Search found 25 matches

by RaulCatena
Mon Mar 04, 2019 10:43 pm
Forum: Reagents
Topic: H&E and IMC staining
Replies: 1
Views: 225

Re: H&E and IMC staining

Hi Matt, Unfortunately, I did that test and it seems that H/E affects strongly antibody signal as the acid pH of H and basic pH of E strip antibodies from their targets. This was by performing the staining after antibody incubations, did never tried to pre-stain with H/E, although probably not a goo...
by RaulCatena
Wed Aug 08, 2018 2:55 pm
Forum: Data analysis
Topic: Histocat++ for windows?
Replies: 1
Views: 595

Re: Histocat++ for windows?

Dear steve, The site is this: http://www.bodenmillerlab.com/research-2/histocal-2/ I paste here the direct link too http://www.bodenmillerlab.org/histoCAT_downloads/histoCAT++.zip Unfortunately, there is no Windows version. That's were MCDViewer and histoCAT++ complement each other. Good news is tha...
by RaulCatena
Wed Aug 08, 2018 2:51 pm
Forum: Data analysis
Topic: Data Plots
Replies: 3
Views: 703

Re: Data Plots

Hi Scott,

Please contact me at raulcatena@gmail.com and let's try to quickly troubleshoot this offline the forum.

Regards,

Raúl
by RaulCatena
Mon Aug 06, 2018 10:41 am
Forum: Data analysis
Topic: Data Plots
Replies: 3
Views: 703

Re: Data Plots

Hi Scott, The functions are not well documented yet. Again, it will all be explained in detail in the upcoming manual. Meanwhile, let me just give you a pointer on how it basically works. Double click on the channels that you are interested. The rows will become orange. Double click to remove them f...
by RaulCatena
Tue Jul 17, 2018 9:46 pm
Forum: Data analysis
Topic: Imctools
Replies: 15
Views: 3652

Re: Imctools

h++ has two procedures. A) A watershed with a few tricks B) Pixel classification in a similar way to what Ilastik does. A is simpler but inferior, so for optimal results, Vito's approach is best. That being said, when you go down the road of pixel classification, the quality depends on the ground tr...
by RaulCatena
Tue Jul 17, 2018 9:40 pm
Forum: Reagents
Topic: Counterstain using RuO4
Replies: 4
Views: 998

Re: Counterstain using RuO4

Correct :)
by RaulCatena
Tue Jul 17, 2018 9:35 pm
Forum: Data analysis
Topic: Imctools
Replies: 15
Views: 3652

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: 5361

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: 5361

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: 998

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....