Post Thu Oct 03, 2019 3:53 am

Trouble with histoCAT and masks

Hi All,

I'm using histoCAT for some IMC analysis and have encountered a strange issue. It appears to be reading my cell mask images as a channel instead of a mask. When I upload my data folders, the mask from each is instead coming up under the 'Channels' bar, and also when I click 'Mask on/off', nothing is happening.

I have encountered a few histoCAT problems over the past months, but this one is new! I am using CellProfiler to create the segmentation mask, except the pipeline I use is the same I have used for all my old sample sets and those didn't have this problem.

Mask file is just a regular 16 bit tiff, file name has 'mask' in it. The files themselves look no different to ones I have used in the past without issue. All the other channels look fine.

Any ideas?

EDIT: Solved the problem by just doing the whole thing again and it appears to have fixed itself, although I'm not sure how. I'll leave this up in case others have a similar issue.