juicr-package {juicr}

Automated, semi-automated, and manual extraction of numerical data from scientific images, plot, charts, and figures

Description

juicr is a GUI interface for automating data extraction from multiple images containing scatter and bar plots, semi-automated tools to tinker with extraction attempts, and a fully-loaded point-and-click manual extractor with image zoom, calibrator, and classifier. Also provides detailed and R-independent extraction reports as fully-embedded .html records. More information about juicr can be found at http://lajeunesse.myweb.usf.edu/.

Details

What to cite?

Lajeunesse, M.J. (2021) Automated, semi-automated, and manual extraction of numerical data from scientific images, plot, charts, and figures. R package, v.0.1

Installation and Dependencies.

juicr has one external dependency that need to be installed and loaded prior to use in R. This is the EBImage R package (Pau et al. 2010) available only from the Bioconductor repository: https://www.bioconductor.org/.

To properly install juicr, start with the following R script that loads the Bioconductor resources needed to install the EBImage (also accept all of its dependencies):

install.packages("BiocManager");
BiocManager::install("EBImage"))
library(metagear)

Finally for Mac OS users, installation is sometimes not straighforward as the GUI_juicr() requires the Tcl/Tk GUI toolkit to be installed. You can get this toolkit by making sure the latest X11 application (xQuartz) is installed from here: https://www.xquartz.org/.

Author(s)

Marc J. Lajeunesse (University of South Florida, Tampa USA)

References

Pau, G., Fuchs, F., Sklyar, O., Boutros, M. and Huber, W. (2010) EBImage: an R package for image processing with applications to cellular phenotypes. Bioinformatics 26: 979-981.