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Merscope Data/Reader mismatch #9

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Farbodch opened this issue May 26, 2024 · 1 comment
Open

Merscope Data/Reader mismatch #9

Farbodch opened this issue May 26, 2024 · 1 comment

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@Farbodch
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The merscope reader-function requires parquet-formatted data for the "cell_boundaries" input, but 16 out of the 17 merscope databases contain purely hdf5-formatted files in their cell_boundaries subfolder.
For reference, the only merscope without this issue is "ush6c__MERSCOPE__HumanUterineCancerPatient2-RACostain", which does have a .parquet cell_boundaries file in the main directory. This db also happens to be the only one with the cell_boundaries data situated in its main directory and not in a subfolder in the main directory.

@LucaMarconato
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Please see some code to make it work here: scverse/spatialdata-io#71.

It would be nice to have this functionality available in spatialdata-io, if any of you end up using the code from Can Ergen I can put you two in contact via Zulip and coordinate a joint PR.

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