Morphometrics Software:
IMPIntegrated Morphometrics Package
Last Updated 7/06/04
IMP is an
integrated 2D Landmarkbased geometric morphometrics software package, with it's own file format system which
loads easily into software such as SPSS and Excel. IMP can also read and write
files in the TPS file format used by F.James Rohlf's TPS series software. Several programs for 3D data
are also available, as are programs to use semilandmarks along curves. I have
a few pieces of 3D morphometrics software only.
IMP currently runs
under Windows only. II have the Mac compiler to port these programs over to
Mac, I need some help with Beta testing, and writing installation do get in
touch if you are interested in Beta testing and are familiar with the Mac X11
system. Keep your fingers crossed...
If you are
considering using IMP, Please read WhatisIMP.pdf Version as of 1/17/02.
New
additions or versions of the IMP software series (appearing after July 1, 2004)
are located at moremorph.html
Also
now available: IMP
7Programs
Using IMP
To use IMP, you will need to download the
selfextracting compressed mathematics and graphics libraries from Mathworks (makers of MATLAB), needed to support IMP. This
set of libraries is large, just over 7 Meg, but it supports all of IMP.
Download: mglinstaller.exe Version as of 2/5/01
If you want to use IMP and want all of the
basic IMP files in one bundle, you may want to download the combined,
selfextracting Zip File IMPBasics, which contains CoordGen, Regress, PCAGen, CVAGen, TwoGroup and TradMorph, the core programs of IMP.
Download IMPBasics.exe
Version 6a
As
of 8/17/02
There are three categories of IMP software: General
Release Software for which there are reasonably complete users
manuals available, Undocumented Software which has little or no
documentation currently available and Beta software, which is the 3D
software which has not been used in a serious research project to date. The
successful use of Undocumented Software or Beta Software most likely relies on
your having had direct contact with one of my direct collaborators, or myself. I will eventually get all the users manuals written,
but you are welcome to download the software at any time. The Undocumented
Software is on this site primarily as a convenience for my direct collaborators
and their students and collaborators.
Individual IMP
files for Download:
General Release IMP
Files for Download
Program 
File 
Manual 
Description 
Latest Update 
CoordGen6 
Also see docs below 
Coordinate Generating Utility, also file translator to/from X1Y1, TPS
file formats 
3/24/03 

CVAGen6 
Also see docs below 
Canonical Variates Analysis Program Try using PCAGen6 before using CVAGen, the 2 programs use the same input files and operational
format. 
3/25/03 

PCAGen6 
Also see docs below 
Principal components analysis based on partial warp scores, outputs
partial warps scores and principle axis scores 
7/10/03 

Regress6 
also see docs below 
Thin Plate Spline and Regression Utility 
4/15/08 

SuperPoser 
not included in the superpac file 
Allows for the exploration of a variety of alternative superimposition
criteriadifferent distance minimization criteriaNot recommended as a
general purpose tool, but provided as an alternative.....written by Dave Liebner, Canisius ’03. 
3/7/03 

TwoGroup6h 
Comparison of statistically significant differences in shape between
two groups 
7/10/03 

TmorphGen6b 
Generates a set of traditional morphometrics variables from a set of
geometric morphometric measurements 
4/5/03 
Additional Documentation On Plotting Updates Additional manuals, commentary, etc.
GridTrimming.pdf A file on how to use the grid trimming feature added to most programs which display deformation grids.
ReferenceRotation.pdf A file on how to use the reference orientation controls added 11/5/02 added to most programs which display deformation
grids
Undocumented
Software, IMP Files for Download
(Some of these actually have limited
amounts of documentation, but the users manuals are
not currently adequate for a general release. If you are familiar enough with
IMP and patient enough, you should be able to get these to work
satisfactorily.) These items are posted here primarily for use by my direct
collaborators.
Program 
File 
Manual 
Description 
Latest Update 
BigFix6 
 
Averages landmarks across a baselinespecial purpose preprocessing of
data 
3/17/01 

