PythonImageConverters

A module that wraps the image data converters bfconvert and bioformats2raw as python functions using the subprocess module.

Requirements

bfconvert and bioformats2raw must be available. The recommended approach is to install the relevant conda packages bftools and bioformats2raw to a (preferably new) conda environment. Then the module can be used by simply activating this environment.

Example use

from DataConverter import bioformats2raw

_ = bioformats2raw('/path/to/input',
                   '/path/to/output.źarr',
                   resolutions = 5,
                   chunk_w = 64,
                   chunk_h = 64,
                   compression = 'blosc',
                   drop_series = True,
                   )