Measuring stomatal and guard cell metrics for plant physiology and growth using StoManager1.

Automated guard cell detection and measurement are vital for understanding plant physiological performance and ecological functioning in global water and carbon cycles. Most current methods for measuring guard cells and stomata are laborious, time-consuming, prone to bias, and limited in scale. We developed StoManager1, a high-throughput tool utilizing geometrical, mathematical algorithms, and convolutional neural networks to automatically detect, count, and measure over 30 guard cell and stomatal metrics, including guard cell and stomatal area, length, width, stomatal aperture area/guard cell area, orientation, stomatal evenness, divergence, and aggregation index. Combined with leaf functional traits, some of these StoManager1-measured guard cell and stomatal metrics explained 90% and 82% of tree biomass and intrinsic water use efficiency (iWUE) variances in hardwoods, making them substantial factors in leaf physiology and tree growth. StoManager1 demonstrated exceptional precision and recall (mAP@0.5 over 0.96), effectively capturing diverse stomatal properties across over 100 species. StoManager1 facilitates the automation of measuring leaf stomatal and guard cells, enabling broader exploration of stomatal control in plant growth and adaptation to environmental stress and climate change. This has implications for global gross primary productivity (GPP) modeling and estimation, as integrating stomatal metrics can enhance predictions of plant growth and resource usage worldwide. Easily accessible open-source code and standalone Windows executable applications are available on a GitHub repository (https://github.com/JiaxinWang123/StoManager1) and Zenodo (https://doi.org/10.5281/zenodo.7686022).

A Multiscale Point-Supervised Network for Counting Maize Tassels in the Wild.

Accurate counting of maize tassels is essential for monitoring crop growth and estimating crop yield. Recently, deep-learning-based object detection methods have been used for this purpose, where plant counts are estimated from the number of bounding boxes detected. However, these methods suffer from 2 issues: (a) The scales of maize tassels vary because of image capture from varying distances and crop growth stage; and (b) tassel areas tend to be affected by occlusions or complex backgrounds, making the detection inefficient. In this paper, we propose a multiscale lite attention enhancement network (MLAENet) that uses only point-level annotations (i.e., objects labeled with points) to count maize tassels in the wild. Specifically, the proposed method includes a new multicolumn lite feature extraction module that generates a scale-dependent density map by exploiting multiple dilated convolutions with different rates, capturing rich contextual information at different scales more effectively. In addition, a multifeature enhancement module that integrates an attention strategy is proposed to enable the model to distinguish between tassel areas and their complex backgrounds. Finally, a new up-sampling module, UP-Block, is designed to improve the quality of the estimated density map by automatically suppressing the gridding effect during the up-sampling process. Extensive experiments on 2 publicly available tassel-counting datasets, maize tassels counting and maize tassels counting from unmanned aerial vehicle, demonstrate that the proposed MLAENet achieves marked advantages in counting accuracy and inference speed compared to state-of-the-art methods. The model is publicly available at https://github.com/ShiratsuyuShigure/MLAENet-pytorch/tree/main.

Field-measured canopy height may not be as accurate and heritable as believed: evidence from advanced 3D sensing.

Canopy height (CH) is an important trait for crop breeding and production. The rapid development of 3D sensing technologies shed new light on high-throughput height measurement. However, a systematic comparison of the accuracy and heritability of different 3D sensing technologies is seriously lacking. Moreover, it is questionable whether the field-measured height is as reliable as believed. This study uncovered these issues by comparing traditional height measurement with four advanced 3D sensing technologies, including terrestrial laser scanning (TLS), backpack laser scanning (BLS), gantry laser scanning (GLS), and digital aerial photogrammetry (DAP). A total of 1920 plots covering 120 varieties were selected for comparison. Cross-comparisons of different data sources were performed to evaluate their performances in CH estimation concerning different CH, leaf area index (LAI), and growth stage (GS) groups. Results showed that 1) All 3D sensing data sources had high correlations with field measurement (r > 0.82), while the correlations between different 3D sensing data sources were even better (r > 0.87). 2) The prediction accuracy between different data sources decreased in subgroups of CH, LAI, and GS. 3) Canopy height showed high heritability from all datasets, and 3D sensing datasets had even higher heritability (H2 = 0.79-0.89) than FM (field measurement) (H2 = 0.77). Finally, outliers of different datasets are analyzed. The results provide novel insights into different methods for canopy height measurement that may ensure the high-quality application of this important trait.

Shortwave Radiation Calculation for Forest Plots Using Airborne LiDAR Data and Computer Graphics.

