Search found 30 matches

by RaulCatena
Tue Jul 17, 2018 9:40 pm
Forum: Reagents
Topic: Counterstain using RuO4
Replies: 4
Views: 1796

Re: Counterstain using RuO4

Correct :)
by RaulCatena
Tue Jul 17, 2018 9:35 pm
Forum: Data analysis
Topic: Imctools
Replies: 15
Views: 5962

Re: Imctools

Santhosh, Linked to the reply to the other thread, and to point 2. Yes, you can apply the compensation in h++ (or other adjustments) and then I recommend you export the channels one by one (but you can do batches of images to make it fast, for instance, export 3 channels for 100 images would be 3 ba...
by RaulCatena
Tue Jul 17, 2018 9:31 pm
Forum: Data analysis
Topic: histoCAT++ manual
Replies: 25
Views: 8816

Re: histoCAT++ manual

Santosh, The reason is that data is saved as 16 bit tiff. So if you have channels that go to a few counts, it will look pretty much black if no automatic adjustment is applied. If you open the files with preview they'll look black. If you open them with Fiji, for instance, and let it use automatic a...
by RaulCatena
Tue Jul 17, 2018 9:25 pm
Forum: Data analysis
Topic: histoCAT++ manual
Replies: 25
Views: 8816

Re: histoCAT++ manual

Hi pBull, The limiting factor is the processor's speed. The standard tSNE implementation uses only one core, so pretty much clock speed (as long as the dataset fits in memory which most likely will, specially if you don't have too many other apps open and the system does not need to keep swapping me...
by RaulCatena
Fri Jul 06, 2018 9:45 pm
Forum: Reagents
Topic: Counterstain using RuO4
Replies: 4
Views: 1796

Re: Counterstain using RuO4

Hi monirathhav, Like Matt says, right after the intercalator should work well. Remember to dilute the RuO4 in raw PBS and not in TBS. Also, make sure there is no serum either. RuO4 would react with the protein in the media (or with TBS too). @Matt. If the signal is too strong just dilute a bit more....
by RaulCatena
Fri Jul 06, 2018 9:30 pm
Forum: Data analysis
Topic: histoCAT++ manual
Replies: 25
Views: 8816

Re: histoCAT++ manual

Hi Santhosh

During the summer I'll update a manual on Analysis. It will be corresponding to the latest version released as of May. Regarding future developments of both histoCAT and histoCAT++ please contact Bernd Bodenmiller.

Regards,

Raúl
by RaulCatena
Fri Apr 27, 2018 10:49 am
Forum: General
Topic: IMC staining - blocking
Replies: 4
Views: 2512

Re: IMC staining - blocking

Hi Santhosh, Theory says that it would be better to do FcBlock first, and then Serum separate. Reason is that mixing them could lead to inactivation of the Fc's that block CD16/32 etc. However, I tried once and did not see anything different, but to be honest with you, I did not do a very through co...
by RaulCatena
Thu Apr 26, 2018 6:44 pm
Forum: General
Topic: IMC staining - blocking
Replies: 4
Views: 2512

Re: IMC staining - blocking

Hi Monirath

I recommend Serum (FBS, Horse...) 0.5-1% and FcBlock (normally 1:100-1:500 if you use Miltenyi’s). The latter one is specially important if you go after immune cells.

Regards,

Raúl
by RaulCatena
Thu Apr 26, 2018 10:06 am
Forum: Data analysis
Topic: histoCAT++ manual
Replies: 25
Views: 8816

Re: histoCAT++ manual

There is an FCS export option for the cell data in histoCAT++ working now. Download the newest version if you want to use this. The generated FCS files can be imported in FlowJo, Accense, flowCore and other tools. For some reason do not work on Cytobank, we will look into that at some point. To gene...
by RaulCatena
Tue Apr 24, 2018 7:45 pm
Forum: Data analysis
Topic: histoCAT++ manual
Replies: 25
Views: 8816

Re: histoCAT++ manual

Hi Marieke, The export FCS function will be available in the near future. Actually, tSNE will be included too, but not immediately. Summarizing, to go down the tSNE road we have the following roadmap. 1) Currently: Export TSV from hCAT++, then use R or Python scripts to convert to FCS, and good to g...