Memory issue in CellProfiler when running Measure_mask pipeline

BodenmillerGroup / ImcSegmentationPipeline

A pixel classification based multiplexed image segmentation pipeline

https://bodenmillergroup.github.io/ImcSegmentationPipeline/

MIT License

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Memory issue in CellProfiler when running Measure_mask pipeline #44

Closed cjauset closed 3 years ago

cjauset commented 4 years ago

Hi Vito,

I am having some issues segmenting an image due to memory, so I was wondering if you had seen this in the past and could suggest any solution.

I am having the following error when doing the last step of the segmentation pipeline (Measure_mask_basic): "Error while processing MeasureObjectNeighbors: (Worker) MemoryError: "

Sizes for the inputs are: Full stack: 680MB Probabilities: 226MB Mask: 35MB

The system I'm using has 620GB of available physical memory.

Thanks!

Best, Cristina

votti commented 4 years ago

Hi Christina,

Sorry for not answering earlier :/ Hm I dont really know what's the issue here: does it happen with all image sets or just with one?

I think that almost might be a question better suited for the Cellprofiler section of the 'image.sc' forum, as it seems to be an issue with your mask/the MeasureObjectNeighbors module.

Generally it is likely that you wont need the results from 'MeasureObjectNeighbors' anyways for a simple analysis, so you may also just disable this step until the problem is identified/resolved.

Cheers!