Programmatic Analysis of Sediment Cores Using Computed Tomography Imaging

Computed tomography (CT) imaging is a powerful tool for understanding the composition of sediment cores. This package streamlines and accelerates the analysis of CT data generated in the context of environmental science. Included are tools for processing raw DICOM images to characterize sediment composition (sand, peat, etc.). Root analyses are also enabled, including measures of external surface area and volumes for user-defined root size classes. For a detailed description of the application of computed tomography imaging for sediment characterization, see: Davey, E., C. Wigand, R. Johnson, K. Sundberg, J. Morris, and C. Roman. (2011) .


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coreCT is an R package for programmatic analysis of sediment cores that have been digitized by computed tomography. The package converts Hounsfield Units to material classes (e.g., peat, root/rhizome, sand) and quantifies component masses and volumes. To get started quickly, check out the package vignette.

Sediment core characterization

coreCT output can be easily plotted using the reshape2 and ggplot2 packages (figures below were produced using the same code included in the help file examples).

Figure 1. Volumes of various compartments in a sediment core

coreCT also quantifies the number of root/rhizome particles in a user-defined range of size classes, and calculates the external surface area and volume attributable to each size class. This allows the estimation of belowground plant organ contributions to total soil volume and, dividing by core area, elevation.

Figure 2. Number (left) and combined volume (right) of root/rhizome particles in each of four size classes.

Installing coreCT

coreCT is available on CRAN and can be installed by typing: install.packages("coreCT")

To install and load the development version of coreCT, run the following commands in R:

install.packages("devtools") # if devtools isn't already installed

devtools::install_github("troyhill/coreCT")

library(coreCT)

News

coreCT version 1.2.3 (release date: 2018-06-24)

Changes:

  • bug fix in conv(): categories with NAs are excluded from calculation of total masses, volumes, etc.

coreCT version 1.2.1 (release date: 2017-09-02)

Changes:

  • Added coreHist(), a function that returns and plots the frequency distribution of Hounsfield units in an image series
  • Efficiency improvements were made to conv()

Reference manual

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install.packages("coreCT")

1.2.3 by Troy D. Hill, 10 months ago


https://github.com/troyhill/coreCT


Browse source code at https://github.com/cran/coreCT


Authors: Troy D. Hill <[email protected]> , Earl Davey


Documentation:   PDF Manual  


GPL-3 license


Depends on raster, igraph, oro.dicom, plyr

Suggests knitr, rmarkdown


See at CRAN