Change the Fiji temp Folder (by passing JVM arguments)

Why? For example if you run Fiji headless on a cluster and you would like it to use a fast local folder instead of a network drive.

This page tells you how you can pass on JVM arguments to Fiji upon start: http://fiji.sc/Java_Options

One can specify the “temp” directory using the following command:

$ fiji -Djava.io.tmpdir=~/tmp -- &

Double dash at the end is required to specify that the given argument is for Java.

Debugging Fiji/ImageJ App

You can reproduce some misbehavior / bug in Fiji – good! But what next?

You could post your problem on the ImageJ mailing list and hope somebody solves the problem  for you, or you could debug the problem yourself. The page below shows you how you can attach eclipse in debug mode to a running (and failing) Fiji/ImageJ instance. Very cool!

http://fiji.sc/Debugging