napari-ndev

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!

See the poster presented at BINA 2024 for an overview of the plugins in action

Try out the Virtual I2K 2024 Workshop 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 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.

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.