS prend en
charge les aspects matheacutematiques et statistiques de
lanalyse de forme Lanalyse se fait en 2 temps
1 Une superposition procruste de lensemble des
speacutecimens
2 Une analyse statistique qui visualise et teste la covariance
entre dune part la conformation et dautre part un facteur
biologique comme la taille lappartenance agrave groupe la
preacutesence ou non dune pathologie
Il est conccedilu pour eacutetudier un ou deux groupes
APS Digitalizar landmarks
DigitX is designed to digitize landmarks on Jpeg or Bitmap picture
middot Select the total number of landmarks to digitize with the second
Combo-Box of the toolbar
middot Select a picture in the graphic file selector on the left
middot Click on to load the link file (optional)
middot Click on to load the consensus file (optional)
middot Digitize landmarks using the left button of the mouse
middot To cancel last landmark position by a click on undo arrow
middot When all landmarks are digitized save the file by a click on save file
APS Crear archivo
Getting started with ApsUtil
ApsUtil create a data file (dat) with specimen ordered by
addition of smaller data files Input and output files are to
APS data format with an header line (number of specimens
number
of landmarks number of dimensions) followed by landmarks
coordinates
NEW button clear all previous data and begin a new data file
ADD button add a file containing one or many specimen
MIX button add a new file to a previous one by mixing the
two file
This ordering of specimen is required before to compute
shape differences
When file is saved specimens are ordered like
specimen 1 of the 1st file
specimen 1 of the 2nd file
specimen 2 of the 1st file
APS analisis
bull New features of Version 241
bull A single specimen or all a sample can be superimposed on any reloaded
bull specimen as consensus (File -gt Reload -gt Consensus)
bull Shape vectors (eg discriminant vectors computed with other software)
bull can be reloaded for visualization (File -gt Reload -gt Pcs)
bull The shape vector must be of norm 1
bull Projections of specimens on shape vectors are automatically computed
Otros
elementos del
esqueleto
A Antarctosaurus wichmannianus B
Saltasaurus loricatus C Neuquensaurus
australis D Neuquensaurus robustus E
Lirainosaurus astibiae F Ampelosaurus atacis
G Magyarosaurus dacus H Magyarosaurus
dacus Jianu I Alamosaurus sanjuanensis J
Aegyptosaurus baharijiensis K
Opisthocoelicaudia skarzynskii
Canudo amp Cuenca Bescos 2004
wwwaragosauruscom
Aegyptosaurus Alamosaurus
Imaacutegenes literatura
Fotos ejemplares
Hacer un poliacutegono con los landmarks
Guardar la misma posicioacuten (en una liacutenea basal por ej)
APS digit
APS util
APS program CP
Opisthocoelicaudia
Resultados
APS Fecha Thu 21 Sep 2006 213918
+0200 [210906 213918 CEST]
De Info Procuste
ltinfoprocustecomgt
Para cuencagunizares
Asunto Re analyse de forme chez
les arvicolides
Cabeceras Mostrar todas las
cabeceras
Chegravere collegravegue
Voici le lien pour teacuteleacutecharger le le
setup dinstallation des 3
logiciels APS ApsDigit et ApsUtil
httpwwwprocustecomprogramsset
up_aps_allexe
Noubliez pas de citer APS dans vos
publications
Bien cordialement
Xavier Penin
Paacuteginas web recomendadas
bull httplifebiosunysbedumorph la mejor paacutegina de
morfometriacutea geomeacutetrica Contiene un listado con todos los
programas de morfometriacutea Universidad de Stony Brook NY
bull httpwwwmorphometricsorgindexhtml es la paacutegina en la
que se mantiene la lista de email morphmet Es la base de la
organizacioacuten de la morfometriacutea en Suny
bull httpwwwflywingsorgukindexhtm iquestporqueacute hay variacioacuten
morfoloacutegica Universidad de Manchester UK
bull httpwwwprocustecomindexhtml anaacutelisis de la forma con
Procruste Aps Xavier Penin Universidad de Paris V
bull Shapehellipy otros ver la paacutegina de Suny
Las ldquoseries TPSrdquo Thin-plate spline
(laacuteminas finas de grosor uniforme)
tpsDIG2
Data acquisition
bull Digitize landmarks amp outlines from image files scanner or video Windows TpsDig is a Windows (95 through XP) program for digitizing landmarks and outlines for geometric morphometric analyses Includes simple image enhancement operations scale factors image brightness profile and support for AVI and MOV files Output is in the TPS file format used by the tps series of programs The TPS file includes the name of the image file for each specimen so that landmarks can always be visualized on the image Since output files are ASCII they can be converted to formats for other software Users should note that the tpsUtil program is useful for both the preparation of the input files to tpsDig as well as for some useful conversions afterwards The program also computes areas of enclosed regions perimeters and linear distances The tpsDig2 link at the left is for the new 205 version
bull Execute the downloaded file to install the program By F James Rohlf
Las ldquoseries TPSrdquo
ordenar los archivos digitalizados
TPS util
bull tps file utility program Windows At present it can randomly scramble the order of specimens in a tps file to minimize bias in digitizing landmark locations restore the original order (eg before statistical analyses are performed) create an empty TPS file from a directory with image files add keywords and values to the variables field of a TPS file combine TPS files into a single TPS file deletereorder landmarks remove outlines from a TPS file and convert TPS and NTS files to NTS M or CSV files It can also split an NTS file into several matrices Graphic editors are included for drawing link and sliders files Unbending a deformed specimen Converting outline and curves points to landmarks
bull Other operations can be added - let me know what you need Execute the TPSUTILW32EXE file to install the program By F James Rohlf Version 138
tpsTree
bull Fit and visualize thin-plate splines on trees Windows Performs a least-squares orthogonal generalized Procrustes analysis to obtain a reference and then estimates the splines for each group (internal node) on a tree Both ultrametric (eg WPGMA and UPGMA trees) and additive trees (using squared change parsimony to estimate the shapes of the HTUs) are supported The estimated shapes can be visualized with estimated images in the background (see the tpsSuper program) The file expands into a Windows setup program and associated files By F James Rohlf Version 118 File containing HTU coordinates and HTU images to demo that feature The older and more limited 16 bit Windows version is still available
tpsRegr
bull Multivariate multiple regression of shape onto independent variables Windows performs a multivariate multiple regression of shape (as captured by partial warp scores and the uniform shape component) onto one or more independent variables By appropriate setting up of independent variables this program can perform various types of MANOVA and MANCOVA Can be used to study allometry By F James Rohlf Version 131
tpsSplin
bull Thin-plate spline Windows Program to
compare pairs of specimens by displaying
a Darcy Thompson style transformation
grid based on a thin-plate spline Several
options are given for sliding
semilandmarks The tpssplnwexe file
expands into a Windows setup program
that will be run automatically By F James
Rohlf Version 120
tpsRelw el anaacutelisis de la
deformacioacuten relativa bull Relative warps analysis Windows Performs a
relative warp (deformacioacuten) analysis This corresponds to a principal components analysis of variation in a sample (relative to bending energy if the alpha parameter is not equal to zero) Displays a plot of relative warp scores and a visualization window that displays the estimated shape for arbitrary points in the ordination Also displays partial warp scores and their visualizations Allows fitting of semilandmark points along curves Version 144 By F James Rohlf
tpsPLS
bull Partial least-squares analysis for shapes Windows Used to explore the covariance between a set of variables and variation in shape or between two shapes It performs a two-block partial least-squares analysis It differs from regression in that both variables and shape are considered equally (one is not considered to be a set of independent variables measured without error) Its use is described in Rohlf and Corti (2000 Systematic Biology 49740-753) By F James Rohlf Version 118
tpsSmall
bull Test for small variation in shape Windows Use to test whether the variation in shape among a set of specimens is too large and thus statistical methods based on the tangent space approximation (eg thin-plate spline methods) cannot be used The program can process both 2D and 3D data files Output files include consensus and aligned specimens By F James Rohlf Version 120
tpsPower
bull Estimate statistical power for comparing shapes Windows Program for estimating statistical power for comparing the mean shapes of two populations Provides methods based on several different approaches Can be used for planning morphometric studies as well as to compare power using different approaches Version 104 By F James Rohlf
Morpheus et al bull Morpheus et al is a software package that will provide a
comprehensive cross-platform environment for morphometric data analysis It is available in graphical and command-line versions for a number of operating systems (see below) More information about new features and previous changes can be found in the release notes
httplifebiosunysbedumorphmorpheus
Multivariate analysis
bull PAST is a free easy-to-use data analysis package aimed at paleontology Windows 95+ Multivariate statistical methods include Principal Components (with Minimal Spanning Tree) Principal Coordinates (ten distance measures) Non-metric Multidimensional Scaling (ten distance measures) Detrended Correspondence Analysis Cluster analysis (three algorithms 11 distance measures) k-means clustering seriation discriminant analysis one-way MANOVA Hotellings t-squared Boxs M Canonical Variates Analysis Also includes Fourier shape analysis thin-plate splines parsimony and time series analysis among others Oslashyvind Hammer University of Oslo
Analysis of outlines
bull Shape Elliptic Fourier WINDOWS Extracts the contour shape from a full color bitmap image delineates the contour shape with the elliptic Fourier descriptors and performs a principal component analysis for summarizing the shape information By Hiroyoshi Iwata For more information see Shape home page tutorial or manual
bull Iwata H and Y Ukai (2002) SHAPE A computer program package for quantitative evaluation of biological shapes based on elliptic Fourier descriptors Journal of Heredity 93 384-385
Eigenshape analysis
bull httpwwwnhmacukhosted_sitespaleonetftpftphtml
bull This archive contains a series of programs designed to perform an eigenshape analysis on xy coordinate data from object outlines Routines include xy -gt phi() transformation phi() -gt xy transformation eigenshape analysis and projection of objects into the eigenshape space Two completely worked example analyses and a users guide are also provided El autor es Norman McLeod del BMNH de Londres
Graphical representation of the four-step morphometric protocol A Quantify raw data
(landmarks recorded on body of cichlid fish) B Remove non-shape variation (landmarks of 412
specimens before and after GPA) C statistical analysis (CVA) and graphical presentation of
results Deformation grids for mean specimen for (right) Eretmodus cyanostictus and (left)
Spathodus erythrodon (magnified by 3X to emphasize shape differences) Data from Ruumlber and
Adams 2001 En Adams Rolhf Slice 2002
Procustes analisis APS
bull Procuste fue un ladroacuten que bien descuartizaba o bien estiraba a sus viacutectimas para ajustarlas al tamantildeo de su cama de ahiacute viene la frase hecha de ldquola cama Procusterdquo que se aplica sobre todo en poliacutetica la censura o para prestaciones puacuteblicas en las que es el usuario el que debe adaptarse y no al reveacuteshellip
bull The APS package
bull The shape analysis softwares APS ApsDigit and ApsUtil are written in English and always free for the students Aps combines Procuste superposition and statistical calculations ApsDigit is used locate landmarks on digital images (JPEG Bitmap tiff GIF) ApsUtil is used to handle files (Selection of points individuals change of classification)
bull httpwwwprocustecom
APS
APS est un logiciel danalyse quantitative de la
variabiliteacute morphologique des formes vivantes La
meacutethode utiliseacutee est la superposition procruste
geacuteneacuteraliseacutee
Destineacute aux biologistes et aux cliniciens APS prend en
charge les aspects matheacutematiques et statistiques de
lanalyse de forme Lanalyse se fait en 2 temps
1 Une superposition procruste de lensemble des
speacutecimens
2 Une analyse statistique qui visualise et teste la covariance
entre dune part la conformation et dautre part un facteur
biologique comme la taille lappartenance agrave groupe la
preacutesence ou non dune pathologie
Il est conccedilu pour eacutetudier un ou deux groupes
APS Digitalizar landmarks
DigitX is designed to digitize landmarks on Jpeg or Bitmap picture
middot Select the total number of landmarks to digitize with the second
Combo-Box of the toolbar
middot Select a picture in the graphic file selector on the left
middot Click on to load the link file (optional)
middot Click on to load the consensus file (optional)
middot Digitize landmarks using the left button of the mouse
middot To cancel last landmark position by a click on undo arrow
middot When all landmarks are digitized save the file by a click on save file
APS Crear archivo
Getting started with ApsUtil
ApsUtil create a data file (dat) with specimen ordered by
addition of smaller data files Input and output files are to
APS data format with an header line (number of specimens
number
of landmarks number of dimensions) followed by landmarks
coordinates
NEW button clear all previous data and begin a new data file
ADD button add a file containing one or many specimen
MIX button add a new file to a previous one by mixing the
two file
This ordering of specimen is required before to compute
shape differences
When file is saved specimens are ordered like
specimen 1 of the 1st file
specimen 1 of the 2nd file
specimen 2 of the 1st file
APS analisis
bull New features of Version 241
bull A single specimen or all a sample can be superimposed on any reloaded
bull specimen as consensus (File -gt Reload -gt Consensus)
bull Shape vectors (eg discriminant vectors computed with other software)
bull can be reloaded for visualization (File -gt Reload -gt Pcs)
bull The shape vector must be of norm 1
bull Projections of specimens on shape vectors are automatically computed
Otros
elementos del
esqueleto
A Antarctosaurus wichmannianus B
Saltasaurus loricatus C Neuquensaurus
australis D Neuquensaurus robustus E
Lirainosaurus astibiae F Ampelosaurus atacis
G Magyarosaurus dacus H Magyarosaurus
dacus Jianu I Alamosaurus sanjuanensis J
Aegyptosaurus baharijiensis K
Opisthocoelicaudia skarzynskii
Canudo amp Cuenca Bescos 2004
wwwaragosauruscom
Aegyptosaurus Alamosaurus
Imaacutegenes literatura
Fotos ejemplares
Hacer un poliacutegono con los landmarks
Guardar la misma posicioacuten (en una liacutenea basal por ej)
APS digit
APS util
APS program CP
Opisthocoelicaudia
Resultados
APS Fecha Thu 21 Sep 2006 213918
+0200 [210906 213918 CEST]
De Info Procuste
ltinfoprocustecomgt
Para cuencagunizares
Asunto Re analyse de forme chez
les arvicolides
Cabeceras Mostrar todas las
cabeceras
Chegravere collegravegue
Voici le lien pour teacuteleacutecharger le le
setup dinstallation des 3
logiciels APS ApsDigit et ApsUtil
httpwwwprocustecomprogramsset
up_aps_allexe
Noubliez pas de citer APS dans vos
publications
Bien cordialement
Xavier Penin
Paacuteginas web recomendadas
bull httplifebiosunysbedumorph la mejor paacutegina de
morfometriacutea geomeacutetrica Contiene un listado con todos los
programas de morfometriacutea Universidad de Stony Brook NY
bull httpwwwmorphometricsorgindexhtml es la paacutegina en la
que se mantiene la lista de email morphmet Es la base de la
organizacioacuten de la morfometriacutea en Suny
bull httpwwwflywingsorgukindexhtm iquestporqueacute hay variacioacuten
morfoloacutegica Universidad de Manchester UK
bull httpwwwprocustecomindexhtml anaacutelisis de la forma con
Procruste Aps Xavier Penin Universidad de Paris V
bull Shapehellipy otros ver la paacutegina de Suny
Las ldquoseries TPSrdquo Thin-plate spline
(laacuteminas finas de grosor uniforme)
tpsDIG2
Data acquisition
bull Digitize landmarks amp outlines from image files scanner or video Windows TpsDig is a Windows (95 through XP) program for digitizing landmarks and outlines for geometric morphometric analyses Includes simple image enhancement operations scale factors image brightness profile and support for AVI and MOV files Output is in the TPS file format used by the tps series of programs The TPS file includes the name of the image file for each specimen so that landmarks can always be visualized on the image Since output files are ASCII they can be converted to formats for other software Users should note that the tpsUtil program is useful for both the preparation of the input files to tpsDig as well as for some useful conversions afterwards The program also computes areas of enclosed regions perimeters and linear distances The tpsDig2 link at the left is for the new 205 version
bull Execute the downloaded file to install the program By F James Rohlf
Las ldquoseries TPSrdquo
ordenar los archivos digitalizados
TPS util
bull tps file utility program Windows At present it can randomly scramble the order of specimens in a tps file to minimize bias in digitizing landmark locations restore the original order (eg before statistical analyses are performed) create an empty TPS file from a directory with image files add keywords and values to the variables field of a TPS file combine TPS files into a single TPS file deletereorder landmarks remove outlines from a TPS file and convert TPS and NTS files to NTS M or CSV files It can also split an NTS file into several matrices Graphic editors are included for drawing link and sliders files Unbending a deformed specimen Converting outline and curves points to landmarks
bull Other operations can be added - let me know what you need Execute the TPSUTILW32EXE file to install the program By F James Rohlf Version 138
tpsTree
bull Fit and visualize thin-plate splines on trees Windows Performs a least-squares orthogonal generalized Procrustes analysis to obtain a reference and then estimates the splines for each group (internal node) on a tree Both ultrametric (eg WPGMA and UPGMA trees) and additive trees (using squared change parsimony to estimate the shapes of the HTUs) are supported The estimated shapes can be visualized with estimated images in the background (see the tpsSuper program) The file expands into a Windows setup program and associated files By F James Rohlf Version 118 File containing HTU coordinates and HTU images to demo that feature The older and more limited 16 bit Windows version is still available
tpsRegr
bull Multivariate multiple regression of shape onto independent variables Windows performs a multivariate multiple regression of shape (as captured by partial warp scores and the uniform shape component) onto one or more independent variables By appropriate setting up of independent variables this program can perform various types of MANOVA and MANCOVA Can be used to study allometry By F James Rohlf Version 131
tpsSplin
bull Thin-plate spline Windows Program to
compare pairs of specimens by displaying
a Darcy Thompson style transformation
grid based on a thin-plate spline Several
options are given for sliding
semilandmarks The tpssplnwexe file
expands into a Windows setup program
that will be run automatically By F James
Rohlf Version 120
tpsRelw el anaacutelisis de la
deformacioacuten relativa bull Relative warps analysis Windows Performs a
relative warp (deformacioacuten) analysis This corresponds to a principal components analysis of variation in a sample (relative to bending energy if the alpha parameter is not equal to zero) Displays a plot of relative warp scores and a visualization window that displays the estimated shape for arbitrary points in the ordination Also displays partial warp scores and their visualizations Allows fitting of semilandmark points along curves Version 144 By F James Rohlf
tpsPLS
bull Partial least-squares analysis for shapes Windows Used to explore the covariance between a set of variables and variation in shape or between two shapes It performs a two-block partial least-squares analysis It differs from regression in that both variables and shape are considered equally (one is not considered to be a set of independent variables measured without error) Its use is described in Rohlf and Corti (2000 Systematic Biology 49740-753) By F James Rohlf Version 118
tpsSmall
bull Test for small variation in shape Windows Use to test whether the variation in shape among a set of specimens is too large and thus statistical methods based on the tangent space approximation (eg thin-plate spline methods) cannot be used The program can process both 2D and 3D data files Output files include consensus and aligned specimens By F James Rohlf Version 120
tpsPower
bull Estimate statistical power for comparing shapes Windows Program for estimating statistical power for comparing the mean shapes of two populations Provides methods based on several different approaches Can be used for planning morphometric studies as well as to compare power using different approaches Version 104 By F James Rohlf
