Help with neighborhood analysis

Looking for ways to analyze your dataset? Need help with a software package?
Computational image analysis of multiplexed Imaging Mass Cytometry acquisitions
Post Reply
mattbliss90
Posts: 10
Joined: Wed Jan 17, 2018 11:37 pm

Help with neighborhood analysis

Post by mattbliss90 » Fri Jul 06, 2018 6:52 pm

Hello,
I am having trouble getting the neighborhood analysis to work on Histocat. As outlined in the manual I select the ROI in Samples/Populations and then click "neighborhood analysis" next to the prepare button and fill in the cluster number on the new pop up window and then select the phenograph. The "please wait" box then appears and remains on the screen for around ~5 min and then goes away. Is the analysis and heat map supposed to be saved in the new matlab file that now appears in the custom gates folder? I can't seem to open this new matlab file on Histocat.

Thanks,
Matt
DenisSchapiro
Posts: 38
Joined: Wed Nov 29, 2017 11:34 am

Re: Help with neighborhood analysis

Post by DenisSchapiro » Sun Jul 08, 2018 8:53 pm

Dear Matt,

I am happy to help! Please provide me/us with some further information:

(1) Did you try to use the published histoCAT session or only your own one?
--> Do you see the same behaviour on the published data set?

(2) The plots should be saved in your custom folder. Make sure there are no folder names above the folder with "spaces" in the folder name.

(3) What histoCAT version are you using? Make sure to always use the newest version here: https://github.com/BodenmillerGroup/histoCAT
--> New update is already coming in the next few days :)

I am looking forward to solve your problem.

Best

Denis
Luis M
Posts: 4
Joined: Tue Oct 23, 2018 8:53 pm

Re: Help with neighborhood analysis

Post by Luis M » Thu Oct 25, 2018 2:49 am

Hi Denis
I have the same issue as Matt. I've tried running the phenograph analysis on both my samples and the publish samples. I am using the latest version of Histocat (1.75) on Windows 10 on an 2017 XPS15. When I attempt to run the analysis, I get a notification sound that usually occurs when I do something the program doesn't like (eg when I once tried to load a custom-named cell mask). The "running phenograph, please wait" dialog box stays on indefinitely.
Luis M
Posts: 4
Joined: Tue Oct 23, 2018 8:53 pm

Re: Help with neighborhood analysis

Post by Luis M » Thu Oct 25, 2018 3:30 am

Hi Denis
I have the same issue as Matt and I have tried on both my samples and the published samples. I am using the latest version of HistoCAT (1.75) on a 2017 XPS laptop with Windows 10. When I try to run the phenotype analysis, initially I get a notification sound and the "Running phenotype analysis, please wait" dialog box, but it stays indefinitely and no analysis occurs. The notification sound I get is the same kind whenever I try to perform a task the program doesn't like (eg when I tired to use a custom-named cell mask).
DenisSchapiro
Posts: 38
Joined: Wed Nov 29, 2017 11:34 am

Re: Help with neighborhood analysis

Post by DenisSchapiro » Mon Oct 29, 2018 1:21 am

The most common problem is the folder naming. Could you check whether you have any spaces in your folder structure where you save the images (including parent-folder). I am working a new version, which should be less sensitive, but this would be a possible workaround for now!

Feel free to share your session with me and I am happy to assist individually.
Luis M
Posts: 4
Joined: Tue Oct 23, 2018 8:53 pm

Re: Help with neighborhood analysis

Post by Luis M » Mon Oct 29, 2018 1:48 am

Hi Dennis
As spaces in folder names previously gave me issues with loading data files and saving sessions, I ensured there were no spaces in any folders or filenames. Are hypens, en/em dashes acceptable? I have some folders and files names with those.
And is the session data the .mat file? I can't seem to attach it to this thread as the website states it is an invalid file format.
DenisSchapiro
Posts: 38
Joined: Wed Nov 29, 2017 11:34 am

Re: Help with neighborhood analysis

Post by DenisSchapiro » Mon Oct 29, 2018 1:58 am

Dashes could be an issue as well. Ideally no special characters.
As I said, I am working on a stable version which should take care of that, but for now please do not use special character. Let me know if this does not help.
Luis M
Posts: 4
Joined: Tue Oct 23, 2018 8:53 pm

Re: Help with neighborhood analysis

Post by Luis M » Tue Oct 30, 2018 8:26 pm

Hi Denis
I've removed all potential special characters but alas the issue still persists. Do you know when the next version will be released?
DenisSchapiro
Posts: 38
Joined: Wed Nov 29, 2017 11:34 am

Re: Help with neighborhood analysis

Post by DenisSchapiro » Tue Oct 30, 2018 8:29 pm

This is an interesting issue. Could you share the .mat file via denis_schapiro(at)hms(dot)harvard(dot)edu
Post Reply