phenoVein - A tool for leaf vein segmentation and analysis

Bühler, Jonas; Rishmawi, Louai; Pflugfelder, Daniel; Huber, Gregor; Scharr, Hanno; Hülskamp, Martin; Koornneef, M.; Schurr, Ulrich; Jahnke, Siegfried

doi:10.1104/pp.15.00974

Cited by 47 publications

(77 citation statements)

References 38 publications

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“…Finally, samples were processed in a series of ethanol solutions at decreasing concentrations and microscopic slides were prepared. Images of small portions of leaves (~5 mm 2 ) were captured with an optical microscope (4× magnification) equipped with a digital camera (model Syrio-2, Pbinternational, Mumbai, India) and VLA min was measured using PhenoVein software [57].…”

Section: Measuring Functional and Mechanistic Traitsmentioning

confidence: 99%

Functional Divergence Drives Invasibility of Plant Communities at the Edges of a Resource Availability Gradient

et al. 2020

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Invasive Alien Species (IAS) are a serious threat to biodiversity, severely affecting natural habitats and species assemblages. However, no consistent empirical evidence emerged on which functional traits or trait combination may foster community invasibility. Novel insights on the functional features promoting community invasibility may arise from the use of mechanistic traits, like those associated with drought resistance, which have been seldom included in trait-based studies.Here, we tested for the functional strategies of native and invasive assemblage (i.e., environmental filtering hypothesis vs. niche divergence), and we assessed how the functional space determined by native species could influence community invasibility at the edges of a resource availability gradient. Our results showed that invasive species pools need to have a certain degree of differentiation in order to persist in highly invaded communities, suggesting that functional niche divergence may foster community invasibility. In addition, resident native communities more susceptible to invasion are those which, on average, have higher resource acquisition capacity, and lower drought resistance coupled with an apparently reduced water-use efficiency. We advocate the use of a mechanistic perspective in future research to comprehensively understand invasion dynamics, providing also new insights on the factors underlying community invasibility in different ecosystems.

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Section: Measuring Functional and Mechanistic Traitsmentioning

confidence: 99%

Functional Divergence Drives Invasibility of Plant Communities at the Edges of a Resource Availability Gradient

et al. 2020

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“…Samples were then dehydrated in a sequence of ethanol solutions at increasing concentrations (25%, 50%, 75%, and 100%), immersed in an alcoholic solution of toluidine blue (3%) overnight, and then treated in a series of ethanol solutions at decreasing concentration before microscopic slides were prepared. Images of leaf portions of~5 mm 2 were captured with a scanner and an optical microscope at 4× magnification equipped with a digital camera, and the VLA of major (VLA maj ) and minor veins (VLA min ) was measured using PhenoVein software [69].…”

Section: Measurements Of Leaf Vein Length Per Unit Areamentioning

confidence: 99%

A Leaf Selfie: Using a Smartphone to Quantify Leaf Vulnerability to Hydraulic Dysfunction

Petruzzellis

Tomasella

Miotto

et al. 2020

Plants

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Accurate predictions of species distribution under current and future climate conditions require modeling efforts based on clear mechanistic relationships between climate variables and plant physiological functions. Vulnerability of leaves to xylem embolism is a key mechanistic trait that might be included in these modeling efforts. Here, we propose a simple set-up to measure leaf vulnerability to embolism on the basis of the optical method using a smartphone, a light source, and a notebook. Our data show that this proposed set-up can adequately quantify the vulnerability to xylem embolism of leaf major veins in Populus nigra and Ostrya carpinifolia, producing values consistent with those obtained in temperate tree species with other methods, allowing virtually any laboratory to quantify species-specific drought tolerance on the basis of a sound mechanistic trait.

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“…We loaded each image into phenoVein (version 1.0; Bühler et al., ), which is a software package within the free MeVisLab SDK suite (version 2.8.2) and is available for Windows, MacOS, and Linux operating systems at https://www.mevislab.de/ (accessed 6 April 2020). Based on a visual inspection, either the R or G color channels gave the best contrast and resolution; therefore, we chose channels on an image‐by‐image basis.…”

Section: Methodsmentioning

confidence: 99%

“…Within phenoVein, we masked these areas from subsequent image analyses. Next, we adjusted the upper and lower sigma values to a range generally falling within 12–26 (following Bühler et al., ), and then allowed phenoVein to estimate a network skeleton representing the vasculature system.…”

Section: Methodsmentioning

confidence: 99%

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Variation within laminae: Semi‐automated methods for quantifying leaf venation using phenoVein

et al. 2020

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PREMISE: Physiological processes may vary within leaf laminae; however, the accompanying heterogeneity in leaf venation is rarely investigated because its quantification can be time consuming. Here we introduce accelerated protocols using existing software to increase sample throughput and ask whether laminae venation varies among three crop types and four subspecies of Brassica rapa. METHODS: FAA (formaldehyde, glacial acetic acid, and ethanol)-fixed samples were stored in ethanol. Without performing any additional clearing or staining, we tested two methods of image acquisition at three locations along the proximal-distal axis of the laminae and estimated the patterns of venation using the program phenoVein. We developed and made available an R script to handle the phenoVein output and then analyzed our data using linear mixed-effects models. RESULTS:Beyond fixation and storage, staining and clearing are not necessary to estimate leaf venation using phenoVein if the images are acquired using a stereomicroscope. All estimates of venation required some manual adjustment. We found a significant effect of location within the laminae for all aspects of venation. DISCUSSION: By removing the clearing and staining steps and utilizing the semi-automated program phenoVein, we quickly and cheaply acquired leaf venation data. Venation may be an important target for crop breeding efforts, particularly if intralaminar variation correlates with variation in physiological processes, which remains an open question. KEY WORDS areole area; Brassica rapa; leaf venation; phenoVein; venation density, venation variation. Applications in Plant Sciences 2020 8(5): e11346 Newsome et al.-Quantifying variation in leaf venation using phenoVein • 2 of 7

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phenoVein - A tool for leaf vein segmentation and analysis

Cited by 47 publications

References 38 publications

Functional Divergence Drives Invasibility of Plant Communities at the Edges of a Resource Availability Gradient

Functional Divergence Drives Invasibility of Plant Communities at the Edges of a Resource Availability Gradient

A Leaf Selfie: Using a Smartphone to Quantify Leaf Vulnerability to Hydraulic Dysfunction

Variation within laminae: Semi‐automated methods for quantifying leaf venation using phenoVein

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