Neighbourhood analysis heatmap problem

[sleungy]

Hi Denis,

Thanks for your help in advance. As mentioned on IMC-forum (https://www.imc-forum.org/viewtopic.php?f=4&t=144), I am detailing my issue here. In sum, I am having issues generating neighbourhood analysis heat maps. Details are below.

(1) Using a single image and it’s phenograph clusters, neighborhood analyses shows a binary yes (red) or no (blue) heatmap (shown below inline).

(2) When a second image is loaded and phenograph clusters generated for this second image, neighborhood analyses similarly shows a binary yes (red) or no (blue) heatmap.

(3) Therefore, I assumed the idea was to select multiple images, generate combined phenograph clusters, then perform neighborhood analysis so there is a "continuum" of frequencies for cells to neighbor each other in a cluster (not just a yes or no). So I selected both the first and second images and generated phenograph clusters, then conducted neighborhood analyses. However, after the usual pop-up (shown below inline), I get an error beep sound (or sometimes no sound at all) and nothing further progresses.

There are no spaces or special characters in the directories and I have been following the Histocat 1.75 manual (but must have misunderstood instructions at some point). I'm using an old Macbook High Sierra v10.13.3. I have emailed you the histocat files privately. Sherman

[DenisSch]

Dear Sherman,

Thank you for your patience. This is indeed a bug, which will be fixed with the next histoCAT version. I have just pushed a bug-fix.

A workaround until I compile the new version would be to run only one clustering method across all samples at the same time. You have run k-means on one sample, but not on the other one, which created an error to cancel the neighborhood analysis.

Best

Denis