Shannon Entropy to quantify cell heterogeneity?

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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

Shannon Entropy to quantify cell heterogeneity?

Post by sbooth » Tue Dec 11, 2018 5:11 pm

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 ... 8.full.pdf

Details of the entropy calculation are on line 371,750, & Fig 11c
"To quantify local heterogeneity, we computed the informational entropy on a-per-channel basis for 10e3 randomly selected cells in each field (Figure 11C, see online Methods for details). In this setting, informational entropy is a measure of cell-to-cell heterogeneity on a mesoscale corresponding to 10-30 cell diameters."

I wonder if something like this could be implemented in Histocat (could be implemented as something like; randomly downsample n cells and select n nearest neighbors, calculate entropy on selected channels). Or does anyone have other ideas of ways to statistically measure cellular heterogeneity within IMC ROIs?

Best,
Steve

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

Re: Shannon Entropy to quantify cell heterogeneity?

Post by DenisSchapiro » Tue Dec 11, 2018 5:23 pm

Dear Steve,

The paper is already published here: https://elifesciences.org/articles/31657

I am working closely with the t-CyCIF team to implement this and other spatial statistics methods into histoCAT. One metric that we have recently implemented is a sliding window approach to quantify cellular heterogeneity.

I will add this feature as priority for the next software release.

Best

Denis

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sbooth
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Joined: Wed Apr 25, 2018 9:40 pm

Re: Shannon Entropy to quantify cell heterogeneity?

Post by sbooth » Tue Dec 11, 2018 5:30 pm

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

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