Description

Takes a single panorama image and fills the empty grid lines with neighbour-weighted values.

Input

Name (Type)
Description
Pattern

meta (map)

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

]

tiff (file)

A tiff file containing gridlines as produced by Molecular Cartography imaging.

*.{tiff}

boxsize (integer)

A larger number allows to overcome large gaps, but makes looses fine details in new filled grid.

loopnum (integer)

The number of times gaussian blur is run consecutively on the gridlines. A smaller number is faster, but the result is less good.

Output

Name (Type)
Description
Pattern

meta (map)

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

]

versions (file)

File containing software versions

versions.yml

tiff (file)

A tiff file with gridlines filled based on consecutive gaussian blurring.

*.{tiff}
included in
molkart
authors
Github user ViriatoII Github user flowuenne
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

mindagap
BSD-3-Clause license

Mindagap is a collection of tools to process multiplexed FISH data, such as produced by Resolve Biosciences Molecular Cartography.

github.com/ViriatoII/MindaGap github.com/ViriatoII/MindaGap/blob/main/README.md https://github.com/ViriatoII/MindaGap