Morpheus et al bull Morpheus et al is a software package that will provide a
comprehensive cross-platform environment for morphometric data analysis It is available in graphical and command-line versions for a number of operating systems (see below) More information about new features and previous changes can be found in the release notes
httplifebiosunysbedumorphmorpheus
Multivariate analysis
bull PAST is a free easy-to-use data analysis package aimed at paleontology Windows 95+ Multivariate statistical methods include Principal Components (with Minimal Spanning Tree) Principal Coordinates (ten distance measures) Non-metric Multidimensional Scaling (ten distance measures) Detrended Correspondence Analysis Cluster analysis (three algorithms 11 distance measures) k-means clustering seriation discriminant analysis one-way MANOVA Hotellings t-squared Boxs M Canonical Variates Analysis Also includes Fourier shape analysis thin-plate splines parsimony and time series analysis among others Oslashyvind Hammer University of Oslo
Analysis of outlines
bull Shape Elliptic Fourier WINDOWS Extracts the contour shape from a full color bitmap image delineates the contour shape with the elliptic Fourier descriptors and performs a principal component analysis for summarizing the shape information By Hiroyoshi Iwata For more information see Shape home page tutorial or manual
bull Iwata H and Y Ukai (2002) SHAPE A computer program package for quantitative evaluation of biological shapes based on elliptic Fourier descriptors Journal of Heredity 93 384-385
Eigenshape analysis
bull httpwwwnhmacukhosted_sitespaleonetftpftphtml
bull This archive contains a series of programs designed to perform an eigenshape analysis on xy coordinate data from object outlines Routines include xy -gt phi() transformation phi() -gt xy transformation eigenshape analysis and projection of objects into the eigenshape space Two completely worked example analyses and a users guide are also provided El autor es Norman McLeod del BMNH de Londres
Graphical representation of the four-step morphometric protocol A Quantify raw data
(landmarks recorded on body of cichlid fish) B Remove non-shape variation (landmarks of 412
specimens before and after GPA) C statistical analysis (CVA) and graphical presentation of
results Deformation grids for mean specimen for (right) Eretmodus cyanostictus and (left)
Spathodus erythrodon (magnified by 3X to emphasize shape differences) Data from Ruumlber and
Adams 2001 En Adams Rolhf Slice 2002
APS
APS est un logiciel danalyse quantitative de la
variabiliteacute morphologique des formes vivantes La
meacutethode utiliseacutee est la superposition procruste
geacuteneacuteraliseacutee
Destineacute aux biologistes et aux cliniciens APS prend en
charge les aspects matheacutematiques et statistiques de
lanalyse de forme Lanalyse se fait en 2 temps
1 Une superposition procruste de lensemble des
speacutecimens
2 Une analyse statistique qui visualise et teste la covariance
entre dune part la conformation et dautre part un facteur
biologique comme la taille lappartenance agrave groupe la
preacutesence ou non dune pathologie
Il est conccedilu pour eacutetudier un ou deux groupes
APS Digitalizar landmarks
DigitX is designed to digitize landmarks on Jpeg or Bitmap picture
middot Select the total number of landmarks to digitize with the second
Combo-Box of the toolbar
middot Select a picture in the graphic file selector on the left
middot Click on to load the link file (optional)
middot Click on to load the consensus file (optional)
middot Digitize landmarks using the left button of the mouse
middot To cancel last landmark position by a click on undo arrow
middot When all landmarks are digitized save the file by a click on save file
APS Crear archivo
Getting started with ApsUtil
ApsUtil create a data file (dat) with specimen ordered by
addition of smaller data files Input and output files are to
APS data format with an header line (number of specimens
number
of landmarks number of dimensions) followed by landmarks
coordinates
NEW button clear all previous data and begin a new data file
ADD button add a file containing one or many specimen
MIX button add a new file to a previous one by mixing the
two file
This ordering of specimen is required before to compute
shape differences
When file is saved specimens are ordered like
specimen 1 of the 1st file
specimen 1 of the 2nd file
specimen 2 of the 1st file
APS analisis
bull New features of Version 241
bull A single specimen or all a sample can be superimposed on any reloaded
bull specimen as consensus (File -gt Reload -gt Consensus)
bull Shape vectors (eg discriminant vectors computed with other software)
bull can be reloaded for visualization (File -gt Reload -gt Pcs)
bull The shape vector must be of norm 1
bull Projections of specimens on shape vectors are automatically computed
Otros
elementos del
esqueleto
A Antarctosaurus wichmannianus B
Saltasaurus loricatus C Neuquensaurus
australis D Neuquensaurus robustus E
Lirainosaurus astibiae F Ampelosaurus atacis
G Magyarosaurus dacus H Magyarosaurus
dacus Jianu I Alamosaurus sanjuanensis J
Aegyptosaurus baharijiensis K
Opisthocoelicaudia skarzynskii
Canudo amp Cuenca Bescos 2004
wwwaragosauruscom
Aegyptosaurus Alamosaurus
Imaacutegenes literatura
Fotos ejemplares
Hacer un poliacutegono con los landmarks
Guardar la misma posicioacuten (en una liacutenea basal por ej)
APS digit
APS util
APS program CP
Opisthocoelicaudia
Resultados
APS Fecha Thu 21 Sep 2006 213918
+0200 [210906 213918 CEST]
De Info Procuste
ltinfoprocustecomgt
Para cuencagunizares
Asunto Re analyse de forme chez
les arvicolides
Cabeceras Mostrar todas las
cabeceras
Chegravere collegravegue
Voici le lien pour teacuteleacutecharger le le
setup dinstallation des 3
logiciels APS ApsDigit et ApsUtil
httpwwwprocustecomprogramsset
up_aps_allexe
Noubliez pas de citer APS dans vos
publications
Bien cordialement
Xavier Penin
Paacuteginas web recomendadas
bull httplifebiosunysbedumorph la mejor paacutegina de
morfometriacutea geomeacutetrica Contiene un listado con todos los
programas de morfometriacutea Universidad de Stony Brook NY
bull httpwwwmorphometricsorgindexhtml es la paacutegina en la
que se mantiene la lista de email morphmet Es la base de la
organizacioacuten de la morfometriacutea en Suny
bull httpwwwflywingsorgukindexhtm iquestporqueacute hay variacioacuten
morfoloacutegica Universidad de Manchester UK
bull httpwwwprocustecomindexhtml anaacutelisis de la forma con
Procruste Aps Xavier Penin Universidad de Paris V
bull Shapehellipy otros ver la paacutegina de Suny
Las ldquoseries TPSrdquo Thin-plate spline
(laacuteminas finas de grosor uniforme)
tpsDIG2
Data acquisition
bull Digitize landmarks amp outlines from image files scanner or video Windows TpsDig is a Windows (95 through XP) program for digitizing landmarks and outlines for geometric morphometric analyses Includes simple image enhancement operations scale factors image brightness profile and support for AVI and MOV files Output is in the TPS file format used by the tps series of programs The TPS file includes the name of the image file for each specimen so that landmarks can always be visualized on the image Since output files are ASCII they can be converted to formats for other software Users should note that the tpsUtil program is useful for both the preparation of the input files to tpsDig as well as for some useful conversions afterwards The program also computes areas of enclosed regions perimeters and linear distances The tpsDig2 link at the left is for the new 205 version
bull Execute the downloaded file to install the program By F James Rohlf
Las ldquoseries TPSrdquo
ordenar los archivos digitalizados
TPS util
bull tps file utility program Windows At present it can randomly scramble the order of specimens in a tps file to minimize bias in digitizing landmark locations restore the original order (eg before statistical analyses are performed) create an empty TPS file from a directory with image files add keywords and values to the variables field of a TPS file combine TPS files into a single TPS file deletereorder landmarks remove outlines from a TPS file and convert TPS and NTS files to NTS M or CSV files It can also split an NTS file into several matrices Graphic editors are included for drawing link and sliders files Unbending a deformed specimen Converting outline and curves points to landmarks
bull Other operations can be added - let me know what you need Execute the TPSUTILW32EXE file to install the program By F James Rohlf Version 138
tpsTree
bull Fit and visualize thin-plate splines on trees Windows Performs a least-squares orthogonal generalized Procrustes analysis to obtain a reference and then estimates the splines for each group (internal node) on a tree Both ultrametric (eg WPGMA and UPGMA trees) and additive trees (using squared change parsimony to estimate the shapes of the HTUs) are supported The estimated shapes can be visualized with estimated images in the background (see the tpsSuper program) The file expands into a Windows setup program and associated files By F James Rohlf Version 118 File containing HTU coordinates and HTU images to demo that feature The older and more limited 16 bit Windows version is still available
tpsRegr
bull Multivariate multiple regression of shape onto independent variables Windows performs a multivariate multiple regression of shape (as captured by partial warp scores and the uniform shape component) onto one or more independent variables By appropriate setting up of independent variables this program can perform various types of MANOVA and MANCOVA Can be used to study allometry By F James Rohlf Version 131
tpsSplin
bull Thin-plate spline Windows Program to
compare pairs of specimens by displaying
a Darcy Thompson style transformation
grid based on a thin-plate spline Several
options are given for sliding
semilandmarks The tpssplnwexe file
expands into a Windows setup program
that will be run automatically By F James
Rohlf Version 120
tpsRelw el anaacutelisis de la
deformacioacuten relativa bull Relative warps analysis Windows Performs a
relative warp (deformacioacuten) analysis This corresponds to a principal components analysis of variation in a sample (relative to bending energy if the alpha parameter is not equal to zero) Displays a plot of relative warp scores and a visualization window that displays the estimated shape for arbitrary points in the ordination Also displays partial warp scores and their visualizations Allows fitting of semilandmark points along curves Version 144 By F James Rohlf
tpsPLS
bull Partial least-squares analysis for shapes Windows Used to explore the covariance between a set of variables and variation in shape or between two shapes It performs a two-block partial least-squares analysis It differs from regression in that both variables and shape are considered equally (one is not considered to be a set of independent variables measured without error) Its use is described in Rohlf and Corti (2000 Systematic Biology 49740-753) By F James Rohlf Version 118
tpsSmall
bull Test for small variation in shape Windows Use to test whether the variation in shape among a set of specimens is too large and thus statistical methods based on the tangent space approximation (eg thin-plate spline methods) cannot be used The program can process both 2D and 3D data files Output files include consensus and aligned specimens By F James Rohlf Version 120
tpsPower
bull Estimate statistical power for comparing shapes Windows Program for estimating statistical power for comparing the mean shapes of two populations Provides methods based on several different approaches Can be used for planning morphometric studies as well as to compare power using different approaches Version 104 By F James Rohlf
Morpheus et al bull Morpheus et al is a software package that will provide a
comprehensive cross-platform environment for morphometric data analysis It is available in graphical and command-line versions for a number of operating systems (see below) More information about new features and previous changes can be found in the release notes
httplifebiosunysbedumorphmorpheus
Multivariate analysis
bull PAST is a free easy-to-use data analysis package aimed at paleontology Windows 95+ Multivariate statistical methods include Principal Components (with Minimal Spanning Tree) Principal Coordinates (ten distance measures) Non-metric Multidimensional Scaling (ten distance measures) Detrended Correspondence Analysis Cluster analysis (three algorithms 11 distance measures) k-means clustering seriation discriminant analysis one-way MANOVA Hotellings t-squared Boxs M Canonical Variates Analysis Also includes Fourier shape analysis thin-plate splines parsimony and time series analysis among others Oslashyvind Hammer University of Oslo
Analysis of outlines
bull Shape Elliptic Fourier WINDOWS Extracts the contour shape from a full color bitmap image delineates the contour shape with the elliptic Fourier descriptors and performs a principal component analysis for summarizing the shape information By Hiroyoshi Iwata For more information see Shape home page tutorial or manual
bull Iwata H and Y Ukai (2002) SHAPE A computer program package for quantitative evaluation of biological shapes based on elliptic Fourier descriptors Journal of Heredity 93 384-385
Eigenshape analysis
bull httpwwwnhmacukhosted_sitespaleonetftpftphtml
bull This archive contains a series of programs designed to perform an eigenshape analysis on xy coordinate data from object outlines Routines include xy -gt phi() transformation phi() -gt xy transformation eigenshape analysis and projection of objects into the eigenshape space Two completely worked example analyses and a users guide are also provided El autor es Norman McLeod del BMNH de Londres
Graphical representation of the four-step morphometric protocol A Quantify raw data
(landmarks recorded on body of cichlid fish) B Remove non-shape variation (landmarks of 412
specimens before and after GPA) C statistical analysis (CVA) and graphical presentation of
results Deformation grids for mean specimen for (right) Eretmodus cyanostictus and (left)
Spathodus erythrodon (magnified by 3X to emphasize shape differences) Data from Ruumlber and
Adams 2001 En Adams Rolhf Slice 2002
APS Digitalizar landmarks
DigitX is designed to digitize landmarks on Jpeg or Bitmap picture
middot Select the total number of landmarks to digitize with the second
Combo-Box of the toolbar
middot Select a picture in the graphic file selector on the left
middot Click on to load the link file (optional)
middot Click on to load the consensus file (optional)
middot Digitize landmarks using the left button of the mouse
middot To cancel last landmark position by a click on undo arrow
middot When all landmarks are digitized save the file by a click on save file
APS Crear archivo
Getting started with ApsUtil
ApsUtil create a data file (dat) with specimen ordered by
addition of smaller data files Input and output files are to
APS data format with an header line (number of specimens
number
of landmarks number of dimensions) followed by landmarks
coordinates
NEW button clear all previous data and begin a new data file
ADD button add a file containing one or many specimen
MIX button add a new file to a previous one by mixing the
two file
This ordering of specimen is required before to compute
shape differences
When file is saved specimens are ordered like
specimen 1 of the 1st file
specimen 1 of the 2nd file
specimen 2 of the 1st file
APS analisis
bull New features of Version 241
bull A single specimen or all a sample can be superimposed on any reloaded
bull specimen as consensus (File -gt Reload -gt Consensus)
bull Shape vectors (eg discriminant vectors computed with other software)
bull can be reloaded for visualization (File -gt Reload -gt Pcs)
bull The shape vector must be of norm 1
bull Projections of specimens on shape vectors are automatically computed
Otros
elementos del
esqueleto
A Antarctosaurus wichmannianus B
Saltasaurus loricatus C Neuquensaurus
australis D Neuquensaurus robustus E
Lirainosaurus astibiae F Ampelosaurus atacis
G Magyarosaurus dacus H Magyarosaurus
dacus Jianu I Alamosaurus sanjuanensis J
Aegyptosaurus baharijiensis K
Opisthocoelicaudia skarzynskii
Canudo amp Cuenca Bescos 2004
wwwaragosauruscom
Aegyptosaurus Alamosaurus
Imaacutegenes literatura
Fotos ejemplares
Hacer un poliacutegono con los landmarks
Guardar la misma posicioacuten (en una liacutenea basal por ej)
APS digit
APS util
APS program CP
Opisthocoelicaudia
Resultados
APS Fecha Thu 21 Sep 2006 213918
+0200 [210906 213918 CEST]
De Info Procuste
ltinfoprocustecomgt
Para cuencagunizares
Asunto Re analyse de forme chez
les arvicolides
Cabeceras Mostrar todas las
cabeceras
Chegravere collegravegue
Voici le lien pour teacuteleacutecharger le le
setup dinstallation des 3
logiciels APS ApsDigit et ApsUtil
httpwwwprocustecomprogramsset
up_aps_allexe
Noubliez pas de citer APS dans vos
publications
Bien cordialement
Xavier Penin
Paacuteginas web recomendadas
bull httplifebiosunysbedumorph la mejor paacutegina de
morfometriacutea geomeacutetrica Contiene un listado con todos los
programas de morfometriacutea Universidad de Stony Brook NY
bull httpwwwmorphometricsorgindexhtml es la paacutegina en la
que se mantiene la lista de email morphmet Es la base de la
organizacioacuten de la morfometriacutea en Suny
bull httpwwwflywingsorgukindexhtm iquestporqueacute hay variacioacuten
morfoloacutegica Universidad de Manchester UK
bull httpwwwprocustecomindexhtml anaacutelisis de la forma con
Procruste Aps Xavier Penin Universidad de Paris V
bull Shapehellipy otros ver la paacutegina de Suny
Las ldquoseries TPSrdquo Thin-plate spline
(laacuteminas finas de grosor uniforme)
tpsDIG2
Data acquisition
bull Digitize landmarks amp outlines from image files scanner or video Windows TpsDig is a Windows (95 through XP) program for digitizing landmarks and outlines for geometric morphometric analyses Includes simple image enhancement operations scale factors image brightness profile and support for AVI and MOV files Output is in the TPS file format used by the tps series of programs The TPS file includes the name of the image file for each specimen so that landmarks can always be visualized on the image Since output files are ASCII they can be converted to formats for other software Users should note that the tpsUtil program is useful for both the preparation of the input files to tpsDig as well as for some useful conversions afterwards The program also computes areas of enclosed regions perimeters and linear distances The tpsDig2 link at the left is for the new 205 version
bull Execute the downloaded file to install the program By F James Rohlf
Las ldquoseries TPSrdquo
ordenar los archivos digitalizados
TPS util
bull tps file utility program Windows At present it can randomly scramble the order of specimens in a tps file to minimize bias in digitizing landmark locations restore the original order (eg before statistical analyses are performed) create an empty TPS file from a directory with image files add keywords and values to the variables field of a TPS file combine TPS files into a single TPS file deletereorder landmarks remove outlines from a TPS file and convert TPS and NTS files to NTS M or CSV files It can also split an NTS file into several matrices Graphic editors are included for drawing link and sliders files Unbending a deformed specimen Converting outline and curves points to landmarks
bull Other operations can be added - let me know what you need Execute the TPSUTILW32EXE file to install the program By F James Rohlf Version 138
tpsTree
bull Fit and visualize thin-plate splines on trees Windows Performs a least-squares orthogonal generalized Procrustes analysis to obtain a reference and then estimates the splines for each group (internal node) on a tree Both ultrametric (eg WPGMA and UPGMA trees) and additive trees (using squared change parsimony to estimate the shapes of the HTUs) are supported The estimated shapes can be visualized with estimated images in the background (see the tpsSuper program) The file expands into a Windows setup program and associated files By F James Rohlf Version 118 File containing HTU coordinates and HTU images to demo that feature The older and more limited 16 bit Windows version is still available
tpsRegr
bull Multivariate multiple regression of shape onto independent variables Windows performs a multivariate multiple regression of shape (as captured by partial warp scores and the uniform shape component) onto one or more independent variables By appropriate setting up of independent variables this program can perform various types of MANOVA and MANCOVA Can be used to study allometry By F James Rohlf Version 131
tpsSplin
bull Thin-plate spline Windows Program to
compare pairs of specimens by displaying
a Darcy Thompson style transformation
grid based on a thin-plate spline Several
options are given for sliding
semilandmarks The tpssplnwexe file
expands into a Windows setup program
that will be run automatically By F James
Rohlf Version 120
tpsRelw el anaacutelisis de la
deformacioacuten relativa bull Relative warps analysis Windows Performs a
relative warp (deformacioacuten) analysis This corresponds to a principal components analysis of variation in a sample (relative to bending energy if the alpha parameter is not equal to zero) Displays a plot of relative warp scores and a visualization window that displays the estimated shape for arbitrary points in the ordination Also displays partial warp scores and their visualizations Allows fitting of semilandmark points along curves Version 144 By F James Rohlf
