Simple reading and writing classes for tiled tiffs using Bioformats.
This tool is a simplified but powerful interface to Bioformats using jpype for direct access to the library. This tool is designed with scalable image analysis in mind, with a simple interface to treat any image like a memory mapped array.
Docker containers with all necessary components are available (see Docker Containers section).
Setting up Java
bfio can be used without Java, but only the
backends will be useable. Only files in tiled OME Tiff or OME Zarr format can be
In order to use the
Java backend, it is necessary to first install the JDK.
bfio package is generally tested with
but JDK 11 and later also appear to work.
bfio package and the core dependencies (numpy, tifffile, imagecodecs) can
be installed using pip:
pip install bfio
bfio with other dependencies can be installed:
pip install bfio[jpype]- Adds support for BioFormats/Java
pip install bfio[zarr]- Adds support for OME Zarr
pip install bfio[all]- Installs all dependencies.
Ubuntu based container with bfio and all dependencies (including Java).
Same as above, except comes with ImageJ and PyImageJ.
Tensorflow container with bfio isntalled.
Documentation and examples are available on Read the Docs.
- Parts of this code were written/modified from existing code found in
- 23 June 2021
- 22 July 2020
- 5 - Production/Stable
- Stars: 4
- Forks: 2
- Issues + PRs: 10
Python versions supported:
- OS Independent
- tifffile (<=2020.11.18)
- imagecodecs (>=2021.2.26)
- numpy (>=1.20.1)