IJ_Rhizo: an open-source software to measure scanned images of root samples

Pierret, Alain; Gonkhamdee, Santimaitree; Jourdan, Christophe; Maeght, Jean‐Luc

doi:10.1007/s11104-013-1795-9

Cited by 112 publications

(100 citation statements)

References 40 publications

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“…Pierret et al (2013) confirmed the good performance of automated measurement of scanned root images using IJ_Rhizo in comparison with the commercial package WinRhizo.…”

Section: Root Image-analysing Softwaresupporting

confidence: 60%

Phenotyping for Root Traits

Chen

Djalović

Rengel

2015

Phenomics in Crop Plants: Trends, Options and Limitations

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Root system architecture determines crop capacity to acquire water and nutrients in the dynamic and variable soil environment. Increasing attention is paid to searching for optimal root traits to improve resource uptake efficiency and adaptation to heterogeneous soil conditions. This chapter summarises genetic variability and plasticity in root traits relevant to increased efficiency of soil resource acquisition. Approaches available for high-throughput phenotyping of root architecture traits at both laboratory and field scales are critically assessed. The advent of several novel imaging technologies such as X-ray computed tomography coupled with image-analysing software packages offers a great opportunity to non-invasively assess root architecture and its interactions with soil environments. The use of three-dimensional structure-function simulation root models is complementary to phenotyping methods, providing assistance in the crop breeding programmes. We also discuss applications and limitations of these novel visualisation technologies in characterising root growth and the root-soil interactions.

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“…Pierret et al (2013) confirmed the good performance of automated measurement of scanned root images using IJ_Rhizo in comparison with the commercial package WinRhizo.…”

Section: Root Image-analysing Softwaresupporting

confidence: 60%

Phenotyping for Root Traits

Chen

Djalović

Rengel

2015

Phenomics in Crop Plants: Trends, Options and Limitations

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“…Nevertheless, our data clearly show that the estimation of average root width of an isogenic population of plants using BRAT is very accurate, while estimating the width of individual plants will result in significantly more variation. While this approach will not capture small important local artifacts that are of clear importance in older and more complex root systems (Ryser, 2006;Pierret et al, 2013), our data show that BRAT is very suitable to measure root diameter of young primary roots for comparing population averages of plants that are genetically different and/or grow in different conditions. BRAT is designed to allow for high-throughput phenotyping of early root growth and development.…”

Section: Resultsmentioning

confidence: 88%

A Scalable Open-Source Pipeline for Large-Scale Root Phenotyping of Arabidopsis

et al. 2014

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Large-scale phenotyping of multicellular organisms is one of the current challenges in biology. We present a comprehensive and scalable pipeline that allows for the efficient phenotyping of root growth traits on a large scale. This includes a highresolution, low-cost acquisition setup as well as the automated image processing software BRAT. We assess the performance of this pipeline in Arabidopsis thaliana under multiple growth conditions and show its utility by performing genome-wide association studies on 16 root growth traits quantified by BRAT each day during a 5-d time-course experiment. The most significantly associated genome region for root growth rate is a locus encoding a calcium sensing receptor. We find that loss of function and overexpression of this gene can significantly alter root growth in a growth condition dependent manner and that the minor natural allele of the Calcium Sensor Receptor locus is highly significantly enriched in populations in coastal areas, demonstrating the power of our approach to identify regulators of root growth that might have adaptive relevance.

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“…Leaf area was measured using an LI-3100C leaf area meter (Li-Cor, Lincoln, NE, USA) and weighed. Washed roots free of soil were photographed against a dark background and analysed using the IJ Rhizo root analysis package (Pierret et al 2013). The entire root system was measured for each seedling.…”

Section: Plant Growth Parameters and Elemental Compositionmentioning

confidence: 99%

The effects of CO2 and nutrient fertilisation on the growth and temperature response of the mangrove Avicennia germinans

et al. 2016

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In order to understand plant responses to both the widespread phenomenon of increased nutrient inputs to coastal zones and the concurrent rise in atmospheric CO2 concentrations, CO2-nutrient interactions need to be considered. In addition to its potential stimulating effect on photosynthesis and growth, elevated CO2 affects the temperature response of photosynthesis. The scarcity of experiments testing how elevated CO2 affects the temperature response of tropical trees hinders our ability to model future primary productivity. In a glasshouse study, we examined the effects of elevated CO2 (800 ppm) and nutrient availability on seedlings of the widespread mangrove Avicennia germinans. We assessed photosynthetic performance, the temperature response of photosynthesis, seedling growth and biomass allocation. We found large synergistic gains in both growth (42 %) and photosynthesis (115 %) when seedlings grown under elevated CO2 were supplied with elevated nutrient concentrations relative to their ambient growing conditions. Growth was significantly enhanced under elevated CO2 only under high-nutrient conditions, mainly in above-ground tissues. Under low-nutrient conditions and elevated CO2, root volume was more than double that of seedlings grown under ambient CO2 levels. Elevated CO2 significantly increased the temperature optimum for photosynthesis by ca. 4 °C. Rising CO2 concentrations are likely to have a significant positive effect on the growth rate of A. germinans over the next century, especially in areas where nutrient availability is high.

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IJ_Rhizo: an open-source software to measure scanned images of root samples

Cited by 112 publications

References 40 publications

Phenotyping for Root Traits

Phenotyping for Root Traits

A Scalable Open-Source Pipeline for Large-Scale Root Phenotyping of Arabidopsis

The effects of CO2 and nutrient fertilisation on the growth and temperature response of the mangrove Avicennia germinans

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