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Martin Stöter edited this page Nov 28, 2017 · 20 revisions

Welcome to the Fiji-Tools-for-HCS wiki!


This wiki supports the documentation of Fiji macros and plugins that have been created to process and analyse images that are come from automatic microscopes and/or need some automated processing. This page was created by MPI-CBG staff HT-TDS and is open to host all useful tools in the field of high-content screening (HCS).


To use the Fiji-Tools-for-HCS you need to install Fiji with the update site 'Fiji-Tools-for-HCS'.
Installation details here...

Content Overview

Currently, all tools are Fiji macros (Imagej macro language) and suppose to run with the latest version of Fiji. A set of plugins (written in Java) is currently under development and suppose to extend the functionalities within the macro language. This plugin is called "FijiToolsForHCSplugin". The macros "Fiji-Tools-for-HCS" are sorted into categories. Details you will find on each macro wiki site.

Automated Microscope Tools

Cell Analysis Tools

File Conversion

Fish Embryo Screen

Image File Filter

Development & Code

this wiki is still under construction (for quick questions send email to the email address below...)


The macros and plugins are hosted here at GitHub and at ImageJ server.


Feel welcome to contact us (stoeter at if you want to contribute to this project, have suggestions, found bugs, or want to be able to edit the wiki (please login and notify stoeter at so that editing permissions can be given).

:Category:Input-Output :Category:Fish-Embryo-Screen :Category:Automated-Microscope-Tools :Category:Misc