BioFormats Input/Ouput (bfio) UtilityΒΆ

The bfio utility is an easy to use, image input/output utility optimized to scalably read and write OME TIFF and OME Zarr images as well as all formats supported by Bioformats . Reading of data makes direct usage of BioFormats (when using the bioformats install option) using JPype, giving bfio the ability to read any of the 150+ formats supported by BioFormats.

For file outputs, only two file formats are supported: tiled OME TIFF, and OME Zarr. These two file formats are supported because they are scalable, permitting tiled writing. This package was created out of a need for speed and scalability so that plugins could be created for the Web Image Processing Pipeline (WIPP).

bfio has a simple to use interface that allows programs to access images as if they were memory mapped numpy arrays operating on the original data file. There are a lot of caveats to data reading and writing, but the goal of this package was to lower the barrier to working with image data that may not fit into memory.