To fix some of the memory issues in Fiji, the following steps can be taken
= Check Fiji Java version =
Make sure you are running a 64bit version of Java
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If you are not, then delete/rename the `java` folder in your fiji installation and download the [[ http://www.oracle.com/technetwork/java/javase/downloads/index.html | 64-bit Java Development Kit (JDK)]]
Make sure that Fiji understands that you are running on this Java Version by setting the [[ https://stackoverflow.com/questions/2619584/how-to-set-java-home-on-windows-7 | JAVA_HOME and PATH variables to the right location in Windows. ]]
= Increase The Allocated Memeory in Fiji =
Go to {nav Edit > Options > Memory & Threads}
And set the memory to about 80% of your available RAM
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= Change ImageJ.cfg file =
You can change the amount of RAM as per the instructions of the [[ http://imagejdocu.tudor.lu/doku.php?id=faq:technical:how_do_i_increase_the_memory_in_imagej | ImageJ wiki ]]
also attached is a file that allocates 60GB to Fiji that you can use as a starting example.
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NOTE: Keep the newlines in the file, otherwise it does not work...
The ImageJ.cfg file is in the same location as the ImageJ/Fiji executable.