Klingenberg lab

MorphoJ

MorphoJ is an integrated program package for doing geometric morphometrics. The goal of the program is to provide a platform for the most important types of analyses in geometric morphometrics in a user-friendly package. The program is written for both 2D and 3D data, with some inevitable differences in the graphical output possibilities etc. MorphoJ is available for free under the Apache License, Version 2.0.

Features presently implemented in the program include:

• Procrustes fit for 2D and 3D data with and without object symmetry
• Import/export of data sets and supplementary information
• Identification of outliers (with choices for including/excluding observations and fixing some problems)
• Generating covariance matrices ('standard' and pooled within-group covariances)
• Principal component analysis
• Matrix correlation (including automatic adjustment for symmetry/asymmetry for configurations with object symmetry)
• Two-block partial least squares
• Regression (arbitrary numbers of dependent and independent variables; also pooled within-group regression, e.g. for allometry correction in multiple groups)
• Evaluation of modularity hypotheses
• Canonical variate analysis
• Linear discriminant analysis, including cross-validation
• Mapping shape variables onto a phylogeny and comparative methods (e.g. independent contrasts)
• Various analyses concerning the quantitative genetics of shape and selection for shape

Additional features will be included in future releases.

Downloads and installation instructions

The MorphoJ software is distributed for MS Windows, Mac OS and Ubuntu/Linux as self-contained software packages (unlike older versions, no external copy of a Java runtime environment is necessary).

The current version of MorphoJ is 1.08.01. See the MorphoJ Change Log for the changes made in the current version of MorphoJ and in previous updates. If you have an older version, it is recommended that you update to the current version.

Current versions of MorphoJ are distributed for MS Windows, Mac OS and Ubuntu/Linux as self-contained software packages (unlike older versions, no external copy of a Java runtime environment is necessary).Program documentation

All these operating systems have security systems that will initially block the user from installing and running the software because it is not from a recognized developer/vendor. Users need to have administrator privileges to install and first run the software, and depending on the operating system, messages may be rather unhelpful (e.g. Mac OS showing a message that the program file is damaged). On computers configured by an institution, e.g. a university, there may be further limits and the help from IT services at the user's institution may be needed.

For instance, on Mac OS, the software normally will not run after installing from the .dmg installer. Instead, the user needs to go to the Applications folder to locate the "MorphoJ.app" file, right-click it and choose the "Run" option. A dialog box (above, left) will appear with the options to cancel or to bin the application; choose "Cancel". Then, right-click "MorphoJ.app" once more, and choose the "Run" option again. Now, a dialog box will appear (above, right) with the options to open, bin or cancel; choose "Open". From now on, the MorphoJ application will open as a standard Mac application.

These steps after downloading the software differ according to operating system, and further differences are to be expected between different versions, according to what security software is installed or whether it is a private or institutional computer. An internet search or asking staff at local IT services usually helps.

Older versions of MorphoJ are available here. Download and use them only for specific purposes. Unless there is a convincing reason for doing so, I strongly advise against this.

Program documentation

The online User's Guide for MorphoJ is available here.

You may want to bookmark the user's guide in your favorite browser.

A copy of the User's Guide is also included with each installation of MorphoJ for offline use, and can be accessed by selecting User's Guide from the Help menu. This will launch your computer's default browser to display the User's Guide.

A brief overview of MorphoJ is available in this paper, which is also the preferred citation for MorphoJ:
Klingenberg, C. P. 2011. MorphoJ: an integrated software package for geometric morphometrics. Molecular Ecology Resources 11: 353-357. PDF file:

Updates

There are occasional updates of the MorphoJ software due to bug fixes or for adding new methods. Updated versions are available for download from this page.

Updates are announced on the Mophmet Google group. Subscribing to the list is therefore a good idea. However, for various reasons, there may be delays or missed postings.

You might therefore want to check on the MorphoJ change log (part of the online User's Guide) whether there have been recent updates (note: use the online version and not the copy included with your MorphoJ installation).