napari-bioformats: Bio-Formats plugin for napari using bffile

Use the classic Java-based OME Bio-Formats reader you know and love from ImageJ/Fiji, QuPath, etc. in napari to open >100 different imaging file formats (for details, see the Bio-Formats documentation).

This plugin leverages bffile, a modern Bio-Formats wrapper for Python:

• "Batteries include": no special Java setup is required
• Layer data is returned as LazyBioArray with full lazy indexing and slicing (with no additional dependencis on dask/xarray/zarr)
• Basic OME metadata handling to identify channel axis and scale
• Automatic handling of multiple resolution levels as napari MultiScaleData

Additionally, it provides a convenient Series selection widget allowing you to choose what to load when a file contains multiple Series.

Installation

You can install the plugin using the built-in napari Plugin manager in the Plugins menu or from either conda-forge or PyPI over a wide range of Python versions (3.10-3.14) using your favorite package manager. E.g.:

conda install napari-bioformats

or

pip install napari-bioformats

Tip

No manual Java installation required!

This package automatically downloads and manages the Java runtime using cjdk (via scyjava).

Contributing

Contributions are welcome!

To get started, fork and clone the repository. For the development environment we recommend using uv:

uv sync

Please be sure to work on contributions in a dedicated branch and then open a pull request for review.

Releasing

Anyone with write access can create a release:

1. Locally:

   checkout the commit you want to release, then run:

   git tag -a vX.Y.Z -m vX.Y.Z
   git push upstream --follow-tags