Description

Contrast-limited adjusted histogram equalization (CLAHE) on single-channel tif images.

Input

name:type
description
pattern

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1']

image{:bash}

:file

Single-channel tiff file to be corrected.

*.{tif,tiff}

Output

name:type
description
pattern

img_clahe{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1']

*.tiff{:bash}

:file

CLAHE corrected tiff file.

*.{tiff}

versions_clahe{:bash}

${task.process}{:bash}

:string

The name of the process

clahe{:bash}

:string

The name of the tool

python /local/scripts/molkart_clahe.py --version{:bash}

:eval

The expression to obtain the version of the tool

versions_scikitimage{:bash}

${task.process}{:bash}

:string

The name of the process

scikit-image{:bash}

:string

The name of the tool

python -c 'import skimage; print(skimage.__version__)'{:bash}

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The name of the process

clahe{:bash}

:string

The name of the tool

python /local/scripts/molkart_clahe.py --version{:bash}

:eval

The expression to obtain the version of the tool

${task.process}{:bash}

:string

The name of the process

scikit-image{:bash}

:string

The name of the tool

python -c 'import skimage; print(skimage.__version__)'{:bash}

:eval

The expression to obtain the version of the tool

Tools

molkartgarage
MIT

One-stop-shop for scripts and tools for processing data for molkart and spatial omics pipelines.

github.com/SchapiroLabor/molkart-local/tree/main https://github.com/SchapiroLabor/molkart-local/blob/main/scripts/molkart_clahe.py
maintainer
Github user kbestak
get in touch
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