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Nanostring TileDB export, new format #85

Open mkattah opened 1 year ago

mkattah commented 1 year ago

Description

Nanostring CosMx datasets have a new file export format through TileDB, https://nanostring.com/wp-content/uploads/2023/01/LiverPublicDataRelease.html They no longer give .csv files for expression matrix and metadata. We are able to generate h5ad files no problem, but the spatial coordinates are different now. Are there any plans to update the tutorial with the new file format? thank you so much, love squidpy and hoping to continue using it for these new datasets. ...

giovp commented 11 months ago

hi @mkattah , I doubt we'll be able to update the reading functions for that, I will move this issue to spatialdata io

Starlitnightly commented 5 months ago

Hi @giovp , spatialdata-io still doesn't seem to be able to read TileDB files directly!

giovp commented 5 months ago

interesting, I took a look again at https://nanostring.com/wp-content/uploads/2023/01/LiverPublicDataRelease.html , it seems like the pipeline from nanostring export the data in tiledb (following soma specs for the gexp matrix). It should be straightforward to read the anndata part, for the images not sure, I can't prioritize it atm but welcome contributions.

pinging @LucaMarconato and @ivirshup just for interest, this is the first time I see a company;'s pipeline adopting tiledb/soma as specification/format for processed data.