Histocat neighborhood analysis

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Computational image analysis of multiplexed Imaging Mass Cytometry acquisitions
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sleungy
Posts: 2
Joined: Mon Dec 31, 2018 4:06 am

Histocat neighborhood analysis

Post by sleungy » Mon Dec 31, 2018 5:00 am

Hi there,

I am having trouble using Histocat's neighborhood analysis for Hyperion imaging cytof data. If anyone could help, I would be very grateful. Details 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).
The attachment Screen Shot 2018-12-31 at 2.43.30 pm.png is no longer available
(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) I presumed the idea is to select multiple images, generate 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 and nothing further progresses.
The attachment Screen Shot 2018-12-31 at 2.54.15 pm.png is no longer available
First image neighborhood output
First image neighborhood output
Screen Shot 2018-12-31 at 2.43.30 pm.png (14.33 KiB) Viewed 1284 times
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.

Regards, Sherman
DenisSchapiro
Posts: 38
Joined: Wed Nov 29, 2017 11:34 am

Re: Histocat neighborhood analysis

Post by DenisSchapiro » Tue Jan 08, 2019 8:24 pm

Dear Sherman,

I am happy to help. Please create an issue on Github and add also the session file so I can reproduce the error:
https://github.com/BodenmillerGroup/histoCAT/issues

Best

Denis
sleungy
Posts: 2
Joined: Mon Dec 31, 2018 4:06 am

Re: Histocat neighborhood analysis

Post by sleungy » Wed Jan 09, 2019 1:32 am

Dear Denis,

Thank you very much. I have described the issue now on GitHub https://github.com/BodenmillerGroup/histoCAT/issues/20

Kind Regards, Sherman
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