Forested environments feature a highly complex radiation regime, and solar radiation is hindered from penetrating into the forest by the 3D canopy structure; hence, canopy shortwave radiation varies spatiotemporally, seasonally, and meteorologically, making the radiant flux challenging to both measure and model. Here, we developed a synergetic method using airborne LiDAR data and computer graphics to model the forest canopy and calculate the radiant fluxes of three forest plots (conifer, broadleaf, and mixed). Directional incident solar beams were emitted according to the solar altitude and azimuth angles, and the forest canopy surface was decomposed into triangular elements. A ray tracing algorithm was utilized to simulate the propagation of reflected and transmitted beams within the forest canopy. Our method accurately modeled the solar radiant fluxes and demonstrated good agreement (R 2 ≥ 0.82) with the plot-scale results of hemispherical photo-based HPEval software and pyranometer measurements. The maximum incident radiant flux appeared in the conifer plot at noon on June 15 due to the largest solar altitude angle (81.21°) and dense clustering of tree crowns; the conifer plot also received the maximum reflected radiant flux (10.91-324.65 kW) due to the higher reflectance of coniferous trees and the better absorption of reflected solar beams. However, the broadleaf plot received more transmitted radiant flux (37.7-226.71 kW) for the trees in the shaded area due to the larger transmittance of broadleaf species. Our method can directly simulate the detailed plot-scale distribution of canopy radiation and is valuable for researching light-dependent biophysiological processes.

Proximal and remote sensing in plant phenomics: 20 years of progress, challenges, and perspectives.

Plant phenomics (PP) has been recognized as a bottleneck in studying the interactions of genomics and environment on plants, limiting the progress of smart breeding and precise cultivation. High-throughput plant phenotyping is challenging owing to the spatio-temporal dynamics of traits. Proximal and remote sensing (PRS) techniques are increasingly used for plant phenotyping because of their advantages in multi-dimensional data acquisition and analysis. Substantial progress of PRS applications in PP has been observed over the last two decades and is analyzed here from an interdisciplinary perspective based on 2972 publications. This progress covers most aspects of PRS application in PP, including patterns of global spatial distribution and temporal dynamics, specific PRS technologies, phenotypic research fields, working environments, species, and traits. Subsequently, we demonstrate how to link PRS to multi-omics studies, including how to achieve multi-dimensional PRS data acquisition and processing, how to systematically integrate all kinds of phenotypic information and derive phenotypic knowledge with biological significance, and how to link PP to multi-omics association analysis. Finally, we identify three future perspectives for PRS-based PP: (1) strengthening the spatial and temporal consistency of PRS data, (2) exploring novel phenotypic traits, and (3) facilitating multi-omics communication.

Simultaneous Prediction of Wheat Yield and Grain Protein Content Using Multitask Deep Learning from Time-Series Proximal Sensing.

Wheat yield and grain protein content (GPC) are two main optimization targets for breeding and cultivation. Remote sensing provides nondestructive and early predictions of yield and GPC, respectively. However, whether it is possible to simultaneously predict yield and GPC in one model and the accuracy and influencing factors are still unclear. In this study, we made a systematic comparison of different deep learning models in terms of data fusion, time-series feature extraction, and multitask learning. The results showed that time-series data fusion significantly improved yield and GPC prediction accuracy with R 2 values of 0.817 and 0.809. Multitask learning achieved simultaneous prediction of yield and GPC with comparable accuracy to the single-task model. We further proposed a two-to-two model that combines data fusion (two kinds of data sources for input) and multitask learning (two outputs) and compared different feature extraction layers, including RNN (recurrent neural network), LSTM (long short-term memory), CNN (convolutional neural network), and attention module. The two-to-two model with the attention module achieved the best prediction accuracy for yield (R 2 = 0.833) and GPC (R 2 = 0.846). The temporal distribution of feature importance was visualized based on the attention feature values. Although the temporal patterns of structural traits and spectral traits were inconsistent, the overall importance of both structural traits and spectral traits at the postanthesis stage was more important than that at the preanthesis stage. This study provides new insights into the simultaneous prediction of yield and GPC using deep learning from time-series proximal sensing, which may contribute to the accurate and efficient predictions of agricultural production.

Design and Analysis of a Microgripper with Three-Stage Amplification Mechanism for Micromanipulation.

