Python 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
- Fiji plugin: URL
- Demo data examples: Dropbox
pip install pybasic-illumination-correction
- You need Poetry.
- Install with
poetry install
This will create a virtual environment and install all the dependencies. To execute the basic_shading_correction.py script,
activate the virtual environment with poetry shell, then execute the script with python <path/to/script.py>
The main script to perform the retrospective shading estimation and correction is basic_shading_correction.
Here is a description of its arguments. Note: You must first activate the pybasic environment to run this script.
>> basic_shading_correction --help
usage: Shading correction algorithm based on the BaSiC method
[-h] [--extension EXTENSION] [--estimate_darkfield]
[--apply_correction] [--use_flatfield USE_FLATFIELD]
[--use_darkfield USE_DARKFIELD] [--epsilon EPSILON] [--l_s L_S]
[--l_d L_D] [--output_flatfield_filename OUTPUT_FLATFIELD_FILENAME]
[--output_darkfield_filename OUTPUT_DARKFIELD_FILENAME]
directory output_directory
positional arguments:
directory Full path a directory containing the tiles to process
output_directory Full path to a directory where the output will be
saved
optional arguments:
-h, --help show this help message and exit
--extension EXTENSION
Image tile extension (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_FLATFIELD
Use existing flatfield (skip estimation)
--use_darkfield USE_DARKFIELD
Use existing darkfield (skip estimation)
--epsilon EPSILON Stability coefficient to use for the shading
correction. (default=1e-06)
--l_s L_S Flat-field regularization parameter (set automatically
if None)
--l_d L_D Dark-field regularization parameter (set automatically
if None)
--output_flatfield_filename OUTPUT_FLATFIELD_FILENAME
Optional output flatfield filename (if none,
flatfield.tif will be saved in the output directory).
--output_darkfield_filename OUTPUT_DARKFIELD_FILENAME
Optional output flatfield filename (if none,
darkfield.tif will be saved in the output directory).
--verbose