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{:bash}

:map

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

image{:bash}

:file

BioFormats-compatible image file to be used for dark and flat field illumination correction

*.{ome.tiff,ome.tif,rcpnl,btf,nd2,tiff,tif,czi}

Output

name:type
description
pattern

profiles{:bash}

meta{:bash}

:map

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

*-dfp.ome.tif{:bash}

:file

OME-TIFF fields for dark field illumination correction

*.{ome.tif}

*-ffp.ome.tif{:bash}

:file

OME-TIFF fields for flat field illumination correction

*.{ome.tif}

versions{:bash}

versions.yml{:bash}

: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.

github.com/peng-lab/BaSiCPy basicpy.readthedocs.io/en/latest https://github.com/peng-lab/BaSiCPy 10.1038/ncomms14836
included in
mcmicro
maintainer
Github user FloWuenne
get in touch
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