Search found 33 matches

by DenisSchapiro
Wed Apr 24, 2019 2:57 am
Forum: Data analysis
Topic: Histocat - Differential cell neighborhood analysis
Replies: 2
Views: 4201

Re: Histocat - Differential cell neighborhood analysis

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...
by DenisSchapiro
Mon Mar 11, 2019 7:58 pm
Forum: Data analysis
Topic: histoCAT on Mac - tiny display fonts
Replies: 1
Views: 585

Re: histoCAT on Mac - tiny display fonts

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
by DenisSchapiro
Tue Jan 08, 2019 8:24 pm
Forum: Data analysis
Topic: Histocat neighborhood analysis
Replies: 2
Views: 723

Re: Histocat neighborhood analysis

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
by DenisSchapiro
Tue Jan 08, 2019 7:52 pm
Forum: Data analysis
Topic: Reproducibility PhenoGraph algorithm in histoCAT
Replies: 3
Views: 1523

Re: Reproducibility PhenoGraph algorithm in histoCAT

Update:
The new histoCAT version provides the possibility to set a seed now.
by DenisSchapiro
Tue Dec 11, 2018 5:23 pm
Forum: Data analysis
Topic: Shannon Entropy to quantify cell heterogeneity?
Replies: 2
Views: 729

Re: Shannon Entropy to quantify cell heterogeneity?

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...
by DenisSchapiro
Tue Nov 20, 2018 9:45 pm
Forum: Data analysis
Topic: Reproducibility PhenoGraph algorithm in histoCAT
Replies: 3
Views: 1523

Re: Reproducibility PhenoGraph algorithm in histoCAT

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
by DenisSchapiro
Tue Nov 20, 2018 5:25 pm
Forum: Data analysis
Topic: Reproducibility PhenoGraph algorithm in histoCAT
Replies: 3
Views: 1523

Re: Reproducibility PhenoGraph algorithm in histoCAT

This will be fixed in the next version of histoCAT
by DenisSchapiro
Tue Nov 20, 2018 12:17 am
Forum: Data analysis
Topic: Please report ALL histoCAT issues in Github
Replies: 0
Views: 1019

Please report ALL histoCAT issues in Github

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...
by DenisSchapiro
Tue Oct 30, 2018 8:29 pm
Forum: Data analysis
Topic: Help with neighborhood analysis
Replies: 8
Views: 2031

Re: Help with neighborhood analysis

This is an interesting issue. Could you share the .mat file via denis_schapiro(at)hms(dot)harvard(dot)edu
by DenisSchapiro
Mon Oct 29, 2018 1:58 am
Forum: Data analysis
Topic: Help with neighborhood analysis
Replies: 8
Views: 2031

Re: Help with neighborhood analysis

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.