tpsPLS
bull Partial least-squares analysis for shapes Windows Used to explore the covariance between a set of variables and variation in shape or between two shapes It performs a two-block partial least-squares analysis It differs from regression in that both variables and shape are considered equally (one is not considered to be a set of independent variables measured without error) Its use is described in Rohlf and Corti (2000 Systematic Biology 49740-753) By F James Rohlf Version 118
tpsSmall
bull Test for small variation in shape Windows Use to test whether the variation in shape among a set of specimens is too large and thus statistical methods based on the tangent space approximation (eg thin-plate spline methods) cannot be used The program can process both 2D and 3D data files Output files include consensus and aligned specimens By F James Rohlf Version 120
tpsPower
bull Estimate statistical power for comparing shapes Windows Program for estimating statistical power for comparing the mean shapes of two populations Provides methods based on several different approaches Can be used for planning morphometric studies as well as to compare power using different approaches Version 104 By F James Rohlf
Morpheus et al bull Morpheus et al is a software package that will provide a
comprehensive cross-platform environment for morphometric data analysis It is available in graphical and command-line versions for a number of operating systems (see below) More information about new features and previous changes can be found in the release notes
httplifebiosunysbedumorphmorpheus
Multivariate analysis
bull PAST is a free easy-to-use data analysis package aimed at paleontology Windows 95+ Multivariate statistical methods include Principal Components (with Minimal Spanning Tree) Principal Coordinates (ten distance measures) Non-metric Multidimensional Scaling (ten distance measures) Detrended Correspondence Analysis Cluster analysis (three algorithms 11 distance measures) k-means clustering seriation discriminant analysis one-way MANOVA Hotellings t-squared Boxs M Canonical Variates Analysis Also includes Fourier shape analysis thin-plate splines parsimony and time series analysis among others Oslashyvind Hammer University of Oslo
Analysis of outlines
bull Shape Elliptic Fourier WINDOWS Extracts the contour shape from a full color bitmap image delineates the contour shape with the elliptic Fourier descriptors and performs a principal component analysis for summarizing the shape information By Hiroyoshi Iwata For more information see Shape home page tutorial or manual
bull Iwata H and Y Ukai (2002) SHAPE A computer program package for quantitative evaluation of biological shapes based on elliptic Fourier descriptors Journal of Heredity 93 384-385
Eigenshape analysis
bull httpwwwnhmacukhosted_sitespaleonetftpftphtml
bull This archive contains a series of programs designed to perform an eigenshape analysis on xy coordinate data from object outlines Routines include xy -gt phi() transformation phi() -gt xy transformation eigenshape analysis and projection of objects into the eigenshape space Two completely worked example analyses and a users guide are also provided El autor es Norman McLeod del BMNH de Londres
Graphical representation of the four-step morphometric protocol A Quantify raw data
(landmarks recorded on body of cichlid fish) B Remove non-shape variation (landmarks of 412
specimens before and after GPA) C statistical analysis (CVA) and graphical presentation of
results Deformation grids for mean specimen for (right) Eretmodus cyanostictus and (left)
Spathodus erythrodon (magnified by 3X to emphasize shape differences) Data from Ruumlber and
Adams 2001 En Adams Rolhf Slice 2002
APS Crear archivo
Getting started with ApsUtil
ApsUtil create a data file (dat) with specimen ordered by
addition of smaller data files Input and output files are to
APS data format with an header line (number of specimens
number
of landmarks number of dimensions) followed by landmarks
coordinates
NEW button clear all previous data and begin a new data file
ADD button add a file containing one or many specimen
MIX button add a new file to a previous one by mixing the
two file
This ordering of specimen is required before to compute
shape differences
When file is saved specimens are ordered like
specimen 1 of the 1st file
specimen 1 of the 2nd file
specimen 2 of the 1st file
APS analisis
bull New features of Version 241
bull A single specimen or all a sample can be superimposed on any reloaded
bull specimen as consensus (File -gt Reload -gt Consensus)
bull Shape vectors (eg discriminant vectors computed with other software)
bull can be reloaded for visualization (File -gt Reload -gt Pcs)
bull The shape vector must be of norm 1
bull Projections of specimens on shape vectors are automatically computed
Otros
elementos del
esqueleto
A Antarctosaurus wichmannianus B
Saltasaurus loricatus C Neuquensaurus
australis D Neuquensaurus robustus E
Lirainosaurus astibiae F Ampelosaurus atacis
G Magyarosaurus dacus H Magyarosaurus
dacus Jianu I Alamosaurus sanjuanensis J
Aegyptosaurus baharijiensis K
Opisthocoelicaudia skarzynskii
Canudo amp Cuenca Bescos 2004
wwwaragosauruscom
Aegyptosaurus Alamosaurus
Imaacutegenes literatura
Fotos ejemplares
Hacer un poliacutegono con los landmarks
Guardar la misma posicioacuten (en una liacutenea basal por ej)
APS digit
APS util
APS program CP
Opisthocoelicaudia
Resultados
APS Fecha Thu 21 Sep 2006 213918
+0200 [210906 213918 CEST]
De Info Procuste
ltinfoprocustecomgt
Para cuencagunizares
Asunto Re analyse de forme chez
les arvicolides
Cabeceras Mostrar todas las
cabeceras
Chegravere collegravegue
Voici le lien pour teacuteleacutecharger le le
setup dinstallation des 3
logiciels APS ApsDigit et ApsUtil
httpwwwprocustecomprogramsset
up_aps_allexe
Noubliez pas de citer APS dans vos
publications
Bien cordialement
Xavier Penin
Paacuteginas web recomendadas
bull httplifebiosunysbedumorph la mejor paacutegina de
morfometriacutea geomeacutetrica Contiene un listado con todos los
programas de morfometriacutea Universidad de Stony Brook NY
bull httpwwwmorphometricsorgindexhtml es la paacutegina en la
que se mantiene la lista de email morphmet Es la base de la
organizacioacuten de la morfometriacutea en Suny
bull httpwwwflywingsorgukindexhtm iquestporqueacute hay variacioacuten
morfoloacutegica Universidad de Manchester UK
bull httpwwwprocustecomindexhtml anaacutelisis de la forma con
Procruste Aps Xavier Penin Universidad de Paris V
bull Shapehellipy otros ver la paacutegina de Suny
Las ldquoseries TPSrdquo Thin-plate spline
(laacuteminas finas de grosor uniforme)
tpsDIG2
Data acquisition
bull Digitize landmarks amp outlines from image files scanner or video Windows TpsDig is a Windows (95 through XP) program for digitizing landmarks and outlines for geometric morphometric analyses Includes simple image enhancement operations scale factors image brightness profile and support for AVI and MOV files Output is in the TPS file format used by the tps series of programs The TPS file includes the name of the image file for each specimen so that landmarks can always be visualized on the image Since output files are ASCII they can be converted to formats for other software Users should note that the tpsUtil program is useful for both the preparation of the input files to tpsDig as well as for some useful conversions afterwards The program also computes areas of enclosed regions perimeters and linear distances The tpsDig2 link at the left is for the new 205 version
bull Execute the downloaded file to install the program By F James Rohlf
Las ldquoseries TPSrdquo
ordenar los archivos digitalizados
TPS util
bull tps file utility program Windows At present it can randomly scramble the order of specimens in a tps file to minimize bias in digitizing landmark locations restore the original order (eg before statistical analyses are performed) create an empty TPS file from a directory with image files add keywords and values to the variables field of a TPS file combine TPS files into a single TPS file deletereorder landmarks remove outlines from a TPS file and convert TPS and NTS files to NTS M or CSV files It can also split an NTS file into several matrices Graphic editors are included for drawing link and sliders files Unbending a deformed specimen Converting outline and curves points to landmarks
bull Other operations can be added - let me know what you need Execute the TPSUTILW32EXE file to install the program By F James Rohlf Version 138
tpsTree
bull Fit and visualize thin-plate splines on trees Windows Performs a least-squares orthogonal generalized Procrustes analysis to obtain a reference and then estimates the splines for each group (internal node) on a tree Both ultrametric (eg WPGMA and UPGMA trees) and additive trees (using squared change parsimony to estimate the shapes of the HTUs) are supported The estimated shapes can be visualized with estimated images in the background (see the tpsSuper program) The file expands into a Windows setup program and associated files By F James Rohlf Version 118 File containing HTU coordinates and HTU images to demo that feature The older and more limited 16 bit Windows version is still available
tpsRegr
bull Multivariate multiple regression of shape onto independent variables Windows performs a multivariate multiple regression of shape (as captured by partial warp scores and the uniform shape component) onto one or more independent variables By appropriate setting up of independent variables this program can perform various types of MANOVA and MANCOVA Can be used to study allometry By F James Rohlf Version 131
tpsSplin
bull Thin-plate spline Windows Program to
compare pairs of specimens by displaying
a Darcy Thompson style transformation
grid based on a thin-plate spline Several
options are given for sliding
semilandmarks The tpssplnwexe file
expands into a Windows setup program
that will be run automatically By F James
Rohlf Version 120
tpsRelw el anaacutelisis de la
deformacioacuten relativa bull Relative warps analysis Windows Performs a
relative warp (deformacioacuten) analysis This corresponds to a principal components analysis of variation in a sample (relative to bending energy if the alpha parameter is not equal to zero) Displays a plot of relative warp scores and a visualization window that displays the estimated shape for arbitrary points in the ordination Also displays partial warp scores and their visualizations Allows fitting of semilandmark points along curves Version 144 By F James Rohlf
tpsPLS
bull Partial least-squares analysis for shapes Windows Used to explore the covariance between a set of variables and variation in shape or between two shapes It performs a two-block partial least-squares analysis It differs from regression in that both variables and shape are considered equally (one is not considered to be a set of independent variables measured without error) Its use is described in Rohlf and Corti (2000 Systematic Biology 49740-753) By F James Rohlf Version 118
tpsSmall
bull Test for small variation in shape Windows Use to test whether the variation in shape among a set of specimens is too large and thus statistical methods based on the tangent space approximation (eg thin-plate spline methods) cannot be used The program can process both 2D and 3D data files Output files include consensus and aligned specimens By F James Rohlf Version 120
tpsPower
bull Estimate statistical power for comparing shapes Windows Program for estimating statistical power for comparing the mean shapes of two populations Provides methods based on several different approaches Can be used for planning morphometric studies as well as to compare power using different approaches Version 104 By F James Rohlf
Morpheus et al bull Morpheus et al is a software package that will provide a
comprehensive cross-platform environment for morphometric data analysis It is available in graphical and command-line versions for a number of operating systems (see below) More information about new features and previous changes can be found in the release notes
httplifebiosunysbedumorphmorpheus
Multivariate analysis
bull PAST is a free easy-to-use data analysis package aimed at paleontology Windows 95+ Multivariate statistical methods include Principal Components (with Minimal Spanning Tree) Principal Coordinates (ten distance measures) Non-metric Multidimensional Scaling (ten distance measures) Detrended Correspondence Analysis Cluster analysis (three algorithms 11 distance measures) k-means clustering seriation discriminant analysis one-way MANOVA Hotellings t-squared Boxs M Canonical Variates Analysis Also includes Fourier shape analysis thin-plate splines parsimony and time series analysis among others Oslashyvind Hammer University of Oslo
Analysis of outlines
bull Shape Elliptic Fourier WINDOWS Extracts the contour shape from a full color bitmap image delineates the contour shape with the elliptic Fourier descriptors and performs a principal component analysis for summarizing the shape information By Hiroyoshi Iwata For more information see Shape home page tutorial or manual
bull Iwata H and Y Ukai (2002) SHAPE A computer program package for quantitative evaluation of biological shapes based on elliptic Fourier descriptors Journal of Heredity 93 384-385
Eigenshape analysis
bull httpwwwnhmacukhosted_sitespaleonetftpftphtml
bull This archive contains a series of programs designed to perform an eigenshape analysis on xy coordinate data from object outlines Routines include xy -gt phi() transformation phi() -gt xy transformation eigenshape analysis and projection of objects into the eigenshape space Two completely worked example analyses and a users guide are also provided El autor es Norman McLeod del BMNH de Londres
Graphical representation of the four-step morphometric protocol A Quantify raw data
(landmarks recorded on body of cichlid fish) B Remove non-shape variation (landmarks of 412
specimens before and after GPA) C statistical analysis (CVA) and graphical presentation of
results Deformation grids for mean specimen for (right) Eretmodus cyanostictus and (left)
Spathodus erythrodon (magnified by 3X to emphasize shape differences) Data from Ruumlber and
Adams 2001 En Adams Rolhf Slice 2002
APS analisis
bull New features of Version 241
bull A single specimen or all a sample can be superimposed on any reloaded
bull specimen as consensus (File -gt Reload -gt Consensus)
bull Shape vectors (eg discriminant vectors computed with other software)
bull can be reloaded for visualization (File -gt Reload -gt Pcs)
bull The shape vector must be of norm 1
bull Projections of specimens on shape vectors are automatically computed
Otros
elementos del
esqueleto
A Antarctosaurus wichmannianus B
Saltasaurus loricatus C Neuquensaurus
australis D Neuquensaurus robustus E
Lirainosaurus astibiae F Ampelosaurus atacis
G Magyarosaurus dacus H Magyarosaurus
dacus Jianu I Alamosaurus sanjuanensis J
Aegyptosaurus baharijiensis K
Opisthocoelicaudia skarzynskii
Canudo amp Cuenca Bescos 2004
wwwaragosauruscom
Aegyptosaurus Alamosaurus
Imaacutegenes literatura
Fotos ejemplares
Hacer un poliacutegono con los landmarks
Guardar la misma posicioacuten (en una liacutenea basal por ej)
APS digit
APS util
APS program CP
Opisthocoelicaudia
Resultados
APS Fecha Thu 21 Sep 2006 213918
+0200 [210906 213918 CEST]
De Info Procuste
ltinfoprocustecomgt
Para cuencagunizares
Asunto Re analyse de forme chez
les arvicolides
Cabeceras Mostrar todas las
cabeceras
Chegravere collegravegue
Voici le lien pour teacuteleacutecharger le le
setup dinstallation des 3
logiciels APS ApsDigit et ApsUtil
httpwwwprocustecomprogramsset
up_aps_allexe
Noubliez pas de citer APS dans vos
publications
Bien cordialement
Xavier Penin
Paacuteginas web recomendadas
bull httplifebiosunysbedumorph la mejor paacutegina de
morfometriacutea geomeacutetrica Contiene un listado con todos los
programas de morfometriacutea Universidad de Stony Brook NY
bull httpwwwmorphometricsorgindexhtml es la paacutegina en la
que se mantiene la lista de email morphmet Es la base de la
organizacioacuten de la morfometriacutea en Suny
bull httpwwwflywingsorgukindexhtm iquestporqueacute hay variacioacuten
morfoloacutegica Universidad de Manchester UK
bull httpwwwprocustecomindexhtml anaacutelisis de la forma con
Procruste Aps Xavier Penin Universidad de Paris V
bull Shapehellipy otros ver la paacutegina de Suny
Las ldquoseries TPSrdquo Thin-plate spline
(laacuteminas finas de grosor uniforme)
tpsDIG2
Data acquisition
bull Digitize landmarks amp outlines from image files scanner or video Windows TpsDig is a Windows (95 through XP) program for digitizing landmarks and outlines for geometric morphometric analyses Includes simple image enhancement operations scale factors image brightness profile and support for AVI and MOV files Output is in the TPS file format used by the tps series of programs The TPS file includes the name of the image file for each specimen so that landmarks can always be visualized on the image Since output files are ASCII they can be converted to formats for other software Users should note that the tpsUtil program is useful for both the preparation of the input files to tpsDig as well as for some useful conversions afterwards The program also computes areas of enclosed regions perimeters and linear distances The tpsDig2 link at the left is for the new 205 version
bull Execute the downloaded file to install the program By F James Rohlf
Las ldquoseries TPSrdquo
ordenar los archivos digitalizados
TPS util
bull tps file utility program Windows At present it can randomly scramble the order of specimens in a tps file to minimize bias in digitizing landmark locations restore the original order (eg before statistical analyses are performed) create an empty TPS file from a directory with image files add keywords and values to the variables field of a TPS file combine TPS files into a single TPS file deletereorder landmarks remove outlines from a TPS file and convert TPS and NTS files to NTS M or CSV files It can also split an NTS file into several matrices Graphic editors are included for drawing link and sliders files Unbending a deformed specimen Converting outline and curves points to landmarks
bull Other operations can be added - let me know what you need Execute the TPSUTILW32EXE file to install the program By F James Rohlf Version 138
tpsTree
bull Fit and visualize thin-plate splines on trees Windows Performs a least-squares orthogonal generalized Procrustes analysis to obtain a reference and then estimates the splines for each group (internal node) on a tree Both ultrametric (eg WPGMA and UPGMA trees) and additive trees (using squared change parsimony to estimate the shapes of the HTUs) are supported The estimated shapes can be visualized with estimated images in the background (see the tpsSuper program) The file expands into a Windows setup program and associated files By F James Rohlf Version 118 File containing HTU coordinates and HTU images to demo that feature The older and more limited 16 bit Windows version is still available
tpsRegr
bull Multivariate multiple regression of shape onto independent variables Windows performs a multivariate multiple regression of shape (as captured by partial warp scores and the uniform shape component) onto one or more independent variables By appropriate setting up of independent variables this program can perform various types of MANOVA and MANCOVA Can be used to study allometry By F James Rohlf Version 131
tpsSplin
bull Thin-plate spline Windows Program to
compare pairs of specimens by displaying
a Darcy Thompson style transformation
grid based on a thin-plate spline Several
options are given for sliding
semilandmarks The tpssplnwexe file
expands into a Windows setup program
that will be run automatically By F James
Rohlf Version 120
tpsRelw el anaacutelisis de la
deformacioacuten relativa bull Relative warps analysis Windows Performs a
relative warp (deformacioacuten) analysis This corresponds to a principal components analysis of variation in a sample (relative to bending energy if the alpha parameter is not equal to zero) Displays a plot of relative warp scores and a visualization window that displays the estimated shape for arbitrary points in the ordination Also displays partial warp scores and their visualizations Allows fitting of semilandmark points along curves Version 144 By F James Rohlf
tpsPLS
bull Partial least-squares analysis for shapes Windows Used to explore the covariance between a set of variables and variation in shape or between two shapes It performs a two-block partial least-squares analysis It differs from regression in that both variables and shape are considered equally (one is not considered to be a set of independent variables measured without error) Its use is described in Rohlf and Corti (2000 Systematic Biology 49740-753) By F James Rohlf Version 118
tpsSmall
bull Test for small variation in shape Windows Use to test whether the variation in shape among a set of specimens is too large and thus statistical methods based on the tangent space approximation (eg thin-plate spline methods) cannot be used The program can process both 2D and 3D data files Output files include consensus and aligned specimens By F James Rohlf Version 120
tpsPower
