Hello!
I've processed an image through the IMC Segmentation pipeline and I am now trying to analyze the single-cell data in histoCAT.
However, histoCAT only seem to recognize 5 cells in total, so I am not sure if my mask is properly created - it has a gradient of four intensities:
When I try to visualize channels in histoCAT using the heatmap I get the same gradient I see in the mask:
If I do the step 3 of the segmentation pipeline, however, I get 126k cells. Is there any pipeline/script for downstream analyses using the single-cell measurements from the segmentation pipeline in histoCAT or R?
Thanks!
Best,
Cristina
Issues with mask/histoCAT segmentation
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- Posts: 43
- Joined: Wed Nov 29, 2017 11:34 am
Re: Issues with mask/histoCAT segmentation
Dear Cristina,
I believe that the issue is that you are saving your mask as 16bit and you should create a 32bit mask instead.
If you have more than 65536 single cells a 16bit mask can not provide unique values to each cell. Just save it as a 32bit mask - histoCAT is supporting 32bit masks.
Best
Denis
I believe that the issue is that you are saving your mask as 16bit and you should create a 32bit mask instead.
If you have more than 65536 single cells a 16bit mask can not provide unique values to each cell. Just save it as a 32bit mask - histoCAT is supporting 32bit masks.
Best
Denis
Re: Issues with mask/histoCAT segmentation
Ah, of course! Thanks Denis! 

Re: Issues with mask/histoCAT segmentation
Hi Denis,
I realized CellProfiler can just save 32bit images as floating points, but Histocat can only read masks in int32 or uint32 if I understood correctly. Is there a way to make this compatible?
Thanks again!
Cristina
I realized CellProfiler can just save 32bit images as floating points, but Histocat can only read masks in int32 or uint32 if I understood correctly. Is there a way to make this compatible?
Thanks again!
Cristina
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- Posts: 43
- Joined: Wed Nov 29, 2017 11:34 am
Re: Issues with mask/histoCAT segmentation
It should be able to load the CellProfiler 32bit float mask - or did you try and it fail?
Re: Issues with mask/histoCAT segmentation
So after the transformation window when loading the images, nothing happens. There's no error message, but it doesn't say that it's loading either, so I assumed it was the mask format.