Bioformats for napari, using pims
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
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"
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
The easiest way to install
napari-bioformats is via conda, from the
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
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.
- 11 August 2021
- 25 June 2021
- Information not submitted
- Stars: 5
- Forks: 2
- Issues + PRs: 2