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This is a repository (update site) containing custom plugins and scripts created at the IMCF / Uni Basel, as well as some collected ImageJ plugins we are using that are not (yet) included in Fiji.


To add the repository to your list of FiJi update sites, use this address:

Please see how to follow a 3rd party update site for detailed instructions how to enable an additional update site in your Fiji installation.

PLEASE NOTE: you also need to enable the “IBMP-CNRS” update site that is already configured in Fiji (it’s just not active by default). Otherwise the ActionBars won’t work.


Macros and Plugins in the IMCF repository

Auto Run
Our custom auto run macros.

location: macros/AutoRun/

Action Bars
Our shortcut toolbars, requires the Action Bar plugin.

location: plugins/ActionBar/

IMCF Tools
Custom macros for users of our facility.

location: plugins/IMCF_Tools/

“Just another Coloc Plugin”: a compilation of co-localization tools.

location: plugins/jacop_.jar

Scripts to record the desktop or a single window.

author: Albert Cardona

location: scripts/Record_*.py

Kinetochore Analysis
Plugin for analyzing kinetochores in 3D.

author / license: unknown, please check!!

location: plugins/Kinetochore_Analysis3D.class

FRAP plugins
FRAP Analysis

Tool for normalized analysis of single-spot FRAP experiments.

author: Philippe Carl (

location: plugins/FRAP_Analysis.class


Automatic detection of bleached and whole cell areas in pictures from FRAP experiments.

author: Joris Meys

location: plugins/frap_norm2.jar

Edge detection
Canny-Deriche filtering for edge detection.

author: Thomas Boudier, repackaged by Joris Meys

location: plugins/image_edge.jar

For more information about the IMCF please have a look at our website:

Imaging Core Facility of the Biozentrum, University of Basel, Switzerland.