Search found 9 matches

by sbooth
Tue Jul 23, 2019 1:11 am
Forum: Data analysis
Topic: Histocat - Differential cell neighborhood analysis
Replies: 2
Views: 4205

Re: Histocat - Differential cell neighborhood analysis

Thanks Dennis, Since the neighborhood analysis is run sample-wise. If it is run on a group of 10 samples then separately on another group of 10 samples, shouldn't the results be the same as running on all 20 samples together? The dendogram will look different obviously, but the actual interaction/av...
by sbooth
Wed Jun 12, 2019 6:34 pm
Forum: Data analysis
Topic: IMC data processing-Normalization & Scaling
Replies: 0
Views: 644

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: 2
Views: 4205

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: 729

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: 729

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: 1114

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: 1114

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: 864

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: 5009

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...