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