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OmicsML / CellPLM

Official repo for CellPLM: Pre-training of Cell Language Model Beyond Single Cells.
BSD 2-Clause "Simplified" License
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Cannot open spatial h5ad files #7

Closed WhirlFirst closed 8 months ago

WhirlFirst commented 8 months ago

Hi,

Thank you for providing the data files. When I tried to open the HumanLiverCancerPatient2_filtered_ensg.h5ad file downloaded from Dropbox, I got an error:

OSError: Can't synchronously read data (filter returned failure during read)
Error raised while reading key '/obs/fov' of <class 'h5py._hl.dataset.Dataset'> to /

I don't know whether it is caused by the different versions or if it means the file is corrupted. Could you give me more information or test to read it on your computer?

Thanks in advance.

wehos commented 8 months ago

Please make sure you installed hdf5plugin (via pip install hdf5plugin) and import it before loading the data. This was included in the tutorial codes.

I don't have other ideas about this issue. I cannot reproduce it and I just successfully loaded the data on my local laptop.

WhirlFirst commented 8 months ago

Please make sure you installed hdf5plugin (via pip install hdf5plugin) and import it before loading the data. This was included in the tutorial codes.

I don't have other ideas about this issue. I cannot reproduce it and I just successfully loaded the data on my local laptop.

Thanks for your help. I thought it was an anndata file and read it by the scanpy function. I will use this package. Thanks