BioFormats Input/Ouput (bfio) Utility¶
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
. 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