Integrated Morphometrics Package (IMP) Suite

In cooperation with Prof. Dr. H. David Sheets, we are happy to announce that we can now provide the full Integrated Morphometrics Package (IMP) Suite here. Prof. H. David Sheets is one of the authors of the well-known book Geometric Morphometrics for Biologists: A Primer by Miriam L. Zeldith, Donald L. Swiderski, H. David Sheets and William L. Fink, which also references the IMP software suite. He is now unable to maintain support for this software and has thus taken down the website on which IMP was previously available. Hence, we have taken it upon us to fill in the distribution role and provide continued access to both current and legacy versions of the IMP software suite. However, all software below will have to be considered as Abandonware, meaning that except for the comment section here as well as potential groups present at other social media, there will be no more support available for this software.

What is IMP?

IMP is a set of compiled software tools with graphic user interfaces that carry out a wide variety of tasks related to the display and analysis of landmark-based geometric morphometric data. IMP can read files in the TPS file format used by F. James Rohlf’s TPS series software. All of the IMP programs use the same file format, and are meant to work in conjunction with one another. Each program in the IMP series is meant to carry out a limited number of specific tasks, so that a complete analysis of your data will require the use of more than one IMP program. Since they share a common file format that also loads easily into other software such as R, SPSS and Excel, progressing through a series of different programs to carry out the analysis is not as daunting as it might seem initially. Each program in the series is meant to be easy to use, and the controls of the various programs operate in similar ways. This is meant to ease the learning curve for the software, and allows for a lot of flexibility in how the software operates. A few programs for 3D morphometric data are also available, as are programs to use semi-landmarks along curves. A more detailed description of the software can be found in the IMP manual.

The most current version of the IMP suite is IMP 8, which runs under Mac OSX 10.7, 10.8 and under Windows 7, 8, 10. IMP 8 was compiled using Matlab 8.2, when you download and run these programs, they will download the Matlab drivers needed to run the programs from the Mathworks Corporation, and install the dynamic link libraries needed to run IMP 8. In IMP8, many previously independent programs have been bundled into a more limited number of packages. CoordGen 8 for example can call TMorphGen, SemiLand, MatchMaker, BigFix and VisProto Editor. CoordGen 8 doesn’t look much different than earlier versions, and isn’t any harder to use, but it now serves as a starting point for the other programs. This should simplify using IMP programs by reducing the sheer number of them. These programs will not run within the Matlab environment, they are compiled versions of the Matlab functions. IMP programs will tend to start slowly, due to the need to load a lot of library files, be a bit patient. The bundling of multiple tools into a single package helps to reduce this problem slightly when you are using a number of different tools.

How to cite IMP?

If you are using IMP in your research, please cite it as follows:
Here, we use CoordGen 8 as an example, please replace this with the respective software that you used. Moreover, the years should be different dependent on which IMP version you used. For IMP 8, cite the year 2014, for IMP 7, the year 2010. The most up-to-date IMP 6 versions should be cited with the year 2007 and the IMP 6 versions frozen at the time the 2003 book was released, the year 2003.

Inline text:
[…]with CoordGen 8 (Integrated Morphometrics Package Suite, H. David Sheets, Canisius College, New York, USA).

Citation:
[…]CoordGen 8 (Sheets, 2014).

Reference:
Sheets, H.D. (2014) Integrated Morphometrics Package (IMP) 8, 2014.

Are there any up-to-date alternatives to IMP?

In case you would like to consider other software, the GeoMorph package for R is a suitable alternative. According to the accompanying paper, it provides routines for all stages of landmark‐based geometric morphometric analyses in 2D and 3D. A Quick Guide for GeoMorph is also available.

