imc-forum.org

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...

Quick update:
In certain situations, I still see the wrong behavior. I made an issue - please stay updated here:
https://github.com/BodenmillerGroup/histoCAT/issues/14

This will be fixed in the next version of histoCAT

Dear all, I am very excited that so many people are using histoCAT across the globe and I am honored to help and fix any issues/questions you have regarding histoCAT. Please report from now on ALL your issues on Github. This would tremendously help to accelerate response time and help prioritize iss...

This is an interesting issue. Could you share the .mat file via denis_schapiro(at)hms(dot)harvard(dot)edu

Dashes could be an issue as well. Ideally no special characters.
As I said, I am working on a stable version which should take care of that, but for now please do not use special character. Let me know if this does not help.