scverse / scverse/squidpy

Vizgen-MERFISH multiple dataset integration/comparison

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#835 1 comment 0 reactions 1 assignee View on GitHub

@giovp is already working on this.

Since Jun 7, 2024.

good first issue question :question:
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Description

...Dear developers.
Thank you for very stable version of squidpy, and very detailed tutorials/scripts. I work with organoid samples. I have sn-seq and VizgenMERFISH 140 genes datasets for 6 different subtypes of organoids. I analyses sn-seq in the seurat in RStudio. Unfortunately, seurat is not working good enough with VizgenMERFISH yet. So, I have to learn python pipelines and I hope you may help me:

  1. Can I merge and integrate all my 6 spatial datasets, so I will be able cluster cell types together and plot them after that per each dataset? I did such clustering it in the https://vizgen.com/resources/merscope-vizualizer-clustering-template/ , and loaded back in the Vizgen visualizer. I failed to read that clustering in the squidpy(
  2. Vizgen visualiser is good visualisation tool, but obviously, has nothing to do with cell type comparisons-analysis. Using squidpy, can I make conclusion like organoids in Dataset 1 has more cells type 1 and 2, and organoids in the dataset 4 have more cell type 5 and 6, that is why organoids in dataset 4 are more mature.
    I am biologist, so I will appreciate any your help

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