Nutil crashes for large datasets

[TomHaran]

Hello,

I'm using Nutil to quantify signals from section of the entire mouse brain. This means I typically run it on ~100 images.

While Nutil handles it fine for spares signals, I noticed that when I try to quantify ubiquitous signals (such as DAPI) in my dataset, Nutil crashes before it is able to finish the analysis. This usually happens when generating the report sheets, so there are missing csv files in the final outcome (always object reports, sometimes also individual sections' reports).

I tried to use more powerful computers, both windows and Linux, but currently I can't make it work even when performing the analysis with 60 threads. It works fine for a single image but not for multiple.

Is there anything I can do to fix this?

Thank you!

Tom

[sharoncy]

Hi Tom,

Sorry to hear you're having problems. I presume it's crashing because Nutil is near its limit in terms of segmentation size (https://nutil.readthedocs.io/en/latest/QuantifierInput.html#preparing-the-segmentations). How big are yout image segmentations on average (pixel height by pixel width)? Nutil supports up to about 10000 x 10000 pixels, although i've got it to work for bigger images before. If possible, I suggest downscaling the segmentations, although this may of course mean you lose some signal.

Another thing you can try is to switch off the coordinate extraction feature in Nutil (coordinate extraction = no). This should also make it run more efficiently. If you do need coordinates, try running coordinate extraction with a lower pixel density (e.g. 10 means 1 coordinate assigned per every 10 pixels).

If you're still having problems and would like me to investigate further, feel free to send me some example files (your JSON file, an atlasmap and corresponding segmentation file) to support@ebrains.eu, stating that the question should be forwarded to Sharon Yates of the brain atlasing team).

Best regards,
Sharon

[TomHaran]

Thank you for your reply!
I checked and found that my segmentation files are large, some exceeding 10,000x10,000 pixels. In accordance with your recommendations,  I tried downscaling them by half. I also disabled coordination extraction, but still Nutil crashed.

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