No project description provided
Project description
ngff-zarr
A lean and kind Open Microscopy Environment (OME) Next Generation File Format (NGFF) Zarr implementation.
Table of Contents
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
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-limit option.
ngff-zarr --memory-limit 50M -i ./LIDCFull.vtk -o ./LIDCFull.zarr
More options
ngff-zarr --help
See also
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
- Generate new test data tarball
cd test/data
tar cvf ../data.tar baseline input
gzip -9 ../data.tar
-
Upload the data to web3.storage
-
Upload the
test_data_ipfs_cid(from web3.storage web UI) andtest_data_sha256(sh256sum ../data.tar.gz) variables in test/_data.py.
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distribution
File details
Details for the file ngff_zarr-0.3.0.tar.gz.
File metadata
- Download URL: ngff_zarr-0.3.0.tar.gz
- Upload date:
- Size: 87.3 MB
- Tags: Source
- Uploaded using Trusted Publishing? No
- Uploaded via: twine/4.0.2 CPython/3.11.0
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | f8fd5b9ab5a61bd4691aea9cdf85d80fe4ecdced8e5fc6f716e7bdc65a8a4e97 |
|
| MD5 | 2e8f5d03a4d17025b9e3b03b1f46e8d9 |
|
| BLAKE2b-256 | 80e3504d54ce4f6622188d976221abb951a27abcb3b1f92ef96a20e07480935a |
Provenance
File details
Details for the file ngff_zarr-0.3.0-py3-none-any.whl.
File metadata
- Download URL: ngff_zarr-0.3.0-py3-none-any.whl
- Upload date:
- Size: 28.8 kB
- Tags: Python 3
- Uploaded using Trusted Publishing? No
- Uploaded via: twine/4.0.2 CPython/3.11.0
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | 04a8d2d975c7ee7a5bd6c9120c7a773466973078abaf567fde2b75dd2896e889 |
|
| MD5 | bb5fa2a086c78b140ffbf81824a84387 |
|
| BLAKE2b-256 | d5a56f1da6ce1a4701146b96e8de011958cd24d05c8c6447e4d197e42eacba73 |
