[ome-users] Memory problem opening Zeiss ZVI with Fiji and Bio-formats

[Pelz Benjamin]

Hey everyone,
I have some problems with opening Zeiss ZVI files with the latest Fiji version on Windows 10 64bit. (ImageJ 2.0.0-rc61/1.51n, Java 1.8.0_101 [64bit], 6004MB memory, bio-formats_plugins-5.5.2). I already posted the issue on the ImageJ forum (http://forum.imagej.net/t/memory-problem-opening-zeiss-zvi-file/5813) and they suggested to also file a bug report here. I uploaded a sample file on http://qa.openmicroscopy.org.uk/qa/upload/ (File ID 17769). The ZVI file contains 200 tiles with 2 channels from scanning with a Zeiss AxioImager M2m.
When I open the ZVI file (not very big around 300MB), Fiji starts opening the Bio-formats options. I open the file with "open all series" and "concatenate series when compatible" activated. In the status bar he says import preparations complete and afterwards I see the memory usage increase in the task manager up to 6000MB. The same in ImageJ and eventually he displays the log message:
>>>>>>>>>>>>>>>>>>>>>>>>>>>
<Out of memory>
<All available memory (5970MB) has been>
<used. To make more available, use the>
<Edit>Options>Memory & Threads command.>
>>>>>>>>>>>>>>>>>>>>>>>>>>>

This works without a problem using ImageJ 2.0.0-rc56/1.51h, Java 1.8.0_66 [64bit], bio-formats_plugins-5.3.3. Here the memory usage in ImageJ is just 300MB.

Has anybody an idea what the problem is?

Thanks
Benjamin

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