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gustaveroussy / sopa

Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoCycler / MACSima / etc)
https://gustaveroussy.github.io/sopa/
BSD 3-Clause "New" or "Revised" License
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How to analyze one tissue section data separately from one capture area which include two tissue sections for Xenium 5k ? #148

Open lidd77 opened 2 days ago

lidd77 commented 2 days ago

Hello,

  For Xenium  5k ,    there are two  tissue sections in one capture area . I need to analyze   every tissue section separately with Seurat.
  So could you please tell me how split every tissue section data   from one caputre area ?
  my Xenium data output name is like this output-*__0041156__Q17_Q16__*__* .

Expecting your reply !

Best

quentinblampey commented 1 day ago

Hello @lidd77, there are two possibilities for splitting the data within Sopa/SpatialData.

1. Before running Sopa

You can create a SpatialData object (with spatialdata_io.xenium), and then use napari-spatialdata to select your regions of interest. Then, based on this, you can crop the SpatialData object based on your regions of interest with this polygon_query. This will create one SpatialData object per polygon query, and then you'll be able to run Sopa on each of the SpatialData objects.

2. After running Sopa

You can also directly run Sopa on all the tissue sections, and split the data afterward. Then, you can use the Xenium Explorer to split your data, as detailed in this tutorial.

Hope this helps, let me know!