andreevg04

Segmented CODEX data in QuPath csv to squidpy

1

Dear Community, I have stitched CODEX images directly after the run and I segemented the image in QuPath. The result is a csv where each row is a cell with...

Import from QuPath or CODEX Dataset

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Dear Community, I am working on CODEX Datasets and want to use squidpy to analyze the spatial charateristics. Unfortunately I cant seem to generate the anndata object from the .csv...

Building neighborhoods

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This is more of a question rather than an issue: I have built my neighborhoods but when I use the function as in the tutrial with 22 phenotypes I find...

CODEX dataset with 200 images

4

I am trying to use scimap (the latest version) on a dataset with 200 images previously segmented with stardist. The intensity range is different as in the MCMICRO pipeline, but...