IRimage: open source software for processing images from infrared thermal cameras

IRimage aims at increasing throughput, accuracy and reproducibility of results obtained from thermal images, especially those produced with affordable, consumer-oriented cameras. IRimage processes thermal images, extracting raw data and calculating temperature values with an open and fully documented algorithm, making this data available for further processing using image analysis software. It also allows the making of reproducible measurements of the temperature of objects in a series of images, and produce visual outputs (images and videos) suitable for scientific reporting. IRimage is implemented in a scripting language of the scientific image analysis software ImageJ, allowing its use through a graphical user interface and also allowing for an easy modification or expansion of its functionality. IRimage’s results were consistent with those of standard software for 15 camera models of the most widely used brand. An example use case is also presented, in which IRimage was used to efficiently process hundreds of thermal images to reveal subtle differences in the daily pattern of leaf temperature of plants subjected to different soil water contents. IRimage’s functionalities make it better suited for research purposes than many currently available alternatives, and could contribute to making affordable consumer-grade thermal cameras useful for reproducible research.EEA BalcarceFil: Pereyra Irujo, Gustavo Adrián. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Balcarce; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Instituto de Innovación para la Producción Agropecuaria y el Desarrollo Sostenible; Argentina

Genetic variability for leaf growth rate and duration under water deficit in sunflower: analysis of responses at cell, organ, and plant level

Plants under water deficit reduce leaf growth, thereby reducing transpiration rate at the expense of reduced photosynthesis. The objective of this work was to analyse the response of leaf growth to water deficit in several sunflower genotypes in order to identify and quantitatively describe sources of genetic variability for this trait that could be used to develop crop varieties adapted to specific scenarios. The genetic variability of the response of leaf growth to water deficit was assessed among 18 sunflower (Helianthus annuus L.) inbred lines representing a broad range of genetic diversity. Plants were subjected to long-term, constant-level, water-deficit treatments, and the response to water deficit quantified by means of growth models at cell-, leaf-, and plant-scale. Significant variation among lines was found for the response of leaf expansion rate and of leaf growth duration, with an equal contribution of these responses to the variability in the reduction of leaf area. Increased leaf growth duration under water deficit is usually suggested to be caused by changes in the activity of cell-wall enzymes, but the present results suggest that the duration of epidermal cell division plays a key role in this response. Intrinsic genotypic responses of rate and duration at a cellular scale were linked to genotypic differences in whole-plant leaf area profile to water deficit. The results suggest that rate and duration responses are the result of different physiological mechanisms, and therefore capable of being combined to increase the variability in leaf area response to water deficit.EEA BalcarceFil: Pereyra Irujo, Gustavo Adrian. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Balcarce. Unidad Integrada. Universidad Nacional de Mar del Plata. Facultad de Ciencias Agrarias; ArgentinaFil: Velazquez, Luciano. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Balcarce. Unidad Integrada. Universidad Nacional de Mar del Plata. Facultad de Ciencias Agrarias; ArgentinaFil: Lechner, Leandra. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Balcarce. Unidad Integrada. Universidad Nacional de Mar del Plata. Facultad de Ciencias Agrarias; Argentina.Fil: Aguirrezábal, Luis Adolfo Nazareno. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Balcarce. Unidad Integrada. Universidad Nacional de Mar del Plata. Facultad de Ciencias Agrarias; Argentina

UAV-based field phenotyping based on low-cost, open-source hardware and software

Here we present a low-cost platform for field phenotyping based on an unmanned aerial vehicle (UAV), which consists mainly of free-to-use or open-source hardware and software. This platform consists of a multirotor helicopter -with 8 rotorsproviding great stability and maneuvrability, which is able to carry a variety of sensors for trait measurement. The platform is controlled by an electronic autopilot board, which can be programmed for GPS-guided, automatic flight through an open-source ground station software. This platform is currently equipped with a low-cost consumer camera modified for the acquisition of near infrared - green - blue images, thus allowing the capture of high-resolution vegetation index images. A pipeline for the processing, geo-referencing and analysis of the images has been developed, which is based on open-source and/or free-to-use software.Sociedad Argentina de Informática e Investigación Operativa (SADIO

Assessing the efficiency of phenotyping early traits in a greenhouse automated platform for predicting drought tolerance of soybean in the field

Conventional field phenotyping for drought tolerance, the most important factor limiting yield at a global scale, is labor-intensive and time-consuming. Automated greenhouse platforms can increase the precision and throughput of plant phenotyping and contribute to a faster release of drought tolerant varieties. The aim of this work was to establish a framework of analysis to identify early traits which could be efficiently measured in a greenhouse automated phenotyping platform, for predicting the drought tolerance of field grown soybean genotypes. A group of genotypes was evaluated, which showed variation in their drought susceptibility index (DSI) for final biomass and leaf area. A large number of traits were measured before and after the onset of a water deficit treatment, which were analyzed under several criteria: the significance of the regression with the DSI, phenotyping cost, earliness, and repeatability. The most efficient trait was found to be transpiration efficiency measured at 13 days after emergence. This trait was further tested in a second experiment with different water deficit intensities, and validated using a different set of genotypes against field data from a trial network in a third experiment. The framework applied in this work for assessing traits under different criteria could be helpful for selecting those most efficient for automated phenotyping.Fil: Peirone, Laura Soledad. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata; Argentina. Universidad Nacional de Mar del Plata. Facultad de Ciencias Agrarias. Departamento de Producción Vegetal; ArgentinaFil: Pereyra Irujo, Gustavo Adrian. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Buenos Aires Sur. Estación Experimental Agropecuaria Balcarce. Área de Investigación en Agronomía; ArgentinaFil: Bolton, Alejandro. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata; Argentina. Universidad Nacional de Mar del Plata. Facultad de Ciencias Agrarias. Departamento de Producción Vegetal; ArgentinaFil: Erreguerena, Ignacio Antonio. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Buenos Aires Sur. Estación Experimental Agropecuaria Balcarce; ArgentinaFil: Aguirrezábal, Luis Adolfo Nazareno. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata; Argentina. Universidad Nacional de Mar del Plata. Facultad de Ciencias Agrarias. Departamento de Producción Vegetal; Argentin

