Metadata-Version: 2.1
Name: zarr-tools
Version: 0.4.5
Summary: Convert nd2 to zarr
Home-page: https://github.com/BaroudLab/zarr-tools
Author: Andrey Aristov
Author-email: aaristov@pasteur.fr
License: BSD-3-Clause
Project-URL: Bug Tracker, https://gitlab.pasteur.fr/aaristov/zarr-tools/issues
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Framework :: napari
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Topic :: Software Development :: Testing
Requires-Python: >=3.8
Description-Content-Type: text/markdown
License-File: LICENSE

# zarr-tools

Convert nd2 to zarr

[![License](https://img.shields.io/pypi/l/zarr-tools.svg?color=green)](https://github.com/BaroudLab/zarr-tools/raw/main/LICENSE)
[![PyPI](https://img.shields.io/pypi/v/zarr-tools.svg?color=green)](https://pypi.org/project/zarr-tools)
[![Python Version](https://img.shields.io/pypi/pyversions/zarr-tools.svg?color=green)](https://python.org)
[![tests](https://github.com/BaroudLab/zarr-tools/workflows/tests/badge.svg)](https://github.com/BaroudLab/zarr-tools/actions)
[![codecov](https://codecov.io/gh/BaroudLab/zarr-tools/branch/main/graph/badge.svg)](https://codecov.io/gh/BaroudLab/zarr-tools)

## Installation

```pip install zarr-tools```

## Usage

### As command line 
``` python -m zarr-tools file.nd2 ```

This will produce the zarr dataset with default 5 steps of binning for xy dimensions.

### As python module

```python
import nd2
import zarr_tools

data = nd2.ND2File("input.nd2").to_dask()
zarr_tools.convert.to_zarr(
    data,
    channel_axis=1,
    path="output.zarr", 
    steps=4, 
    name=['BF','TRITC'], 
    colormap=['gray','green'],
    lut=((1000,30000),(440, 600)),
)
```