GrowProfile6 
 
Growth Profiles 
3/17/01 

DisparityBox6 
 
Disparity Box, designed for calculation of Morpological
Disparity 
2/16/07 

LMEdit6 
LMEdit6 is an editting tool for altering
landmark configurations, allowing for averaging of measurements across an
axis of symetry and eventually other tasks 
6/17/03 

MakeFan 3^{rd} Beta Version (Works reliably, limited manuals) 
None Yet! 
MakeFan, a tool for drawing alignment
“fans” at equal angular spacing on an image prior to digitizationcan be used
with TPSDig, or as a really primitive standalone
digitizer 
8/27/09 

Extra DLL needed for MakeFanexpand this into
the Bin\win32 directory where MakeFan is
installed, if MakeFan doesn’t work properly
initially 

PLSAngle Version 6b 
Partialincluded in compressed file 
Partial Least Squares tool for comparing patterns of covariance between
blocks, using two data of 2 blocks each 
7/10/03 

PLSMaker (was listed as PLSBlock, same program) 
PLSMaker _manual.pdf included 
Partial Least Squares Tool for studying patterns of covariance using
shape data 
3/23/03 

SemiLand6 6^{th} Beta Version 
Partial manual included in compressed files 
A tool for processing semilandmarks, prior to use in other programs.
Now includes a zoom function 
6/19/09 

ShuffleAllometry6 
 
Computes range of vector correlations that can be generated by random
shuffling of a vector 
2/03/01 

SpaceAngle 
Limited manual 
Compares the angle between the spaces defined by the PC axis of
different groups 
8/19/02 

Splice6 
No manual, simple program 
A tool to splice together ASCII files, either IMP or TPS 
3/18/04 

Standard6a 
Standardization Utilityremoves linear dependences of shape on some
variable 
8/19/02 

TBox 
No manual yet 
Computes a ttest score, given the means, samples sizes and standard errors
in the measurements. Note the use of the standard error, rather than standard
deviation. 
7/10/03 

VecDisplay6 
Displays thin plate spline vectors for
comparison purposes 
3/25/03 

VecCompare6 
 
Computes a growth angle between two groups. Resampling
statistics. 
3/17/01 

VecLand6 
 
Displays landmark by landmark differences between two groups USE OF VECLAND NOT RECOMMENDUSE VECDISPLAY INSTEAD 
3/17/01 

VecLand6b Substantially altered version, with documentation! 
includes manual 
Displays landmark by landmark Differences in regress models between two groups 
2/10/04 
IMP 3D Beta Programs
Below are a set of the basic programs needed to work with 3D landmark based morphometric data. Simple3D does file conversion and pairwise tests of differences in shape between two groups (ala TwoGroup6). Regress3 and ThreeDPCA carry out regression analysis and PCA using partial warp scores for three dimensional data. The three dimensional display is rather limited at the moment, but all the mathematics is in place. Take a look at these programs if you are interested and let me know what additions/changes/improvements might prove helpful. Brief manuals and example files are included with each of these programs.
Program 
File 
Description 
Latest Update 
Regress3D 
Regression analysis of 3D landmark data using partial warp scores. 
8/21/02 

Simple3D 
File conversion, Procrustes Superimposition, Goodall’s Ftest for differences in means, calculation of Procrustes distances between means for 3D landmark data. Also, 3D Bookstein Coordinates, matrices of all pairwise interspecimen distances. 
5/07/09 

