Search found 43 matches

by DenisSchapiro
Fri Aug 28, 2020 2:10 pm
Forum: Data analysis
Topic: Issues with mask/histoCAT segmentation
Replies: 5
Views: 808

Re: Issues with mask/histoCAT segmentation

It should be able to load the CellProfiler 32bit float mask - or did you try and it fail?
by DenisSchapiro
Wed Aug 26, 2020 3:03 pm
Forum: Data analysis
Topic: Issues with mask/histoCAT segmentation
Replies: 5
Views: 808

Re: Issues with mask/histoCAT segmentation

Dear Cristina, I believe that the issue is that you are saving your mask as 16bit and you should create a 32bit mask instead. If you have more than 65536 single cells a 16bit mask can not provide unique values to each cell. Just save it as a 32bit mask - histoCAT is supporting 32bit masks. Best Denis
by DenisSchapiro
Sun Feb 16, 2020 8:28 pm
Forum: Data analysis
Topic: Graphs from cvs and txt files.
Replies: 1
Views: 2984

Re: Graphs from cvs and txt files.

Graphs in terms of histograms, scatter plots, tSNE etc? If yes, than histoCAT can do this through command line, but not directly in the GUI.
by DenisSchapiro
Tue Dec 17, 2019 8:27 pm
Forum: Data analysis
Topic: question about the neighborhood analysis heatmap
Replies: 1
Views: 2584

Re: question about the neighborhood analysis heatmap

Thank you for the question. I will post a detailed response on Github.
by DenisSchapiro
Mon Dec 16, 2019 5:06 pm
Forum: Data analysis
Topic: HistoCAT 1.76 from github repo not installing on Mac - Matlab Runtime issue?
Replies: 1
Views: 2246

Re: HistoCAT 1.76 from github repo not installing on Mac - Matlab Runtime issue?

Dear Trevor,

I am investigating the issue. So far I couldn't reproduce it.

Would you mind trying it again and double-checking that you have a stable internet connection?

Best

Denis
by DenisSchapiro
Wed Nov 06, 2019 9:49 pm
Forum: Data analysis
Topic: Loading a new HistoCAT Session with previous Phenographs/gates?
Replies: 1
Views: 3066

Re: Loading a new HistoCAT Session with previous Phenographs/gates?

Dear Julian,

Would you mind sharing the .mat file with me via direct message?
Regarding the parameters: The "custom_gates_0" folder should include a txt file with all the requested parameters.

Best

Denis
by DenisSchapiro
Mon Oct 07, 2019 10:28 pm
Forum: Data analysis
Topic: HistoCAT reading mask as a channel, not a mask
Replies: 1
Views: 2461

Re: HistoCAT reading mask as a channel, not a mask

Thank you for reporting this issue. If you can reproduce this behavior, please create an issue here:
https://github.com/BodenmillerGroup/histoCAT/issues
by DenisSchapiro
Wed Sep 04, 2019 3:38 pm
Forum: Data analysis
Topic: IMC data transformation and normalisation across ROI
Replies: 2
Views: 3521

Re: IMC data transformation and normalisation across ROI

Dear Anna, Your question is highly dependent on the underlying dataset/distribution and therefore difficult to answer in general. - We are currently using raw values for IMC and log-transform for Immunofluorescence based on the underlying dynamic range. - We have used 99-percentile for tSNE and Phen...
by DenisSchapiro
Fri Aug 02, 2019 6:33 pm
Forum: Data analysis
Topic: Cell population frequencies in HistoCat
Replies: 12
Views: 12242

Re: Cell population frequencies in HistoCat

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
by DenisSchapiro
Wed Jul 31, 2019 7:38 pm
Forum: Data analysis
Topic: Histocat - Differential cell neighborhood analysis
Replies: 3
Views: 8087

Re: Histocat - Differential cell neighborhood analysis

Dear Steve,

This is a pretty unique and tailored question. I will respond via email with your data example.

For the Clustergram, use the command: view(Delta)

Best

Denis