title: RootGraph: a graphic optimization tool for automated image analysis of plant roots.
abstract: This paper outlines a numerical scheme for accurate, detailed, and high-throughput image analysis of plant roots. In contrast to existing root image analysis tools that focus on root system-average traits, a novel, fully automated and robust approach for the detailed characterization of root traits, based on a graph optimization process is presented. The scheme, firstly, distinguishes primary roots from lateral roots and, secondly, quantifies a broad spectrum of root traits for each identified primary and lateral root. Thirdly, it associates lateral roots and their properties with the specific primary root from which the laterals emerge. The performance of this approach was evaluated through comparisons with other automated and semi-automated software solutions as well as against results based on manual measurements. The comparisons and subsequent application of the algorithm to an array of experimental data demonstrate that this method outperforms existing methods in terms of accuracy, robustness, and the ability to process root images under high-throughput conditions.
authors.affiliation: Phenomics and Bioinformatics Research Centre, University of South Australia, Mawson Lakes SA 5095, Australia Australian Centre for Plant Functional Genomics, University of Adelaide, Hartley Grove, Urrbrae SA 5064, Australia.
authors.forename: Jinhai
authors.initials: J
authors.lastname: Cai
authors.affiliation: Australian Centre for Plant Functional Genomics, University of Adelaide, Hartley Grove, Urrbrae SA 5064, Australia.
authors.forename: Zhanghui
authors.initials: Z
authors.lastname: Zeng
authors.affiliation: Phenomics and Bioinformatics Research Centre, University of South Australia, Mawson Lakes SA 5095, Australia Australian Centre for Plant Functional Genomics, University of Adelaide, Hartley Grove, Urrbrae SA 5064, Australia.
authors.forename: Jason N
authors.initials: JN
authors.lastname: Connor
authors.affiliation: Australian Centre for Plant Functional Genomics, University of Adelaide, Hartley Grove, Urrbrae SA 5064, Australia.
authors.forename: Chun Yuan
authors.initials: CY
authors.lastname: Huang
authors.affiliation: Australian Centre for Plant Functional Genomics, University of Adelaide, Hartley Grove, Urrbrae SA 5064, Australia.
authors.forename: Vanessa
authors.initials: V
authors.lastname: Melino
authors.affiliation: Phenomics and Bioinformatics Research Centre, University of South Australia, Mawson Lakes SA 5095, Australia Australian Centre for Plant Functional Genomics, University of Adelaide, Hartley Grove, Urrbrae SA 5064, Australia.
authors.forename: Pankaj
authors.initials: P
authors.lastname: Kumar
authors.affiliation: Phenomics and Bioinformatics Research Centre, University of South Australia, Mawson Lakes SA 5095, Australia Australian Centre for Plant Functional Genomics, University of Adelaide, Hartley Grove, Urrbrae SA 5064, Australia stan.miklavcic@unisa.edu.au.
authors.forename: Stanley J
authors.initials: SJ
authors.lastname: Miklavcic
mesh_terms: D000465:Algorithms; D001330:Electronic Data Processing / Q000379:methods*; D001467:Hordeum / Q000033:anatomy & histology*; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D018517:Plant Roots / Q000033:anatomy & histology*; D012984:Software; D014908:Triticum / Q000033:anatomy & histology*
keywords: 2D; fully automated; graphic optimization; high throughput; image analysis; root network analysis; root phenotyping; wheat and barley.