ngff-zarr

---

A lean and kind Open Microscopy Environment (OME) Next Generation File Format (NGFF) Zarr implementation.

Table of Contents

• Installation
• Features
• Usage
• See also
• License

Installation

To install the command line interface (CLI):

pip install 'ngff-zarr[cli]'

Features

• Minimal dependencies
• Work with arbitrary Zarr store types
• Lazy, parallel, and web ready -- no local filesystem required
• Process extremely large datasets
• Multiple downscaling methods
• Supports Python>=3.7
• Implements version 0.4 of the OME-Zarr NGFF specification

Usage

Convert an image file

Convert any scientific image file format supported by either itk, tifffile, or imageio.

Example:

ngff-zarr -i ./MR-head.nrrd -o ./MR-head.zarr

Convert an image volume slice series

Note the quotes:

ngff-zarr -i "series/*.tif" -o ome-ngff.zarr

Print information about generated multiscales

To print information about the input, omit the output argument.

ngff-zarr -i ./MR-head.nrrd

Specify output chunks

ngff-zarr -c 64 -i ./MR-head.nrrd

Specify metadata

ngff-zarr --dims "z" "y" "x" --scale x 1.4 y 1.4 z 2.5 --translation x 6.24 y 360.0 z 332.5 --name LIDC2 -i "series/*.tif"

Limit memory consumption

Limit memory consumption by passing a rough memory limit in human-readable units, e.g. 8GB with the --memory-target option.

ngff-zarr --memory-target 50M -i ./LIDCFull.vtk -o ./LIDCFull.zarr

More options

ngff-zarr --help

See also

• ome-zarr-py
• multiscale-spatial-image

License

ngff-zarr is distributed under the terms of the MIT license.

Development

Contributions are welcome and appreciated.

To run the unit tests:

pip install -e ".[test,dask-image,itk,cli]"
pytest

Updating test data

1. Generate new test data tarball

cd test/data
tar cvf ../data.tar baseline input
gzip -9 ../data.tar

2. Upload the data to web3.storage

3. Upload the test_data_ipfs_cid (from web3.storage web UI) and test_data_sha256 (sh256sum ../data.tar.gz) variables in test/_data.py.