Search found 26 matches

by votti
Wed Jul 18, 2018 8:36 am
Forum: Data analysis
Topic: Imctools
Replies: 15
Views: 16690

Re: Imctools

Hi Vito, I am a beginner with Python and IMCtools, just a couple of questions: 1) Is IMCtools package supposed to be 'installed' via terminal or Jupyter notebook? Or am I supposed to copy it somewhere and call it? Sorry if terminology I'm using is wrong 2) is there a way to use histocat++ in this p...
by votti
Tue Jun 12, 2018 4:33 pm
Forum: Data analysis
Topic: Imctools
Replies: 15
Views: 16690

Re: Imctools

I suffered from this con Hi, This is probably a very silly question and more of a quality of life issue, but is there any way to expand the tab with all the channel labels? If I expand the window, the box containing the channels stays exactly the same size. I'm constantly scrolling back and forth to...
by votti
Thu Apr 26, 2018 12:40 pm
Forum: Data analysis
Topic: Imctools
Replies: 15
Views: 16690

Re: Imctools

Hi Votti, I am trying to use the imctools as a Fiji plugin as you described. The 'open multichannel ome' function works fine, but the 'open imc' function (which is the one that I need) is throwing the following error in my hands, could you take a look and let me know what you think? Using the lates...
by votti
Wed Apr 11, 2018 6:14 pm
Forum: Data analysis
Topic: IMC segmentation pipeline
Replies: 0
Views: 9934

IMC segmentation pipeline

This thread should collect question about the IMC segmentation pipeline developed in the Bodenmiller lab, described here: https://github.com/BodenmillerGroup/ImcSegmentationPipeline The open source software based pipeline combines the powerful CellProfiller segmentation software (http://cellprofiler...
by votti
Wed Apr 11, 2018 6:05 pm
Forum: Data analysis
Topic: Visualization of Compensated Images
Replies: 7
Views: 9213

Re: Visualization of Compensated Images

For completeness: we published all our code for the compensation paper on our github: https://github.com/BodenmillerGroup/cyTOFcompensation In particular the scripts: imc_generatespillmat_short.Rmd and imc_comp_txt_example.Rmd should be useful. A beginner friendly simple workflow could be to estimat...
by votti
Wed Apr 11, 2018 5:56 pm
Forum: Reagents
Topic: Compensation slide
Replies: 6
Views: 7953

Re: Compensation slide

Hi Santhosh, CATALYSTlight (http://imlspenticton.uzh.ch:3838/CATALYSTLite/) seems really to have a severe issues right now. I opened an issue with the developer: https://github.com/HelenaLC/CATALYST/issues/30 and hope that it will be fixed soon. @Compensation slide: Happy to hear that the protocol w...
by votti
Thu Mar 29, 2018 11:08 am
Forum: Reagents
Topic: Compensation slide
Replies: 6
Views: 7953

Re: Compensation slide

Hi Santhosh, Sorry that this took so long! You asked this question already in January and I somehow forgot about it :? Here is the link to the protocol to generate the spillover slide: https://docs.google.com/document/d/195eViUqHoYRKrkoy_NkIdJPmyx1-OuDaSjiWQBy4weA/edit?usp=sharing To your question: ...
by votti
Thu Feb 22, 2018 2:56 pm
Forum: Data analysis
Topic: ImcSegmentationPipeline issue with ome.tiff
Replies: 2
Views: 3581

Re: ImcSegmentationPipeline issue with ome.tiff

Hi there, I just noticed that problem myself last week: somehow the 'tifffile' python dependency updated the way that the attributes of the tiffs are called internally, which causes problems. I fixed this already in the development version of the imctools You can install it by: pip install -U git+ht...
by votti
Thu Feb 08, 2018 5:28 pm
Forum: Data analysis
Topic: Visualization of Compensated Images
Replies: 7
Views: 9213

Re: Visualization of Compensated Images

Thanks for clarifying the rational behind the OME TIFF, I am also not a big fan of the mcd format and would alos prefer a different format, the problem is a you also pointed out that you anyway need to convert it again for most other applications. We store the txtfiles as rds in the R pipeline (and...
by votti
Tue Feb 06, 2018 8:59 am
Forum: General
Topic: Best instrument for heat retreaval in FFPE
Replies: 9
Views: 13491

Re: Best instrument for heat retreaval in FFPE

Hi there,

In the Bodenmiller lab we use a pressure cooker for doing the FFPE heat retrieval.
In the IMC conference in summer I heard also stories of people finding expensive microwaves being the best way to do heat retrieval.