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Running scripts with an open Virtual Hyperstack

Posted by Greg on Mar 25, 2015; 1:51pm
URL: http://imagej.273.s1.nabble.com/Running-scripts-with-an-open-Virtual-Hyperstack-tp5012163.html

Hi,

today I witnessed a rather odd behavior of Fiji when trying to run my jython scripts on a opened virtual hyperstack. So basically it took ages to run my script so I stripped it down to the point, where I realized that you just have to try to run an empty (!) script from the script editor to see all your RAM eaten up. I tested that for jython and javascript.

So what I did:

opened a 7gb ome.tiff with Bio Formats Importer in virtual hyperstack mode
opened the script editor via file -> new -> script
choosed python/java script as language
pressed run on the empty(!) script

What I see:

When monitoring the RAM, I see it gets filled rather quickly by Fiji up to the size of 9.5Gb. For bigger input files more RAM gets 'used' accordingly. So for files exceeding my physical amount of Memory Fiji becomes unresponsive rather quickly. I experienced the same behavior for nd2 files.

Is there a way to cirmumvent this ? I guess Fiji tries to load the whole image stack despite having chosen 'virtual stack' in the first place ?

Best,
Greg