Search found 11 matches

by monirathhav
Tue Dec 11, 2018 5:57 am
Forum: General
Topic: IMC staining on bone marrow trephine
Replies: 1
Views: 256

IMC staining on bone marrow trephine

Hi,

Is anyone here working with decalcified bone marrow trephine? Our lab has had issue with getting some markers and Iridium to work on BM trephine biopsies.

I would appreciate input on this matter.

Monirath
by monirathhav
Wed Oct 31, 2018 8:39 pm
Forum: Data analysis
Topic: Bug with HistoCAT
Replies: 7
Views: 735

Re: Bug with HistoCAT

Hi Denis,

Can you provide me with the version that can fix the seed problem?

Thank you.

Monirath
by monirathhav
Thu Oct 18, 2018 7:00 pm
Forum: Data analysis
Topic: Bug with HistoCAT
Replies: 7
Views: 735

Re: Bug with HistoCAT

Hi Denis, Have you ever had this problem where HistoCAT generated different numbers of clusters each time you run phenograph? The expression of each marker changes to some extent as well. Take CCR4 expression as an example. We can clearly see the difference. See attached. These phenotypes and heatma...
by monirathhav
Wed Oct 17, 2018 5:09 pm
Forum: Data analysis
Topic: Bug with HistoCAT
Replies: 7
Views: 735

Re: Bug with HistoCAT

Hi Denis,

The issue has been solved. It was due to special character in my file and folder names. I used dot instead of underscore. I changed the file names and HistoCAT is displaying the right masks now. Thank you very much.

Monirath
by monirathhav
Tue Oct 16, 2018 3:42 pm
Forum: Data analysis
Topic: Bug with HistoCAT
Replies: 7
Views: 735

Re: Bug with HistoCAT

Hi Denis, I have attached 3 examples for you where the same mask from case 8_3939 was applied to all other cases. At first, I thought that I mistakenly copied and pasted the wrong mask file into the other two TIFF folders. But I already checked in the original TIFF folders and saw that I had the rig...
by monirathhav
Mon Oct 15, 2018 11:06 pm
Forum: Data analysis
Topic: Bug with HistoCAT
Replies: 7
Views: 735

Bug with HistoCAT

Hi, I uploaded several images onto HistoCAT. When I overlayed the mask on "Apply RGB image", the mask was completely off, smaller and with different shape. It was a different mask from the mask of the image. Has anyone encountered similar problem? Thanks for helping to troubleshoot this issue. Monir...
by monirathhav
Thu Oct 04, 2018 3:57 am
Forum: Data analysis
Topic: Checking uncertainty in Ilastik
Replies: 1
Views: 360

Checking uncertainty in Ilastik

Hi,

Is there a way to quantitatively check uncertainty during pixel classification training in Ilastik besides looking at the cyan color opacity?

Thank you.

Monirath
by monirathhav
Tue Jul 10, 2018 6:11 pm
Forum: Reagents
Topic: Counterstain using RuO4
Replies: 4
Views: 787

Re: Counterstain using RuO4

Hi Matt and Raul,

Thanks for the comments. Raul, do you mean diluting 0.5% RuO4 1000 times in PBS to get the 0.0005% RuO4 counterstain solution?

Monirath
by monirathhav
Fri Jul 06, 2018 6:17 pm
Forum: Reagents
Topic: Counterstain using RuO4
Replies: 4
Views: 787

Counterstain using RuO4

Hi, Has anyone tried counterstaining with Ruthenium Tetroxide as suggested in this latest IMC paper? https://www.ncbi.nlm.nih.gov/pubmed/29405336 I was wondering if RuO4 step comes before or after the intercalator step. Or is intercalator not necessary at all here if we already include Histone3 as n...
by monirathhav
Thu Apr 26, 2018 6:16 pm
Forum: General
Topic: IMC staining - blocking
Replies: 4
Views: 1147

IMC staining - blocking

Hi,

Can anyone share which blocking solutions work well for IMC staining?

Thank you.

Monirath