modules/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.

illumiation_correctionbackground_correctionmicroscopyimaging

https://github.com/nf-core/modules/[...]/modules/nf-core/basicpy

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.

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