Software Overview


GEOCHEM–EZ is a multi-purpose chemical speciation program, used in plant nutrition and in soil and environmental chemistry research to perform equilibrium speciation computations, that allows users to estimate solution ion activities and to consider simple complexes and solid phases (Shaff et al., 2010). Programs of this type allow users to estimate the interactions between metals and ligands and to calculate the free activities of the ions of interest. In doing so, scientists can make a solution in which requisite conditions are satisfied and the design is intelligent.


The Plant Root Imaging and Data Acquisiton (PRIDA) control system was developed in response to the need of data maintenance and access for 2D and 3D digital image root phenotyping. PRIDA is an open-source Python-based software for the collection, storage and organization of digital images along with all the relevant experimental details that builds on top of the 3D imaging framework introduced in Clark et al. (2011) and includes the updates described in Piñeros et al. (2015).

Image Analysis

Currently, the Plant Root Image Analysis (PRIA) is a Python-based command-line program that is used to prepare the digital images taken of root systems for trait measurement software (e.g., RootReader2D and RootReader3D). This processing software converts color images to binary (i.e., black and white) in such a way as to represent the plant roots as true (i.e., white) against a false (i.e., black) background. During the binarization process, the image foreground (i.e., root system) is partitioned from the background based on a variety of image-processing techniques.


RootReader2D software is a Java-based stand-alone program designed to assist with root length measurements from digital images. This software allows for high-throughput analysis of total root system length as well as measurements of selected root types of interest. RootReader2D has been adapted to work with a variety of growth systems, including hydroponics, gellan gum, sand, agarose plates and paper pouch systems. See Clark et al., 2013 for more details.


RootReader3D is a custom software, written in the Java programming language (Oracle), that reconstructs 3D root system models from 2D image sequences and quantifies 3D root system traits. This software generates 3D root volume and skeleton models. Various viewing interfaces and mouse and keyboard commands are incorporated into RootReader3D to assist in visualizing and interacting with the 3D reconstructions. See Clark et al., 2011 for more details.