This paper proposes a novel microgripper with two working modes. The microgripper is designed with symmetric structure and each part is actuated by one piezoelectric actuator, respectively. To achieve desired output displacement, each part of the microgripper is designed with three-stage amplification mechanism to amplify the displacement of the PZT actuator. According to the size of the microobjects, the grasping operation can be completed by one finger moving or two fingers moving simultaneously. Then, the theoretical analysis is carried out to calculated the key characteristics, including amplification, input stiffness and frequency. Finite element analysis (FEA) is conducted to optimize the structural parameters and investigate the performance of the microgripper. Finally, a prototype is machined by wire electro-discharge machining (WEDM) method and experiments are carried out to verify the performance of the microgripper. The results indicate that the amplification is 10.41 and the motion stroke of one jaw is 118.34 µm when the input voltage is 100 V. The first natural frequency is 746.56 Hz. By picking and placing the wires with different diameters and slices with different thickness, the grasping stability is verified.

Large-scale field phenotyping using backpack LiDAR and CropQuant-3D to measure structural variation in wheat.

Plant phenomics bridges the gap between traits of agricultural importance and genomic information. Limitations of current field-based phenotyping solutions include mobility, affordability, throughput, accuracy, scalability, and the ability to analyze big data collected. Here, we present a large-scale phenotyping solution that combines a commercial backpack Light Detection and Ranging (LiDAR) device and our analytic software, CropQuant-3D, which have been applied jointly to phenotype wheat (Triticum aestivum) and associated 3D trait analysis. The use of LiDAR can acquire millions of 3D points to represent spatial features of crops, and CropQuant-3D can extract meaningful traits from large, complex point clouds. In a case study examining the response of wheat varieties to three different levels of nitrogen fertilization in field experiments, the combined solution differentiated significant genotype and treatment effects on crop growth and structural variation in the canopy, with strong correlations with manual measurements. Hence, we demonstrate that this system could consistently perform 3D trait analysis at a larger scale and more quickly than heretofore possible and addresses challenges in mobility, throughput, and scalability. To ensure our work could reach non-expert users, we developed an open-source graphical user interface for CropQuant-3D. We, therefore, believe that the combined system is easy-to-use and could be used as a reliable research tool in multi-location phenotyping for both crop research and breeding. Furthermore, together with the fast maturity of LiDAR technologies, the system has the potential for further development in accuracy and affordability, contributing to the resolution of the phenotyping bottleneck and exploiting available genomic resources more effectively.

Exploring Seasonal and Circadian Rhythms in Structural Traits of Field Maize from LiDAR Time Series.

Plant growth rhythm in structural traits is important for better understanding plant response to the ever-changing environment. Terrestrial laser scanning (TLS) is a well-suited tool to study structural rhythm under field conditions. Recent studies have used TLS to describe the structural rhythm of trees, but no consistent patterns have been drawn. Meanwhile, whether TLS can capture structural rhythm in crops is unclear. Here, we aim to explore the seasonal and circadian rhythms in maize structural traits at both the plant and leaf levels from time-series TLS. The seasonal rhythm was studied using TLS data collected at four key growth periods, including jointing, bell-mouthed, heading, and maturity periods. Circadian rhythms were explored by using TLS data acquired around every 2 hours in a whole day under standard and cold stress conditions. Results showed that TLS can quantify the seasonal and circadian rhythm in structural traits at both plant and leaf levels. (1) Leaf inclination angle decreased significantly between the jointing stage and bell-mouthed stage. Leaf azimuth was stable after the jointing stage. (2) Some individual-level structural rhythms (e.g., azimuth and projected leaf area/PLA) were consistent with leaf-level structural rhythms. (3) The circadian rhythms of some traits (e.g., PLA) were not consistent under standard and cold stress conditions. (4) Environmental factors showed better correlations with leaf traits under cold stress than standard conditions. Temperature was the most important factor that significantly correlated with all leaf traits except leaf azimuth. This study highlights the potential of time-series TLS in studying outdoor agricultural chronobiology.

A Novel Computational Framework for Precision Diagnosis and Subtype Discovery of Plant With Lesion.

Plants are often attacked by various pathogens during their growth, which may cause environmental pollution, food shortages, or economic losses in a certain area. Integration of high throughput phenomics data and computer vision (CV) provides a great opportunity to realize plant disease diagnosis in the early stage and uncover the subtype or stage patterns in the disease progression. In this study, we proposed a novel computational framework for plant disease identification and subtype discovery through a deep-embedding image-clustering strategy, Weighted Distance Metric and the t-stochastic neighbor embedding algorithm (WDM-tSNE). To verify the effectiveness, we applied our method on four public datasets of images. The results demonstrated that the newly developed tool is capable of identifying the plant disease and further uncover the underlying subtypes associated with pathogenic resistance. In summary, the current framework provides great clustering performance for the root or leave images of diseased plants with pronounced disease spots or symptoms.

