RootAnalyzer: A Cross-Section Image Analysis Tool for Automated Characterization of Root Cells and Tissues

Chopin, Joshua; Laga, Hamid; Huang, Chih‐Wei; Heuer, Sigrid; Miklavcic, Stanley J.

doi:10.1371/journal.pone.0137655

Cited by 36 publications

(27 citation statements)

References 37 publications

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“…The GRANAR model generates cell networks of root cross sections from a small set of root anatomical features ( 23 . Briefly, the anatomy generation process is based on the placing of cell layers around the center of the root.…”

Section: Resultsmentioning

confidence: 99%

GRANAR, a new computational tool to better understand the functional importance of root anatomy

Heymans

Couvreur

LaRue

et al. 2019

Preprint

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Root hydraulic conductivity is an important determinant of plant water uptake capacity. In particular, the root radial conductivity is often thought to be a limiting factor along the water pathways between the soil and the leaf. The root radial conductivity is itself defined by cell scale hydraulic properties and anatomical features. However, quantifying the influence of anatomical features on the radial conductivity remains challenging due to complex, and time-consuming, experimental procedures. We present a new computation tool, the Generator of Root ANAtomy in R (GRANAR) that can be used to rapidly generate digital versions of root anatomical networks. GRANAR uses a limited set of root anatomical parameters, easily acquired with existing image analysis tools. The generated anatomical network can then be used in combination with hydraulic models to estimate the corresponding hydraulic properties. Heymans et al. 2019 -GRANAR -A Generator of Root ANAtomy in R -Preprint We used GRANAR to re-analyse large maize (Zea mays) anatomical datasets from the literature. Our model was successful at creating virtual anatomies for each experimental observation. We also used GRANAR to generate anatomies not observed experimentally, over wider ranges of anatomical parameters. The generated anatomies were then used to estimate the corresponding radial conductivities with the hydraulic model MECHA. This enabled us to quantify the effect of individual anatomical features on the root radial conductivity. In particular, our simulations highlight the large importance of the width of the stele and the cortex. GRANAR is an open-source project available here: http://granar.github.io Keywords Root anatomy, radial conductivity, anatomical model, Zea mays , aerenchyma, reanalysis One-Sentence summary: Generator of Root ANAtomy in R (GRANAR) is a new open-source computational tool that can be used to rapidly generate digital versions of root anatomical networks.

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Section: Resultsmentioning

confidence: 99%

GRANAR, a new computational tool to better understand the functional importance of root anatomy

Heymans

Couvreur

LaRue

et al. 2019

Preprint

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“…Genetic variation in rice root traits has been reported such as root thickness (Babu et al, 2001) and deep rooting (Nemoto, Suga, Ishihara & Okutsu, 1998), and the latter has been shown to be useful for drought avoidance (Kato et al, 2007;Yoshida & Hasegawa, 1982) and for watersaving (Deshmukh, Kamoshita, Norisada & Uga, 2017) to lead to higher yield (Uga et al, 2013). However, studies of root anatomical traits are less reported probably due to its tedious and time-consuming phenotyping (Atkinson & Wells, 2017;Burton, Williams, Lynch & Brown, 2012;Chopin, Laga, Huang, Heuer & Miklavcic, 2015;Uga, Okuno & Yano, 2008).…”

Section: Introductionmentioning

confidence: 99%

Eco-physiological evaluation of Stele Transversal Area 1 for rice root anatomy and shoot growth

