LeTra: a leaf tracking workflow based on convolutional neural networks and intersection over union

BACKGROUND

The study of plant photosynthesis is essential for productivity and yield. Thanks to the development of high-throughput phenotyping (HTP) facilities, based on chlorophyll fluorescence imaging, photosynthetic traits can be measured in a reliable, reproducible and efficient manner. In most state-of-the-art HTP platforms, these traits are automatedly analyzed at individual plant level, but information at leaf level is often restricted by the use of manual annotation. Automated leaf tracking over time is therefore highly desired. Methods for tracking individual leaves are still uncommon, convoluted, or require large datasets. Hence, applications and libraries with different techniques are required. New phenotyping platforms are initiated now more frequently than ever; however, the application of advanced computer vision techniques, such as convolutional neural networks, is still growing at a slow pace. Here, we provide a method for leaf segmentation and tracking through the fine-tuning of Mask R-CNN and intersection over union as a solution for leaf tracking on top-down images of plants. We also provide datasets and code for training and testing on both detection and tracking of individual leaves, aiming to stimulate the community to expand the current methodologies on this topic.

RESULTS

We tested the results for detection and segmentation on 523 Arabidopsis thaliana leaves at three different stages of development from which we obtained a mean F-score of 0.956 on detection and 0.844 on segmentation overlap through the intersection over union (IoU). On the tracking side, we tested nine different plants with 191 leaves. A total of 161 leaves were tracked without issues, accounting to a total of 84.29% correct tracking, and a Higher Order Tracking Accuracy (HOTA) of 0.846. In our case study, leaf age and leaf order influenced photosynthetic capacity and photosynthetic response to light treatments. Leaf-dependent photosynthesis varies according to the genetic background.

CONCLUSION

The method provided is robust for leaf tracking on top-down images. Although one of the strong components of the method is the low requirement in training data to achieve a good base result (based on fine-tuning), most of the tracking issues found could be solved by expanding the training dataset for the Mask R-CNN model.

Interpreting the variation in particle size of ground spice by high-resolution visual and spectral imaging: A ginger case study

High-resolution (HR) visual imaging and spectral imaging are common computer vision-based techniques used for food quality analysis and/or authentication based on the interaction of light and material surface and/or composition. The particle size of ground spices is an important morphological feature that affects the physico-chemical properties of food products containing such particles. This study aimed to interpret the impact of particle size of ground spice on its HR visual profile and spectral imaging profile using ginger powder as a representative spice powder model. The results revealed an increase in the light reflection with the decrease of particle size of ginger powder, which was manifested by the lighter colour (higher percentage of the colour code with lighter yellow colour) of the HR visual image and stronger reflection with spectral imaging. The study also revealed that, in spectral imaging, the influence of the particle size of ginger powder increased with rising wavelengths. Finally, the results indicated a relationship between spectral wavelengths, ginger particle size, and other natural variables of the products which might be generated from cultivation to processing. Ultimately, the impact of natural variables arising during the food production process on the physico-chemical properties of the product should be fully considered or even additionally evaluated prior to the application of specific food quality and/or authentication analytical techniques.

Insect exuviae as soil amendment affect flower reflectance and increase flower production and plant volatile emission

Soil composition and herbivory are two environmental factors that can affect plant traits including flower traits, thus potentially affecting plant-pollinator interactions. Importantly, soil composition and herbivory may interact in these effects, with consequences for plant fitness. We assessed the main effects of aboveground insect herbivory and soil amendment with exuviae of three different insect species on visual and olfactory traits of Brassica nigra plants, including interactive effects. We combined various methodological approaches including gas chromatography/mass spectrometry, spectroscopy and machine learning to evaluate changes in flower morphology, colour and the emission of volatile organic compounds (VOCs). Soil amended with insect exuviae increased the total number of flowers per plant and VOC emission, whereas herbivory reduced petal area and VOC emission. Soil amendment and herbivory interacted in their effect on the floral reflectance spectrum of the base part of petals and the emission of 10 VOCs. These findings demonstrate the effects of insect exuviae as soil amendment on plant traits involved in reproduction, with a potential for enhanced reproductive success by increasing the strength of signals attracting pollinators and by mitigating the negative effects of herbivory.

High-Resolution Analysis of Growth and Transpiration of Quinoa Under Saline Conditions

The Plantarray 3.0 phenotyping platform^® was used to monitor the growth and water use of the quinoa varieties Pasto and selRiobamba under salinity (0-300 mM NaCl). Salinity reduced the cumulative transpiration of both varieties by 60% at 200 mM NaCl and by 75 and 82% at 300 mM NaCl for selRiobamba and Pasto, respectively. Stomatal conductance was reduced by salinity, but at 200 mM NaCl Pasto showed a lower reduction (15%) than selRiobamba (35%), along with decreased specific leaf area. Diurnal changes in water use parameters indicate that under salt stress, daily transpiration in quinoa is less responsive to changes in light irradiance, and stomatal conductance is modulated to maximize CO₂ uptake and minimize water loss following the changes in VPD (vapor pressure deficit). These changes might contribute to the enhanced water use efficiency of both varieties under salt stress. The mechanistic crop model LINTUL was used to integrate physiological responses into the radiation use efficiency of the plants (RUE), which was more reduced in Pasto than selRiobamba under salinity. By the end of the experiment (eleven weeks after sowing, six weeks after stress), the growth of Pasto was significantly lower than selRiobamba, fresh biomass was 50 and 35% reduced at 200 mM and 70 and 50% reduced at 300 mM NaCl for Pasto and selRiobamba, respectively. We argue that contrasting water management strategies can at least partly explain the differences in salt tolerance between Pasto and selRiobamba. Pasto adopted a "conservative-growth" strategy, saving water at the expense of growth, while selRiobamba used an "acquisitive-growth" strategy, maximizing growth in spite of the stress. The implementation of high-resolution phenotyping could help to dissect these complex growth traits that might be novel breeding targets for abiotic stress tolerance.

