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RootscanR (version 0.0.1)

Stitching and Analyzing Root Scans

Description

Minirhizotrons are widely used to observe and explore roots and their growth. This package provides the means to stitch images and divide them into depth layers. Please note that this R package was developed alongside the following manuscript: Stitching root scans and extracting depth layer information -- a workflow and practical examples, S. Kersting, L. Knüver, and M. Fischer. The manuscript is currently in preparation and should be citet as soon as it is available. This project was supported by the project ArtIGROW, which is a part of the WIR!-Alliance ArtIFARM – Artificial Intelligence in Farming funded by the German Federal Ministry of Research, Technology and Space (No. 03WIR4805).

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Version

Install

install.packages('RootscanR')

Monthly Downloads

135

Version

0.0.1

License

GPL (>= 3)

Maintainer

Sophie Kersting

Last Published

October 30th, 2025

Functions in RootscanR (0.0.1)

getDepthLayerInfo_par

Extract depth layer information from root scans (parallel)
getOverviewInput

Get an overview of the given root scans
skelPxWidth

Count skeleton root pixels with certain widths in the base root image
showImgMask

Depict images with masking layers
stitchImgs

Stitch images
kimuraLength

Computation of the Kimura length
getNeighborCoords

Get coordinates of neighbors of specified distance
findAvgSurface

Find the average surface level
createDepthLayerMasks

Create masking layers for the depth layers
findSurface

Find the surface level and split images
findAvgOverlap

Find average image overlaps
cm2px

Functions for converting pixels and centimeters
findOverlap

Find image overlaps
combineStatsWithDL

Get an overview of the given root scans
ppcm2ppi

Functions for converting resolutions: ppi and ppcm
checkInput

Check if the root scan directories contain everything necessary
getDepthLayerInfo

Extract depth layer information from root scans