best way to extract anndata ( h5ad ) from hdf5 file

[afshinmoradi]

Dear,

I run cell segmentation and saved h5 files.
I loaded with bellow command
f= h5py.File('a.h5', "r")
I want to extract annadata or csv from that. Could please let me know what is the best option

I used bellow comment it works
f['counts']['X'][()]

but I got bellow error when I called obs dataset

f['counts']['obs'][()]
Traceback (most recent call last):
File "", line 1, in
File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
File "/scratch/medicine/afshin/app/miniconda3/envs/H5/lib/python3.10/site-packages/h5py/_hl/group.py", line 330, in getitem
raise TypeError("Accessing a group is done with bytes or str, "
TypeError: Accessing a group is done with bytes or str, not <class 'tuple'>

Thanks for your help

[jacob-rosenthal]

I suggest using SlideData instead of interacting with the raw h5 file for this. For example, try something like:

wsi = SlideData('a.h5')
counts = wsi.counts