Published and Released Results

We use two different systems to analyze root system architecture (RSA): an x-ray based system developed by Phenotype Screening Corporation ( and a gel-based system we recently developed in our lab. For the gel-based system, seeds are germinated directly in gellan gum and roots are imaged with a digital camera (see preliminary data). For imaging with the the x-ray system, rice plants are grown in a carbon-based foam substrate and imaged at different timepoints during growth. Seeds germinate directly in the foam substrate. A nutrient solution drips at periodic intervals onto the plants (see preliminary data).

1. Preliminary Data:

2. Preliminary Analysis:

We use descriptors such as root width and length to characterize the root systems and are developing additional features to describe RSA. We are also implementing an imaging pipeline to analyze our data. Our preliminary analysis shows that rice varieties can be distinguished based on their root system architecture (see results of PCA for three varieties).

Please contact Philip Benfey ( for more information.

3. GiA Roots: High-throughput software for the analysis of root system architecture

The Weitz group led the development of GiA Roots (General Image Analysis of Roots), a semi-automated software tool designed specifically for the high-throughput analysis of root images. GiA Roots includes a user-assisted segmentation component to distinguish root from background, and a fully automated pipeline that extracts dozens of root system phenotypes (with the ability to extend the software to estimate novel phenotypes). Quantitative information on each phenotype, along with intermediate steps for full reproducibility, is returned to the end-user for downstream analysis using an XML-compliant input and output interface. The phenotypic traits currently available in GiA Roots represent traits of interest to plant biologists studying complex monocot root networks. GiA Roots also has a fully functional command-line interface for interweaving the software into large-scale work flows.

GiA Roots is available for download. The manuscript associated with the release of GiA Roots is available at BMC Plant Biology.

Please contact Joshua Wetz ( for more information.

4. Root Reader 2D and 3D
The Kochian group led the development of Root Reader 2D and 3D. The RootReader software package provides free, publically available image processing and analysis tools for root system images taken from various fixed imaging sources.

Root Reader software is available online. Follow this download link. The manuscript associated with RootReader 3D is available at Plant Physiology.

5. 3D reconstruction software

The Edelsbrunner group led the development of algorithms for the reconstruction of 3D root networks from a sequence of 2D images. The paper describing the software is available in the Proceedings of the 13th International Conference on Computer Vision (ICCV), 2011. Requests for code should be directed to: Herbert Edelsbrunner, Duke University.

6. Topp et al. PNAS 2013

The Benfey, Weitz, Mitchell-Olds, Edelsbrunner and Harer groups collaborated on the project: "3D phenotyping and quantitative trait locus mapping identify core regions of the rice genome controlling root architecture" (Topp et al., PNAS, in press). This paper includes analysis of >1,400 3D root models and >57,000 2D images of root systems. The original images, analyzed images, and 3D models are available for download here.