IMP file list

Software name

Description

Download

IMP 8 (most up-to-date version, requires Windows 7 or later)
2D IMP Programs
CoordGen 8 Utility tool for file conversion, checking for digitizing errors and other data management tasks, and simple statistics on a single data set.
Now included within CoordGen: TMorphGen (Traditional Morphometrics Generator, calculates lengths and angles based on landmark data), SemiLand (Semi-Landmark alignment based on distance minimization), BigFlip (Tool for reflecting and averaging bilaterally symmetric specimens), MatchMaker (Tools for searching for ‘matches’ within a specified measurement error), VisProto (An editing tool for creating protocol files for other IMP programs, including TMorphGen, also allows for extraction of subsets of data, with specified landmarks).
TwoGroup 8 Tool for comparing the means of two groups, and displaying differences in mean shape.
PCAGen 8 PCA tool in the IMP series, also includes NMMDSGen8 (Non-metric multidimensional scaling), PCAGen8SP (PCA of size and shape), CorrExplore (Testing models of correlation structure), DisparityBox ( Investigating morphological disparity), AsymBoxTwo (Calculation of asymmetry, PCA+CVA of asymmetry based on LM data).
CVAGen 8 Canonical Variates Analysis of landmark data
Regress 8 Regression tools for landmark data, also includes Standard8 (size standardization for residual analysis of shape), VecLand8 (display and compare ontogenetic growth vectors), VecCompare8 (compute and angles between regression vectors), ShuffleAllometry8 (specialized allometry tests).
PLSMaker 8 2 Block Partial Least squares, also includes PLSAngle8 (Tools for comparing variance+covariance patterns in multiple groups), SpaceAngle (Calculation of angles between subspaces defined by PCA axes of groups), OModel.
MakeFan 8 Tool for drawing ‘fans’ or guidelines for digitizing semi-landmarks on images.
3D IMP Programs
Simple3D8 Basic utility for 3D shape data, including simple states, comparison of the means of two groups, variance calculations, file conversion, traditional measurements calculations etc. The 3D equivalent of CoordGen 8. Includes the following tools: ChainMan3D (Conversion of chain-coded outlines in 2D or 3D to semilandmarks), WireMan (This is an editor for creating wire frames or protocols for use with other IMP 3D tools), Pts_2_tps (converts .pts format files from LandMark to tps format), MatchMaker3D (the 3D shape matching tool).
ThreeDPCA 8 PCA analysis of 3D shape data. Also includes: DisparityBox3D8 ( analysis of disparity patterns).
ThreeDCVA 8 CVA of 3D shape data.
ThreeDRegress Regression Tools in 3D. Also includes VecCompare3D (3D comparisons of ontogenetic trajectories), Standardize3D (Standardization tool for residual analysis in 3D).
ThreeDPLS 8 Partial Least Squares analysis. Includes ThreeDPLS_Angle8 ( Comparison of covariance patterns in multiple groups).
IMP 7 (for Windows XP and later)
MATLAB Compiler Runtime Password-protected MATLAB Compiler Runtime from MathWorks Corp, needed to support IMP7. Username: ‘guest’, Password: ‘morph’. Windows installation routine: 1) Create a directory on your hard drive, so that it appears as C:\IMP7, 2) Download MCRInstaller into your C:\IMP7 directory, 3) Expand MCRInstaller in this directory, by running it. It will install the Matlab components needed to run the IMP7 modules, 4) Download IMP7 programs/modules as desired, and load them into the directory C:\IMP7\V78\bin\win32, 5) Run the files from this directory. Alternatively, you can also include the directory C:\IMP7\V78\bin\win32 in the PATH variable on your computer, and then the IMP7 programs can be installed and run from anywhere on your computer. A copy of this installer for the Mac is included in the Mac version of the Coordgen 7a file.
2D IMP Programs
CoordGen7a Includes TMorphGen and SemiLand, called from within CoordGen7. Now includes Procrustes SP.
CVAGen 7b CVAGen program- with single factor MANOVA.
DisparityBox7 Disparity Box tool for Disparity/Variance Calculation.
LMEdit7 Landmark and data set editor.
MakeFan7
MatchMaker7 Searches for “matches” in shape databases based on a stated measurement resolution – meant for forensics.
PCAGen7a PCAGen – PCA of shape data.
PCAGen7SP PCAGen variant using Procrustes SP (size-preserving) superimpositions. Meant for forensic applications.
PLSMaker7 Partial Least Squares Analysis of Shape Data.
PLSAngle7 Angular comparisons of PLS axes and PCA axes.
RegPac7 Regression of shape data.
Regression7a Regress7a – highly revised user interface.
Standard7 Standardization program, for residual analysis.
TwoGroup7 Pairwise comparisons of populations.
VecCompare7 Growth Vector Comparison.
VecLand7 Growth Vector Comparison plots.
Vis_Proto7 Visual Protocol Editor.
3D IMP Programs
DisparityBox3D Disparity Box in 3D.
MatchMaker3D7 3D version of the MatchMaker matching program.
PLS3D7 Partial Least Squares in 3D.
ThreeDCVA CVA of 3D landmark data. N/A
ThreeDPCA PCA of 3D landmark data.
ThreeDRegress7 Regression of 3D landmark data.
ThreeDPLS7 Partial Least Squares of 3D landmark data.
WireMan7 Utility tool for creating 3D wireframe. Files for use with other 3D tools.
IMP 6 (most updated versions)
Matlab drivers version 6.5 Download this file and install it in a new directory, not, repeat, not, the same directory as the mglinstaller for version 6, which you presumably already have installed.
2D IMP Programs
