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labsyspharm / mcmicro

Multiple-choice microscopy pipeline
https://mcmicro.org/
MIT License
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Exemplar-001 nuclei segmentation is identical to the cell segmentation #531

Closed LucaMarconato closed 6 months ago

LucaMarconato commented 6 months ago

It appears that the nuclei segmentation in exemplar-001 is incorrect as it coincides with the cell segmentation (see screenshot from FIJI).

Screenshot 2024-01-06 at 14 06 33

The two files are located in exemplar-001/segmentation/unmicst-exemplar_001/ and have filenames cell.ome.tif and nuclei.ome.tif.

CC @keller-mark, who originally reported the bug in https://github.com/scverse/spatialdata-notebooks/issues/52.

LucaMarconato commented 6 months ago

I see a similar problem also with exemplar-002, in fact the segmentation files in qc/s3seg/unmicst-1/ for cells and nuclei (cellOutlines.ome.tif and nucleiOutlines.ome.tif), show the same segmentation.

Screenshot 2024-01-06 at 15 11 08
ArtemSokolov commented 6 months ago

Thanks, @LucaMarconato. Is this with default parameters?

@clarenceyapp Can you take a look when you have a chance?

LucaMarconato commented 6 months ago

The files have been generated by @melonora; can you please comment on this?

clarenceyapp commented 6 months ago

By default, cytoplasm segmentation is switched off. So only nuclei are segmented. Users have historically wanted a mask called cell to always get written out even if it's drawing intensities from the nucleus so both files (nucleus and cell) will be duplicates. To get a true cell, cytoplasm, and nucleus mask, the segment cytoplasm flag must be on.

Clarence

From: LucaMarconato @.> Sent: Saturday, January 6, 2024 11:11:18 AM To: labsyspharm/mcmicro @.> Cc: Yapp, Clarence @.>; Mention @.> Subject: Re: [labsyspharm/mcmicro] Exemplar-001 nuclei segmentation is identical to the cell segmentation (Issue #531)

The files have been generated by @melonorahttps://github.com/melonora; can you please comment on this?

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LucaMarconato commented 6 months ago

Thank you for the clarification @clarenceyapp!