• Version:

    • 0.2.1
  • Release date:

    • 11 August 2021
  • First released:

    • 25 June 2021
  • Development status:

    • 4 - Beta
  • License:

    • GPL-3.0

Github Activity

  • Stars: 4
  • Forks: 2
  • Issues + PRs: 1
  • Python versions supported:

    • >=3.7
  • Operating system:

    • OS Independent
  • Requirements:

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

napari-bioformats

Bioformats for napari, using pims

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.

  • Version:

    • 0.2.1
  • Release date:

    • 11 August 2021
  • First released:

    • 25 June 2021
  • Development status:

    • 4 - Beta
  • License:

    • GPL-3.0

Github Activity

  • Stars: 4
  • Forks: 2
  • Issues + PRs: 1
  • Python versions supported:

    • >=3.7
  • Operating system:

    • OS Independent
  • Requirements:

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

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