The bfio package can be installed with a variety of options designed in consideration of containerization.

Base Package

The base package can only read/write tiled, OME TIFF images. It can be installed using:

pip install bfio

To install all reading and writing options, install with all dependencies:

pip install bfio[all]

NOTE: See the Java and Bioformats note about licensing considerations when installing using the bfio[all] option.

Java and Bioformats

To use Bioformats, it is necessary to install Java 8 or later. Once Java is installed, bfio can be installed with support for Java using:

pip install bfio[‘bioformats’]

NOTE: The bioformats_jar package and BioFormats are licensed under GPL, while bfio is licensed under MIT. This may have consequences when packaging any software that uses bfio as a dependency when this option is used.


To use the zarr backend, you need to have Zarr already installed, or you can install it when installing bfio using:

pip install bfio[‘zarr’]