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Bug with HistoCAT

Posted: Mon Oct 15, 2018 11:06 pm
by monirathhav
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

Re: Bug with HistoCAT

Posted: Tue Oct 16, 2018 2:36 am
by DenisSchapiro
Dear Monirath,

Would you mind to share an example mask and image?

Best

Denis

Re: Bug with HistoCAT

Posted: Tue Oct 16, 2018 3:42 pm
by monirathhav
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

Re: Bug with HistoCAT

Posted: Tue Oct 16, 2018 3:50 pm
by DenisSchapiro
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

Re: Bug with HistoCAT

Posted: Wed Oct 17, 2018 5:09 pm
by monirathhav
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

Re: Bug with HistoCAT

Posted: Thu Oct 18, 2018 7:00 pm
by monirathhav
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

Re: Bug with HistoCAT

Posted: Thu Oct 18, 2018 7:10 pm
by DenisSchapiro
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.

Re: Bug with HistoCAT

Posted: Wed Oct 31, 2018 8:39 pm
by monirathhav
Hi Denis,

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

Thank you.

Monirath