scverse / scverse/squidpy

Bring minimal `stalign` function

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#1,146 1 comment 0 reactions 1 assignee View on GitHub

@selmanozleyen is already working on this.

Since Apr 2, 2026.

squidpy2.0
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Python
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Description

Description of feature

Ok here is the plan I have for this.

  • We will only support point cloud case for now, later we can make additions.
  • Will call it stalign and won't expose it as if it's a function that aligns everything. So that we can add other methods and have our monolith align function later as this goes
  • If there is serious preprocessing needs to be done on point clouds it should be a different function called stalign_preprocess. If that is the case then there might be more optimal ways to handle this but let's just go with something we can ship as is.
  • We shouldn't make guarantees on the stability of these unexposed API's
  • plotting/scoring will be a separate issue
  • I will do it in jax as it's better than torch and stalign doesn't rely on it so heavily

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