README.md

Headless Fiji

This repository demonstrates how to download, update and run a Fiji script in headless mode, as proof of principle to deploy our scripts to the users of the image analysis facility. This was developed for and tested on a Linux machine.

1. Run the download script to get a fresh Fiji install:

   sh download_fiji.sh myfiji

2. Change the sites.json file:

   {
       "IJPB-plugins": "IJPB-plugins",
       "Labkit": "Labkit"
   }

   The first entry (key) is the name of the update site, the second (value) is the path in the update site. So if in the add update site window of Fiji, the name of the site is Foo and the update site is https://sites.imagej.net/bar, then enter "Foo": "bar".
3. Run the update script:

   sh update_fiji.sh --fiji myfiji/Fiji.app/ --sites sites.json

4. Run the example script:

   myfiji/Fiji.app/ImageJ-linux64 --ij2 --headless --run  macro.ijm 'output=""'

   Here output can be an absolute or relative path, always between quotation marks: 'output="example/path/to/folder"'.