CVAGen6L This is an update of CVAGen6 with a jackknife procedure for assessing how well the discriminant function and assignment test work for a given data set. There is a newer version of CVAGen available below, listed as PCA_CVA.
PLSMaker6g This is a version of PLSMaker with a trace correlation calculation available. The trace correlation may be calculated between the two blocks, and the use of a generalized inverse calculation is available within this calculation.
BigFlip6a This is an updated version of the Big Flip program which can use pairs of off-axis landmarks to estimate the location of the symmetry axis when carrying out reflection and averaging of data.
REGPAC6P This is an update of Regress6k called Regress6K+, it is a Beta version that checks the correlation of the linear tangent space distances with the Procrustes distance in curved space. Includes a Word file called “Correlation of Euclidean and Procrustes” that explains how it works.
PCAGen6p This version has a summed variance calculation in it (the summed squared partial procrustes distance about the mean form divided by (n-1), where n is the sample size). It also has a better window resizing function. I also updated the write to eps files option and added more error trapping.
TMorphGen6c This expanded version of Tmorphgen computes angles on organismal structures based on landmark coordinates, as well as lengths along structures based on landmarks. Users specify the angles to be measured using a protocol and angles are output in degrees and radians.
CoordGen6h This version will compute a matrix of all pairwise Partial Procrustes Distances between specimens in the input file. The option is available on the file menu to run this calculation. Also has the ability to display individual specimens one by one, and a zoom function has been added.
PairDisparity This is a program for testing whether the disparity of one group of organisms/species (ie. a clade, local population, ecologically related group) is statistically significantly larger or smaller than that of another group using a permutation test. This compliments DisparityBox6.
Vis_Proto This is a tool for visually editing a number of different “protocols” used in other pieces of software. It is currently under development, so I would like to restrict it’s use to direct collaborators only please.
TMCorr -Traditional Morphometrics Correlation Structure Tool. Currently under development, so I would like to restrict it’s use to direct collaborators only please.
ChainMan This is the ChainMan tool for outline data. It can carry out a PCA of outline-based data, and can extract evenly spaced semi-landmarks from chain-codes or curves into semi-landmarks. This is currently under development, so direct collaborators only please. ChainMan runs under Matlab version 6.5 so it needs the mglinstaller version 6.5 drivers.
ChainMan3D This is a 3D version of the ChainMan tool. It runs under the Matlab 6.0 drivers, and now includes the ability to handle 2D data also. Still in Beta, let me know about problems!
PCA_CVA This is a version of CVAGen (CVAGen6o) which is capable of performing a PCA on the data first, and then carrying out the CVA on a subset of the PC scores to reduce the dimensionality of the data. This program is currently in Beta Form. There is also a Jackknife test of the assignment of specimens to groups, as well as the more complex assignment test. I also fixed some problems with the save eps format file and other issues.
CCoder This is the utility tool for producing customized group codes for use with CVAGen and PCAGen.
3D IMP Programs
ThreeDPCA6 I have added the ability to save the eigenvalues and eigenvectors (PC axis loadings) from the PCA analysis. The save options are on the File menu. Beta 2.
V3pac This is a program called V3Comp6, which is a version of VecCompare meant for use with 3 dimensional data. Very limited
manual. Beta 2.
TDSPAC This is a three dimensional version of Standard6, for removing variance attributable to an independent variable, using a
regression model. The program enclosed is ThreeDStand6 (which means Three Dimensional Standardization). It can load
either IMP or TPS files. Beta 2.
WireMan6 Visual editing tool for constructing wireframes, traditional measurements data sets and block structures using 3D landmark data. There is a manual for this, but it is in Beta form. Beta 2.
PLS3PAC This is a three dimensional version of the PLSBlock program, called PLS3D, for carrying out Partial Least Squares
analysis of 3D data. It is in beta form, with only the sketchiest of users manuals. Direct collaborators only please. Beta 3.
SAT6 This is a three dimensional version of the SpaceAngle program, called SpaceAngleThree6. Beta 2.
R3PAC This is the the 3D regression tool ThreeDRegress.
CVAPAC3 This is an the 3D alpha version of a 3D CVA tool-very rough-collaborators only, thanks!
Other software
WalkPac This is the Walkbox6 tool for testing time series against the null model of a random walks, and contains some of the tests discussed
in Sheets, H. D. and Michell C.E., 2001. Why the Null Matters: statistical tests, random walks and evolution. Genetica 112-113 pg 105-125. There is a pdf manual included that should be reasonably complete.
WalkPac 6.5 This is WalkBox65 with multivariate random walk models included. It requires the matlab version 6.5 driver files. This is a program for direct collaborators only, thanks.
