Cpp implementation of the BaSiC shading correction method.
- Original paper: T. Peng et al., “A BaSiC tool for background and shading correction of optical microscopy images,” Nat. Commun., vol. 8, p. 14836, Jun. 2017. DOI:10.1038/ncomms14836
- Nature Supplementary Materials: PDF
- Matlab implementation: https://github.com/QSCD/BaSiC
- Demo data examples: Dropbox
- Referenced python implementation: PyBaSiC
Usage: basic_cpp [--help] [--version] [--extension VAR] [--estimate_darkfield] [--apply_correction] [--use_flatfield VAR] [--use_darkfield VAR] [--epsilon VAR] [--l_s VAR] [--l_d VAR] [--output_flatfield_filename VAR] [--output_darkfield_filename VAR] [--verbose] directory output_directory
Positional arguments:
directory Full path to a directory containing the tiles to process [required]
output_directory Full path to a directory where the output will be saved [required]
Optional arguments:
-h, --help shows help message and exits
-v, --version prints version information and exits
--extension Image tile extension (default=%(default)s) [nargs=0..1] [default: ".tif"]
--estimate_darkfield Estimate the darkfield in addition to the flatfield.
--apply_correction Apply the shading correction with the estimated or loaded profiles.
--use_flatfield Use existing flatfield (skip estimation) [default: ""]
--use_darkfield Use existing darkfield (skip estimation) [default: ""]
--epsilon Stability coefficient to use for the shading correction. [nargs=0..1] [default: 1e-06]
--l_s Flat-field regularization parameter (set automatically if None)
--l_d Dark-field regularization parameter (set automatically if None)
--output_flatfield_filename Optional output flatfield filename (if none, flatfield.tif will be saved in the output directory). [default: ""]
--output_darkfield_filename Optional output flatfield filename (if none, darkfield.tif will be saved in the output directory). [default: ""]
--verbose Enable verbose output