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theislab / spatialdata-db

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Visium dbs with multiple subfolders/types in the ./spatial subfolder #11

Open Farbodch opened 5 months ago

Farbodch commented 5 months ago

Two of the visium readers' inputs are fullres_image_file and scalefactors_file. Some of the visium dbs (below) have multiple subfolders/types in their ./spatial subfolder, each with their own distinct image & scalefactors files. It is unclear how these should be parsed into the visium reader, which expects only one file for each of the two inputs.

The visium dbs in question:

with

in ./spatial/*

note also: the above dbs are the only "proper" visium dbs without a tissue_positions_file file. ("proper" as opposed to the two dbs 3554v & 0nuqa that are missing the major .h5 file. Refer to another issue for these two)

Farbodch commented 5 months ago

The following db doesn't have their sub-sections individually and separately downloaded:

https://github.com/theislab/spatialdata-db/issues/28

Farbodch commented 5 months ago

The x2 subsections of the following aggregated DB already exists:

They are the following:

https://github.com/theislab/spatialdata-db/issues/25

Farbodch commented 5 months ago

The x2 subsections of the following aggregated DB already exists:

They are the following:

https://github.com/theislab/spatialdata-db/issues/26

Farbodch commented 5 months ago

The x11 subsections of the following aggregated DB already exists:

They are the following:

https://github.com/theislab/spatialdata-db/issues/27