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Bioformats for napari, using pims

Project description

napari-bioformats

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

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.

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

Project details


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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

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