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Nanostring-Biostats / CosMx-Analysis-Scratch-Space

This repository is an exploratory resource to accelerate opensource analysis of CosMx® Spatial Molecular Imager (SMI) data. Contained here are and writeups and vignettes addressing a variety of topics discussed when analyzing single-cell spatial data.
https://nanostring-biostats.github.io/CosMx-Analysis-Scratch-Space/
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adjusting for cell contamination (segmentation error) in models #127

Open acjordan333 opened 21 hours ago

acjordan333 commented 21 hours ago

Hi team,

In the blog post titled, "Impact of segmentation errors on DE", Dr. Danaher wrote that a paper was coming (and a corresponding blog post) that will provide some solutions on how to account for segmentation error (but not fully remove it). Is the blog post coming soon? If not, would I be able to request the code on how to implement this solution? What would be preferred - adjusting for the segmentation error or attempting to remove it with an algorithm like FastReseg?

eveilyeverafter commented 19 hours ago

I think the post you are referring to in currently in review. You can take a look at the draft here: https://github.com/Nanostring-Biostats/CosMx-Analysis-Scratch-Space/pull/123