Metadata-Version: 2.4
Name: napari-ndev
Version: 0.11.8
Summary: napari widgets to (batch) process images from start to finish.
Author-email: Tim Monko <timmonko@gmail.com>
License: BSD-3-Clause
Project-URL: Bug Tracker, https://github.com/TimMonko/napari-ndev/issues
Project-URL: Documentation, https://ndev-kit.github.io/
Project-URL: Source Code, https://github.com/TimMonko/napari-ndev
Classifier: Development Status :: 3 - Alpha
Classifier: Framework :: napari
Classifier: Intended Audience :: Education
Classifier: Intended Audience :: Science/Research
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 :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Topic :: Scientific/Engineering :: Image Processing
Classifier: Topic :: Scientific/Engineering :: Visualization
Classifier: Topic :: Software Development :: User Interfaces
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Classifier: Topic :: Utilities
Requires-Python: >=3.9
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: numpy<2.0,>=1.26
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Requires-Dist: napari-workflows
Requires-Dist: napari-pyclesperanto-assistant
Requires-Dist: napari-segment-blobs-and-things-with-membranes
Requires-Dist: natsort
Requires-Dist: seaborn
Requires-Dist: stackview
Requires-Dist: tifffile<2025.2.18,>=2023.3.15
Requires-Dist: scikit-image>=0.18.0
Requires-Dist: ngff-zarr>0.10.0
Requires-Dist: zarr<3
Requires-Dist: bioio>=1.1.0
Requires-Dist: bioio-base==1.0.4
Requires-Dist: bioio-imageio>=1
Requires-Dist: bioio-tifffile>=1
Requires-Dist: bioio-ome-tiff>=1
Requires-Dist: bioio-ome-zarr>=1
Requires-Dist: bioio-nd2>=1
Requires-Dist: matplotlib-scalebar>=0.8.1
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Requires-Dist: napari[all]; extra == "testing"
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Requires-Dist: bioio-czi>=1.0.1; extra == "testing"
Requires-Dist: napari-ndev[extras]; extra == "testing"
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Provides-Extra: pyside
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Provides-Extra: extras
Requires-Dist: napari-simpleitk-image-processing; extra == "extras"
Provides-Extra: gpl-extras
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Requires-Dist: bioio-lif>=1; extra == "gpl-extras"
Provides-Extra: all
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Requires-Dist: napari-ndev[extras]; extra == "all"
Requires-Dist: napari-ndev[gpl_extras]; extra == "all"
Dynamic: license-file

# napari-ndev

[![License BSD-3](https://img.shields.io/pypi/l/napari-ndev.svg?color=green)](https://github.com/TimMonko/napari-ndev/raw/main/LICENSE)
[![PyPI](https://img.shields.io/pypi/v/napari-ndev.svg?color=green)](https://pypi.org/project/napari-ndev)
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[![Python Version](https://img.shields.io/pypi/pyversions/napari-ndev.svg?color=green)](https://python.org)
[![tests](https://github.com/TimMonko/napari-ndev/workflows/tests/badge.svg)](https://github.com/TimMonko/napari-ndev/actions)
[![codecov](https://codecov.io/gh/TimMonko/napari-ndev/branch/main/graph/badge.svg)](https://codecov.io/gh/TimMonko/napari-ndev)
[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-ndev)](https://napari-hub.org/plugins/napari-ndev)
![Static Badge](https://img.shields.io/badge/plugin-npe2-brightgreen?style=flat-square&label=plugin)
[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.14787853.svg)](https://doi.org/10.5281/zenodo.14787853)

<img src="./resources/nDev-logo-large.png" alt="logo" width="400" style="display: block; margin: auto;">

A collection of widgets intended to serve any person seeking to process microscopy images from start to finish, *with no coding necessary*. `napari-ndev` was designed to address the **gap between the napari viewer and batch python scripting**.

* Accepts **diverse image formats**, dimensionality, file size, and maintains key metadata.
* Allows **advanced, arbitrary image processing** workflows to be used by novices.
* **User-friendly** sparse annotation and batch training of **machine learning classifiers**.
* Flexible label measurements, parsing of metadata, and summarization for **easily readable datasets**.
* Designed for ease of use, modification, and reproducibility.

## [Check out the Docs to learn more!](https://ndev-kit.github.io)

### See the [poster presented at BINA 2024](https://ndev-kit.github.io/BINA_poster/) for an overview of the plugins in action

### Try out the [Virtual I2K 2024 Workshop](https://ndev-kit.github.io/tutorial/00_setup/) for an interactive tutorial

## Installation

**napari-ndev** is a pure Python package, and can be installed with [pip]:

```bash
pip install napari-ndev
```

If napari is currently not installed in your environment, you will also need to include a QtPy backend:

```bash
pip install napari-ndev[qtpy-backend]
```

The easiest way to get started with **napari-ndev** is to install all the optional dependencies (see note below) with:

```bash
pip install napari-ndev[all]
```

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

### Optional Libraries

**napari-ndev** is most useful when interacting with some other napari plugins (e.g. napari-assistant) and can read additional filetypes. A few extra BSD3 compatible napari-plugins may be installed with [pip]:

```bash
pip install napari-ndev[extras]
```

**napari-ndev** can optionally use GPL-3 licensed libraries to enhance its functionality, but are not required. If you choose to install and use these optional dependencies, you must comply with the GPL-3 license terms. The main functional improvement is from some `bioio` libraries to support extra image formats, including `czi` and `lif` files. These libraries can be installed with [pip]:

```bash
pip install napari-ndev[gpl-extras]
```

In addition, you may need to install specific [`bioio` readers](https://github.com/bioio-devs/bioio) to support your specific image, such as `bioio-czi` and `bioio-lif` (included in `[gpl-extras]`) or `bioio-bioformats`.

### Development Libraries

For development use the `[dev]` optional libraries to verify your changes, which includes the `[docs]` and `[testing]` optional groups. However, the Github-CI will test pull requests with `[testing]` only.

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

The wide breadth of this plugin's scope is only made possible by the amazing libraries and plugins from the python and napari community, especially [Robert Haase](https://github.com/haesleinhuepf).

This [napari] plugin was generated with [Cookiecutter] using [napari]'s [cookiecutter-napari-plugin] template.

## 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-ndev" is free and open source software.

Some optional libraries can be installed to add functionality to `napari-ndev`, including some that may be more restrictive than this package's BSD-3-Clause.

## Issues

If you encounter any problems, please [file an issue] along with a detailed description.

[napari]: https://github.com/napari
[Cookiecutter]: https://github.com/audreyr/cookiecutter
[BSD-3]: http://opensource.org/licenses/BSD-3-Clause
[cookiecutter-napari-plugin]: https://github.com/napari/cookiecutter-napari-plugin

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