Description

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.

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’ ]

image (file)

Tiff file to be used for dark and flat field illumination correction

*.{tiff,tif}

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’ ]

versions (file)

File containing software versions

versions.yml

fields (file)

Tiff fields for dark and flat field illumination correction

*.{tiff,tif}
included in
mcmicro
author
Github user FloWuenne
get in touch
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Tools

basicpy
MIT License

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. The container of this tool needs to be initialized with an empty Entrypoint. See the nextflow.config of the tests for details.

github.com/peng-lab/BaSiCPy basicpy.readthedocs.io/en/latest https://github.com/peng-lab/BaSiCPy 10.1038/ncomms14836