OME-Zarr Download Guide

This guide shows an easy way to download OME-Zarr datasets from the QIM data repository and other sources using Python and the qim3d library.

Step 1: Install qim3d

The official qim3d README recommends this setup:

conda create -n qim3d python=3.11
conda activate qim3d
pip install qim3d

Important: activate the environment each time before using qim3d:

conda activate qim3d

Step 2a: Download using the qim3d.io.Downloader()

This codeblock downloads the Escargot OME-Zarr file into a local downloads folder.

Ome-Zarr can be large and downloads can take a long time. Keep the process running until completion.

import qim3d

downloader = qim3d.io.Downloader()

escargot_path = downloader(
    url="https://platform.qim.dk/qim-public/escargot/escargot.zarr",
    output_dir="downloads",
    load_file=False,
)

print("Downloaded to:", escargot_path)

Step 2b: Download and explore the data using qim3d

virtual_stack=True is recommended for larger datasets because it avoids loading everything into RAM immediately, and uses a dask.Array.

The loaded scale can also be configured, by default it loads the highest definition level. Look at the qim3d documentation for more details.

import qim3d

downloader = qim3d.io.Downloader()

escargot = downloader(
    url="https://platform.qim.dk/qim-public/escargot/escargot.zarr",
    output_dir="downloads",
    load_file=True,
    virtual_stack=True,
)

print(type(escargot))
print(escargot.shape)