BaSiCPy

Type
Collection
Author
Nicholas Schaub
Tim Morello
Tingying Peng
Yohsuke T. Fukai
Yu Liu
Requires
Python
Execution Platform
Linux
Mac
Windows
Implementation Type
library
Programming Language
Python
Supported image dimension
2D
time-series
Interaction Level
Manual
License/Openness
Free and open source
License
MIT
Description

A python package for background and shading correction of optical microscopy images


BaSiCPy is a python package for background and shading correction of optical microscopy images. It is developed based on the Matlab version of BaSiC tool with major improvements in the algorithm.

Post date
11/07/2025 - 03:54
Last modified
11/07/2025 - 04:08
Download Page
https://github.com/peng-lab/BaSiCPy
Documentation Link
https://basicpy.readthedocs.io/en/latest
attribution instructions
Reference:
BaSiCPy: A robust and scalable shadow correction tool for optical microscopy images (in prep.)
A BaSiC Tool for Background and Shading Correction of Optical Microscopy Images by Tingying Peng, Kurt Thorn, Timm Schroeder, Lichao Wang, Fabian J Theis, Carsten Marr*, Nassir Navab*, Nature Communication 8:14836 (2017). doi: 10.1038/ncomms14836.
Usage Example Link
Link to colab notebooks on github page
Backlinks