bull Estimate statistical power for comparing shapes Windows Program for estimating statistical power for comparing the mean shapes of two populations Provides methods based on several different approaches Can be used for planning morphometric studies as well as to compare power using different approaches Version 104 By F James Rohlf
Morpheus et al bull Morpheus et al is a software package that will provide a
comprehensive cross-platform environment for morphometric data analysis It is available in graphical and command-line versions for a number of operating systems (see below) More information about new features and previous changes can be found in the release notes
httplifebiosunysbedumorphmorpheus
Multivariate analysis
bull PAST is a free easy-to-use data analysis package aimed at paleontology Windows 95+ Multivariate statistical methods include Principal Components (with Minimal Spanning Tree) Principal Coordinates (ten distance measures) Non-metric Multidimensional Scaling (ten distance measures) Detrended Correspondence Analysis Cluster analysis (three algorithms 11 distance measures) k-means clustering seriation discriminant analysis one-way MANOVA Hotellings t-squared Boxs M Canonical Variates Analysis Also includes Fourier shape analysis thin-plate splines parsimony and time series analysis among others Oslashyvind Hammer University of Oslo
Analysis of outlines
bull Shape Elliptic Fourier WINDOWS Extracts the contour shape from a full color bitmap image delineates the contour shape with the elliptic Fourier descriptors and performs a principal component analysis for summarizing the shape information By Hiroyoshi Iwata For more information see Shape home page tutorial or manual
bull Iwata H and Y Ukai (2002) SHAPE A computer program package for quantitative evaluation of biological shapes based on elliptic Fourier descriptors Journal of Heredity 93 384-385
Eigenshape analysis
bull httpwwwnhmacukhosted_sitespaleonetftpftphtml
bull This archive contains a series of programs designed to perform an eigenshape analysis on xy coordinate data from object outlines Routines include xy -gt phi() transformation phi() -gt xy transformation eigenshape analysis and projection of objects into the eigenshape space Two completely worked example analyses and a users guide are also provided El autor es Norman McLeod del BMNH de Londres
Graphical representation of the four-step morphometric protocol A Quantify raw data
(landmarks recorded on body of cichlid fish) B Remove non-shape variation (landmarks of 412
specimens before and after GPA) C statistical analysis (CVA) and graphical presentation of
results Deformation grids for mean specimen for (right) Eretmodus cyanostictus and (left)
Spathodus erythrodon (magnified by 3X to emphasize shape differences) Data from Ruumlber and
Adams 2001 En Adams Rolhf Slice 2002
Otros
elementos del
esqueleto
A Antarctosaurus wichmannianus B
Saltasaurus loricatus C Neuquensaurus
australis D Neuquensaurus robustus E
Lirainosaurus astibiae F Ampelosaurus atacis
G Magyarosaurus dacus H Magyarosaurus
dacus Jianu I Alamosaurus sanjuanensis J
Aegyptosaurus baharijiensis K
Opisthocoelicaudia skarzynskii
Canudo amp Cuenca Bescos 2004
wwwaragosauruscom
Aegyptosaurus Alamosaurus
Imaacutegenes literatura
Fotos ejemplares
Hacer un poliacutegono con los landmarks
Guardar la misma posicioacuten (en una liacutenea basal por ej)
APS digit
APS util
APS program CP
Opisthocoelicaudia
Resultados
APS Fecha Thu 21 Sep 2006 213918
+0200 [210906 213918 CEST]
De Info Procuste
ltinfoprocustecomgt
Para cuencagunizares
Asunto Re analyse de forme chez
les arvicolides
Cabeceras Mostrar todas las
cabeceras
Chegravere collegravegue
Voici le lien pour teacuteleacutecharger le le
setup dinstallation des 3
logiciels APS ApsDigit et ApsUtil
httpwwwprocustecomprogramsset
up_aps_allexe
Noubliez pas de citer APS dans vos
publications
Bien cordialement
Xavier Penin
Paacuteginas web recomendadas
bull httplifebiosunysbedumorph la mejor paacutegina de
morfometriacutea geomeacutetrica Contiene un listado con todos los
programas de morfometriacutea Universidad de Stony Brook NY
bull httpwwwmorphometricsorgindexhtml es la paacutegina en la
que se mantiene la lista de email morphmet Es la base de la
organizacioacuten de la morfometriacutea en Suny
bull httpwwwflywingsorgukindexhtm iquestporqueacute hay variacioacuten
morfoloacutegica Universidad de Manchester UK
bull httpwwwprocustecomindexhtml anaacutelisis de la forma con
Procruste Aps Xavier Penin Universidad de Paris V
bull Shapehellipy otros ver la paacutegina de Suny
Las ldquoseries TPSrdquo Thin-plate spline
(laacuteminas finas de grosor uniforme)
tpsDIG2
Data acquisition
bull Digitize landmarks amp outlines from image files scanner or video Windows TpsDig is a Windows (95 through XP) program for digitizing landmarks and outlines for geometric morphometric analyses Includes simple image enhancement operations scale factors image brightness profile and support for AVI and MOV files Output is in the TPS file format used by the tps series of programs The TPS file includes the name of the image file for each specimen so that landmarks can always be visualized on the image Since output files are ASCII they can be converted to formats for other software Users should note that the tpsUtil program is useful for both the preparation of the input files to tpsDig as well as for some useful conversions afterwards The program also computes areas of enclosed regions perimeters and linear distances The tpsDig2 link at the left is for the new 205 version
bull Execute the downloaded file to install the program By F James Rohlf
Las ldquoseries TPSrdquo
ordenar los archivos digitalizados
TPS util
bull tps file utility program Windows At present it can randomly scramble the order of specimens in a tps file to minimize bias in digitizing landmark locations restore the original order (eg before statistical analyses are performed) create an empty TPS file from a directory with image files add keywords and values to the variables field of a TPS file combine TPS files into a single TPS file deletereorder landmarks remove outlines from a TPS file and convert TPS and NTS files to NTS M or CSV files It can also split an NTS file into several matrices Graphic editors are included for drawing link and sliders files Unbending a deformed specimen Converting outline and curves points to landmarks
bull Other operations can be added - let me know what you need Execute the TPSUTILW32EXE file to install the program By F James Rohlf Version 138
tpsTree
bull Fit and visualize thin-plate splines on trees Windows Performs a least-squares orthogonal generalized Procrustes analysis to obtain a reference and then estimates the splines for each group (internal node) on a tree Both ultrametric (eg WPGMA and UPGMA trees) and additive trees (using squared change parsimony to estimate the shapes of the HTUs) are supported The estimated shapes can be visualized with estimated images in the background (see the tpsSuper program) The file expands into a Windows setup program and associated files By F James Rohlf Version 118 File containing HTU coordinates and HTU images to demo that feature The older and more limited 16 bit Windows version is still available
tpsRegr
bull Multivariate multiple regression of shape onto independent variables Windows performs a multivariate multiple regression of shape (as captured by partial warp scores and the uniform shape component) onto one or more independent variables By appropriate setting up of independent variables this program can perform various types of MANOVA and MANCOVA Can be used to study allometry By F James Rohlf Version 131
tpsSplin
bull Thin-plate spline Windows Program to
compare pairs of specimens by displaying
a Darcy Thompson style transformation
grid based on a thin-plate spline Several
options are given for sliding
semilandmarks The tpssplnwexe file
expands into a Windows setup program
that will be run automatically By F James
Rohlf Version 120
tpsRelw el anaacutelisis de la
deformacioacuten relativa bull Relative warps analysis Windows Performs a
relative warp (deformacioacuten) analysis This corresponds to a principal components analysis of variation in a sample (relative to bending energy if the alpha parameter is not equal to zero) Displays a plot of relative warp scores and a visualization window that displays the estimated shape for arbitrary points in the ordination Also displays partial warp scores and their visualizations Allows fitting of semilandmark points along curves Version 144 By F James Rohlf
tpsPLS
bull Partial least-squares analysis for shapes Windows Used to explore the covariance between a set of variables and variation in shape or between two shapes It performs a two-block partial least-squares analysis It differs from regression in that both variables and shape are considered equally (one is not considered to be a set of independent variables measured without error) Its use is described in Rohlf and Corti (2000 Systematic Biology 49740-753) By F James Rohlf Version 118
tpsSmall
bull Test for small variation in shape Windows Use to test whether the variation in shape among a set of specimens is too large and thus statistical methods based on the tangent space approximation (eg thin-plate spline methods) cannot be used The program can process both 2D and 3D data files Output files include consensus and aligned specimens By F James Rohlf Version 120
tpsPower
bull Estimate statistical power for comparing shapes Windows Program for estimating statistical power for comparing the mean shapes of two populations Provides methods based on several different approaches Can be used for planning morphometric studies as well as to compare power using different approaches Version 104 By F James Rohlf
Morpheus et al bull Morpheus et al is a software package that will provide a
comprehensive cross-platform environment for morphometric data analysis It is available in graphical and command-line versions for a number of operating systems (see below) More information about new features and previous changes can be found in the release notes
httplifebiosunysbedumorphmorpheus
Multivariate analysis
bull PAST is a free easy-to-use data analysis package aimed at paleontology Windows 95+ Multivariate statistical methods include Principal Components (with Minimal Spanning Tree) Principal Coordinates (ten distance measures) Non-metric Multidimensional Scaling (ten distance measures) Detrended Correspondence Analysis Cluster analysis (three algorithms 11 distance measures) k-means clustering seriation discriminant analysis one-way MANOVA Hotellings t-squared Boxs M Canonical Variates Analysis Also includes Fourier shape analysis thin-plate splines parsimony and time series analysis among others Oslashyvind Hammer University of Oslo
Analysis of outlines
bull Shape Elliptic Fourier WINDOWS Extracts the contour shape from a full color bitmap image delineates the contour shape with the elliptic Fourier descriptors and performs a principal component analysis for summarizing the shape information By Hiroyoshi Iwata For more information see Shape home page tutorial or manual
bull Iwata H and Y Ukai (2002) SHAPE A computer program package for quantitative evaluation of biological shapes based on elliptic Fourier descriptors Journal of Heredity 93 384-385
Eigenshape analysis
bull httpwwwnhmacukhosted_sitespaleonetftpftphtml
bull This archive contains a series of programs designed to perform an eigenshape analysis on xy coordinate data from object outlines Routines include xy -gt phi() transformation phi() -gt xy transformation eigenshape analysis and projection of objects into the eigenshape space Two completely worked example analyses and a users guide are also provided El autor es Norman McLeod del BMNH de Londres
Graphical representation of the four-step morphometric protocol A Quantify raw data
(landmarks recorded on body of cichlid fish) B Remove non-shape variation (landmarks of 412
specimens before and after GPA) C statistical analysis (CVA) and graphical presentation of
results Deformation grids for mean specimen for (right) Eretmodus cyanostictus and (left)
Spathodus erythrodon (magnified by 3X to emphasize shape differences) Data from Ruumlber and
Adams 2001 En Adams Rolhf Slice 2002
Canudo amp Cuenca Bescos 2004
wwwaragosauruscom
Aegyptosaurus Alamosaurus
Imaacutegenes literatura
Fotos ejemplares
Hacer un poliacutegono con los landmarks
Guardar la misma posicioacuten (en una liacutenea basal por ej)
APS digit
APS util
APS program CP
Opisthocoelicaudia
Resultados
APS Fecha Thu 21 Sep 2006 213918
+0200 [210906 213918 CEST]
De Info Procuste
ltinfoprocustecomgt
Para cuencagunizares
Asunto Re analyse de forme chez
les arvicolides
Cabeceras Mostrar todas las
cabeceras
Chegravere collegravegue
Voici le lien pour teacuteleacutecharger le le
setup dinstallation des 3
logiciels APS ApsDigit et ApsUtil
httpwwwprocustecomprogramsset
up_aps_allexe
Noubliez pas de citer APS dans vos
publications
Bien cordialement
Xavier Penin
Paacuteginas web recomendadas
bull httplifebiosunysbedumorph la mejor paacutegina de
morfometriacutea geomeacutetrica Contiene un listado con todos los
programas de morfometriacutea Universidad de Stony Brook NY
bull httpwwwmorphometricsorgindexhtml es la paacutegina en la
que se mantiene la lista de email morphmet Es la base de la
organizacioacuten de la morfometriacutea en Suny
bull httpwwwflywingsorgukindexhtm iquestporqueacute hay variacioacuten
morfoloacutegica Universidad de Manchester UK
bull httpwwwprocustecomindexhtml anaacutelisis de la forma con
Procruste Aps Xavier Penin Universidad de Paris V
bull Shapehellipy otros ver la paacutegina de Suny
Las ldquoseries TPSrdquo Thin-plate spline
(laacuteminas finas de grosor uniforme)
tpsDIG2
Data acquisition
bull Digitize landmarks amp outlines from image files scanner or video Windows TpsDig is a Windows (95 through XP) program for digitizing landmarks and outlines for geometric morphometric analyses Includes simple image enhancement operations scale factors image brightness profile and support for AVI and MOV files Output is in the TPS file format used by the tps series of programs The TPS file includes the name of the image file for each specimen so that landmarks can always be visualized on the image Since output files are ASCII they can be converted to formats for other software Users should note that the tpsUtil program is useful for both the preparation of the input files to tpsDig as well as for some useful conversions afterwards The program also computes areas of enclosed regions perimeters and linear distances The tpsDig2 link at the left is for the new 205 version
bull Execute the downloaded file to install the program By F James Rohlf
Las ldquoseries TPSrdquo
ordenar los archivos digitalizados
TPS util
bull tps file utility program Windows At present it can randomly scramble the order of specimens in a tps file to minimize bias in digitizing landmark locations restore the original order (eg before statistical analyses are performed) create an empty TPS file from a directory with image files add keywords and values to the variables field of a TPS file combine TPS files into a single TPS file deletereorder landmarks remove outlines from a TPS file and convert TPS and NTS files to NTS M or CSV files It can also split an NTS file into several matrices Graphic editors are included for drawing link and sliders files Unbending a deformed specimen Converting outline and curves points to landmarks
bull Other operations can be added - let me know what you need Execute the TPSUTILW32EXE file to install the program By F James Rohlf Version 138
tpsTree
bull Fit and visualize thin-plate splines on trees Windows Performs a least-squares orthogonal generalized Procrustes analysis to obtain a reference and then estimates the splines for each group (internal node) on a tree Both ultrametric (eg WPGMA and UPGMA trees) and additive trees (using squared change parsimony to estimate the shapes of the HTUs) are supported The estimated shapes can be visualized with estimated images in the background (see the tpsSuper program) The file expands into a Windows setup program and associated files By F James Rohlf Version 118 File containing HTU coordinates and HTU images to demo that feature The older and more limited 16 bit Windows version is still available
tpsRegr
bull Multivariate multiple regression of shape onto independent variables Windows performs a multivariate multiple regression of shape (as captured by partial warp scores and the uniform shape component) onto one or more independent variables By appropriate setting up of independent variables this program can perform various types of MANOVA and MANCOVA Can be used to study allometry By F James Rohlf Version 131
tpsSplin
bull Thin-plate spline Windows Program to
compare pairs of specimens by displaying
a Darcy Thompson style transformation
grid based on a thin-plate spline Several
options are given for sliding
semilandmarks The tpssplnwexe file
expands into a Windows setup program
that will be run automatically By F James
Rohlf Version 120
tpsRelw el anaacutelisis de la
deformacioacuten relativa bull Relative warps analysis Windows Performs a
relative warp (deformacioacuten) analysis This corresponds to a principal components analysis of variation in a sample (relative to bending energy if the alpha parameter is not equal to zero) Displays a plot of relative warp scores and a visualization window that displays the estimated shape for arbitrary points in the ordination Also displays partial warp scores and their visualizations Allows fitting of semilandmark points along curves Version 144 By F James Rohlf
tpsPLS
bull Partial least-squares analysis for shapes Windows Used to explore the covariance between a set of variables and variation in shape or between two shapes It performs a two-block partial least-squares analysis It differs from regression in that both variables and shape are considered equally (one is not considered to be a set of independent variables measured without error) Its use is described in Rohlf and Corti (2000 Systematic Biology 49740-753) By F James Rohlf Version 118
tpsSmall
bull Test for small variation in shape Windows Use to test whether the variation in shape among a set of specimens is too large and thus statistical methods based on the tangent space approximation (eg thin-plate spline methods) cannot be used The program can process both 2D and 3D data files Output files include consensus and aligned specimens By F James Rohlf Version 120
tpsPower
bull Estimate statistical power for comparing shapes Windows Program for estimating statistical power for comparing the mean shapes of two populations Provides methods based on several different approaches Can be used for planning morphometric studies as well as to compare power using different approaches Version 104 By F James Rohlf
Morpheus et al bull Morpheus et al is a software package that will provide a
comprehensive cross-platform environment for morphometric data analysis It is available in graphical and command-line versions for a number of operating systems (see below) More information about new features and previous changes can be found in the release notes
httplifebiosunysbedumorphmorpheus
Multivariate analysis
bull PAST is a free easy-to-use data analysis package aimed at paleontology Windows 95+ Multivariate statistical methods include Principal Components (with Minimal Spanning Tree) Principal Coordinates (ten distance measures) Non-metric Multidimensional Scaling (ten distance measures) Detrended Correspondence Analysis Cluster analysis (three algorithms 11 distance measures) k-means clustering seriation discriminant analysis one-way MANOVA Hotellings t-squared Boxs M Canonical Variates Analysis Also includes Fourier shape analysis thin-plate splines parsimony and time series analysis among others Oslashyvind Hammer University of Oslo
Analysis of outlines
bull Shape Elliptic Fourier WINDOWS Extracts the contour shape from a full color bitmap image delineates the contour shape with the elliptic Fourier descriptors and performs a principal component analysis for summarizing the shape information By Hiroyoshi Iwata For more information see Shape home page tutorial or manual
bull Iwata H and Y Ukai (2002) SHAPE A computer program package for quantitative evaluation of biological shapes based on elliptic Fourier descriptors Journal of Heredity 93 384-385
Eigenshape analysis
bull httpwwwnhmacukhosted_sitespaleonetftpftphtml
bull This archive contains a series of programs designed to perform an eigenshape analysis on xy coordinate data from object outlines Routines include xy -gt phi() transformation phi() -gt xy transformation eigenshape analysis and projection of objects into the eigenshape space Two completely worked example analyses and a users guide are also provided El autor es Norman McLeod del BMNH de Londres
Graphical representation of the four-step morphometric protocol A Quantify raw data
(landmarks recorded on body of cichlid fish) B Remove non-shape variation (landmarks of 412
specimens before and after GPA) C statistical analysis (CVA) and graphical presentation of
results Deformation grids for mean specimen for (right) Eretmodus cyanostictus and (left)
Spathodus erythrodon (magnified by 3X to emphasize shape differences) Data from Ruumlber and
Adams 2001 En Adams Rolhf Slice 2002
Aegyptosaurus Alamosaurus
Imaacutegenes literatura
Fotos ejemplares
Hacer un poliacutegono con los landmarks
Guardar la misma posicioacuten (en una liacutenea basal por ej)
APS digit
APS util
APS program CP
Opisthocoelicaudia
Resultados
APS Fecha Thu 21 Sep 2006 213918
+0200 [210906 213918 CEST]
