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BodenmillerGroup / ImcSegmentationPipeline

A pixel classification based multiplexed image segmentation pipeline
https://bodenmillergroup.github.io/ImcSegmentationPipeline/
MIT License
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TIFF output all black #135

Closed alyoung85 closed 10 months ago

alyoung85 commented 11 months ago

Hello,

When running through _IMCSEGPIPE.PY within create_analysis_stacks it appears like the acquisition_img array contains the appropriate intensity values. But, when the analysis_img is outputted with tifffile.imwrite the resulting tiff file is all black.

I have turned off hpf, so it's not a hot pixel filtering issue.

What other information do you need from me to troubleshoot this?

Thanks Andrew

nilseling commented 11 months ago

@Milad4849 could you please have a look? My assumption is that the contrast hasn't been adjusted when visualizing the images.

Milad4849 commented 11 months ago

Hi @alyoung85 Thank you for reaching out. From your description I cannot really tell if you are having a visualization issue or a data processing one. Can you check if the image that you write is fine by reading the file with tifffile.imreadand checking that the intensity values are as expected. If that is the case then the issue is likely with the visualization settings as @nilseling suspects.

nilseling commented 10 months ago

Hi @alyoung85

Please close this issue if it has been resolved.

alyoung85 commented 10 months ago

Hello Nils,

Sorry. I can close the issue.

Andrew

From: Nils Eling @.> Sent: Wednesday, November 15, 2023 11:03 AM To: BodenmillerGroup/ImcSegmentationPipeline @.> Cc: Young, Andrew @.>; Mention @.> Subject: Re: [BodenmillerGroup/ImcSegmentationPipeline] TIFF output all black (Issue #135)

Hi @alyoung85https://github.com/alyoung85

Please close this issue if it has been resolved.

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