napari-bioformats

Bioformats for napari, using pims


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    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.

    Version:

    • 0.2.1

    Release date:

    • 11 August 2021

    First released:

    • 25 June 2021

    License:

    • GPL-3.0

    Supported data:

    • Information not submitted

    GitHub activity:

    • Stars: 4
    • Forks: 2
    • Issues + PRs: 2

    Python versions supported:

    Operating system:

    Requirements:

    • jpype1
    • napari-plugin-engine (>=0.1.4)
    • numpy
    • ome-types
    • pims
    • requests

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