napari-bioformats

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:

• Zeiss (.czi): napari-aicsimageio, napari-czifile2
• Nikon (.nd2): napari-nikon-nd2, nd2-dask
• Leica (.lif): napari-aicsimageio
• Olympus (.oif): no plugin? (but see oiffile )
• DeltaVision (.dv, .mrc): napari-dv

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

Installation

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.

License

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

Issues

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

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