Search found 8 matches

by sbooth
Wed Jun 12, 2019 6:34 pm
Forum: Data analysis
Topic: IMC data processing-Normalization & Scaling
Replies: 0
Views: 57

IMC data processing-Normalization & Scaling

Hi there, I am wondering if anyone has a some example code that shows how to 1-99% normalize and 0-1 scale the IMC intensity data - in R hopefully :) After extracting the cell and image intensity values from cellprofiler using the Measure_Mask_Basic pipeline from the Bodenmiller group I have a HUGE ...
by sbooth
Tue Apr 23, 2019 11:36 pm
Forum: Data analysis
Topic: Histocat - Differential cell neighborhood analysis
Replies: 1
Views: 4062

Histocat - Differential cell neighborhood analysis

Hi all, hope you are well! We have 70 samples analyzed by IMC, and they are graded 1-4 in disease severity. Is there a way to see if cell types interact differently between the severity stages? For example, should we tsne+phenograph on all the samples together, and then run the neighborhood analysis...
by sbooth
Tue Dec 11, 2018 5:30 pm
Forum: Data analysis
Topic: Shannon Entropy to quantify cell heterogeneity?
Replies: 2
Views: 582

Re: Shannon Entropy to quantify cell heterogeneity?

Thanks Denis for the quick reply, and for directing to the correct reference.

Sounds like a great update to Histocat, look forward to seeing the new release!

Steve
by sbooth
Tue Dec 11, 2018 5:11 pm
Forum: Data analysis
Topic: Shannon Entropy to quantify cell heterogeneity?
Replies: 2
Views: 582

Shannon Entropy to quantify cell heterogeneity?

Hi everyone, hope you are well. I just came across this quite impressive pre-print of a new multiplex IF technique. In the paper they used a measure of entropy to examine local cell heterogeneity. https://www.biorxiv.org/content/biorxiv/early/2018/05/10/151738.full.pdf Details of the entropy calcula...
by sbooth
Thu Nov 15, 2018 11:03 pm
Forum: Data analysis
Topic: Compensation slide acquisition
Replies: 3
Views: 896

Re: Compensation slide acquisition

Thanks Vito, Santhosh. Your suggestions are great.

Fingers crossed I guess!

Steve
by sbooth
Mon Nov 12, 2018 6:27 pm
Forum: Data analysis
Topic: Compensation slide acquisition
Replies: 3
Views: 896

Compensation slide acquisition

Hi all, We are running a 33x Ab panel on the Hyperion at the moment and I would like to try to generate a compensation slide. I think the protocol from Vito is very clear for preparing the slide, but I am wondering how you actually acquire such a slide on the Hyperion? i.e. do you do a single acquis...
by sbooth
Tue Jul 17, 2018 10:40 pm
Forum: Data analysis
Topic: Histocat++ for windows?
Replies: 1
Views: 735

Histocat++ for windows?

Hi there, hope you are all well! I have been using Fluidigm MCD viewer, Ilastik, Cell profiler, Histocat & Cytofkit to do IMC analysis thus far. But I was just reading in the forum that compensation & segmentation will be built into Histocat ++. I can't seem to find where I can download Histocat ++ ...
by sbooth
Wed Apr 25, 2018 9:52 pm
Forum: Data analysis
Topic: Imctools
Replies: 15
Views: 4431

Re: Imctools

Hi Votti, I am trying to use the imctools as a Fiji plugin as you described. The 'open multichannel ome' function works fine, but the 'open imc' function (which is the one that I need) is throwing the following error in my hands, could you take a look and let me know what you think? Using the latest...