feature_slice.h5 Error when running spatialdata_io.visium_hd

[Hanxi-002]

Hi there,

When I run the following code:

base_dir = '/Visium_HD_5_2024/SpaceRanger_OUT/' folder = 'Control3/' sdata = spatialdata_io.visium_hd(base_dir+folder+'outs/', dataset_id='Control3', bin_size = 16, filtered_counts_file=True)

I get this error:
FileNotFoundError: [Errno 2] Unable to open file (unable to open file: name = '/Visium_HD_5_2024/SpaceRanger_OUT/Control3/outs/Control3_feature_slice.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Just FYI, this is the content of the base_dir+folder+'outs/' directory, which I believe follows the1 10X output format:
binned_outputs
cloupe_008um.cloupe
Control3_web_summary.html
feature_slice.h5
metrics_summary.csv
molecule_info.h5
possorted_genome_bam.bam
possorted_genome_bam.bam.bai
probe_set.csv
spatial

Not sure why this is happening and any help is appreciated!
Thanks!

[LucaMarconato]

Thank you for reporting, seems like a duplicate of #212; please follow that issue for getting updates on the solution.

[LucaMarconato]

The issue should now be addressed thanks to #264. Please if you test the new fixed code, it would be great to learn your feedback.