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
Search found 38 matches
- Wed Nov 06, 2019 9:49 pm
- Forum: Data analysis
- Topic: Loading a new HistoCAT Session with previous Phenographs/gates?
- Replies: 1
- Views: 714
- Mon Oct 07, 2019 10:28 pm
- Forum: Data analysis
- Topic: HistoCAT reading mask as a channel, not a mask
- Replies: 1
- Views: 300
Re: HistoCAT reading mask as a channel, not a mask
Thank you for reporting this issue. If you can reproduce this behavior, please create an issue here:
https://github.com/BodenmillerGroup/histoCAT/issues
https://github.com/BodenmillerGroup/histoCAT/issues
- Wed Sep 04, 2019 3:38 pm
- Forum: Data analysis
- Topic: IMC data transformation and normalisation across ROI
- Replies: 2
- Views: 548
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...
- Fri Aug 02, 2019 6:33 pm
- Forum: Data analysis
- Topic: Cell population frequencies in HistoCat
- Replies: 12
- Views: 4536
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
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
- Wed Jul 31, 2019 7:38 pm
- Forum: Data analysis
- Topic: Histocat - Differential cell neighborhood analysis
- Replies: 3
- Views: 4941
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
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
- Wed Apr 24, 2019 2:57 am
- Forum: Data analysis
- Topic: Histocat - Differential cell neighborhood analysis
- Replies: 3
- Views: 4941
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...
- Mon Mar 11, 2019 7:58 pm
- Forum: Data analysis
- Topic: histoCAT on Mac - tiny display fonts
- Replies: 1
- Views: 1072
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
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
- Tue Jan 08, 2019 8:24 pm
- Forum: Data analysis
- Topic: Histocat neighborhood analysis
- Replies: 2
- Views: 1335
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
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
- Tue Jan 08, 2019 7:52 pm
- Forum: Data analysis
- Topic: Reproducibility PhenoGraph algorithm in histoCAT
- Replies: 3
- Views: 2144
Re: Reproducibility PhenoGraph algorithm in histoCAT
Update:
The new histoCAT version provides the possibility to set a seed now.
The new histoCAT version provides the possibility to set a seed now.
- Tue Dec 11, 2018 5:23 pm
- Forum: Data analysis
- Topic: Shannon Entropy to quantify cell heterogeneity?
- Replies: 2
- Views: 1235
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...