Install

The bfio package and the core dependencies (numpy, tifffile, imagecodecs, scyjava) can be installed using pip:

pip install bfio

A conda distribution is also available in the conda-forge channel. To install it in conda environment, use this:

conda install bfio -c conda-forge

Java and Bio-Formats

bfio can be used without Java, but only the python and zarr backends will be usable. This means only files in tiled OME Tiff or OME Zarr format can be read/written.

In order to use the bioformats backend, it is necessary to first install the JDK and Maven. The bfio package is generally tested with JDK 8, but JDK 11 and later also appear to work. Here are some info on installing Maven on various OS (Windows | Linux | Mac).

NOTE: Bio-Formats is licensed under GPL, while bfio is licensed under MIT. This may have consequences when packaging any software that uses bfio as a dependency. During the first invocation of bfio, scyjava will try to download Bio-Formats package from the Maven repository. The current version of bfio uses Bio-Formats v7.2.0 .