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

profiles

meta:map

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

*-dfp.tiff:file

Tiff fields for dark field illumination correction

*.{tiff}

*-ffp.tiff:file

Tiff fields for flat field illumination correction

*.{tiff}

versions

versions.yml:file

File containing software versions

versions.yml

Tools

basicpy

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.