AgroPac This is the GrowChoice software tool used in Zelditch, M.L, B.L. Lundrigan, H.D. Sheets and T.Garland, Jr. 2003. Do precocial mammals develop at a faster rate? A comparison of rates of skull development in Sigmodon fulviventer and Mus musculus domesticus. Journal of Evolutionary Biology, Volume 16, pgs not known at present. The manual may be a bit sketchy for this program at the moment, let me know how it goes.
DefCat This is the DefCat retrodeformation operations test frame software, not currently intended for general distribution, collaborators only, thanks!
FMC This is the FMC Finite Mixture Coding Program for phylogenetic coding, test frame software, not currently intended for general distribution, collaborators only, thanks!
CorrExplore6 This is a tool for exploring matrix correlations. Collaborators only, thanks.
OmitBox This is a tool for selecting taxa to omit in a rarefaction study-very limited, direct collaborators only, thanks!
ManPac This is the Manova/Mancova tool for 2D geometric morphometric data, allowing up to 2 classification variables and 1 covariate. This is currently in a very early beta version, direct collaborators only, thanks!
CardWalkPac This is a simulation designed for classroom laboratory use, direct collaborators only at the moment, thanks!
RepManPac This is a repeated measures manova tool, using permutations and procrustes distances, direct collaborators only, thanks!
IMP 6 versions frozen at the time the book Geometric Morphometrics for Biologists: A Primer by Miriam L. Zeldith, Donald L. Swiderski, H. David Sheets and William L. Fink was published
MathWorks libraries Self-extracting compressed mathematics and graphics libraries from Mathworks (makers of MATLAB), needed to support IMP.
IMPBasics If you want to use IMP and want all of the basic IMP files in one bundle, you may want to download the combined, self-extracting Zip File IMPBasics, which contains CoordGen, Regress, PCAGen, CVAGen, TwoGroup and TradMorph, the core programs of IMP.
General Release Software
CoordGen6 Coordinate Generating Utility, also file translator to/from X1Y1, TPS file formats.
CVAGen6 Canonical Variates Analysis Program. Try using PCAGen6 before using CVAGen, the 2 programs use the same input files and operational format.
PCAGen6 Principal components analysis based on partial warp scores, outputs partial warps scores and principle axis scores.
Regress6 Thin Plate Spline and Regression Utility.
SuperPoser Allows for the exploration of a variety of alternative superimposition criteria-different distance minimization criteria-Not recommended as a general purpose tool, but provided as an alternative…..written by Dave Liebner, Canisius.
TwoGroup6h Comparison of statistically significant differences in shape between two groups.
TmorphGen6b Generates a set of traditional morphometrics variables from a set of geometric morphometric measurements.
GridTrimming A manual on how to use the grid trimming feature added to most programs which display deformation grids.
ReferenceRotation A manual on how to use the reference orientation controls added to most programs which display deformation grids.
Undocumented Software
BigFix6 Averages landmarks across a baseline-special purpose preprocessing of data.
GrowProfile6 Growth Profiles
DisparityBox6 Disparity Box, designed for calculation of Morpological Disparity.
LMEdit6 LMEdit6 is an editting tool for altering landmark configurations, allowing for averaging of measurements across an axis of symetry and eventually other tasks.
MakeFan MakeFan, a tool for drawing alignment “fans” at equal angular spacing on an image prior to digitization-can be used with TPSDig, or as a really primitive stand-alone digitizer.
MakeFan EXTRADLL Extra DLL needed for MakeFan-expand this into the Bin\win32 directory where MakeFan is installed, if MakeFan doesn’t work properly initially.
PLSAngle 6b Partial Least Squares tool for comparing patterns of covariance between blocks, using two data of 2 blocks each.
PLSMaker Partial Least Squares Tool for studying patterns of covariance using shape data.
SemiLand6 A tool for processing semi-landmarks, prior to use in other programs. Now includes a zoom function.
ShuffleAllometry6 Computes range of vector correlations that can be generated by random shuffling of a vector.
SpaceAngle Compares the angle between the spaces defined by the PC axis of different groups.
Splice6 A tool to splice together ASCII files, either IMP or TPS.
Standard6a Standardization Utility-removes linear dependences of shape on some variable.
TBox Computes a t-test score, given the means, samples sizes and standard errors in the measurements. Note the use of the standard error, rather than standard deviation.
VecDisplay6 Displays thin plate spline vectors for comparison purposes.
VecCompare6 Computes a growth angle between two groups. Resampling statistics.
VecLand6 Displays landmark by landmark differences between two groups. USE OF VECLAND NOT RECOMMEND – USE VECDISPLAY INSTEAD!
VecLand6b Displays landmark by landmark differences in regress models between two groups.
3D Beta Software
Regress3D Regression analysis of 3D landmark data using partial warp scores.
Simple3D File conversion, Procrustes Superimposition, Goodall’s F-test for differences in means, calculation of Procrustes distances between means for 3D landmark data. Also, 3D Bookstein Coordinates, matrices of all pairwise interspecimen distances.
ThreeDPCA PCA for 3D landmark data, based on partial warp scores.

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