ThreeDPCA 
PCA for 3D landmark data, based on partial warp scores 
8/21/02 
Update
Information:
3/17/01 There are a number of updates as of 3/17/01. Most notable is the
PCA program PCAGen6, which does Principal Components Analysis of data based on
thin plate spline decompositions of shape. Groups are
color coded for display, and the shape deformation implied by a pair of PCA
scores can be illustrated. It may also be used purely to generate thin plate spline scores.
Most of the rest of the software got relatively minor graphics upgrades,
including the ability to write .EPS files (encapsulated post script) that may
be loaded into Adobe Illustrator and the like.
3/28/01 I loaded an updated manual for PCAGen6, and a mild update of
PCGen6a, which now includes Scree plots of the eigenvalues for each PC, and a statistical test of which PC
axes are significantly different from one another.
4/01/01 Loaded a new version of PCAGen6, called PCAGen6b. There was an
error in the statistical test of PC axes significant in PCAGen6a, it reported 1
too many significant axes, sorry folks, load the new version.
6/06/01Loaded a new version of Regress6, called Regress6c. This how has
updates in the statistics (it calculates significance levels for you now) and
it also allows you of plotting the reference form, the deformed shape (or
target form), or both. TwoGroup6 also got some updates, specifically the
calculation of alpha levels from the Fvalues. Also CoordGen6b now includes the
ability to generate a RFTRA (Resistant Fit ThetaRho Fitting) superimpositioning, if that’s what you need!
8/01/01Added a user supplied reference option to PCAGen6.
10/9/01 Put CVAGen up for downloads.
1/17/02 Updated Manuals
5/28/02 Fixed a couple of problems in TwoGroup6c
and Regress6. TwoGroup6c will now output a “dummy coded” file to be used in
Regress6 to depict the differences between the mean form of two groups. The
problem copying the Procrustes distances vs CS plots
that occurred in Regress6 has now been fixed.
7/27/02 Added Updated versions of PCAGen6 and VecCompare6More updates
soon!
7/31/02 Added updates of PCAGen6F, Regress6F and CVAGen6D, so that these
programs now round the reference form (to 5 decimal places) in exactly the same
fashion, so that they generate the same values for PW scores when generating an
reference form internally, or when loading a user reference. Earlier
differences due to how references were rounded and superimpositions were handled
should now be eliminated.
All these programs now have the grid plus vectors display option,
PCAGen6F and CVAGen6D can now plot the mean PCA/CVA scores of each group on the
PC/CVA axes plots, CVAGen6 can now assign “unknown” specimens to a known group
based on CVA scores and has an assignment test for the validity of assignments.
Regress6F has a permutation test based on a form of a Generalized Goodall’s Ftest for the significance of the regression
model. All of them also have the “Grid Trimming” feature
as well, which will allow better user control of the size of the grid (which I
still have to write the manual for! If you want to try it, let me know, I’ll
try to write a quick explanation.)
8/15/02 Added updates of PCAGen6g,CVAGen6e and
Regress6g which have a more stable calculation of the GLS Procrustes Mean form.
The earlier versions had a subroutine which could be unstable under some
conditions, producing a reference with a centroid sized that deviated from 1
(by several percent). This should not pose a severe problem for analyses done
using earlier reference forms, so long as the linear approximation to the
curved shape space is valid. If your data occupies enough of shape space to
depart from linearity, you should recheck your results with the newer versions.
Sorry about the problem, it was an error that appeared erratically. I have
checked the PW scores and reference form produced against those from TPSRegress, and they are currently in agreement.
Also, I have added an update of DisparityBox6d that allows for automated
loading of a sequence of files, and also has a variety of nearestneighbor
calculations available within it. The manual for DisparityBox
needs updating though.
Added MakeFan (an alignment
tool) and PLSBlock (a partial least square tool), and
an updated version of IMPBasics.
8/19/02 Added updates of CVAGen, CoordGen, PCAGen, Regress, DisparityBox, Standard 6, which fixed an error in how these
programs rotated specimens to align with the PC axis
of variation of the reference. In some situations earlier versions of these
programs could produced affine distortions of the
data, particularly when the reference was rotated substantially during the
procedure. DOWNLOAD THE NEW VERSIONS OF THESE PROGRAMS AND RECHECK YOUR
RESULTS. The distortion was affine and applied evenly to all specimens, which