Phoura

Kamoshita

Norisada

et al. 2020

Plant Production Science

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Larger stele size with greater xylem area or endodermis thickness in rice roots may lead to higher plant water status and maintain yield. Sta1-NIL, a near-isogenic line of IR64 introgressed with Stele Transversal Area 1 (Sta1), a quantitative trait locus controlling stele transversal area (STA) was investigated together with IR64 for their root anatomy and physiological parameters, at seedling, heading and maturity stages in greenhouse and fields of water deficit and well-watered conditions in 2017 and 2018. Combined analysis of STA from nine observations of overall four experiments showed that STA was increased by 7% (35,400 to 37,800 μm 2 ) by the introduction of Sta1 into IR64. Total late metaxylem area also increased by 6% (5,840 to 6,180 μm 2 ), which came mainly from its single area rather than its number, whereas small increase in endodermis thickness was also noted. Genotype x observation for STA was marginal, but Sta1-NIL had larger STA under water deficit environments. Sta1-NIL also maintained higher mid-day leaf water potential (−2.34 ± 0.3 MPa) than IR64 (−2.57 ± 0.3 MPa). Meta-analysis of seven experiments under 14 environments showed tendency of the positive effect of Sta1 on grain yield increment (579 to 604 g m −2 ), which came from the increment of harvest index. This study indicated the importance of wider stele size for maintenance of higher plant water status and yield across different water regimes. ARTICLE HISTORY

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“…This method was used to investigate and understand the formation of emboli in saplings’ xylem during cycles from drought to re-watering [16]. The plant root formation in the soil is another research focus to utilize HRCT imaging and analysis [17-19]. This method enables scientists to trace the development of roots and foresee the plant’s growth status.…”

Section: Introductionmentioning

confidence: 99%

The microstructure investigation of plant architecture with X-ray microscopy

Zhang

Guo

Chen

et al. 2019

Preprint

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18Background 19 In recent years, the plant morphology has been well studied by multiple approaches at 20 cellular and subcellular levels. Two-dimensional (2D) microscopy techniques offer 21 imaging of plant structures on a wide range of magnifications for researchers. However, 22 subcellular imaging is still challenging in plant tissues like roots and seeds. 23 Results 24Here we use a three-dimensional (3D) imaging technology based on the ZEISS X-ray 25 microscope (XRM) Versa and analyze several plant tissues from different plant species. 26 The XRM provides new insights into plant structures using non-destructive imaging at 27 high-resolution and high contrast. We also developed a workflow aiming to acquire 28 accurate and high-quality images in the context of the whole specimen. Multiple plant 29 samples including rice, tobacco, Arabidopsis and maize were used to display the 30 differences of phenotypes, which indicates that the XRM is a powerful tool to 31 investigate plant microstructure. 32 Conclusions 33 Our work provides a novel observation method to evaluate and quantify tissue specific 34 differences for a range of plant species. This new tool is suitable for non-destructive 35 seed observation and screening. 36 37 Keywords: X-ray microscopy, plant morphology, plant development, plant 3D 38 reconstruction 39 Background 40 Since the invention and development of microscopes, it has extended human vision 41 substantially. The observation of cellular and subcellular structures using microscopes 42 have broadened our knowledge to understand the biological world more efficiently [1]. 43 ZEISS and many other microscopy manufacturing companies are spending an 44 enormous amount of time and resources developing higher resolution microscopy 45 systems to assist scientists acquire more detailed images in their research fields. From 46 the single cell organism blue-green algae (Cyanobacteria) to over a hundred-meter-tall 47 giant tree (Eucalyptus regnans), plants display versatile morphologies to survive in 48 different environments. Therefore, utilizing microscopy techniques to study the cellular 49 and subcellular and physiological traits is essential in plant research.50 51 In the 21 st century, microscopy companies provide a variety of measurement techniques 52 for scientists. With the assistance of electron microscopy, plant scientists can observe 53 the cell surface and the detailed structure of organelles, and even decipher the structure 54 of proteins [2-4]. Optical microscopes, including upright and inverted microscopes, 55 provide powerful solutions for cellular observations as well [5, 6]. Since the application 56 of green fluorescent protein, confocal microscopy and various fluorescence related 57 techniques advanced the biological research field [7]. Furthermore, the methods to 58 analyze the corresponding data have been developed at a similar pace [8]. For larger 59 sample observation, stereoscopic microscopy offers non-destructive and detailed 60 insights to identify the tiny differences in betw...

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RootAnalyzer: A Cross-Section Image Analysis Tool for Automated Characterization of Root Cells and Tissues

Cited by 36 publications

References 37 publications

GRANAR, a new computational tool to better understand the functional importance of root anatomy

GRANAR, a new computational tool to better understand the functional importance of root anatomy

Eco-physiological evaluation of Stele Transversal Area 1 for rice root anatomy and shoot growth

The microstructure investigation of plant architecture with X-ray microscopy

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