Search found 4 matches

by cjauset
Fri Aug 28, 2020 2:17 pm
Forum: Data analysis
Topic: Issues with mask/histoCAT segmentation
Replies: 5
Views: 714

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.
by cjauset
Fri Aug 28, 2020 11:40 am
Forum: Data analysis
Topic: Issues with mask/histoCAT segmentation
Replies: 5
Views: 714

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
by cjauset
Thu Aug 27, 2020 4:08 pm
Forum: Data analysis
Topic: Issues with mask/histoCAT segmentation
Replies: 5
Views: 714

Re: Issues with mask/histoCAT segmentation

Ah, of course! Thanks Denis! :D
by cjauset
Mon Aug 24, 2020 1:42 pm
Forum: Data analysis
Topic: Issues with mask/histoCAT segmentation
Replies: 5
Views: 714

Issues with mask/histoCAT segmentation

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: Screenshot 2020-08...