Histocat - Differential cell neighborhood analysis

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Computational image analysis of multiplexed Imaging Mass Cytometry acquisitions
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sbooth
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Joined: Wed Apr 25, 2018 9:40 pm

Histocat - Differential cell neighborhood analysis

Post by sbooth » Tue Apr 23, 2019 11:36 pm

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 on the different severity groups separately? So we would have 4 neighborhood analyses, then compare the significant interactions among them somehow.

Our hypothesis is that inflammatory cells may interact with structural cells more as the disease severity increases, leading to tissue destruction.

Any thoughts on this would be much appreciated!
Best,
Steve

DenisSchapiro
Posts: 33
Joined: Wed Nov 29, 2017 11:34 am

Re: Histocat - Differential cell neighborhood analysis

Post by DenisSchapiro » Wed Apr 24, 2019 2:57 am

Hi Steve,

I would run tSNE + PhenoGraph on all samples and run neighborhood analysis (1) on 4 different disease states for comparison and on all disease states together. When you run all together, do you see hierarchical clusters enriched in certain cell-cell interactions? When you run them individual, you can compare the heat maps. We have done something similar in the original histoCAT paper.

Best

Denis

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