Search found 30 matches

by ssivajothi
Mon Feb 04, 2019 2:52 pm
Forum: Reagents
Topic: Standardized retrieval conditions?
Replies: 1
Views: 220

Standardized retrieval conditions?

Hi all, As you all know, retrieval is key to staining on FFPE tissues, especially when trying to get 35 antibodies to work well together. What retrieval conditions have you been having most success with for the broadest range of antibodies and tissues? (Citr/EDTA, temp, time) I have tried multiple o...
by ssivajothi
Mon Jan 07, 2019 4:16 pm
Forum: Reagents
Topic: CD56 clone?
Replies: 1
Views: 288

CD56 clone?

Hi all,

Does anyone have the 123C3 clone of CD56 working on human FFPE tissue? If not can you point me to a clone that works?

Thank you,
Santhosh
by ssivajothi
Thu Dec 13, 2018 5:03 pm
Forum: General
Topic: IMC staining on bone marrow trephine
Replies: 1
Views: 423

Re: IMC staining on bone marrow trephine

Hi Monirath,

I haven't worked with this tissue, but can I ask what issue you are having with the Ir and what markers are you having trouble getting to work?

Santhosh
by ssivajothi
Thu Dec 13, 2018 4:54 pm
Forum: Reagents
Topic: Inter cellular stain on mouse frozen tissue
Replies: 1
Views: 969

Re: Inter cellular stain on mouse frozen tissue

Hi Matt,

I am wondering if you found any solution to this. Is a separate permeabilization step even required? In my trials with human frozen tissue, Ki-67 worked pretty well without any change to the standard protocol, but that was the only non-surface antigen I looked for.

Santhosh
by ssivajothi
Mon Nov 12, 2018 6:40 pm
Forum: Data analysis
Topic: Compensation slide acquisition
Replies: 3
Views: 681

Re: Compensation slide acquisition

Hi Steve, Your diagram is on track. That is how I have patterned the comp slide. The way I do the acquisition is to generate a panorama of the entire spotted region and go in and draw 5px tall ROIs inside each spot. Use the output from this to generate your compensation matrix. Hope this helps. Best...
by ssivajothi
Mon Oct 29, 2018 12:50 pm
Forum: Data analysis
Topic: histoCAT++ manual
Replies: 25
Views: 5361

Re: histoCAT++ manual

Hi Raul,

Just wanted to ask if there are any updates to Histocat++ and the associated manual?

Thank you,
Santhosh
by ssivajothi
Fri Oct 26, 2018 4:05 pm
Forum: Reagents
Topic: Mouse FFPE antibodies
Replies: 5
Views: 1149

Re: Mouse FFPE antibodies

Matt,

Just wanted to ask if you were able to troubleshoot your issue with the mouse FFPE antibodies working?

Santhosh
by ssivajothi
Mon Aug 20, 2018 1:56 pm
Forum: Data analysis
Topic: Cell population frequencies in HistoCat
Replies: 10
Views: 1926

Re: Cell population frequencies in HistoCat

Hi Denis,

Is the new 1.75 version same as the 1.8 version with major changes you spoke about earlier?

Thanks for the continued improvement.

Santhosh
by ssivajothi
Mon Aug 20, 2018 1:50 pm
Forum: Reagents
Topic: Mouse FFPE antibodies
Replies: 5
Views: 1149

Re: Mouse FFPE antibodies

Hi Matt, Adding to Hart's response, the issue is not with the conjugation procedure but the specific clones you are using. Antigens on FFPE tissues are slightly altered and flow antibodies which usually work on frozen sections will not work on FFPE tissue. You need to source and test clones known to...
by ssivajothi
Wed Jul 18, 2018 3:21 pm
Forum: Data analysis
Topic: Imctools
Replies: 15
Views: 3652

Re: Imctools

Hi Vito,

Thank for that, I got it working. Yes, Raul's comments clarified some things about histocat++.

Does "old_example_preprocessing_pipeline.ipynb" contain all steps from start to finish of the pipeline?

Sorry for many beginner questions.

Thanks,
Santhosh