ArticleBMC plant biology2012
GiA Roots: software for the high throughput analysis of plant root system architecture.
Article in BMC plant biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 128 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
128 citing papers in PubMed.
- Advances in root phenotyping: high-throughput imaging, computational tools, and integrative approaches for crop improvement.Journal of experimental botany · 2026Review
- Uncovering the early and conserved molecular mechanisms of root nitrogen foraging in model and crops.BMC genomics · 2026Article
- Uncovering the potential MTAs, candidate genes and microRNAs regulatory networks involved in salinity stress tolerance triggered in Iranian Aegilops tauschii.Scientific reports · 2026Article
- Editorial: Signaling in roots: the brain of the plant.Frontiers in plant science · 2026Article
- Root system architecture and drought adaptation: emerging tools and genetic insights.Frontiers in plant science · 2026Review
- Legume-grass mixtures with arbuscular mycorrhizal fungi improve plant physiology, optimizing carbon and nitrogen dynamics and forage quality in perennial living mulches.Frontiers in plant science · 2026Article
- Exploring drought adaptation strategies in pistachios through morpho-physiological analysis under deficit irrigation.Scientific reports · 2025Article
- Integrating 3D imaging, GWAS, and single-cell transcriptome approaches to elucidate root system architecture in Populus.Plant physiology · 2025Article
- Impact of drought stress memory and variations in type and degree on root characteristic, yield stability and drought tolerance in Orchardgrass.BMC plant biology · 2025Article
- Improved root architecture and seedling performance in pistachio (Pistacia vera L.) via radicle-tip excision.BMC plant biology · 2025Article
- Phenotyping, genome-wide dissection, and prediction of maize root architecture for temperate adaptability.iMeta · 2025Article
- Role of genetic diversity and salicylic acid in drought stress memory of tall fescue.Scientific reports · 2025Article
- Physiological and molecular responses of two contrasting drought resistance pistachio interspecific hybrid rootstocks.Frontiers in plant science · 2025Article
- Article
- Genome-Wide Association study for root system architecture traits in field soybean [Glycine max (L.) Merr.].Scientific reports · 2024Article
- The role of magnesium oxide foliar sprays in enhancing mint (Mentha crispa L.) tolerance to cadmium stress.Scientific reports · 2024Article
- Distinct growth patterns in seedling and tillering wheat plants suggests a developmentally restricted role of HYD2 in salt-stress response.Plant cell reports · 2024Article
- Fast and Efficient Root Phenotyping via Pose Estimation.Plant phenomics (Washington, D.C.) · 2024Article
- Salt stress memory in tall fescue: Interaction of different stress stages, pollination system and genetic diversity.PloS one · 2024Article
- Multi-locus genome-wide association study for phosphorus use efficiency in a tropical maize germplasm.Frontiers in plant science · 2024Article
68 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
13 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundCharacterizing root system architecture (RSA) is essential to understanding the development and function of vascular plants. Identifying RSA-associated genes also represents an underexplored opportunity for crop improvement. Software tools are needed to accelerate the pace at which quantitative traits of RSA are estimated from images of root networks.
resultsWe have developed GiA Roots (General Image Analysis of Roots), a semi-automated software tool designed specifically for the high-throughput analysis of root system images. GiA Roots includes user-assisted algorithms to distinguish root from background and a fully automated pipeline that extracts dozens of root system phenotypes. Quantitative information on each phenotype, along with intermediate steps for full reproducibility, is returned to the end-user for downstream analysis. GiA Roots has a GUI front end and a command-line interface for interweaving the software into large-scale workflows. GiA Roots can also be extended to estimate novel phenotypes specified by the end-user.
conclusionsWe demonstrate the use of GiA Roots on a set of 2393 images of rice roots representing 12 genotypes from the species Oryza sativa. We validate trait measurements against prior analyses of this image set that demonstrated that RSA traits are likely heritable and associated with genotypic differences. Moreover, we demonstrate that GiA Roots is extensible and an end-user can add functionality so that GiA Roots can estimate novel RSA traits. In summary, we show that the software can function as an efficient tool as part of a workflow to move from large numbers of root images to downstream analysis.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.