Bug with HistoCAT

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Computational image analysis of multiplexed Imaging Mass Cytometry acquisitions
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monirathhav
Posts: 17
Joined: Sat Feb 24, 2018 6:33 am

Bug with HistoCAT

Post by monirathhav » Mon Oct 15, 2018 11:06 pm

Hi,

I uploaded several images onto HistoCAT. When I overlayed the mask on "Apply RGB image", the mask was completely off, smaller and with different shape. It was a different mask from the mask of the image. Has anyone encountered similar problem?

Thanks for helping to troubleshoot this issue.

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

Re: Bug with HistoCAT

Post by DenisSchapiro » Tue Oct 16, 2018 2:36 am

Dear Monirath,

Would you mind to share an example mask and image?

Best

Denis
monirathhav
Posts: 17
Joined: Sat Feb 24, 2018 6:33 am

Re: Bug with HistoCAT

Post by monirathhav » Tue Oct 16, 2018 3:42 pm

Hi Denis,

I have attached 3 examples for you where the same mask from case 8_3939 was applied to all other cases. At first, I thought that I mistakenly copied and pasted the wrong mask file into the other two TIFF folders. But I already checked in the original TIFF folders and saw that I had the right masks in their respective folders. I'm not sure why HistoCAT keeps displaying the same mask on other cases.

Monirath
Attachments
wrong mask
wrong mask
case 8_3937.JPG (946.81 KiB) Viewed 2614 times
right mask
right mask
Case 8.JPG (1016.81 KiB) Viewed 2614 times
wrong mask
wrong mask
case 6.JPG (1.03 MiB) Viewed 2614 times
DenisSchapiro
Posts: 38
Joined: Wed Nov 29, 2017 11:34 am

Re: Bug with HistoCAT

Post by DenisSchapiro » Tue Oct 16, 2018 3:50 pm

Thank you for reporting and sharing this issue. If possible, could you please share the original tiff files and masks?
Feel free to send me the files via denis.schapiro(at)uzh(dot)ch

Best

Denis
monirathhav
Posts: 17
Joined: Sat Feb 24, 2018 6:33 am

Re: Bug with HistoCAT

Post by monirathhav » Wed Oct 17, 2018 5:09 pm

Hi Denis,

The issue has been solved. It was due to special character in my file and folder names. I used dot instead of underscore. I changed the file names and HistoCAT is displaying the right masks now. Thank you very much.

Monirath
monirathhav
Posts: 17
Joined: Sat Feb 24, 2018 6:33 am

Re: Bug with HistoCAT

Post by monirathhav » Thu Oct 18, 2018 7:00 pm

Hi Denis,

Have you ever had this problem where HistoCAT generated different numbers of clusters each time you run phenograph? The expression of each marker changes to some extent as well. Take CCR4 expression as an example. We can clearly see the difference. See attached. These phenotypes and heatmaps were generated using exactly the same input data.

Best,

Monirath
Attachments
Heatmap 28 clusters new.jpeg
Heatmap 28 clusters new.jpeg (402.57 KiB) Viewed 2586 times
Attachment 3_Pheno8022_30 clusters.jpeg
Attachment 3_Pheno8022_30 clusters.jpeg (425.81 KiB) Viewed 2586 times
Attachment 3_Pheno8022_30 clusters.jpeg
Attachment 3_Pheno8022_30 clusters.jpeg (425.81 KiB) Viewed 2588 times
Last edited by monirathhav on Thu Oct 18, 2018 7:13 pm, edited 1 time in total.
DenisSchapiro
Posts: 38
Joined: Wed Nov 29, 2017 11:34 am

Re: Bug with HistoCAT

Post by DenisSchapiro » Thu Oct 18, 2018 7:10 pm

PhenoGraph is using a random seed in the current implementation. If you run the analysis again, it will generate a new set of clusters with different clusters.
If this is a problem, please let me know and I am happy to provide you with a version where you can fix the seed.
monirathhav
Posts: 17
Joined: Sat Feb 24, 2018 6:33 am

Re: Bug with HistoCAT

Post by monirathhav » Wed Oct 31, 2018 8:39 pm

Hi Denis,

Can you provide me with the version that can fix the seed problem?

Thank you.

Monirath
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