User Tools

Site Tools


Setting up ij tools in Galaxy


This is just a proof of concept. Only tested on my 10.8.5 Mac.

So far only TIF as input, TIF as output.


Galaxy is an open, web-based platform for data intensive biomedical research. You have tools for making data available and to process these data. Galaxy offers a toolshed with extra tools you can install. The toolshed has a 'Image processing' section, but it was empty. A similar project by CSIRO makes some custom IP tools available, but not ImageJ, so I'm giving a try.


Just follow this tutorial:

It was enough to get Galaxy running on my mac.

Add ImageJ tools

  • Create an imagej folder in your galaxy-dist/tools folder
  • put ij.jar in the fresh galaxy-dist/tools/imagej folder
  • add the new tools definition files in galaxy-dist/tools/imagej as well
in my case, each new tool consists of a tool definition file (xml) that describes inputs, outputs and a script (pyhton) that takes care of creating a proper ImageJ macro and calls it.

Get them all from GitHub :

  • edit galaxy-dist/tool_conf.xml to account for the new tools
  add this section to existing configuration
  <section id="imagej" name="Image Processing">
    <tool file="data_source/upload.xml" />
    <tool file="imagej/extractChannelAs32bit.xml" />
    <tool file="imagej/ijFilters.xml" />   
    <tool file="imagej/pixelMath.xml" />   
    <tool file="imagej/calculatorMacro.xml" />   
    <tool file="imagej/applyMacro.xml" />
  • stop and reload your Galaxy instance


Once you have working tools, you can also chain them into workflows.

howto/working/setting_up_ij_tools_in_galaxy.txt ยท Last modified: 2019/04/12 13:13 by

Donate Powered by PHP Valid HTML5 Valid CSS Driven by DokuWiki