Skip to main content

Bioformats for napari, using pims

Project description


License PyPI Conda Python Version tests codecov

Bioformats plugin for napari using pims-bioformats

Use this plugin as a fallback!

Anyone coming to napari from the Fiji/ImageJ world will likely be aware of the incredible Bio-Formats library. A heroic effort, built over years, to read more than a 100 file formats. Naturally, we want some of that goodness for napari ... hence this plugin.

However: it's important to note that this plugin still requires having a java runtime engine installed. This is easy enough to do (the plugin will ask to install it for you if you're in a conda environment), but it definitely makes for a more complicated environment setup, it's not very "pythonic", and the performance will likely not feel as snappy as a native "pure" python module.

So, before you reflexively install this plugin to fill that bio-formats sized hole in your python heart, consider trying some of the other pure-python plugins designed to read your format of interest:

if you have a pure-python reader for a bio-formats-supported file format that you'd like to see added to this list, please open an issue


The easiest way to install napari-bioformats is via conda, from the conda-forge channel:

conda install -c conda-forge napari-bioformats

It is also possible to install via pip, but you will need to have a working JVM installed, and may need to set the JAVA_HOME environment variable

pip install napari-bioformats

First Usage

The first time you attempt to open a file with napari-bioformats, you will likely notice a long delay as pims downloads the loci_tools.jar (speed will depend on your internet connection). Subsequent files should open more quickly.


Distributed under the terms of the GPLv3 license, "napari-bioformats" is free and open source software


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

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

Project details

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Files for napari-bioformats, version 0.2.1
Filename, size File type Python version Upload date Hashes
Filename, size napari_bioformats-0.2.1.tar.gz (41.8 MB) File type Source Python version None Upload date Hashes View
Filename, size napari_bioformats-0.2.1-py3-none-any.whl (41.8 MB) File type Wheel Python version py3 Upload date Hashes View

Supported by

AWS AWS Cloud computing Datadog Datadog Monitoring Facebook / Instagram Facebook / Instagram PSF Sponsor Fastly Fastly CDN Google Google Object Storage and Download Analytics Huawei Huawei PSF Sponsor Microsoft Microsoft PSF Sponsor NVIDIA NVIDIA PSF Sponsor Pingdom Pingdom Monitoring Salesforce Salesforce PSF Sponsor Sentry Sentry Error logging StatusPage StatusPage Status page