Zarr version
2.17.1
Numcodecs version
0.12.1
Python Version
3.11
Operating System
linux-ubuntu
Installation
pip
Description
Hi Guys,
I need to convert my h5 file from Visium to zarr to open it with spatial napari, but I did not work, and I can open the final zarr file.
root = zarr.group(dest_file, overwrite=True) root.tree()
=> Tree(nodes=(Node(disabled=True, name='/'),))
How can I succeed at it, please?
Best
Nazim
Steps to reproduce
`import h5py
import zarr
import numpy as np
from sys import stdout
sp_data_file = "/media/ben/Elements/Recherche/ETUDE230 visium plag1/data/Visium PA data/nazim/N1Abis/N1Ab.h5" ## h5 file
source = h5py.File(sp_data_file, mode='r')
dest_file = "/home/ben/Documents/VISIUM/PA/lame V1b/test.zarr"
dest = zarr.open_group(dest_file, mode='w')
zarr.copy_all(source, dest, log=stdout)`
Additional output
No response
Zarr version
2.17.1
Numcodecs version
0.12.1
Python Version
3.11
Operating System
linux-ubuntu
Installation
pip
Description
Hi Guys,
I need to convert my h5 file from Visium to zarr to open it with spatial napari, but I did not work, and I can open the final zarr file.
root = zarr.group(dest_file, overwrite=True) root.tree()=> Tree(nodes=(Node(disabled=True, name='/'),))
How can I succeed at it, please?
Best
Nazim
Steps to reproduce
`import h5py
import zarr
import numpy as np
from sys import stdout
sp_data_file = "/media/ben/Elements/Recherche/ETUDE230 visium plag1/data/Visium PA data/nazim/N1Abis/N1Ab.h5" ## h5 file
source = h5py.File(sp_data_file, mode='r')
dest_file = "/home/ben/Documents/VISIUM/PA/lame V1b/test.zarr"
dest = zarr.open_group(dest_file, mode='w')
zarr.copy_all(source, dest, log=stdout)`
Additional output
No response