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

[David Gault (Staff)]

Hi Benjamin,

Thank you for providing the sample file. I was able to reproduce the issue using the settings you stated.
>From debugging the import process it appears the build of memory is caused due to the metadata being temporarily stored for each series before the concatenation occurs. The metadata in this particular case happens too be quite large, however it should not need to be stored multiple times as it is currently doing so.

I believe I might have a fix for this issue although it requires further testing. I have added a card with more details on the Bio-Formats Trello inbox to track the issue and is linked below:
https://trello.com/c/evfYjQ4y/15-imagej-concatenate-memory-usage

With Thanks,
David Gault

> On 27 Jun 2017, at 13:44, Pelz Benjamin <benjamin.pelz at epfl.ch> wrote:
>
> 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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