Search found 30 matches

by RaulCatena
Mon Apr 23, 2018 10:45 pm
Forum: Data analysis
Topic: histoCAT++ manual
Replies: 25
Views: 8816

Re: histoCAT++ manual

Hi Santhosh, The spillover matrix could be quite different depending on the instrument, tuning, etc. However, by looking to our images and a few others from other labs and simply applying Stephane´s matrix (the so-called factory matrix in hCAT++) it does a very good job off-the-bat. Reason is that o...
by RaulCatena
Fri Apr 20, 2018 3:14 pm
Forum: Data analysis
Topic: histoCAT++ manual
Replies: 25
Views: 8816

Re: histoCAT++ manual

Found the problem regarding the TXT files after compensation. The line returns in those files as they come from the CyTOF software are \r\n , which is the typical for windows. The file you generated had only \n (linux and mac), which led to a parser failure. Just patched the version (you can already...
by RaulCatena
Fri Apr 20, 2018 2:27 pm
Forum: Data analysis
Topic: histoCAT++ manual
Replies: 25
Views: 8816

Re: histoCAT++ manual

One more thing, If you download the last version that I just uploaded a minute ago, you can activate the compensation checkbox and the matrix published in Chevrier´s/Zanotelli´s paper is applied. You can further customize the compensation matrix by going to the edit->compensation matrix... menú. You...
by RaulCatena
Fri Apr 20, 2018 2:20 pm
Forum: Data analysis
Topic: histoCAT++ manual
Replies: 25
Views: 8816

Re: histoCAT++ manual

Santhosh, Actually have not tried to load such files yet as histoCAT++ comes with a compensation module already (based on Vito´s paper). Probably is some minor issue on the format of the produced TXT. Would you mind sharing one of those TXT files so that I can take a quick look? raul.catenafelipe@uz...
by RaulCatena
Fri Apr 20, 2018 10:35 am
Forum: Data analysis
Topic: histoCAT++ manual
Replies: 25
Views: 8816

Re: histoCAT++ manual

Hi Marieke,

I just checked and the version is the last one. Perhaps it could be that the older one "shadows" the newest one if you try opening a workspace by double clicking. I recommend that you erase the old binary (.app file) and move the new download to the Applications folder.

Regards,
by RaulCatena
Tue Apr 17, 2018 4:01 pm
Forum: Data analysis
Topic: histoCAT++ manual
Replies: 25
Views: 8816

Re: histoCAT++ manual

Dear histoCAT++ users We finally have the promised manual ready. http://www.bodenmillerlab.org/histoCAT_manual/index.php/manual_plus/ The format chosen is a typical blog site. This will save us from having different versions circulating. Simply reach out the Bodenmiller laboratory's histoCAT++ site ...
by RaulCatena
Thu Mar 22, 2018 3:30 pm
Forum: Publications & Resources
Topic: Ruthenium Counterstain
Replies: 3
Views: 1806

Ruthenium Counterstain

Since a few people have asked, I think it is worth putting the word out on this. We recently published a method for counterstaining in IMC. It is an equivalent to Eosin in classic histology, and together with Iridium gives a very good H&E approximation (Which we call I&R). Check out the paper here (...
by RaulCatena
Thu Mar 22, 2018 12:14 pm
Forum: Data analysis
Topic: histoCAT++ manual
Replies: 25
Views: 8816

Re: histoCAT++ manual

Hi Sky We are a few days away of getting out a first basic manual. Is going to be in web format so it will dynamically grow with additional tutorials for more advanced topics. We will advertise the manual here in the forum as soon as it is available. In the meantime, if you have any urgent question ...
by RaulCatena
Mon Mar 12, 2018 2:30 pm
Forum: General
Topic: Gas usage
Replies: 1
Views: 1577

Re: Gas usage

Hi Santosh, Of course depends on the gas tanks that you have. Roughly we get at least around 72h of continuous running with 2 Cytofs (for one it would be more like 4.5 days) with the same Argon tank. The argon tanks we use are 250L give or take. The helium usually lasts for much longer (2/3 weeks pe...
by RaulCatena
Wed Jan 24, 2018 6:38 pm
Forum: Data analysis
Topic: Imctools
Replies: 15
Views: 5962

Re: Imctools

Hello

If you happen to have a Macintosh, you can use histoCAT++ to convert txt, mcd, or tiff into a folder of single channel tiffs that work with histoCAT.

You can download histoCAT++ at
http://www.bodenmillerlab.com/research-2/histocat-2/

Let us know whether you succeed

Regards