ome-zarr-py

Use the ome-zarr-py library for inspecting and downloading OME-Zarrs from s3

Remote OME-Zarr data stored in a public s3 bucket can be inspected and downloaded using the ome-zarr-py tool via terminal or Python code.

Activate the conda environment ngff_workshop:

conda activate ngff_workshop

Terminal

Inspect remote data

Inspect 3 different remote datasets:

ome_zarr info https://uk1s3.embassy.ebi.ac.uk/EuBI/anna_steyer0/20160112_C.elegans_std_fullhead.zarr

ome_zarr info https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0062A/6001240.zarr

ome_zarr info https://s3.embl.de/i2k-2020/platy-raw.ome.zarr

Download remote data

Create a directory named downloaded_omezarrs in your home directory, browse into it and download the dataset 6001240.zarr from s3:

cd /path/to/data/downloaded_omezarrs

ome_zarr download https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0062A/6001240.zarr

Inspect the local dataset (optional):

ome_zarr info /path/to/data/downloaded_omezarrs/6001240.zarr

Python

Access Python

python

Import the relevant tools

from ome_zarr import utils

Inspect remote data

list(utils.info("https://uk1s3.embassy.ebi.ac.uk/EuBI/anna_steyer0/20160112_C.elegans_std_fullhead.zarr"))

Download remote data

utils.download(input_path = "https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0062A/6001240.zarr",
               output_dir = "./downloaded_omezarrs")