BioFormats Input/Ouput (bfio) UtilityΒΆ

The bfio utility builds off of multiple existing projects to streamline and optimize the reading of formats supported by Bioformats . Writing of files is done using the the OME-TIFF file specification, using compressed image tiling to make the file conform to the Web Image Processing Pipeline (WIPP) standard image format.

This tool makes extensive usage of tifffile, python-bioformats, and python-javabridge. The need for the bfio utility stems from issues in dealing with large images in python-bioformats, slow loading and saving of files in ome.tif format, and difficulty of maintaining OME metadata. Individually, each package has advantages and disadvantages, but bfio merges and optimizes the best qualities of each package and simplifies working with large images.