ndevio 0.5.0

Read, write, and manage images in napari

ndevio

Read, write, and manage images in napari

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This napari plugin was generated with copier using the napari-plugin-template.

Installation

You can install ndevio via pip:

pip install ndevio

If napari is not already installed, you can install ndevio with napari and Qt via:

pip install "ndevio[all]"

To install the latest development version:

pip install git+https://github.com/ndev-kit/ndevio.git

Additional Image Format Support

ndevio uses bioio for flexible image reading. Basic formats (TIFF, OME-TIFF, OME-Zarr, PNG, etc.) are supported out of the box via:

• bioio-ome-tiff - OME-TIFF files
• bioio-ome-zarr - OME-Zarr files
• bioio-tifffile - General TIFF files
• bioio-imageio - PNG, JPEG, and other common formats

If your image format is not supported by the default readers, then you will get a warning and (by default in napari) a widget to install the suggested reader. If you know of your additional proprietary formats, install the appropriate bioio reader.

# CZI files (GPL-3 licensed)
pip install bioio-czi

# LIF files (GPL-3 licensed)
pip install bioio-lif

# Bio-Formats for many formats (behavior not guaranteed)
pip install bioio-bioformats

See the bioio documentation for the full list of available readers.

Pixi Usage

You can use Pixi for reproducible development environments:

git clone https://github.com/ndev-kit/ndevio.git
cd ndevio
pixi install -e dev
pixi run -e dev test

Or activate the environment and run commands directly:

pixi shell -e dev
pytest -v

Development

For development, clone the repository and install with the dev dependency group:

git clone https://github.com/ndev-kit/ndevio.git
cd ndevio
pip install -e . --group dev

This includes pytest, pytest-cov, pytest-qt, tox-uv, napari, and pyqt6.

Run tests with:

pytest -v --cov=ndevio --cov-report=html

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, "ndevio" is free and open source software

Issues

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