BioFormats Input/Ouput (bfio) Utility¶
bfio utility builds off of multiple existing projects to streamline and
optimize the reading of formats supported by
. 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
and python-javabridge. The need
bfio utility stems from issues in dealing with large images in
python-bioformats, slow loading and saving of files in
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.