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

Hi Steve, I would run tSNE + PhenoGraph on all samples and run neighborhood analysis (1) on 4 different disease states for comparison and on all disease states together. When you run all together, do you see hierarchical clusters enriched in certain cell-cell interactions? When you run them individu...

Dear Stoh,

The only way to customize the font size is to change the properties in Matlab GUIDE:
1) Right click on histoCAT.fig --> Open in GUIDE
2) Click on the elements you would like to customize and select a larger FontSize

Best

Denis

Dear Sherman,

I am happy to help. Please create an issue on Github and add also the session file so I can reproduce the error:
https://github.com/BodenmillerGroup/histoCAT/issues

Best

Denis

Update:
The new histoCAT version provides the possibility to set a seed now.

Dear Steve, The paper is already published here: https://elifesciences.org/articles/31657 I am working closely with the t-CyCIF team to implement this and other spatial statistics methods into histoCAT. One metric that we have recently implemented is a sliding window approach to quantify cellular he...