IMP 8- Runs under Mac OSX 10.7,10.8, Windows 7,8

 

     Software for Land-mark based Geometric Morphometric Analysis of Shape

Tools available for both 2D and 3D data

 

 

sheets@canisius.edu, hsheets@buffalo.edu

 

This version of IMP 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 IMP8.

 

In IMP8, many previously independent programs have been bundled into a more limited number of packages.   CoordGen8 for example can “call  TMorphGen, SemiLand, MatchMaker, BigFix and VisProto Editor.   CoordGen doesn’t look much different that 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.   It will make my life easier in maintaining them as well (fingers crossed!).

 

All users should download CoordGen first and make sure it works before proceeding to other programs.   CoordGen also installs the dynamic link libraries, the other programs assume CoordGen has already taken care of this.  CoordGen should create a directory in your program files (Win) or applications (Mac) directory called IMP8.   Within this directory, you will find CoordGen.  Save the other zipped or compressed files into the directory created by CoordGen, and then expand them.   You may have to use the Mac “Open” command to avoid a system warning that the program is from an unrecognized developer.

 

Note: 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.

 

Zip File Contents- These typically include the software tool and some example files.   Users manuals are now online and accessed from inside the program, using your default system browser.

 

What is IMP?

 

2D IMP Programs

 

Versions updated the week of 3/7/14

Mac versions need OSX 10.7 or later, Windows needs Windows 7 or later

 

Programs                                                    Comments/Description

 

CoordGen8_Mac      CoordGen8_Win              Utility tool for file conversion, checking for digitizing errors and

                                                                 Other data management tasks, and simple statistics on a single data set

 

                                                                 Now Included witnin 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

 

                                                                                                            User’s Manual for CoordGen8

 

 

 

TwoGroup8_Mac     TwoGroup8_Win             TwoGroup8- Tool for comparing the means of two groups, and displaying                                                                                               

                                                                                      differences in mean shape. 

 

 

PCAGen8_Mac        PCAGen8_Win                PCAGen8- PCA tool in the IMP series, also includes

       Compiled 5/5/2014                                                  

                                                                        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

 

CVAGen8_Mac        CVAGen8_Win               CVAGen8- Canonical Variates Analysis of landmark data

 

Regress8_Mac        Regress8_Win               Regress8- 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

 

PLSMaker8_Mac    PLSMaker8_Win            PLSMaker8- 2 Block Partial Least squares, also includes

       Compiled 5/5/2014

                                                                               PLSAngle8- tools for comparing variance+covariance patterns

                                                                                      in multiple groups

             

                                                                               SpaceAngle- Calculate of angles between subspaces defined

                                                                                      by PCA axes of groups

                                                                                                    

                                                                               OModel-

 

MakeFan8_Mac     MakeFan8_Win             Make Fan- Tool for drawing “fans” or guidelines for digitizing semi-landmarks                                                                           on images.

 

 

 

 

                                                                 3D IMP Programs

                                    Updated the week of 3/14/14

 

 

Note: If you are using the IMP3D tools, you must still install CoordGen8 (above) first, to install the necessary Matlab drivers.  Install and check CoordGen8 before proceeding with the 3D tools below.

 

Simple3D_Mac               Simple3D_Win        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

 

                                                                               Now 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

 

                                                                

ThreeD_PCA_Mac           ThreeD_PCA_Win    ThreeDPCA8- PCA analysis of 3D shape data

 

                                                                 Also includes:

 

                                                                 DisparityBox3D8- analysis of disparity patterns

 

 

ThreeD_CVA_Mac           ThreeD_CVA_Win    ThreeDCVA8- CVA of 3D shape data

 

 

ThreeD_Regress_Mac                                  ThreeDRegress- Regression Tools in 3D

 

                             ThreeD_Regress_Win             also includes

 

                                                                 VecCompare3D- 3D comparisons of ontogenetic trajectories

                                                         

                                                                 Standardize3D- Standardization tool for residual analysis in 3D

 

ThreeD_PLS_Mac            ThreeD_PLS_Win     ThreeDPLS8- Partial Least Squares analysis

 

                                                                        Includes

      

                                                                        ThreeDPLS_Angle8- Comparison of covariance patterns in multiple groups