Search found 26 matches

by votti
Thu Jan 25, 2018 7:33 pm
Forum: Reagents
Topic: Nuclear/DNA staining with frozen sections (OCT embedded)
Replies: 5
Views: 9535

Re: Nuclear/DNA staining with frozen sections (OCT embedded)

Hi there, Unfortunately I cannot provide much advice: I fix my in vitro tissues with PFA before cutting and never had problems with Iridum. Also I remember seeing a quite good correlation with IMC Ir and IF Dapi/Hoechst. In general I recommend to allways use Hoechst after the overnight IMC staining ...
by votti
Thu Jan 25, 2018 4:45 pm
Forum: Data analysis
Topic: Visualization of Compensated Images
Replies: 7
Views: 9213

Re: Visualization of Compensated Images

Hey there, We are currently pushing hard to finalize everything concerning compensation, so we should also put out a detailed protocol shortly. Thanks for your patience! We never tested it thoroughly but usually metals on a slide are really stable when stored dry (as atoms very rarely decay). So whe...
by votti
Thu Jan 25, 2018 4:36 pm
Forum: Data analysis
Topic: Imctools
Replies: 15
Views: 16690

Re: Imctools

:) Thanks for sharing this tool and histocat. My knowledge in the use of python is very limited, something i realise is nescesarry and i am working hard on to improve. I have been able to get the ome.tiff file by using the imctool plugin in Fiji but i was wondering if there is a way to also get the ...
by votti
Fri Jan 12, 2018 8:33 pm
Forum: Data analysis
Topic: Visualization of Compensated Images
Replies: 7
Views: 9213

Re: Visualization of Compensated Images

Ok, txt files compensation in R is easy! I will make sure that there will also be an example provided with the final version of the paper and I can look that it gets maybe even integrated in Catalyst directly. I am currently skiing for a week, but I will already make an example available when I am b...
by votti
Fri Jan 12, 2018 4:50 pm
Forum: Data analysis
Topic: Imctools
Replies: 15
Views: 16690

Imctools

https://github.com/BodenmillerGroup/imctools Imctools is a python based IMC file conversion library that aims to convert IMC rawfiles (.mcd, .txt) into an intermediary, vendor independent ome.tiff format, containing all the relevant metadata. Further it contains tools to generate simpler tiff files ...
by votti
Fri Jan 12, 2018 4:26 pm
Forum: Data analysis
Topic: Visualization of Compensated Images
Replies: 7
Views: 9213

Visualization of Compensated Images

Question per Email from Erik Gerdtsson, Research Lab Specialist, The Bridge@USC: We have your segmentation pipeline set up and it is really great, thanks again for sharing. I was able to create the spillovermatrix using CATALYST and the Cellprofiler module but only on the 32bit images (_full.tiff) b...