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tables referring to multiple regions #99
Description
in both nanostring cosmx and xenium we available info on labels and labels' centroids. Therefore, the spatialdata object will (could) have 2 regions representing the same instance (with potentially same instance_id) and a single table annotating both.
I believe we discussed this but I don't remember how we ended up resolving this issue.
I think one option we discussed was that the centroids labels would just be stored in table.obsm["spatial"] essentially as an annotation on the labels (and useful for plotting etc) but without any constraint or specifications (e.g. no coordinate systems and/or transforms). If that's the case, then there would be no Shapes region for the centroids.
Any idea on how to resolve this issue?
related to #43
Activity
LucaMarconato commentedon Jan 8, 2023
Hi, from the discussion we settled, as you mentioned, on storing the centroids in the table as a separate column, and if I recall correctly we said to store the centroids in the implicit coordinates. This is meant to be a way to unblock this now and not the definitive solutions, since if for instance the centroids come from a labels and they are cropped, then the implicit coordinates stored in the table would not be correct anymore. I also agree of removing the
Shapesfrom storage, they could be created in-place at any time if needed.kevinyamauchi commentedon Jan 9, 2023
My recollection is the same as @LucaMarconato 's.
LucaMarconato commentedon Feb 22, 2024
Closed as duplicate of #34 and #123.