Cell population frequencies in HistoCat

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Computational image analysis of multiplexed Imaging Mass Cytometry acquisitions
mattbliss90
Posts: 10
Joined: Wed Jan 17, 2018 11:37 pm

Cell population frequencies in HistoCat

Post by mattbliss90 » Tue Jul 24, 2018 6:12 pm

Hello,
Is it possible to obtain cell population frequencies/numbers directly in the HistoCat software without having to export the FCS or CSV file into another software such as FloJo?

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

Re: Cell population frequencies in HistoCat

Post by DenisSchapiro » Tue Jul 24, 2018 6:21 pm

Hi Matt,

We are in the process of releasing a major new version (1.8) in the next few days which will include this function. If you need it urgently, please let me know and I am happy to provide you with a pre-release version.

Best

Denis
mattbliss90
Posts: 10
Joined: Wed Jan 17, 2018 11:37 pm

Re: Cell population frequencies in HistoCat

Post by mattbliss90 » Thu Jul 26, 2018 8:12 pm

Hello Denis,
We would be happy to test out the pre-release HistoCat 1.8

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

Re: Cell population frequencies in HistoCat

Post by DenisSchapiro » Mon Jul 30, 2018 9:24 pm

Somehow I can't send you a private message, so I will post a public link here in the next few days! Can't wait to have a beta-tester for our newest version :)

Best

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

Re: Cell population frequencies in HistoCat

Post by DenisSchapiro » Wed Aug 01, 2018 10:08 pm

Dear Matt,

You can find the newest version of the source code here: https://github.com/BodenmillerGroup/histoCAT
If you need a compiled version, please contact me via email and let me know which operating system is used.

Please see here a few cases how to visualise the data: https://github.com/BodenmillerGroup/histoCAT/issues/9

Best

Denis
ssivajothi
Posts: 31
Joined: Thu Jan 11, 2018 9:00 pm

Re: Cell population frequencies in HistoCat

Post by ssivajothi » Mon Aug 20, 2018 1:56 pm

Hi Denis,

Is the new 1.75 version same as the 1.8 version with major changes you spoke about earlier?

Thanks for the continued improvement.

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

Re: Cell population frequencies in HistoCat

Post by DenisSchapiro » Mon Aug 20, 2018 2:01 pm

Dear Santhosh,

Exactly, I called it 1.75, since I am planning to add many more features for the 1.8 version in the next few month.

I am looking forward to your feedback.

Best

Denis
douglas.linn
Posts: 17
Joined: Mon Jan 22, 2018 4:20 pm

Re: Cell population frequencies in HistoCat

Post by douglas.linn » Mon Oct 01, 2018 2:20 pm

Denis, thanks for adding the cell number function in the latest version of Histocat! Is there a way to determine the contribution of each individual ROI/image to those numbers? Perhaps I missed it, but plotting ImageId vs Amount_cells_in_sample doesn't seem to work
DenisSchapiro
Posts: 38
Joined: Wed Nov 29, 2017 11:34 am

Re: Cell population frequencies in HistoCat

Post by DenisSchapiro » Tue Oct 09, 2018 3:05 pm

Does this issue address your question:
https://github.com/BodenmillerGroup/histoCAT/issues/11
douglas.linn
Posts: 17
Joined: Mon Jan 22, 2018 4:20 pm

Re: Cell population frequencies in HistoCat

Post by douglas.linn » Fri Oct 19, 2018 3:17 am

DenisSchapiro wrote:
Tue Oct 09, 2018 3:05 pm
Does this issue address your question:
https://github.com/BodenmillerGroup/histoCAT/issues/11
It works, but I have to manually count the number of rows from each respective ImageID/ROI. This would become quite tedious when there is a lot of clusters across a large set of ROIs, so I was hoping those numbers would be generated automatically or more readily accessible.
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