ImageJ Documentation Wiki

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====== Setting up ij tools in Galaxy ======

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===== Disclaimer =====

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

<note> 
So far only TIF as input, TIF as output.
</note>

===== Background =====

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 http://cloudimaging.blogspot.com.au/ makes some custom IP tools available, but not ImageJ, so I'm giving a try.

===== Installation =====

Just follow this tutorial: https://wiki.galaxyproject.org/Admin/GetGalaxy

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

<note info>
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 : https://github.com/mutterer/ij-galaxy
</note>

  * edit **galaxy-dist/tool_conf.xml** to account for the new tools

<file java galaxy-dist/tool_conf.xml>
  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" />
  </section>

</file>

  * stop and reload your Galaxy instance


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

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