Skip to content


Folders and files

Last commit message
Last commit date

Latest commit


Repository files navigation

MSOT Cluster Analysis Toolkit (Mcat)



Copyright by Dr. Bianca Hoffmann, Ruman Gerst, Dr. Zoltán Cseresnyés and Prof. Dr. Marc Thilo Figge

Research Group Applied Systems Biology - Head: Prof. Dr. Marc Thilo Figge
HKI-Center for Systems Biology of Infection
Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Insitute (HKI)
Adolf-Reichwein-Straße 23, 07745 Jena, Germany

The project code is licensed under BSD 2-Clause. See the LICENSE file provided with the code for the full license.

System Requirements

Mcat is Java-based and generally platform-independent. It was tested on Windows 10 and Linux Ubuntu 20.10.


If you don’t have ImageJ installed yet, you can get it here. To integrate Mcat into your ImageJ distribution you can either install it via its ImageJ Update Site or manually.

Installation via Update Site:

  • In ImageJ go to Help > Update...
  • Click Manage Update Sites.
  • Scroll down the list and tick the check box for Mcat.
  • Close the Manage Update Sites window.
  • Click Apply Changes.
  • Restart ImageJ when prompted so.
  • Mcat should now appear at the bottom of the Plugins menu.

Manual installation:

  • Download the package (under Releases on the right hand side) and unzip the *.zip archive.
  • Copy all files from the unzipped folder (Mcat-1.0.0.jar and dependencies folder) into the plugins directory of your ImageJ installation.
  • Restart ImageJ.
  • Mcat should now appear at the bottom of the Plugins menu.


See User Manual for instructions on how to run Mcat and the expected output data.

Running MCAT from command line

You can run an MCAT project from command line:

./ImageJ-linux64 --pass-classpath --full-classpath --main-class org.hkijena.mcat.Main --project-file=<Project file> --output-path=<Output path>


Breeze icons

Our plugin uses the Breeze icon pack by KDE, licensed under lesser GPL.

Font awesome icons

Our plugin uses icons from Font Awesome by Fonticons, Inc. We obtained the icons via the Font-Awesome-SVG-PNG project by Code Charm. The Font Awesome font is licensed under the SIL OFL 1.1. Font-Awesome-SVG-PNG is licensed under MIT.