pybasic is a python package for background and shading correction of microscopy images. It implements the algorithm as described in the below reference.
Peng, T., Thorn, K., Schroeder, T. et al. A BaSiC tool for background and shading correction of optical microscopy images. Nat Commun 8, 14836 (2017). https://doi.org/10.1038/ncomms14836
A MATLAB implementation from the above lab is available here.
pip install git+https://github.com/biomicrodev/pybasic.git
We recommend installing in a virtual environment.
| Image set | Link |
|---|---|
| Cell culture | notebook |
| WSI brain | notebook |
To run the jupyter notebook examples, download sample images from the MATLAB repository's Dropbox link, and place into examples/images.