De Info Procuste
ltinfoprocustecomgt
Para cuencagunizares
Asunto Re analyse de forme chez
les arvicolides
Cabeceras Mostrar todas las
cabeceras
Chegravere collegravegue
Voici le lien pour teacuteleacutecharger le le
setup dinstallation des 3
logiciels APS ApsDigit et ApsUtil
httpwwwprocustecomprogramsset
up_aps_allexe
Noubliez pas de citer APS dans vos
publications
Bien cordialement
Xavier Penin
Paacuteginas web recomendadas
bull httplifebiosunysbedumorph la mejor paacutegina de
morfometriacutea geomeacutetrica Contiene un listado con todos los
programas de morfometriacutea Universidad de Stony Brook NY
bull httpwwwmorphometricsorgindexhtml es la paacutegina en la
que se mantiene la lista de email morphmet Es la base de la
organizacioacuten de la morfometriacutea en Suny
bull httpwwwflywingsorgukindexhtm iquestporqueacute hay variacioacuten
morfoloacutegica Universidad de Manchester UK
bull httpwwwprocustecomindexhtml anaacutelisis de la forma con
Procruste Aps Xavier Penin Universidad de Paris V
bull Shapehellipy otros ver la paacutegina de Suny
Las ldquoseries TPSrdquo Thin-plate spline
(laacuteminas finas de grosor uniforme)
tpsDIG2
Data acquisition
bull Digitize landmarks amp outlines from image files scanner or video Windows TpsDig is a Windows (95 through XP) program for digitizing landmarks and outlines for geometric morphometric analyses Includes simple image enhancement operations scale factors image brightness profile and support for AVI and MOV files Output is in the TPS file format used by the tps series of programs The TPS file includes the name of the image file for each specimen so that landmarks can always be visualized on the image Since output files are ASCII they can be converted to formats for other software Users should note that the tpsUtil program is useful for both the preparation of the input files to tpsDig as well as for some useful conversions afterwards The program also computes areas of enclosed regions perimeters and linear distances The tpsDig2 link at the left is for the new 205 version
bull Execute the downloaded file to install the program By F James Rohlf
Las ldquoseries TPSrdquo
ordenar los archivos digitalizados
TPS util
bull tps file utility program Windows At present it can randomly scramble the order of specimens in a tps file to minimize bias in digitizing landmark locations restore the original order (eg before statistical analyses are performed) create an empty TPS file from a directory with image files add keywords and values to the variables field of a TPS file combine TPS files into a single TPS file deletereorder landmarks remove outlines from a TPS file and convert TPS and NTS files to NTS M or CSV files It can also split an NTS file into several matrices Graphic editors are included for drawing link and sliders files Unbending a deformed specimen Converting outline and curves points to landmarks
bull Other operations can be added - let me know what you need Execute the TPSUTILW32EXE file to install the program By F James Rohlf Version 138
tpsTree
bull Fit and visualize thin-plate splines on trees Windows Performs a least-squares orthogonal generalized Procrustes analysis to obtain a reference and then estimates the splines for each group (internal node) on a tree Both ultrametric (eg WPGMA and UPGMA trees) and additive trees (using squared change parsimony to estimate the shapes of the HTUs) are supported The estimated shapes can be visualized with estimated images in the background (see the tpsSuper program) The file expands into a Windows setup program and associated files By F James Rohlf Version 118 File containing HTU coordinates and HTU images to demo that feature The older and more limited 16 bit Windows version is still available
tpsRegr
bull Multivariate multiple regression of shape onto independent variables Windows performs a multivariate multiple regression of shape (as captured by partial warp scores and the uniform shape component) onto one or more independent variables By appropriate setting up of independent variables this program can perform various types of MANOVA and MANCOVA Can be used to study allometry By F James Rohlf Version 131
tpsSplin
bull Thin-plate spline Windows Program to
compare pairs of specimens by displaying
a Darcy Thompson style transformation
grid based on a thin-plate spline Several
options are given for sliding
semilandmarks The tpssplnwexe file
expands into a Windows setup program
that will be run automatically By F James
Rohlf Version 120
tpsRelw el anaacutelisis de la
deformacioacuten relativa bull Relative warps analysis Windows Performs a
relative warp (deformacioacuten) analysis This corresponds to a principal components analysis of variation in a sample (relative to bending energy if the alpha parameter is not equal to zero) Displays a plot of relative warp scores and a visualization window that displays the estimated shape for arbitrary points in the ordination Also displays partial warp scores and their visualizations Allows fitting of semilandmark points along curves Version 144 By F James Rohlf
tpsPLS
bull Partial least-squares analysis for shapes Windows Used to explore the covariance between a set of variables and variation in shape or between two shapes It performs a two-block partial least-squares analysis It differs from regression in that both variables and shape are considered equally (one is not considered to be a set of independent variables measured without error) Its use is described in Rohlf and Corti (2000 Systematic Biology 49740-753) By F James Rohlf Version 118
tpsSmall
bull Test for small variation in shape Windows Use to test whether the variation in shape among a set of specimens is too large and thus statistical methods based on the tangent space approximation (eg thin-plate spline methods) cannot be used The program can process both 2D and 3D data files Output files include consensus and aligned specimens By F James Rohlf Version 120
tpsPower
bull Estimate statistical power for comparing shapes Windows Program for estimating statistical power for comparing the mean shapes of two populations Provides methods based on several different approaches Can be used for planning morphometric studies as well as to compare power using different approaches Version 104 By F James Rohlf
Morpheus et al bull Morpheus et al is a software package that will provide a
comprehensive cross-platform environment for morphometric data analysis It is available in graphical and command-line versions for a number of operating systems (see below) More information about new features and previous changes can be found in the release notes
httplifebiosunysbedumorphmorpheus
Multivariate analysis
bull PAST is a free easy-to-use data analysis package aimed at paleontology Windows 95+ Multivariate statistical methods include Principal Components (with Minimal Spanning Tree) Principal Coordinates (ten distance measures) Non-metric Multidimensional Scaling (ten distance measures) Detrended Correspondence Analysis Cluster analysis (three algorithms 11 distance measures) k-means clustering seriation discriminant analysis one-way MANOVA Hotellings t-squared Boxs M Canonical Variates Analysis Also includes Fourier shape analysis thin-plate splines parsimony and time series analysis among others Oslashyvind Hammer University of Oslo
Analysis of outlines
bull Shape Elliptic Fourier WINDOWS Extracts the contour shape from a full color bitmap image delineates the contour shape with the elliptic Fourier descriptors and performs a principal component analysis for summarizing the shape information By Hiroyoshi Iwata For more information see Shape home page tutorial or manual
bull Iwata H and Y Ukai (2002) SHAPE A computer program package for quantitative evaluation of biological shapes based on elliptic Fourier descriptors Journal of Heredity 93 384-385
Eigenshape analysis
bull httpwwwnhmacukhosted_sitespaleonetftpftphtml
bull This archive contains a series of programs designed to perform an eigenshape analysis on xy coordinate data from object outlines Routines include xy -gt phi() transformation phi() -gt xy transformation eigenshape analysis and projection of objects into the eigenshape space Two completely worked example analyses and a users guide are also provided El autor es Norman McLeod del BMNH de Londres
Graphical representation of the four-step morphometric protocol A Quantify raw data
(landmarks recorded on body of cichlid fish) B Remove non-shape variation (landmarks of 412
specimens before and after GPA) C statistical analysis (CVA) and graphical presentation of
results Deformation grids for mean specimen for (right) Eretmodus cyanostictus and (left)
Spathodus erythrodon (magnified by 3X to emphasize shape differences) Data from Ruumlber and
Adams 2001 En Adams Rolhf Slice 2002
Resultados
APS Fecha Thu 21 Sep 2006 213918
+0200 [210906 213918 CEST]
De Info Procuste
ltinfoprocustecomgt
Para cuencagunizares
Asunto Re analyse de forme chez
les arvicolides
Cabeceras Mostrar todas las
cabeceras
Chegravere collegravegue
Voici le lien pour teacuteleacutecharger le le
setup dinstallation des 3
logiciels APS ApsDigit et ApsUtil
httpwwwprocustecomprogramsset
up_aps_allexe
Noubliez pas de citer APS dans vos
publications
Bien cordialement
Xavier Penin
Paacuteginas web recomendadas
bull httplifebiosunysbedumorph la mejor paacutegina de
morfometriacutea geomeacutetrica Contiene un listado con todos los
programas de morfometriacutea Universidad de Stony Brook NY
bull httpwwwmorphometricsorgindexhtml es la paacutegina en la
que se mantiene la lista de email morphmet Es la base de la
organizacioacuten de la morfometriacutea en Suny
bull httpwwwflywingsorgukindexhtm iquestporqueacute hay variacioacuten
morfoloacutegica Universidad de Manchester UK
bull httpwwwprocustecomindexhtml anaacutelisis de la forma con
Procruste Aps Xavier Penin Universidad de Paris V
bull Shapehellipy otros ver la paacutegina de Suny
Las ldquoseries TPSrdquo Thin-plate spline
(laacuteminas finas de grosor uniforme)
tpsDIG2
Data acquisition
bull Digitize landmarks amp outlines from image files scanner or video Windows TpsDig is a Windows (95 through XP) program for digitizing landmarks and outlines for geometric morphometric analyses Includes simple image enhancement operations scale factors image brightness profile and support for AVI and MOV files Output is in the TPS file format used by the tps series of programs The TPS file includes the name of the image file for each specimen so that landmarks can always be visualized on the image Since output files are ASCII they can be converted to formats for other software Users should note that the tpsUtil program is useful for both the preparation of the input files to tpsDig as well as for some useful conversions afterwards The program also computes areas of enclosed regions perimeters and linear distances The tpsDig2 link at the left is for the new 205 version
bull Execute the downloaded file to install the program By F James Rohlf
Las ldquoseries TPSrdquo
ordenar los archivos digitalizados
TPS util
bull tps file utility program Windows At present it can randomly scramble the order of specimens in a tps file to minimize bias in digitizing landmark locations restore the original order (eg before statistical analyses are performed) create an empty TPS file from a directory with image files add keywords and values to the variables field of a TPS file combine TPS files into a single TPS file deletereorder landmarks remove outlines from a TPS file and convert TPS and NTS files to NTS M or CSV files It can also split an NTS file into several matrices Graphic editors are included for drawing link and sliders files Unbending a deformed specimen Converting outline and curves points to landmarks
bull Other operations can be added - let me know what you need Execute the TPSUTILW32EXE file to install the program By F James Rohlf Version 138
tpsTree
bull Fit and visualize thin-plate splines on trees Windows Performs a least-squares orthogonal generalized Procrustes analysis to obtain a reference and then estimates the splines for each group (internal node) on a tree Both ultrametric (eg WPGMA and UPGMA trees) and additive trees (using squared change parsimony to estimate the shapes of the HTUs) are supported The estimated shapes can be visualized with estimated images in the background (see the tpsSuper program) The file expands into a Windows setup program and associated files By F James Rohlf Version 118 File containing HTU coordinates and HTU images to demo that feature The older and more limited 16 bit Windows version is still available
tpsRegr
bull Multivariate multiple regression of shape onto independent variables Windows performs a multivariate multiple regression of shape (as captured by partial warp scores and the uniform shape component) onto one or more independent variables By appropriate setting up of independent variables this program can perform various types of MANOVA and MANCOVA Can be used to study allometry By F James Rohlf Version 131
tpsSplin
bull Thin-plate spline Windows Program to
compare pairs of specimens by displaying
a Darcy Thompson style transformation
grid based on a thin-plate spline Several
options are given for sliding
semilandmarks The tpssplnwexe file
expands into a Windows setup program
that will be run automatically By F James
Rohlf Version 120
tpsRelw el anaacutelisis de la
deformacioacuten relativa bull Relative warps analysis Windows Performs a
relative warp (deformacioacuten) analysis This corresponds to a principal components analysis of variation in a sample (relative to bending energy if the alpha parameter is not equal to zero) Displays a plot of relative warp scores and a visualization window that displays the estimated shape for arbitrary points in the ordination Also displays partial warp scores and their visualizations Allows fitting of semilandmark points along curves Version 144 By F James Rohlf
tpsPLS
bull Partial least-squares analysis for shapes Windows Used to explore the covariance between a set of variables and variation in shape or between two shapes It performs a two-block partial least-squares analysis It differs from regression in that both variables and shape are considered equally (one is not considered to be a set of independent variables measured without error) Its use is described in Rohlf and Corti (2000 Systematic Biology 49740-753) By F James Rohlf Version 118
tpsSmall
bull Test for small variation in shape Windows Use to test whether the variation in shape among a set of specimens is too large and thus statistical methods based on the tangent space approximation (eg thin-plate spline methods) cannot be used The program can process both 2D and 3D data files Output files include consensus and aligned specimens By F James Rohlf Version 120
tpsPower
bull Estimate statistical power for comparing shapes Windows Program for estimating statistical power for comparing the mean shapes of two populations Provides methods based on several different approaches Can be used for planning morphometric studies as well as to compare power using different approaches Version 104 By F James Rohlf
Morpheus et al bull Morpheus et al is a software package that will provide a
comprehensive cross-platform environment for morphometric data analysis It is available in graphical and command-line versions for a number of operating systems (see below) More information about new features and previous changes can be found in the release notes
httplifebiosunysbedumorphmorpheus
Multivariate analysis
bull PAST is a free easy-to-use data analysis package aimed at paleontology Windows 95+ Multivariate statistical methods include Principal Components (with Minimal Spanning Tree) Principal Coordinates (ten distance measures) Non-metric Multidimensional Scaling (ten distance measures) Detrended Correspondence Analysis Cluster analysis (three algorithms 11 distance measures) k-means clustering seriation discriminant analysis one-way MANOVA Hotellings t-squared Boxs M Canonical Variates Analysis Also includes Fourier shape analysis thin-plate splines parsimony and time series analysis among others Oslashyvind Hammer University of Oslo
Analysis of outlines
bull Shape Elliptic Fourier WINDOWS Extracts the contour shape from a full color bitmap image delineates the contour shape with the elliptic Fourier descriptors and performs a principal component analysis for summarizing the shape information By Hiroyoshi Iwata For more information see Shape home page tutorial or manual
bull Iwata H and Y Ukai (2002) SHAPE A computer program package for quantitative evaluation of biological shapes based on elliptic Fourier descriptors Journal of Heredity 93 384-385
Eigenshape analysis
bull httpwwwnhmacukhosted_sitespaleonetftpftphtml
bull This archive contains a series of programs designed to perform an eigenshape analysis on xy coordinate data from object outlines Routines include xy -gt phi() transformation phi() -gt xy transformation eigenshape analysis and projection of objects into the eigenshape space Two completely worked example analyses and a users guide are also provided El autor es Norman McLeod del BMNH de Londres
Graphical representation of the four-step morphometric protocol A Quantify raw data
(landmarks recorded on body of cichlid fish) B Remove non-shape variation (landmarks of 412
specimens before and after GPA) C statistical analysis (CVA) and graphical presentation of
results Deformation grids for mean specimen for (right) Eretmodus cyanostictus and (left)
Spathodus erythrodon (magnified by 3X to emphasize shape differences) Data from Ruumlber and
Adams 2001 En Adams Rolhf Slice 2002
APS Fecha Thu 21 Sep 2006 213918
+0200 [210906 213918 CEST]
De Info Procuste
ltinfoprocustecomgt
Para cuencagunizares
Asunto Re analyse de forme chez
les arvicolides
Cabeceras Mostrar todas las
cabeceras
Chegravere collegravegue
Voici le lien pour teacuteleacutecharger le le
setup dinstallation des 3
logiciels APS ApsDigit et ApsUtil
httpwwwprocustecomprogramsset
up_aps_allexe
Noubliez pas de citer APS dans vos
publications
Bien cordialement
Xavier Penin
Paacuteginas web recomendadas
bull httplifebiosunysbedumorph la mejor paacutegina de
morfometriacutea geomeacutetrica Contiene un listado con todos los
programas de morfometriacutea Universidad de Stony Brook NY
bull httpwwwmorphometricsorgindexhtml es la paacutegina en la
que se mantiene la lista de email morphmet Es la base de la
organizacioacuten de la morfometriacutea en Suny
bull httpwwwflywingsorgukindexhtm iquestporqueacute hay variacioacuten
morfoloacutegica Universidad de Manchester UK
bull httpwwwprocustecomindexhtml anaacutelisis de la forma con
Procruste Aps Xavier Penin Universidad de Paris V
bull Shapehellipy otros ver la paacutegina de Suny
Las ldquoseries TPSrdquo Thin-plate spline
(laacuteminas finas de grosor uniforme)
tpsDIG2
Data acquisition
bull Digitize landmarks amp outlines from image files scanner or video Windows TpsDig is a Windows (95 through XP) program for digitizing landmarks and outlines for geometric morphometric analyses Includes simple image enhancement operations scale factors image brightness profile and support for AVI and MOV files Output is in the TPS file format used by the tps series of programs The TPS file includes the name of the image file for each specimen so that landmarks can always be visualized on the image Since output files are ASCII they can be converted to formats for other software Users should note that the tpsUtil program is useful for both the preparation of the input files to tpsDig as well as for some useful conversions afterwards The program also computes areas of enclosed regions perimeters and linear distances The tpsDig2 link at the left is for the new 205 version
bull Execute the downloaded file to install the program By F James Rohlf
Las ldquoseries TPSrdquo
ordenar los archivos digitalizados
TPS util
bull tps file utility program Windows At present it can randomly scramble the order of specimens in a tps file to minimize bias in digitizing landmark locations restore the original order (eg before statistical analyses are performed) create an empty TPS file from a directory with image files add keywords and values to the variables field of a TPS file combine TPS files into a single TPS file deletereorder landmarks remove outlines from a TPS file and convert TPS and NTS files to NTS M or CSV files It can also split an NTS file into several matrices Graphic editors are included for drawing link and sliders files Unbending a deformed specimen Converting outline and curves points to landmarks
bull Other operations can be added - let me know what you need Execute the TPSUTILW32EXE file to install the program By F James Rohlf Version 138
tpsTree
bull Fit and visualize thin-plate splines on trees Windows Performs a least-squares orthogonal generalized Procrustes analysis to obtain a reference and then estimates the splines for each group (internal node) on a tree Both ultrametric (eg WPGMA and UPGMA trees) and additive trees (using squared change parsimony to estimate the shapes of the HTUs) are supported The estimated shapes can be visualized with estimated images in the background (see the tpsSuper program) The file expands into a Windows setup program and associated files By F James Rohlf Version 118 File containing HTU coordinates and HTU images to demo that feature The older and more limited 16 bit Windows version is still available
tpsRegr
