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>
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.
Just follow this tutorial: https://wiki.galaxyproject.org/Admin/GetGalaxy
It was enough to get Galaxy running on my mac.
<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>
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>
Once you have working tools, you can also chain them into workflows.