bioio-ome-zarr 1.1.0

A BioIO reader plugin for reading Zarr files in the OME format.

bioio-ome-zarr

A BioIO reader plugin for reading OME ZARR images using ome-zarr

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Documentation

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

Installation

Stable Release: pip install bioio-ome-zarr
Development Head: pip install git+https://github.com/bioio-devs/bioio-ome-zarr.git

Example Usage (see full documentation for more examples)

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

Reading from AWS S3

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())

If using an s3:// path to access a public S3 bucket, the BioImage constructor must be given a dictionary with anon: True in the fs_kwargs argument.

from bioio import BioImage
path = "s3://allencell/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, fs_kwargs=dict(anon=True))
print(image.get_image_dask_data())

Issues

Click here to view all open issues in bioio-devs organization at once or check this repository's issue tab.

Development

See CONTRIBUTING.md for information related to developing the code.