bull Multivariate multiple regression of shape onto independent variables Windows performs a multivariate multiple regression of shape (as captured by partial warp scores and the uniform shape component) onto one or more independent variables By appropriate setting up of independent variables this program can perform various types of MANOVA and MANCOVA Can be used to study allometry By F James Rohlf Version 131
tpsSplin
bull Thin-plate spline Windows Program to
compare pairs of specimens by displaying
a Darcy Thompson style transformation
grid based on a thin-plate spline Several
options are given for sliding
semilandmarks The tpssplnwexe file
expands into a Windows setup program
that will be run automatically By F James
Rohlf Version 120
tpsRelw el anaacutelisis de la
deformacioacuten relativa bull Relative warps analysis Windows Performs a
relative warp (deformacioacuten) analysis This corresponds to a principal components analysis of variation in a sample (relative to bending energy if the alpha parameter is not equal to zero) Displays a plot of relative warp scores and a visualization window that displays the estimated shape for arbitrary points in the ordination Also displays partial warp scores and their visualizations Allows fitting of semilandmark points along curves Version 144 By F James Rohlf
tpsPLS
bull Partial least-squares analysis for shapes Windows Used to explore the covariance between a set of variables and variation in shape or between two shapes It performs a two-block partial least-squares analysis It differs from regression in that both variables and shape are considered equally (one is not considered to be a set of independent variables measured without error) Its use is described in Rohlf and Corti (2000 Systematic Biology 49740-753) By F James Rohlf Version 118
tpsSmall
bull Test for small variation in shape Windows Use to test whether the variation in shape among a set of specimens is too large and thus statistical methods based on the tangent space approximation (eg thin-plate spline methods) cannot be used The program can process both 2D and 3D data files Output files include consensus and aligned specimens By F James Rohlf Version 120
tpsPower
bull Estimate statistical power for comparing shapes Windows Program for estimating statistical power for comparing the mean shapes of two populations Provides methods based on several different approaches Can be used for planning morphometric studies as well as to compare power using different approaches Version 104 By F James Rohlf
Morpheus et al bull Morpheus et al is a software package that will provide a
comprehensive cross-platform environment for morphometric data analysis It is available in graphical and command-line versions for a number of operating systems (see below) More information about new features and previous changes can be found in the release notes
httplifebiosunysbedumorphmorpheus
Multivariate analysis
bull PAST is a free easy-to-use data analysis package aimed at paleontology Windows 95+ Multivariate statistical methods include Principal Components (with Minimal Spanning Tree) Principal Coordinates (ten distance measures) Non-metric Multidimensional Scaling (ten distance measures) Detrended Correspondence Analysis Cluster analysis (three algorithms 11 distance measures) k-means clustering seriation discriminant analysis one-way MANOVA Hotellings t-squared Boxs M Canonical Variates Analysis Also includes Fourier shape analysis thin-plate splines parsimony and time series analysis among others Oslashyvind Hammer University of Oslo
Analysis of outlines
bull Shape Elliptic Fourier WINDOWS Extracts the contour shape from a full color bitmap image delineates the contour shape with the elliptic Fourier descriptors and performs a principal component analysis for summarizing the shape information By Hiroyoshi Iwata For more information see Shape home page tutorial or manual
bull Iwata H and Y Ukai (2002) SHAPE A computer program package for quantitative evaluation of biological shapes based on elliptic Fourier descriptors Journal of Heredity 93 384-385
Eigenshape analysis
bull httpwwwnhmacukhosted_sitespaleonetftpftphtml
bull This archive contains a series of programs designed to perform an eigenshape analysis on xy coordinate data from object outlines Routines include xy -gt phi() transformation phi() -gt xy transformation eigenshape analysis and projection of objects into the eigenshape space Two completely worked example analyses and a users guide are also provided El autor es Norman McLeod del BMNH de Londres
Graphical representation of the four-step morphometric protocol A Quantify raw data
(landmarks recorded on body of cichlid fish) B Remove non-shape variation (landmarks of 412
specimens before and after GPA) C statistical analysis (CVA) and graphical presentation of
results Deformation grids for mean specimen for (right) Eretmodus cyanostictus and (left)
Spathodus erythrodon (magnified by 3X to emphasize shape differences) Data from Ruumlber and
Adams 2001 En Adams Rolhf Slice 2002
Paacuteginas web recomendadas
bull httplifebiosunysbedumorph la mejor paacutegina de
morfometriacutea geomeacutetrica Contiene un listado con todos los
programas de morfometriacutea Universidad de Stony Brook NY
bull httpwwwmorphometricsorgindexhtml es la paacutegina en la
que se mantiene la lista de email morphmet Es la base de la
organizacioacuten de la morfometriacutea en Suny
bull httpwwwflywingsorgukindexhtm iquestporqueacute hay variacioacuten
morfoloacutegica Universidad de Manchester UK
bull httpwwwprocustecomindexhtml anaacutelisis de la forma con
Procruste Aps Xavier Penin Universidad de Paris V
bull Shapehellipy otros ver la paacutegina de Suny
Las ldquoseries TPSrdquo Thin-plate spline
(laacuteminas finas de grosor uniforme)
tpsDIG2
Data acquisition
bull Digitize landmarks amp outlines from image files scanner or video Windows TpsDig is a Windows (95 through XP) program for digitizing landmarks and outlines for geometric morphometric analyses Includes simple image enhancement operations scale factors image brightness profile and support for AVI and MOV files Output is in the TPS file format used by the tps series of programs The TPS file includes the name of the image file for each specimen so that landmarks can always be visualized on the image Since output files are ASCII they can be converted to formats for other software Users should note that the tpsUtil program is useful for both the preparation of the input files to tpsDig as well as for some useful conversions afterwards The program also computes areas of enclosed regions perimeters and linear distances The tpsDig2 link at the left is for the new 205 version
bull Execute the downloaded file to install the program By F James Rohlf
Las ldquoseries TPSrdquo
ordenar los archivos digitalizados
TPS util
bull tps file utility program Windows At present it can randomly scramble the order of specimens in a tps file to minimize bias in digitizing landmark locations restore the original order (eg before statistical analyses are performed) create an empty TPS file from a directory with image files add keywords and values to the variables field of a TPS file combine TPS files into a single TPS file deletereorder landmarks remove outlines from a TPS file and convert TPS and NTS files to NTS M or CSV files It can also split an NTS file into several matrices Graphic editors are included for drawing link and sliders files Unbending a deformed specimen Converting outline and curves points to landmarks
bull Other operations can be added - let me know what you need Execute the TPSUTILW32EXE file to install the program By F James Rohlf Version 138
tpsTree
bull Fit and visualize thin-plate splines on trees Windows Performs a least-squares orthogonal generalized Procrustes analysis to obtain a reference and then estimates the splines for each group (internal node) on a tree Both ultrametric (eg WPGMA and UPGMA trees) and additive trees (using squared change parsimony to estimate the shapes of the HTUs) are supported The estimated shapes can be visualized with estimated images in the background (see the tpsSuper program) The file expands into a Windows setup program and associated files By F James Rohlf Version 118 File containing HTU coordinates and HTU images to demo that feature The older and more limited 16 bit Windows version is still available
tpsRegr
bull Multivariate multiple regression of shape onto independent variables Windows performs a multivariate multiple regression of shape (as captured by partial warp scores and the uniform shape component) onto one or more independent variables By appropriate setting up of independent variables this program can perform various types of MANOVA and MANCOVA Can be used to study allometry By F James Rohlf Version 131
tpsSplin
bull Thin-plate spline Windows Program to
compare pairs of specimens by displaying
a Darcy Thompson style transformation
grid based on a thin-plate spline Several
options are given for sliding
semilandmarks The tpssplnwexe file
expands into a Windows setup program
that will be run automatically By F James
Rohlf Version 120
tpsRelw el anaacutelisis de la
deformacioacuten relativa bull Relative warps analysis Windows Performs a
relative warp (deformacioacuten) analysis This corresponds to a principal components analysis of variation in a sample (relative to bending energy if the alpha parameter is not equal to zero) Displays a plot of relative warp scores and a visualization window that displays the estimated shape for arbitrary points in the ordination Also displays partial warp scores and their visualizations Allows fitting of semilandmark points along curves Version 144 By F James Rohlf
tpsPLS
bull Partial least-squares analysis for shapes Windows Used to explore the covariance between a set of variables and variation in shape or between two shapes It performs a two-block partial least-squares analysis It differs from regression in that both variables and shape are considered equally (one is not considered to be a set of independent variables measured without error) Its use is described in Rohlf and Corti (2000 Systematic Biology 49740-753) By F James Rohlf Version 118
tpsSmall
bull Test for small variation in shape Windows Use to test whether the variation in shape among a set of specimens is too large and thus statistical methods based on the tangent space approximation (eg thin-plate spline methods) cannot be used The program can process both 2D and 3D data files Output files include consensus and aligned specimens By F James Rohlf Version 120
tpsPower
bull Estimate statistical power for comparing shapes Windows Program for estimating statistical power for comparing the mean shapes of two populations Provides methods based on several different approaches Can be used for planning morphometric studies as well as to compare power using different approaches Version 104 By F James Rohlf
Morpheus et al bull Morpheus et al is a software package that will provide a
comprehensive cross-platform environment for morphometric data analysis It is available in graphical and command-line versions for a number of operating systems (see below) More information about new features and previous changes can be found in the release notes
httplifebiosunysbedumorphmorpheus
Multivariate analysis
bull PAST is a free easy-to-use data analysis package aimed at paleontology Windows 95+ Multivariate statistical methods include Principal Components (with Minimal Spanning Tree) Principal Coordinates (ten distance measures) Non-metric Multidimensional Scaling (ten distance measures) Detrended Correspondence Analysis Cluster analysis (three algorithms 11 distance measures) k-means clustering seriation discriminant analysis one-way MANOVA Hotellings t-squared Boxs M Canonical Variates Analysis Also includes Fourier shape analysis thin-plate splines parsimony and time series analysis among others Oslashyvind Hammer University of Oslo
Analysis of outlines
bull Shape Elliptic Fourier WINDOWS Extracts the contour shape from a full color bitmap image delineates the contour shape with the elliptic Fourier descriptors and performs a principal component analysis for summarizing the shape information By Hiroyoshi Iwata For more information see Shape home page tutorial or manual
bull Iwata H and Y Ukai (2002) SHAPE A computer program package for quantitative evaluation of biological shapes based on elliptic Fourier descriptors Journal of Heredity 93 384-385
Eigenshape analysis
bull httpwwwnhmacukhosted_sitespaleonetftpftphtml
bull This archive contains a series of programs designed to perform an eigenshape analysis on xy coordinate data from object outlines Routines include xy -gt phi() transformation phi() -gt xy transformation eigenshape analysis and projection of objects into the eigenshape space Two completely worked example analyses and a users guide are also provided El autor es Norman McLeod del BMNH de Londres
Graphical representation of the four-step morphometric protocol A Quantify raw data
(landmarks recorded on body of cichlid fish) B Remove non-shape variation (landmarks of 412
specimens before and after GPA) C statistical analysis (CVA) and graphical presentation of
results Deformation grids for mean specimen for (right) Eretmodus cyanostictus and (left)
Spathodus erythrodon (magnified by 3X to emphasize shape differences) Data from Ruumlber and
Adams 2001 En Adams Rolhf Slice 2002
Las ldquoseries TPSrdquo Thin-plate spline
(laacuteminas finas de grosor uniforme)
tpsDIG2
Data acquisition
bull Digitize landmarks amp outlines from image files scanner or video Windows TpsDig is a Windows (95 through XP) program for digitizing landmarks and outlines for geometric morphometric analyses Includes simple image enhancement operations scale factors image brightness profile and support for AVI and MOV files Output is in the TPS file format used by the tps series of programs The TPS file includes the name of the image file for each specimen so that landmarks can always be visualized on the image Since output files are ASCII they can be converted to formats for other software Users should note that the tpsUtil program is useful for both the preparation of the input files to tpsDig as well as for some useful conversions afterwards The program also computes areas of enclosed regions perimeters and linear distances The tpsDig2 link at the left is for the new 205 version
bull Execute the downloaded file to install the program By F James Rohlf
Las ldquoseries TPSrdquo
ordenar los archivos digitalizados
TPS util
bull tps file utility program Windows At present it can randomly scramble the order of specimens in a tps file to minimize bias in digitizing landmark locations restore the original order (eg before statistical analyses are performed) create an empty TPS file from a directory with image files add keywords and values to the variables field of a TPS file combine TPS files into a single TPS file deletereorder landmarks remove outlines from a TPS file and convert TPS and NTS files to NTS M or CSV files It can also split an NTS file into several matrices Graphic editors are included for drawing link and sliders files Unbending a deformed specimen Converting outline and curves points to landmarks
bull Other operations can be added - let me know what you need Execute the TPSUTILW32EXE file to install the program By F James Rohlf Version 138
tpsTree
bull Fit and visualize thin-plate splines on trees Windows Performs a least-squares orthogonal generalized Procrustes analysis to obtain a reference and then estimates the splines for each group (internal node) on a tree Both ultrametric (eg WPGMA and UPGMA trees) and additive trees (using squared change parsimony to estimate the shapes of the HTUs) are supported The estimated shapes can be visualized with estimated images in the background (see the tpsSuper program) The file expands into a Windows setup program and associated files By F James Rohlf Version 118 File containing HTU coordinates and HTU images to demo that feature The older and more limited 16 bit Windows version is still available
tpsRegr
bull Multivariate multiple regression of shape onto independent variables Windows performs a multivariate multiple regression of shape (as captured by partial warp scores and the uniform shape component) onto one or more independent variables By appropriate setting up of independent variables this program can perform various types of MANOVA and MANCOVA Can be used to study allometry By F James Rohlf Version 131
tpsSplin
bull Thin-plate spline Windows Program to
compare pairs of specimens by displaying
a Darcy Thompson style transformation
grid based on a thin-plate spline Several
options are given for sliding
semilandmarks The tpssplnwexe file
expands into a Windows setup program
that will be run automatically By F James
Rohlf Version 120
tpsRelw el anaacutelisis de la
deformacioacuten relativa bull Relative warps analysis Windows Performs a
relative warp (deformacioacuten) analysis This corresponds to a principal components analysis of variation in a sample (relative to bending energy if the alpha parameter is not equal to zero) Displays a plot of relative warp scores and a visualization window that displays the estimated shape for arbitrary points in the ordination Also displays partial warp scores and their visualizations Allows fitting of semilandmark points along curves Version 144 By F James Rohlf
tpsPLS
bull Partial least-squares analysis for shapes Windows Used to explore the covariance between a set of variables and variation in shape or between two shapes It performs a two-block partial least-squares analysis It differs from regression in that both variables and shape are considered equally (one is not considered to be a set of independent variables measured without error) Its use is described in Rohlf and Corti (2000 Systematic Biology 49740-753) By F James Rohlf Version 118
tpsSmall
bull Test for small variation in shape Windows Use to test whether the variation in shape among a set of specimens is too large and thus statistical methods based on the tangent space approximation (eg thin-plate spline methods) cannot be used The program can process both 2D and 3D data files Output files include consensus and aligned specimens By F James Rohlf Version 120
tpsPower
bull Estimate statistical power for comparing shapes Windows Program for estimating statistical power for comparing the mean shapes of two populations Provides methods based on several different approaches Can be used for planning morphometric studies as well as to compare power using different approaches Version 104 By F James Rohlf
Morpheus et al bull Morpheus et al is a software package that will provide a
comprehensive cross-platform environment for morphometric data analysis It is available in graphical and command-line versions for a number of operating systems (see below) More information about new features and previous changes can be found in the release notes
httplifebiosunysbedumorphmorpheus
Multivariate analysis
bull PAST is a free easy-to-use data analysis package aimed at paleontology Windows 95+ Multivariate statistical methods include Principal Components (with Minimal Spanning Tree) Principal Coordinates (ten distance measures) Non-metric Multidimensional Scaling (ten distance measures) Detrended Correspondence Analysis Cluster analysis (three algorithms 11 distance measures) k-means clustering seriation discriminant analysis one-way MANOVA Hotellings t-squared Boxs M Canonical Variates Analysis Also includes Fourier shape analysis thin-plate splines parsimony and time series analysis among others Oslashyvind Hammer University of Oslo
Analysis of outlines
bull Shape Elliptic Fourier WINDOWS Extracts the contour shape from a full color bitmap image delineates the contour shape with the elliptic Fourier descriptors and performs a principal component analysis for summarizing the shape information By Hiroyoshi Iwata For more information see Shape home page tutorial or manual
bull Iwata H and Y Ukai (2002) SHAPE A computer program package for quantitative evaluation of biological shapes based on elliptic Fourier descriptors Journal of Heredity 93 384-385
Eigenshape analysis
bull httpwwwnhmacukhosted_sitespaleonetftpftphtml
bull This archive contains a series of programs designed to perform an eigenshape analysis on xy coordinate data from object outlines Routines include xy -gt phi() transformation phi() -gt xy transformation eigenshape analysis and projection of objects into the eigenshape space Two completely worked example analyses and a users guide are also provided El autor es Norman McLeod del BMNH de Londres
Graphical representation of the four-step morphometric protocol A Quantify raw data
(landmarks recorded on body of cichlid fish) B Remove non-shape variation (landmarks of 412
specimens before and after GPA) C statistical analysis (CVA) and graphical presentation of
results Deformation grids for mean specimen for (right) Eretmodus cyanostictus and (left)
Spathodus erythrodon (magnified by 3X to emphasize shape differences) Data from Ruumlber and
Adams 2001 En Adams Rolhf Slice 2002
Las ldquoseries TPSrdquo
ordenar los archivos digitalizados
TPS util
bull tps file utility program Windows At present it can randomly scramble the order of specimens in a tps file to minimize bias in digitizing landmark locations restore the original order (eg before statistical analyses are performed) create an empty TPS file from a directory with image files add keywords and values to the variables field of a TPS file combine TPS files into a single TPS file deletereorder landmarks remove outlines from a TPS file and convert TPS and NTS files to NTS M or CSV files It can also split an NTS file into several matrices Graphic editors are included for drawing link and sliders files Unbending a deformed specimen Converting outline and curves points to landmarks
