Thursday, December 16, 2010

Set maximum memory limit in Fiji

Fiji is a "bundle version" of ImageJ, i.e., ImageJ + a lot of plugins already developed and installed.

I use it on a daily basis for my image processing/analysis tasks.

When there is need to import a sequence of images as a stack and such stack is quite big, you may need to setup a larger maximum memory limit than what it comes with the standard setup.

In order to do that, open the menu Edit -> Options -> Memory & Threads and fix the maximum memory limit.

This operation essentially writes into Fiji startup configuration file, called jvm.cfg and located within Fiji's root folder. If you open it, you can see the Java Virtual Machine option -Xmx????m, where ????m indicates the maximum memory limit expressed in MBytes.