A BioIO reader plugin for reading OME ZARR images using ome-zarr
See the full documentation on our GitHub pages site - the generic use and installation instructions there will work for this package.
Information about the base reader this package relies on can be found in the bioio-base
repository here
Stable Release: pip install bioio-ome-zarr
Development Head: pip install git+https://github.com/bioio-devs/bioio-ome-zarr.git
Install bioio-ome-zarr alongside bioio:
pip install bioio bioio-ome-zarr
This example shows a simple use case for just accessing the pixel data of the image
by explicitly passing this Reader
into the BioImage
. Passing the Reader
into
the BioImage
instance is optional as bioio
will automatically detect installed
plug-ins and auto-select the most recently installed plug-in that supports the file
passed in.
from bioio import BioImage
import bioio_ome_zarr
img = BioImage("my_file.zarr", reader=bioio_ome_zarr.Reader)
img.data
To read from private S3 buckets, credentials must be configured. Public buckets can be accessed without credentials.
from bioio import BioImage
path = "https://allencell.s3.amazonaws.com/aics/nuc-morph-dataset/hipsc_fov_nuclei_timelapse_dataset/hipsc_fov_nuclei_timelapse_data_used_for_analysis/baseline_colonies_fov_timelapse_dataset/20200323_09_small/raw.ome.zarr"
image = BioImage(path)
print(image.get_image_dask_data())
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See CONTRIBUTING.md for information related to developing the code.