bull Other operations can be added - let me know what you need Execute the TPSUTILW32EXE file to install the program By F James Rohlf Version 138
tpsTree
bull Fit and visualize thin-plate splines on trees Windows Performs a least-squares orthogonal generalized Procrustes analysis to obtain a reference and then estimates the splines for each group (internal node) on a tree Both ultrametric (eg WPGMA and UPGMA trees) and additive trees (using squared change parsimony to estimate the shapes of the HTUs) are supported The estimated shapes can be visualized with estimated images in the background (see the tpsSuper program) The file expands into a Windows setup program and associated files By F James Rohlf Version 118 File containing HTU coordinates and HTU images to demo that feature The older and more limited 16 bit Windows version is still available
tpsRegr
bull Multivariate multiple regression of shape onto independent variables Windows performs a multivariate multiple regression of shape (as captured by partial warp scores and the uniform shape component) onto one or more independent variables By appropriate setting up of independent variables this program can perform various types of MANOVA and MANCOVA Can be used to study allometry By F James Rohlf Version 131
tpsSplin
bull Thin-plate spline Windows Program to
compare pairs of specimens by displaying
a Darcy Thompson style transformation
grid based on a thin-plate spline Several
options are given for sliding
semilandmarks The tpssplnwexe file
expands into a Windows setup program
that will be run automatically By F James
Rohlf Version 120
tpsRelw el anaacutelisis de la
deformacioacuten relativa bull Relative warps analysis Windows Performs a
relative warp (deformacioacuten) analysis This corresponds to a principal components analysis of variation in a sample (relative to bending energy if the alpha parameter is not equal to zero) Displays a plot of relative warp scores and a visualization window that displays the estimated shape for arbitrary points in the ordination Also displays partial warp scores and their visualizations Allows fitting of semilandmark points along curves Version 144 By F James Rohlf
tpsPLS
bull Partial least-squares analysis for shapes Windows Used to explore the covariance between a set of variables and variation in shape or between two shapes It performs a two-block partial least-squares analysis It differs from regression in that both variables and shape are considered equally (one is not considered to be a set of independent variables measured without error) Its use is described in Rohlf and Corti (2000 Systematic Biology 49740-753) By F James Rohlf Version 118
tpsSmall
bull Test for small variation in shape Windows Use to test whether the variation in shape among a set of specimens is too large and thus statistical methods based on the tangent space approximation (eg thin-plate spline methods) cannot be used The program can process both 2D and 3D data files Output files include consensus and aligned specimens By F James Rohlf Version 120
tpsPower
bull Estimate statistical power for comparing shapes Windows Program for estimating statistical power for comparing the mean shapes of two populations Provides methods based on several different approaches Can be used for planning morphometric studies as well as to compare power using different approaches Version 104 By F James Rohlf
Morpheus et al bull Morpheus et al is a software package that will provide a
comprehensive cross-platform environment for morphometric data analysis It is available in graphical and command-line versions for a number of operating systems (see below) More information about new features and previous changes can be found in the release notes
httplifebiosunysbedumorphmorpheus
Multivariate analysis
bull PAST is a free easy-to-use data analysis package aimed at paleontology Windows 95+ Multivariate statistical methods include Principal Components (with Minimal Spanning Tree) Principal Coordinates (ten distance measures) Non-metric Multidimensional Scaling (ten distance measures) Detrended Correspondence Analysis Cluster analysis (three algorithms 11 distance measures) k-means clustering seriation discriminant analysis one-way MANOVA Hotellings t-squared Boxs M Canonical Variates Analysis Also includes Fourier shape analysis thin-plate splines parsimony and time series analysis among others Oslashyvind Hammer University of Oslo
Analysis of outlines
bull Shape Elliptic Fourier WINDOWS Extracts the contour shape from a full color bitmap image delineates the contour shape with the elliptic Fourier descriptors and performs a principal component analysis for summarizing the shape information By Hiroyoshi Iwata For more information see Shape home page tutorial or manual
bull Iwata H and Y Ukai (2002) SHAPE A computer program package for quantitative evaluation of biological shapes based on elliptic Fourier descriptors Journal of Heredity 93 384-385
Eigenshape analysis
bull httpwwwnhmacukhosted_sitespaleonetftpftphtml
bull This archive contains a series of programs designed to perform an eigenshape analysis on xy coordinate data from object outlines Routines include xy -gt phi() transformation phi() -gt xy transformation eigenshape analysis and projection of objects into the eigenshape space Two completely worked example analyses and a users guide are also provided El autor es Norman McLeod del BMNH de Londres
Graphical representation of the four-step morphometric protocol A Quantify raw data
(landmarks recorded on body of cichlid fish) B Remove non-shape variation (landmarks of 412
specimens before and after GPA) C statistical analysis (CVA) and graphical presentation of
results Deformation grids for mean specimen for (right) Eretmodus cyanostictus and (left)
Spathodus erythrodon (magnified by 3X to emphasize shape differences) Data from Ruumlber and
Adams 2001 En Adams Rolhf Slice 2002
tpsTree
bull Fit and visualize thin-plate splines on trees Windows Performs a least-squares orthogonal generalized Procrustes analysis to obtain a reference and then estimates the splines for each group (internal node) on a tree Both ultrametric (eg WPGMA and UPGMA trees) and additive trees (using squared change parsimony to estimate the shapes of the HTUs) are supported The estimated shapes can be visualized with estimated images in the background (see the tpsSuper program) The file expands into a Windows setup program and associated files By F James Rohlf Version 118 File containing HTU coordinates and HTU images to demo that feature The older and more limited 16 bit Windows version is still available
tpsRegr
bull Multivariate multiple regression of shape onto independent variables Windows performs a multivariate multiple regression of shape (as captured by partial warp scores and the uniform shape component) onto one or more independent variables By appropriate setting up of independent variables this program can perform various types of MANOVA and MANCOVA Can be used to study allometry By F James Rohlf Version 131
tpsSplin
bull Thin-plate spline Windows Program to
compare pairs of specimens by displaying
a Darcy Thompson style transformation
grid based on a thin-plate spline Several
options are given for sliding
semilandmarks The tpssplnwexe file
expands into a Windows setup program
that will be run automatically By F James
Rohlf Version 120
tpsRelw el anaacutelisis de la
deformacioacuten relativa bull Relative warps analysis Windows Performs a
relative warp (deformacioacuten) analysis This corresponds to a principal components analysis of variation in a sample (relative to bending energy if the alpha parameter is not equal to zero) Displays a plot of relative warp scores and a visualization window that displays the estimated shape for arbitrary points in the ordination Also displays partial warp scores and their visualizations Allows fitting of semilandmark points along curves Version 144 By F James Rohlf
tpsPLS
bull Partial least-squares analysis for shapes Windows Used to explore the covariance between a set of variables and variation in shape or between two shapes It performs a two-block partial least-squares analysis It differs from regression in that both variables and shape are considered equally (one is not considered to be a set of independent variables measured without error) Its use is described in Rohlf and Corti (2000 Systematic Biology 49740-753) By F James Rohlf Version 118
tpsSmall
bull Test for small variation in shape Windows Use to test whether the variation in shape among a set of specimens is too large and thus statistical methods based on the tangent space approximation (eg thin-plate spline methods) cannot be used The program can process both 2D and 3D data files Output files include consensus and aligned specimens By F James Rohlf Version 120
tpsPower
bull Estimate statistical power for comparing shapes Windows Program for estimating statistical power for comparing the mean shapes of two populations Provides methods based on several different approaches Can be used for planning morphometric studies as well as to compare power using different approaches Version 104 By F James Rohlf
Morpheus et al bull Morpheus et al is a software package that will provide a
comprehensive cross-platform environment for morphometric data analysis It is available in graphical and command-line versions for a number of operating systems (see below) More information about new features and previous changes can be found in the release notes
httplifebiosunysbedumorphmorpheus
Multivariate analysis
bull PAST is a free easy-to-use data analysis package aimed at paleontology Windows 95+ Multivariate statistical methods include Principal Components (with Minimal Spanning Tree) Principal Coordinates (ten distance measures) Non-metric Multidimensional Scaling (ten distance measures) Detrended Correspondence Analysis Cluster analysis (three algorithms 11 distance measures) k-means clustering seriation discriminant analysis one-way MANOVA Hotellings t-squared Boxs M Canonical Variates Analysis Also includes Fourier shape analysis thin-plate splines parsimony and time series analysis among others Oslashyvind Hammer University of Oslo
Analysis of outlines
bull Shape Elliptic Fourier WINDOWS Extracts the contour shape from a full color bitmap image delineates the contour shape with the elliptic Fourier descriptors and performs a principal component analysis for summarizing the shape information By Hiroyoshi Iwata For more information see Shape home page tutorial or manual
bull Iwata H and Y Ukai (2002) SHAPE A computer program package for quantitative evaluation of biological shapes based on elliptic Fourier descriptors Journal of Heredity 93 384-385
Eigenshape analysis
bull httpwwwnhmacukhosted_sitespaleonetftpftphtml
bull This archive contains a series of programs designed to perform an eigenshape analysis on xy coordinate data from object outlines Routines include xy -gt phi() transformation phi() -gt xy transformation eigenshape analysis and projection of objects into the eigenshape space Two completely worked example analyses and a users guide are also provided El autor es Norman McLeod del BMNH de Londres
Graphical representation of the four-step morphometric protocol A Quantify raw data
(landmarks recorded on body of cichlid fish) B Remove non-shape variation (landmarks of 412
specimens before and after GPA) C statistical analysis (CVA) and graphical presentation of
results Deformation grids for mean specimen for (right) Eretmodus cyanostictus and (left)
Spathodus erythrodon (magnified by 3X to emphasize shape differences) Data from Ruumlber and
Adams 2001 En Adams Rolhf Slice 2002
tpsRegr
bull Multivariate multiple regression of shape onto independent variables Windows performs a multivariate multiple regression of shape (as captured by partial warp scores and the uniform shape component) onto one or more independent variables By appropriate setting up of independent variables this program can perform various types of MANOVA and MANCOVA Can be used to study allometry By F James Rohlf Version 131
tpsSplin
bull Thin-plate spline Windows Program to
compare pairs of specimens by displaying
a Darcy Thompson style transformation
grid based on a thin-plate spline Several
options are given for sliding
semilandmarks The tpssplnwexe file
expands into a Windows setup program
that will be run automatically By F James
Rohlf Version 120
tpsRelw el anaacutelisis de la
deformacioacuten relativa bull Relative warps analysis Windows Performs a
relative warp (deformacioacuten) analysis This corresponds to a principal components analysis of variation in a sample (relative to bending energy if the alpha parameter is not equal to zero) Displays a plot of relative warp scores and a visualization window that displays the estimated shape for arbitrary points in the ordination Also displays partial warp scores and their visualizations Allows fitting of semilandmark points along curves Version 144 By F James Rohlf
tpsPLS
bull Partial least-squares analysis for shapes Windows Used to explore the covariance between a set of variables and variation in shape or between two shapes It performs a two-block partial least-squares analysis It differs from regression in that both variables and shape are considered equally (one is not considered to be a set of independent variables measured without error) Its use is described in Rohlf and Corti (2000 Systematic Biology 49740-753) By F James Rohlf Version 118
tpsSmall
bull Test for small variation in shape Windows Use to test whether the variation in shape among a set of specimens is too large and thus statistical methods based on the tangent space approximation (eg thin-plate spline methods) cannot be used The program can process both 2D and 3D data files Output files include consensus and aligned specimens By F James Rohlf Version 120
tpsPower
bull Estimate statistical power for comparing shapes Windows Program for estimating statistical power for comparing the mean shapes of two populations Provides methods based on several different approaches Can be used for planning morphometric studies as well as to compare power using different approaches Version 104 By F James Rohlf
Morpheus et al bull Morpheus et al is a software package that will provide a
comprehensive cross-platform environment for morphometric data analysis It is available in graphical and command-line versions for a number of operating systems (see below) More information about new features and previous changes can be found in the release notes
httplifebiosunysbedumorphmorpheus
Multivariate analysis
bull PAST is a free easy-to-use data analysis package aimed at paleontology Windows 95+ Multivariate statistical methods include Principal Components (with Minimal Spanning Tree) Principal Coordinates (ten distance measures) Non-metric Multidimensional Scaling (ten distance measures) Detrended Correspondence Analysis Cluster analysis (three algorithms 11 distance measures) k-means clustering seriation discriminant analysis one-way MANOVA Hotellings t-squared Boxs M Canonical Variates Analysis Also includes Fourier shape analysis thin-plate splines parsimony and time series analysis among others Oslashyvind Hammer University of Oslo
Analysis of outlines
bull Shape Elliptic Fourier WINDOWS Extracts the contour shape from a full color bitmap image delineates the contour shape with the elliptic Fourier descriptors and performs a principal component analysis for summarizing the shape information By Hiroyoshi Iwata For more information see Shape home page tutorial or manual
bull Iwata H and Y Ukai (2002) SHAPE A computer program package for quantitative evaluation of biological shapes based on elliptic Fourier descriptors Journal of Heredity 93 384-385
Eigenshape analysis
bull httpwwwnhmacukhosted_sitespaleonetftpftphtml
bull This archive contains a series of programs designed to perform an eigenshape analysis on xy coordinate data from object outlines Routines include xy -gt phi() transformation phi() -gt xy transformation eigenshape analysis and projection of objects into the eigenshape space Two completely worked example analyses and a users guide are also provided El autor es Norman McLeod del BMNH de Londres
Graphical representation of the four-step morphometric protocol A Quantify raw data
(landmarks recorded on body of cichlid fish) B Remove non-shape variation (landmarks of 412
specimens before and after GPA) C statistical analysis (CVA) and graphical presentation of
results Deformation grids for mean specimen for (right) Eretmodus cyanostictus and (left)
Spathodus erythrodon (magnified by 3X to emphasize shape differences) Data from Ruumlber and
Adams 2001 En Adams Rolhf Slice 2002
tpsSplin
bull Thin-plate spline Windows Program to
compare pairs of specimens by displaying
a Darcy Thompson style transformation
grid based on a thin-plate spline Several
options are given for sliding
semilandmarks The tpssplnwexe file
expands into a Windows setup program
that will be run automatically By F James
Rohlf Version 120
tpsRelw el anaacutelisis de la
deformacioacuten relativa bull Relative warps analysis Windows Performs a
relative warp (deformacioacuten) analysis This corresponds to a principal components analysis of variation in a sample (relative to bending energy if the alpha parameter is not equal to zero) Displays a plot of relative warp scores and a visualization window that displays the estimated shape for arbitrary points in the ordination Also displays partial warp scores and their visualizations Allows fitting of semilandmark points along curves Version 144 By F James Rohlf
tpsPLS
bull Partial least-squares analysis for shapes Windows Used to explore the covariance between a set of variables and variation in shape or between two shapes It performs a two-block partial least-squares analysis It differs from regression in that both variables and shape are considered equally (one is not considered to be a set of independent variables measured without error) Its use is described in Rohlf and Corti (2000 Systematic Biology 49740-753) By F James Rohlf Version 118
tpsSmall
bull Test for small variation in shape Windows Use to test whether the variation in shape among a set of specimens is too large and thus statistical methods based on the tangent space approximation (eg thin-plate spline methods) cannot be used The program can process both 2D and 3D data files Output files include consensus and aligned specimens By F James Rohlf Version 120
tpsPower
bull Estimate statistical power for comparing shapes Windows Program for estimating statistical power for comparing the mean shapes of two populations Provides methods based on several different approaches Can be used for planning morphometric studies as well as to compare power using different approaches Version 104 By F James Rohlf
Morpheus et al bull Morpheus et al is a software package that will provide a
comprehensive cross-platform environment for morphometric data analysis It is available in graphical and command-line versions for a number of operating systems (see below) More information about new features and previous changes can be found in the release notes
httplifebiosunysbedumorphmorpheus
Multivariate analysis
bull PAST is a free easy-to-use data analysis package aimed at paleontology Windows 95+ Multivariate statistical methods include Principal Components (with Minimal Spanning Tree) Principal Coordinates (ten distance measures) Non-metric Multidimensional Scaling (ten distance measures) Detrended Correspondence Analysis Cluster analysis (three algorithms 11 distance measures) k-means clustering seriation discriminant analysis one-way MANOVA Hotellings t-squared Boxs M Canonical Variates Analysis Also includes Fourier shape analysis thin-plate splines parsimony and time series analysis among others Oslashyvind Hammer University of Oslo
Analysis of outlines
bull Shape Elliptic Fourier WINDOWS Extracts the contour shape from a full color bitmap image delineates the contour shape with the elliptic Fourier descriptors and performs a principal component analysis for summarizing the shape information By Hiroyoshi Iwata For more information see Shape home page tutorial or manual
bull Iwata H and Y Ukai (2002) SHAPE A computer program package for quantitative evaluation of biological shapes based on elliptic Fourier descriptors Journal of Heredity 93 384-385
Eigenshape analysis
bull httpwwwnhmacukhosted_sitespaleonetftpftphtml
bull This archive contains a series of programs designed to perform an eigenshape analysis on xy coordinate data from object outlines Routines include xy -gt phi() transformation phi() -gt xy transformation eigenshape analysis and projection of objects into the eigenshape space Two completely worked example analyses and a users guide are also provided El autor es Norman McLeod del BMNH de Londres
Graphical representation of the four-step morphometric protocol A Quantify raw data
(landmarks recorded on body of cichlid fish) B Remove non-shape variation (landmarks of 412
specimens before and after GPA) C statistical analysis (CVA) and graphical presentation of
results Deformation grids for mean specimen for (right) Eretmodus cyanostictus and (left)
Spathodus erythrodon (magnified by 3X to emphasize shape differences) Data from Ruumlber and
Adams 2001 En Adams Rolhf Slice 2002
tpsRelw el anaacutelisis de la
