Open lidd77 opened 3 weeks ago
Hello @lidd77, there are two possibilities for splitting the data within Sopa/SpatialData.
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.
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!
Hello,
Expecting your reply !
Best