Search found 36 matches

by DenisSchapiro
Wed Sep 04, 2019 3:38 pm
Forum: Data analysis
Topic: IMC data transformation and normalisation across ROI
Replies: 2
Views: 153

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: 3708

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: 4566

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
by DenisSchapiro
Wed Apr 24, 2019 2:57 am
Forum: Data analysis
Topic: Histocat - Differential cell neighborhood analysis
Replies: 3
Views: 4566

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: 824

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: 1022

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: 1827

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: 982

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: 1827

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: 1827

Re: Reproducibility PhenoGraph algorithm in histoCAT

This will be fixed in the next version of histoCAT