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 .