It should be able to load the CellProfiler 32bit float mask - or did you try and it fail?

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

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.

Thank you for the question. I will post a detailed response on Github.

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

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

Thank you for reporting this issue. If you can reproduce this behavior, please create an issue here:
https://github.com/BodenmillerGroup/histoCAT/issues

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...

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

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