Papatrónica – dispositivo de código abierto para la medición de golpes y prevención de daños mecánicos

En Argentina, según datos de la Secretaría de Agroindustria, se pierden y desperdician anualmente 14,5 millones de toneladas de alimentos en las etapas de producción, almacenamiento, transporte y procesamiento, siendo la cadena frutihortícola la que presenta mayor proporción de pérdidas. Los daños mecánicos generados por golpes ocasionan una parte importante de estas pérdidas, directamente como consecuencia de la ruptura de células y tejidos, e indirectamente por generar lesiones que permiten el ingreso de patógenos que producen necrosis o pudriciones. El objetivo de este trabajo fue prototipar una plataforma abierta y modular de código abierto y bajo costo que permita determinar los puntos donde se producen golpes que puedan afectar los tubérculos de papa, pero también fácilmente adaptable a otros cultivos o productos, o a la medición de otras variables.Sociedad Argentina de Informática e Investigación Operativ

UAV-based field phenotyping based on low-cost, open-source hardware and software

Here we present a low-cost platform for field phenotyping based on an unmanned aerial vehicle (UAV), which consists mainly of free-to-use or open-source hardware and software. This platform consists of a multirotor helicopter -with 8 rotorsproviding great stability and maneuvrability, which is able to carry a variety of sensors for trait measurement. The platform is controlled by an electronic autopilot board, which can be programmed for GPS-guided, automatic flight through an open-source ground station software. This platform is currently equipped with a low-cost consumer camera modified for the acquisition of near infrared - green - blue images, thus allowing the capture of high-resolution vegetation index images. A pipeline for the processing, geo-referencing and analysis of the images has been developed, which is based on open-source and/or free-to-use software.Sociedad Argentina de Informática e Investigación Operativa (SADIO

Foliar Abscisic Acid-To-Ethylene Accumulation and Response Regulate Shoot Growth Sensitivity to Mild Drought in Wheat

Although, plant hormones play an important role in adjusting growth in response to environmental perturbation, the relative contributions of abscisic acid (ABA) and ethylene remain elusive. Using six spring wheat genotypes differing for stress tolerance, we show that young seedlings of the drought-tolerant (DT) group maintained or increased shoot dry weight (SDW) while the drought-susceptible (DS) group decreased SDW in response to mild drought. Both the DT and DS groups increased endogenous ABA and ethylene concentrations under mild drought compared to control. The DT and DS groups exhibited different SDW response trends, whereby the DS group decreased while the DT group increased SDW, to increased concentrations of ABA and ethylene under mild drought, although both groups decreased ABA/ethylene ratio under mild drought albeit at different levels. We concluded that SDW of the DT and DS groups might be distinctly regulated by specific ABA:ethylene ratio. Further, a foliar-spray of low concentrations (0.1 μM) of ABA increased shoot relative growth rate (RGR) in the DS group while ACC (1-aminocyclopropane-1-carboxylic acid, ethylene precursor) spray increased RGR in both groups compared to control. Furthermore, the DT group accumulated a significantly higher galactose while a significantly lower maltose in the shoot compared to the DS group. Taken all together, these results suggest an impact of ABA, ethylene, and ABA:ethylene ratio on SDW of wheat seedlings that may partly underlie a genotypic variability of different shoot growth sensitivities to drought among crop species under field conditions. We propose that phenotyping based on hormone accumulation, response and hormonal ratio would be a viable, rapid, and an early–stage selection tool aiding genotype selection for stress tolerance

Biomass Allocation Patterns Are Linked to Genotypic Differences in Whole-Plant Transpiration Efficiency in Sunflower

Increased transpiration efficiency (the ratio of biomass to water transpired, TE) could lead to increased drought tolerance under some water deficit scenarios. Intrinsic (i.e., leaf-level) TE is usually considered as the primary source of variation in whole-plant TE, but empirical data usually contradict this assumption. Sunflower has a significant variability in TE, but a better knowledge of the effect of leaf and plant-level traits could be helpful to obtain more efficient genotypes for water use. The objective of this study was, therefore, to assess if genotypic variation in whole-plant TE is better related to leaf- or plant-level traits. Three experiments were conducted, aimed at verifying the existence of variability in whole-plant TE and whole-plant and leaf-level traits, and to assess their correlation. Sunflower public inbred lines and a segregating population of recombinant inbred lines were grown under controlled conditions and subjected to well-watered and water-deficit treatments. Significant genotypic variation was found for TE and related traits. These differences in whole-plant transpiration efficiency, both between genotypes and between plants within each genotype, showed no association to leaf-level traits, but were significantly and negatively correlated to biomass allocation to leaves and to the ratio of leaf area to total biomass. These associations are likely of a physiological origin, and not only a consequence of genetic linkage in the studied population. These results suggest that genotypic variation for biomass allocation could be potentially exploited as a source for increased transpiration efficiency in sunflower breeding programmes. It is also suggested that phenotyping for TE in this species should not be restricted to leaf-level measurements, but also include measurements of plant-level traits, especially those related to biomass allocation between photosynthetic and non-photosynthetic organs