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BodenmillerGroup / ImcSegmentationPipeline

A pixel classification based multiplexed image segmentation pipeline
https://bodenmillergroup.github.io/ImcSegmentationPipeline/
MIT License
83 stars 35 forks source link

Generation of histocat folders with mask #71

Closed veenstje closed 2 years ago

veenstje commented 3 years ago

Hi @votti

When trying to create histocat folders with the final mask I'm having an issue with the mask file getting created properly. After the _mask.tiff files are successfully created in the tiffs folder using the CP segment_ilastik pipeline, I run the last line of jupyter script to "generate the histocat folder with masks," which completes successfully. However, the _mask file that is created in each histocat folder has no extension or defined file type and does not register as a mask in histocat (see screen shot below). I've tried this with the example data set as well as several others with the same result. Do you know how to correct this issue?

error

I'm using IMC tools 2.1.6 along with the most up to date segmentation pipeline

Thanks

veenstje commented 3 years ago

Thank you

votti commented 3 years ago

Sorry for the trouble with this - should be fixed soon.

I think as a workaround until BodenmillerGroup/imctools#111 is fixed you could just manually add the '.tiff' extension to the files and this should work.

Best, Vito

veenstje commented 3 years ago

Thanks Vito

Jesse Veenstra MD, PhD, MS, FAAD Staff Dermatologist Department of Dermatology​ Henry Ford Health System 3031 West Grand Blvd, Suite 800 Detroit, MI 48202 Office: 313-916-2151 Fax: 313-916-5334 [cid:8d72ac44-90b1-491b-8ce1-9c896e98a59d]

From: Vito Zanotelli @.> Sent: Thursday, May 20, 2021 5:08 PM To: BodenmillerGroup/ImcSegmentationPipeline @.> Cc: Veenstra, Jesse @.>; Author @.> Subject: Re: [BodenmillerGroup/ImcSegmentationPipeline] Generation of histocat folders with mask (#71)

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I think as a workaround until BodenmillerGroup/imctools#111https://urldefense.com/v3/__https://github.com/BodenmillerGroup/imctools/issues/111__;!!PFzsKvxRBh-H!OonUuIj5bDwxjNbv_soGZDFzl4qvfuFTnI9h6tvNi9L5isiBIOlLLDJNuZwJRlo$ is fixed you could just manually add the '.tiff' extension to the files and this should work.

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