napari-basicpy 0.0.3
BaSiCPy illumination correction for napari
License: BSD-3-Clause
Requires Python: >=3.8

# napari-basicpy

[![License](https://img.shields.io/pypi/l/napari-basicpy.svg?color=green)](https://github.com/tdmorello/napari-basicpy/raw/main/LICENSE)
[![PyPI](https://img.shields.io/pypi/v/napari-basicpy.svg?color=green)](https://pypi.org/project/napari-basicpy)
[![Python Version](https://img.shields.io/pypi/pyversions/napari-basicpy.svg?color=green)](https://python.org)
[![tests](https://github.com/tdmorello/napari-basicpy/workflows/tests/badge.svg)](https://github.com/tdmorello/napari-basicpy/actions)
[![codecov](https://codecov.io/gh/tdmorello/napari-basicpy/branch/main/graph/badge.svg)](https://codecov.io/gh/tdmorello/napari-basicpy)
[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-basicpy)](https://napari-hub.org/plugins/napari-basicpy)

BaSiCPy illumination correction for [napari]

## Example

![example](resources/example.gif)

----------------------------------

## Installation

### Recommended Installation Method

We highly recommend using a `conda` virtual environment to install and operate this plugin.

To use Python 3.9, for example:

    conda create -n basicpy -c conda-forge python=3.9 napari pyqt && \
    conda activate basicpy && \
    pip install napari-basicpy

For further instructions on installing `napari`, visit their [install guide](https://napari.org/stable/tutorials/fundamentals/installation).

---

**IMPORTANT NOTE FOR APPLE SILICON AND WINDOWS USERS:**

If the above instructions fail with Apple silicon (e.g., M1/M2 chip) or Windows, you may need to install the `jax` and `jaxlib` following the instruction [here](https://github.com/peng-lab/BaSiCPy#installation).

---

### Other Installation Methods

You can also install `napari-basicpy` via [pip]:

    pip install napari-basicpy


To install latest development version:

    pip install git+https://github.com/peng-lab/napari-basicpy.git

or

    pip install git+https://github.com/tdmorello/napari-basicpy.git

## Usage

### General Usage

This plugin expects a stack of tiles as input. Mosaic images should be deconstructed into their tiled components before processing. Individual tiles should be two-dimensional.

There are many options to customize the performance of BaSiCPy. Please refer to the BaSiCPy documentation on parameters [here](https://basicpy.readthedocs.io/en/latest/api.html#basicpy.basicpy.BaSiC) for details.

### Batch Processing

Coming soon...

## Contributing

Contributions are very welcome. Tests can be run with [tox], please ensure
the coverage at least stays the same before you submit a pull request.

## License

Distributed under the terms of the [BSD-3] license,
"napari-basicpy" is free and open source software

## Issues

If you encounter any problems, please [file an issue](https://github.com/peng-lab/napari-basicpy/issues) along with a detailed description.

[napari]: https://github.com/napari/napari
[@napari]: https://github.com/napari
[BSD-3]: http://opensource.org/licenses/BSD-3-Clause

[tox]: https://tox.readthedocs.io/en/latest/
[pip]: https://pypi.org/project/pip/
[PyPI]: https://pypi.org/