deformacioacuten relativa bull Relative warps analysis Windows Performs a
relative warp (deformacioacuten) analysis This corresponds to a principal components analysis of variation in a sample (relative to bending energy if the alpha parameter is not equal to zero) Displays a plot of relative warp scores and a visualization window that displays the estimated shape for arbitrary points in the ordination Also displays partial warp scores and their visualizations Allows fitting of semilandmark points along curves Version 144 By F James Rohlf
tpsPLS
bull Partial least-squares analysis for shapes Windows Used to explore the covariance between a set of variables and variation in shape or between two shapes It performs a two-block partial least-squares analysis It differs from regression in that both variables and shape are considered equally (one is not considered to be a set of independent variables measured without error) Its use is described in Rohlf and Corti (2000 Systematic Biology 49740-753) By F James Rohlf Version 118
tpsSmall
bull Test for small variation in shape Windows Use to test whether the variation in shape among a set of specimens is too large and thus statistical methods based on the tangent space approximation (eg thin-plate spline methods) cannot be used The program can process both 2D and 3D data files Output files include consensus and aligned specimens By F James Rohlf Version 120
tpsPower
bull Estimate statistical power for comparing shapes Windows Program for estimating statistical power for comparing the mean shapes of two populations Provides methods based on several different approaches Can be used for planning morphometric studies as well as to compare power using different approaches Version 104 By F James Rohlf
Morpheus et al bull Morpheus et al is a software package that will provide a
comprehensive cross-platform environment for morphometric data analysis It is available in graphical and command-line versions for a number of operating systems (see below) More information about new features and previous changes can be found in the release notes
httplifebiosunysbedumorphmorpheus
Multivariate analysis
bull PAST is a free easy-to-use data analysis package aimed at paleontology Windows 95+ Multivariate statistical methods include Principal Components (with Minimal Spanning Tree) Principal Coordinates (ten distance measures) Non-metric Multidimensional Scaling (ten distance measures) Detrended Correspondence Analysis Cluster analysis (three algorithms 11 distance measures) k-means clustering seriation discriminant analysis one-way MANOVA Hotellings t-squared Boxs M Canonical Variates Analysis Also includes Fourier shape analysis thin-plate splines parsimony and time series analysis among others Oslashyvind Hammer University of Oslo
Analysis of outlines
bull Shape Elliptic Fourier WINDOWS Extracts the contour shape from a full color bitmap image delineates the contour shape with the elliptic Fourier descriptors and performs a principal component analysis for summarizing the shape information By Hiroyoshi Iwata For more information see Shape home page tutorial or manual
bull Iwata H and Y Ukai (2002) SHAPE A computer program package for quantitative evaluation of biological shapes based on elliptic Fourier descriptors Journal of Heredity 93 384-385
Eigenshape analysis
bull httpwwwnhmacukhosted_sitespaleonetftpftphtml
bull This archive contains a series of programs designed to perform an eigenshape analysis on xy coordinate data from object outlines Routines include xy -gt phi() transformation phi() -gt xy transformation eigenshape analysis and projection of objects into the eigenshape space Two completely worked example analyses and a users guide are also provided El autor es Norman McLeod del BMNH de Londres
Graphical representation of the four-step morphometric protocol A Quantify raw data
(landmarks recorded on body of cichlid fish) B Remove non-shape variation (landmarks of 412
specimens before and after GPA) C statistical analysis (CVA) and graphical presentation of
results Deformation grids for mean specimen for (right) Eretmodus cyanostictus and (left)
Spathodus erythrodon (magnified by 3X to emphasize shape differences) Data from Ruumlber and
Adams 2001 En Adams Rolhf Slice 2002
tpsPLS
bull Partial least-squares analysis for shapes Windows Used to explore the covariance between a set of variables and variation in shape or between two shapes It performs a two-block partial least-squares analysis It differs from regression in that both variables and shape are considered equally (one is not considered to be a set of independent variables measured without error) Its use is described in Rohlf and Corti (2000 Systematic Biology 49740-753) By F James Rohlf Version 118
tpsSmall
bull Test for small variation in shape Windows Use to test whether the variation in shape among a set of specimens is too large and thus statistical methods based on the tangent space approximation (eg thin-plate spline methods) cannot be used The program can process both 2D and 3D data files Output files include consensus and aligned specimens By F James Rohlf Version 120
tpsPower
bull Estimate statistical power for comparing shapes Windows Program for estimating statistical power for comparing the mean shapes of two populations Provides methods based on several different approaches Can be used for planning morphometric studies as well as to compare power using different approaches Version 104 By F James Rohlf
Morpheus et al bull Morpheus et al is a software package that will provide a
comprehensive cross-platform environment for morphometric data analysis It is available in graphical and command-line versions for a number of operating systems (see below) More information about new features and previous changes can be found in the release notes
httplifebiosunysbedumorphmorpheus
Multivariate analysis
bull PAST is a free easy-to-use data analysis package aimed at paleontology Windows 95+ Multivariate statistical methods include Principal Components (with Minimal Spanning Tree) Principal Coordinates (ten distance measures) Non-metric Multidimensional Scaling (ten distance measures) Detrended Correspondence Analysis Cluster analysis (three algorithms 11 distance measures) k-means clustering seriation discriminant analysis one-way MANOVA Hotellings t-squared Boxs M Canonical Variates Analysis Also includes Fourier shape analysis thin-plate splines parsimony and time series analysis among others Oslashyvind Hammer University of Oslo
Analysis of outlines
bull Shape Elliptic Fourier WINDOWS Extracts the contour shape from a full color bitmap image delineates the contour shape with the elliptic Fourier descriptors and performs a principal component analysis for summarizing the shape information By Hiroyoshi Iwata For more information see Shape home page tutorial or manual
bull Iwata H and Y Ukai (2002) SHAPE A computer program package for quantitative evaluation of biological shapes based on elliptic Fourier descriptors Journal of Heredity 93 384-385
Eigenshape analysis
bull httpwwwnhmacukhosted_sitespaleonetftpftphtml
bull This archive contains a series of programs designed to perform an eigenshape analysis on xy coordinate data from object outlines Routines include xy -gt phi() transformation phi() -gt xy transformation eigenshape analysis and projection of objects into the eigenshape space Two completely worked example analyses and a users guide are also provided El autor es Norman McLeod del BMNH de Londres
Graphical representation of the four-step morphometric protocol A Quantify raw data
(landmarks recorded on body of cichlid fish) B Remove non-shape variation (landmarks of 412
specimens before and after GPA) C statistical analysis (CVA) and graphical presentation of
results Deformation grids for mean specimen for (right) Eretmodus cyanostictus and (left)
Spathodus erythrodon (magnified by 3X to emphasize shape differences) Data from Ruumlber and
Adams 2001 En Adams Rolhf Slice 2002
tpsSmall
bull Test for small variation in shape Windows Use to test whether the variation in shape among a set of specimens is too large and thus statistical methods based on the tangent space approximation (eg thin-plate spline methods) cannot be used The program can process both 2D and 3D data files Output files include consensus and aligned specimens By F James Rohlf Version 120
tpsPower
bull Estimate statistical power for comparing shapes Windows Program for estimating statistical power for comparing the mean shapes of two populations Provides methods based on several different approaches Can be used for planning morphometric studies as well as to compare power using different approaches Version 104 By F James Rohlf
Morpheus et al bull Morpheus et al is a software package that will provide a
comprehensive cross-platform environment for morphometric data analysis It is available in graphical and command-line versions for a number of operating systems (see below) More information about new features and previous changes can be found in the release notes
httplifebiosunysbedumorphmorpheus
Multivariate analysis
bull PAST is a free easy-to-use data analysis package aimed at paleontology Windows 95+ Multivariate statistical methods include Principal Components (with Minimal Spanning Tree) Principal Coordinates (ten distance measures) Non-metric Multidimensional Scaling (ten distance measures) Detrended Correspondence Analysis Cluster analysis (three algorithms 11 distance measures) k-means clustering seriation discriminant analysis one-way MANOVA Hotellings t-squared Boxs M Canonical Variates Analysis Also includes Fourier shape analysis thin-plate splines parsimony and time series analysis among others Oslashyvind Hammer University of Oslo
Analysis of outlines
bull Shape Elliptic Fourier WINDOWS Extracts the contour shape from a full color bitmap image delineates the contour shape with the elliptic Fourier descriptors and performs a principal component analysis for summarizing the shape information By Hiroyoshi Iwata For more information see Shape home page tutorial or manual
bull Iwata H and Y Ukai (2002) SHAPE A computer program package for quantitative evaluation of biological shapes based on elliptic Fourier descriptors Journal of Heredity 93 384-385
Eigenshape analysis
bull httpwwwnhmacukhosted_sitespaleonetftpftphtml
bull This archive contains a series of programs designed to perform an eigenshape analysis on xy coordinate data from object outlines Routines include xy -gt phi() transformation phi() -gt xy transformation eigenshape analysis and projection of objects into the eigenshape space Two completely worked example analyses and a users guide are also provided El autor es Norman McLeod del BMNH de Londres
Graphical representation of the four-step morphometric protocol A Quantify raw data
(landmarks recorded on body of cichlid fish) B Remove non-shape variation (landmarks of 412
specimens before and after GPA) C statistical analysis (CVA) and graphical presentation of
results Deformation grids for mean specimen for (right) Eretmodus cyanostictus and (left)
Spathodus erythrodon (magnified by 3X to emphasize shape differences) Data from Ruumlber and
Adams 2001 En Adams Rolhf Slice 2002
tpsPower
bull Estimate statistical power for comparing shapes Windows Program for estimating statistical power for comparing the mean shapes of two populations Provides methods based on several different approaches Can be used for planning morphometric studies as well as to compare power using different approaches Version 104 By F James Rohlf
Morpheus et al bull Morpheus et al is a software package that will provide a
comprehensive cross-platform environment for morphometric data analysis It is available in graphical and command-line versions for a number of operating systems (see below) More information about new features and previous changes can be found in the release notes
httplifebiosunysbedumorphmorpheus
Multivariate analysis
bull PAST is a free easy-to-use data analysis package aimed at paleontology Windows 95+ Multivariate statistical methods include Principal Components (with Minimal Spanning Tree) Principal Coordinates (ten distance measures) Non-metric Multidimensional Scaling (ten distance measures) Detrended Correspondence Analysis Cluster analysis (three algorithms 11 distance measures) k-means clustering seriation discriminant analysis one-way MANOVA Hotellings t-squared Boxs M Canonical Variates Analysis Also includes Fourier shape analysis thin-plate splines parsimony and time series analysis among others Oslashyvind Hammer University of Oslo
Analysis of outlines
bull Shape Elliptic Fourier WINDOWS Extracts the contour shape from a full color bitmap image delineates the contour shape with the elliptic Fourier descriptors and performs a principal component analysis for summarizing the shape information By Hiroyoshi Iwata For more information see Shape home page tutorial or manual
bull Iwata H and Y Ukai (2002) SHAPE A computer program package for quantitative evaluation of biological shapes based on elliptic Fourier descriptors Journal of Heredity 93 384-385
Eigenshape analysis
bull httpwwwnhmacukhosted_sitespaleonetftpftphtml
bull This archive contains a series of programs designed to perform an eigenshape analysis on xy coordinate data from object outlines Routines include xy -gt phi() transformation phi() -gt xy transformation eigenshape analysis and projection of objects into the eigenshape space Two completely worked example analyses and a users guide are also provided El autor es Norman McLeod del BMNH de Londres
Graphical representation of the four-step morphometric protocol A Quantify raw data
(landmarks recorded on body of cichlid fish) B Remove non-shape variation (landmarks of 412
specimens before and after GPA) C statistical analysis (CVA) and graphical presentation of
results Deformation grids for mean specimen for (right) Eretmodus cyanostictus and (left)
Spathodus erythrodon (magnified by 3X to emphasize shape differences) Data from Ruumlber and
Adams 2001 En Adams Rolhf Slice 2002
Morpheus et al bull Morpheus et al is a software package that will provide a
comprehensive cross-platform environment for morphometric data analysis It is available in graphical and command-line versions for a number of operating systems (see below) More information about new features and previous changes can be found in the release notes
httplifebiosunysbedumorphmorpheus
Multivariate analysis
bull PAST is a free easy-to-use data analysis package aimed at paleontology Windows 95+ Multivariate statistical methods include Principal Components (with Minimal Spanning Tree) Principal Coordinates (ten distance measures) Non-metric Multidimensional Scaling (ten distance measures) Detrended Correspondence Analysis Cluster analysis (three algorithms 11 distance measures) k-means clustering seriation discriminant analysis one-way MANOVA Hotellings t-squared Boxs M Canonical Variates Analysis Also includes Fourier shape analysis thin-plate splines parsimony and time series analysis among others Oslashyvind Hammer University of Oslo
Analysis of outlines
bull Shape Elliptic Fourier WINDOWS Extracts the contour shape from a full color bitmap image delineates the contour shape with the elliptic Fourier descriptors and performs a principal component analysis for summarizing the shape information By Hiroyoshi Iwata For more information see Shape home page tutorial or manual
bull Iwata H and Y Ukai (2002) SHAPE A computer program package for quantitative evaluation of biological shapes based on elliptic Fourier descriptors Journal of Heredity 93 384-385
Eigenshape analysis
bull httpwwwnhmacukhosted_sitespaleonetftpftphtml
bull This archive contains a series of programs designed to perform an eigenshape analysis on xy coordinate data from object outlines Routines include xy -gt phi() transformation phi() -gt xy transformation eigenshape analysis and projection of objects into the eigenshape space Two completely worked example analyses and a users guide are also provided El autor es Norman McLeod del BMNH de Londres
Graphical representation of the four-step morphometric protocol A Quantify raw data
(landmarks recorded on body of cichlid fish) B Remove non-shape variation (landmarks of 412
specimens before and after GPA) C statistical analysis (CVA) and graphical presentation of
results Deformation grids for mean specimen for (right) Eretmodus cyanostictus and (left)
Spathodus erythrodon (magnified by 3X to emphasize shape differences) Data from Ruumlber and
Adams 2001 En Adams Rolhf Slice 2002
Multivariate analysis
bull PAST is a free easy-to-use data analysis package aimed at paleontology Windows 95+ Multivariate statistical methods include Principal Components (with Minimal Spanning Tree) Principal Coordinates (ten distance measures) Non-metric Multidimensional Scaling (ten distance measures) Detrended Correspondence Analysis Cluster analysis (three algorithms 11 distance measures) k-means clustering seriation discriminant analysis one-way MANOVA Hotellings t-squared Boxs M Canonical Variates Analysis Also includes Fourier shape analysis thin-plate splines parsimony and time series analysis among others Oslashyvind Hammer University of Oslo
Analysis of outlines
bull Shape Elliptic Fourier WINDOWS Extracts the contour shape from a full color bitmap image delineates the contour shape with the elliptic Fourier descriptors and performs a principal component analysis for summarizing the shape information By Hiroyoshi Iwata For more information see Shape home page tutorial or manual
bull Iwata H and Y Ukai (2002) SHAPE A computer program package for quantitative evaluation of biological shapes based on elliptic Fourier descriptors Journal of Heredity 93 384-385
Eigenshape analysis
bull httpwwwnhmacukhosted_sitespaleonetftpftphtml
bull This archive contains a series of programs designed to perform an eigenshape analysis on xy coordinate data from object outlines Routines include xy -gt phi() transformation phi() -gt xy transformation eigenshape analysis and projection of objects into the eigenshape space Two completely worked example analyses and a users guide are also provided El autor es Norman McLeod del BMNH de Londres
Graphical representation of the four-step morphometric protocol A Quantify raw data
(landmarks recorded on body of cichlid fish) B Remove non-shape variation (landmarks of 412
specimens before and after GPA) C statistical analysis (CVA) and graphical presentation of
results Deformation grids for mean specimen for (right) Eretmodus cyanostictus and (left)
Spathodus erythrodon (magnified by 3X to emphasize shape differences) Data from Ruumlber and
Adams 2001 En Adams Rolhf Slice 2002
Analysis of outlines
bull Shape Elliptic Fourier WINDOWS Extracts the contour shape from a full color bitmap image delineates the contour shape with the elliptic Fourier descriptors and performs a principal component analysis for summarizing the shape information By Hiroyoshi Iwata For more information see Shape home page tutorial or manual
bull Iwata H and Y Ukai (2002) SHAPE A computer program package for quantitative evaluation of biological shapes based on elliptic Fourier descriptors Journal of Heredity 93 384-385
Eigenshape analysis
bull httpwwwnhmacukhosted_sitespaleonetftpftphtml
bull This archive contains a series of programs designed to perform an eigenshape analysis on xy coordinate data from object outlines Routines include xy -gt phi() transformation phi() -gt xy transformation eigenshape analysis and projection of objects into the eigenshape space Two completely worked example analyses and a users guide are also provided El autor es Norman McLeod del BMNH de Londres
Graphical representation of the four-step morphometric protocol A Quantify raw data
(landmarks recorded on body of cichlid fish) B Remove non-shape variation (landmarks of 412
specimens before and after GPA) C statistical analysis (CVA) and graphical presentation of
results Deformation grids for mean specimen for (right) Eretmodus cyanostictus and (left)
Spathodus erythrodon (magnified by 3X to emphasize shape differences) Data from Ruumlber and
Adams 2001 En Adams Rolhf Slice 2002
Eigenshape analysis
bull httpwwwnhmacukhosted_sitespaleonetftpftphtml
bull This archive contains a series of programs designed to perform an eigenshape analysis on xy coordinate data from object outlines Routines include xy -gt phi() transformation phi() -gt xy transformation eigenshape analysis and projection of objects into the eigenshape space Two completely worked example analyses and a users guide are also provided El autor es Norman McLeod del BMNH de Londres
Graphical representation of the four-step morphometric protocol A Quantify raw data
(landmarks recorded on body of cichlid fish) B Remove non-shape variation (landmarks of 412
specimens before and after GPA) C statistical analysis (CVA) and graphical presentation of
results Deformation grids for mean specimen for (right) Eretmodus cyanostictus and (left)
Spathodus erythrodon (magnified by 3X to emphasize shape differences) Data from Ruumlber and
Adams 2001 En Adams Rolhf Slice 2002
Graphical representation of the four-step morphometric protocol A Quantify raw data
(landmarks recorded on body of cichlid fish) B Remove non-shape variation (landmarks of 412
specimens before and after GPA) C statistical analysis (CVA) and graphical presentation of
results Deformation grids for mean specimen for (right) Eretmodus cyanostictus and (left)
Spathodus erythrodon (magnified by 3X to emphasize shape differences) Data from Ruumlber and
Adams 2001 En Adams Rolhf Slice 2002
