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.

See the MorphoJ Change Log for the current version of MorphoJ and the changes made in recent updates.

The software is written in Java, and includes external libraries that are also written in Java. As a result, the program is more or less platform-independent. At the moment, there are distributions of the test versions for Windows, Macintosh OS X (10.5 and higher) and Unix/Linux (tested under Ubuntu Linux only). All you will need to run it is a recent Java Runtime Environment (minimum Version 6.0) for your operating system, which is available for free from http://www.java.com (Windows and Unix/Linux) or comes with your operating system (Mac; users of OS X 10.5 may have to upgrade to version 6.0).

Downloads and installation instructions

The following links provide installer programs and web pages with installation instructions for the operating systems that are currently supported.

For each operating system, there are two types of installer: a standard installer, which is self-contained and provides the complete software, and a web installer, which is smaller and will download the required files in three separate parcels from the MorphoJ web site during installation. This installer can only be used for computers that are connected to the internet during the installation process. It is recommended for users whose internet connection does not allow files of about 7MB to be downloaded. Other users should download the standard installer.

The use of both types of installer is very similar.

Standard installer
(download)

Web installer
(download)
Installation instructions
(web page)

Updated versions of the program will be posted here periodically.

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 MORPHMET mailing list. Subscribing to the list is therefore a good idea. However, due to recent technical problems wth the list, there have been delays with 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).