Hyperspectral imaging system based on a single-pixel camera design for detecting differences in tissue properties

Optical spectroscopy can be used to distinguish between healthy and diseased tissue. In this study, the design and testing of a single-pixel hyperspectral imaging (HSI) system that uses autofluorescence emission from collagen (400 nm) and nicotinamide adenine dinucleotide phosphate (475 nm) along with differences in the optical reflectance spectra to differentiate between healthy and thermally damaged tissue is discussed. The changes in protein autofluorescence and reflectance due to thermal damage are studied in ex vivo porcine tissue models. Thermal lesions were created in porcine skin (n=12) and liver (n=15) samples using an IR laser. The damaged regions were clearly visible in the hyperspectral images. Sizes of the thermally damaged regions as measured via HSI are compared to sizes of these regions as measured in white-light images and via physical measurement. Good agreement between the sizes measured in the hyperspectral images, white-light imaging, and physical measurements were found. The HSI system can differentiate between healthy and damaged tissue. Possible applications of this imaging system include determination of tumor margins during surgery/biopsy and cancer diagnosis and staging.

Interactions of zinc and arachidonic acid

To probe the interaction of zinc with polyunsaturated fatty acids we have studied the effect of zinc on the cooxygenation of ferrous iron and arachidonic acid. Zinc inhibited the process of cooxygenation in a concentration dependent fashion. Further evaluation of the interaction of zinc and arachidonic acid gave spectroscopic evidence that zinc, oxygen and arachidonic acid can form an unstable hydroperoxide-like complex similar to that postulated earlier for iron, oxygen and arachidonic acid. However, in the case of zinc the complex will not proceed further to form stable peroxides and the unstable complex falls apart to give zinc and arachidonic acid intact. The findings have implications for the role of zinc in enzyme reactions and for antioxidant reactions of zinc within the cell. The influence of zinc on platelet aggregation was also evaluated. Zinc was found to inhibit cell-cell aggregation. However, in contrast to the known ability of zinc to inhibit prostaglandin synthesis in a broken cell preparation, zinc did not inhibit prostaglandin or thromboxane synthesis in the intact platelet. Inhibition of platelet aggregation by zinc must result from some other action of this cation.

Lysophosphatidic acids. Influence on platelet aggregation and intracellular calcium flux

Decanoyl-, palmitoyl-, and oleoyl-lysophosphatidic acid (LPA) were studied for their effects on platelet aggregation and intracellular calcium flux. Palmitoyl-LPA and oleoyl-LPA both caused a concentration-dependent aggregation of human blood platelets at concentrations of 12--300 microM. Aggregation by adenosine diphosphate (ADP) was enhanced at slightly lower concentrations. First-wave aggregation induced by these LPAs was not blocked by aspirin, indomethacin, or heparin, suggesting similarities to ADP aggregation. However, in washed platelets with a high calcium concentration, no serotonin secretion was observed, even though full aggregation occurred, suggesting that aggregation was not due to released ADP. This concept was supported by studies of platelets deficient in the storage pool of ADP and serotonin, which had a normal first-wave aggregation response to palmitoyl-LPA. Aggregation induced by palmitoyl LPA was inhibited by prostaglandin E1 (PGE1), theophylline, and ethylenediaminotetraacetate (EDTA), though in the presence of EDTA shape change occurred. Aggregation stimulated by palmitoyl-LPA or oleoyl-LPA was characterized by changes in the shape of the platelets with development of pseudopods and centralization of granules closely surrounded by contractile microfilaments and supporting microtubules. The addition of palmitoyl-LPA and oleoyl-LPA, but not decanoyl-LPA, caused the release of calcium from a platelet membrane fraction that contains elements of the intracellular calcium storage system and actively concentrates this cation in the presence of adenosine triphosphate (ATP) and magnesium. It is suggested that LPAs cause aggregation by stimulating the release of calcium intracellularly.

Vitamin E inhibits the release of calcium from a platelet fraction in vitro

Vitamin E, an inhibitor of platelet aggregation, was evaluated for its effects on platelet intracellular calcium flux. These studies used a platelet membrane fraction containing membranes of the dense tubular system which actively sequesters calcium in the presence of ATP and magnesium. After these membrane vesicles have accumulated calcium, the cation can be released by addition of the calcium ionophore A23187. Vitamin E had no effect on uptake of calcium by the membrane vesicles, but showed a concentration dependent inhibition of the release of calcium induced by A23187. In similar or slightly higher concentrations than inhibited calcium release, vitamin E also inhibited platelet aggregation, internal contraction and secretion, but had no effect on prostaglandin and thromboxane synthesis and potentiated phospholipase A2 activity. It is suggested that vitamin E acts to inhibit platelet internal contraction and secretion by preventing efflux of calcium from the dense tubular system. The potentiation of phospholiplase A2 by vitamin E could be explained by a localized increase of calcium at the site of the phospholipase A2 on the inner side of the dense tubular system membrane proximal to the vitamin E block.