Cell population frequencies in HistoCat

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Computational image analysis of multiplexed Imaging Mass Cytometry acquisitions
DenisSchapiro
Posts: 38
Joined: Wed Nov 29, 2017 11:34 am

Re: Cell population frequencies in HistoCat

Post by DenisSchapiro » Fri Oct 19, 2018 8:58 pm

I have sent you a private message to get all the necessary details. If this is a bug, I will update everyone here.
tc28
Posts: 1
Joined: Thu Feb 28, 2019 5:53 pm

Re: Cell population frequencies in HistoCat

Post by tc28 » Thu Feb 28, 2019 6:43 pm

Hi Denis,

I have a question along the same lines as Douglas. I'd like to be able to export the frequency of cells comprising a specific phenograph cluster per ROI. I cannot seem to be able to visualize the clusters by ROI. I also cannot export the data in a csv that will provide this information. Any help you have would be greatly appreciated. Many thanks in advance!
DenisSchapiro
Posts: 38
Joined: Wed Nov 29, 2017 11:34 am

Re: Cell population frequencies in HistoCat

Post by DenisSchapiro » Fri Aug 02, 2019 6:33 pm

Dear tc28,

Could you create an issue on https://github.com/BodenmillerGroup/histoCAT/issues describing the necessary workflow?

Right now the work around would be to export the CSV files for each (or merge all and export one CSV) and count the clusters outside histoCAT.

Best

Denis
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