makes it hard to pick out visually, and probably means that it won’t effect inferences, but do recheck your results. Thanks to
Mark Webster at UC Riverside for locating this problem.
I have also posted a semilandmark tool, SemiLand6, which will allow
processing of semilandmarks placed along curve, and
also PLSAngle for comparing PLS\SVD vectors between
groups, or comparing SVD axes to PC axis.
8/21/02 Added the three dimensional programs in Beta form.
8/23/02 Updated Three Dimensional ProgramsAdded a permutation Ftest and
rudimentary plot controls.
8/27/02 Added better image controls to PLSMaker6. Added
the pdf on grid trimming.
9/12/02 Posted the 2^{nd} Beta versions
of SemiLand 6 and MakeFan.
There was a change in the algorithm used in SemiLand6 to estimate the local
slope at the endpoints of openended curves, which seems to improve the
accuracy of semilandmark positioning when sliding semilandmarks along curves.
Additional image controls were also added to SemiLand6. Some additional
features were added to MakeFan to improve it’s utility as a digitizer,
allowing user control of landmark color and number, and the ability to erase
fans.
11/11/02 Posted updated versions of PCAGen, CVAGen,Regress, PLSMaker, PLSAngle and VecDisplay. The plotting routines were updated, fixing an
error in the routine that in some cases produced an affine error in the plots
(but not in statistical inference). The new routine also allows for accurate
user control of the orientation of the reference during display.
12/06/02 Posted an updated version of SemiLand6
which aligns semilandmarks to minimize Procrustes distance between
semilandmarks on a curve and semilandmarks on a reference form. The
minimization based on bending energy is not currently operating in a stable
manner, and so it has been disabled until such time as I can produce a stable,
consistent version.
1/14/03 Added a “comb” alignment tool to MakeFan6, as an alternative to
fans.
2/1/03 Minor alterations to the “comb” function in MakeFan6, to draw
perpendicular lines at the end of the comb.
3/7/03 Added versions of PCAGEN, CVAGen and
Regress with a default reference orientation setting, making the reference
rotation optional, which sound increase the speed of use. I also put up the SuperPoser tool written by my student Dave Liebner which allows use of a variety of robust error
functions to be used in superposition (as alternative approaches to resistant
fit methods), for those who want to work with this type of mathematical
approach.
3/10/03 Added versions of VecDisplay, PLSMaker and PLSAngle with the
default reference orientation setting. Also added a version
of CoordGen which orients the Procrustes reference
form with the specified axis as close to horizontal or vertical as possible,
given the need to align the GLS Procrustes Reference with the principal axis of
the specimen.
3/14/03 Added the ability to display deformation
grids and vectors depicting the differences between the means of two groups of
specimens to the TwoGroup progam.
3/24/03 I have worked out an approach to the calculation of the uniform
component that does not require that the reference form be in principal axis
alignment. This approach is now implemented in PCAGEN and PLSMaker.
Also, CoordGen now offers Procrustes Superimposition
with or without principle axis (PA) alignment.
3/26/03. Added revised versions of Regress, PLSAngle, VecDisplay and CVAGen with the updated display routines, which do not
require principle axis rotation. PCAGen was
also updated to fix an error that crept into the last update that caused the
software to fail to reload data properly. Also, I made minor adjustments in the
size of the white space in the copy to clipboard and copy to eps file functions that should eliminate or reduce some
copy problems.
6/18/03. I have added an “exaggeration” control into TwoGroup,
and also have put up the lmedit6 tool which can “edit”, renumber and reflect
landmark configurations, and can also “backreflect” landmarks on one side of a
bilaterally symmetric organism to form symmetric landmark configurations.
7/10/03 I noticed that PCAGen didn’t number
specimens correctly when the axes are reversed (changing the axis polarity), so
I fixed that and posted a new version of PCAGen.
There is also a new MakeFan up since the last compile
had errors in the line weight control and in digitizing, so get a new copy of
that one. There are new copies of DisparityBox, TwoGroup and PLSAngle up which
have the standard error estimates for all statistics displayed. There is also a
new tool up called Tbox which calculates ttest
scores given the means, standard errors and sample sizes of two measurements.
This is a bit different from the standard ttest in that it takes the standard
error as an input, rather than a standard deviation.
7/06/04 Final update to this page, creation of the new moremorph page