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add tooling to access and compute on large embeddings #9

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kevinyamauchi opened this issue Feb 7, 2024 · 3 comments
Open
3 tasks

add tooling to access and compute on large embeddings #9

kevinyamauchi opened this issue Feb 7, 2024 · 3 comments

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@kevinyamauchi
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In order to support larger-than-memory embeddings, we need some tooling for performant lazy loading. A few features/characteristics:

  • should support most numpy style indexing
  • should allow for simple queries (e.g., ball point)
  • must support zarr both local and remote (e.g., S3)

Libraries for IO:

  • TensorStore. this seems like it's the most flexible backend-wise
  • xarray
  • dask (@kephale noted some performace limitations with large numbers of chunks in the napari tiled rendering work)
@kephale
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kephale commented Feb 7, 2024

For the size of typical tomograms we might be ok with Dask

@kephale
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kephale commented Feb 8, 2024

I'm up for giving TensorStore a whirl.

@kephale
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kephale commented Mar 1, 2024

I have been able to use this album solution to segment whole tomograms:
https://album.cellcanvas.org/cellcanvas/segment-tomogram/0.0.4

after computing the embedding with this album solution:
http://cold-storage.kyleharrington.com/tomotwin/generate-embedding-zarr/0.0.15

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