Non-destructive estimation of field maize biomass using terrestrial lidar: an evaluation from plot level to individual leaf level.

BACKGROUND: Precision agriculture is an emerging research field that relies on monitoring and managing field variability in phenotypic traits. An important phenotypic trait is biomass, a comprehensive indicator that can reflect crop yields. However, non-destructive biomass estimation at fine levels is unknown and challenging due to the lack of accurate and high-throughput phenotypic data and algorithms. RESULTS: In this study, we evaluated the capability of terrestrial light detection and ranging (lidar) data in estimating field maize biomass at the plot, individual plant, leaf group, and individual organ (i.e., individual leaf or stem) levels. The terrestrial lidar data of 59 maize plots with more than 1000 maize plants were collected and used to calculate phenotypes through a deep learning-based pipeline, which were then used to predict maize biomass through simple regression (SR), stepwise multiple regression (SMR), artificial neural network (ANN), and random forest (RF). The results showed that terrestrial lidar data were useful for estimating maize biomass at all levels (at each level, R2 was greater than 0.80), and biomass estimation at leaf group level was the most precise (R2 = 0.97, RMSE = 2.22 g) among all four levels. All four regression techniques performed similarly at all levels. However, considering the transferability and interpretability of the model itself, SR is the suggested method for estimating maize biomass from terrestrial lidar-derived phenotypes. Moreover, height-related variables showed to be the most important and robust variables for predicting maize biomass from terrestrial lidar at all levels, and some two-dimensional variables (e.g., leaf area) and three-dimensional variables (e.g., volume) showed great potential as well. CONCLUSION: We believe that this study is a unique effort on evaluating the capability of terrestrial lidar on estimating maize biomass at difference levels, and can provide a useful resource for the selection of the phenotypes and models required to estimate maize biomass in precision agriculture practices.

An updated Vegetation Map of China (1:1000000).

Vegetation maps are important sources of information for biodiversity conservation, ecological studies, vegetation management and restoration, and national strategic decision making. The current Vegetation Map of China (1:1000000) was generated by a team of more than 250 scientists in an effort that lasted over 20 years starting in the 1980s. However, the vegetation distribution of China has experienced drastic changes during the rapid development of China in the last three decades, and it urgently needs to be updated to better represent the distribution of current vegetation types. Here, we describe the process of updating the Vegetation Map of China (1:1000000) generated in the 1980s using a "crowdsourcing-change detection-classification-expert knowledge" vegetation mapping strategy. A total of 203,024 field samples were collected, and 50 taxonomists were involved in the updating process. The resulting updated map has 12 vegetation type groups, 55 vegetation types/subtypes, and 866 vegetation formation/sub-formation types. The overall accuracy and kappa coefficient of the updated map are 64.8% and 0.52 at the vegetation type group level, 61% and 0.55 at the vegetation type/subtype level and 40% and 0.38 at the vegetation formation/sub-formation level. When compared to the original map, the updated map showed that 3.3 million km2 of vegetated areas of China have changed their vegetation type group during the past three decades due to anthropogenic activities and climatic change. We expect this updated map to benefit the understanding and management of China's terrestrial ecosystems.

Evaluating maize phenotype dynamics under drought stress using terrestrial lidar.

BACKGROUND: Maize (Zea mays L.) is the third most consumed grain in the world and improving maize yield is of great importance of the world food security, especially under global climate change and more frequent severe droughts. Due to the limitation of phenotyping methods, most current studies only focused on the responses of phenotypes on certain key growth stages. Although light detection and ranging (lidar) technology showed great potential in acquiring three-dimensional (3D) vegetation information, it has been rarely used in monitoring maize phenotype dynamics at an individual plant level. RESULTS: In this study, we used a terrestrial laser scanner to collect lidar data at six growth stages for 20 maize varieties under drought stress. Three drought-related phenotypes, i.e., plant height, plant area index (PAI) and projected leaf area (PLA), were calculated from the lidar point clouds at the individual plant level. The results showed that terrestrial lidar data can be used to estimate plant height, PAI and PLA at an accuracy of 96%, 70% and 92%, respectively. All three phenotypes showed a pattern of first increasing and then decreasing during the growth period. The high drought tolerance group tended to keep lower plant height and PAI without losing PLA during the tasseling stage. Moreover, the high drought tolerance group inclined to have lower plant area density in the upper canopy than the low drought tolerance group. CONCLUSION: The results demonstrate the feasibility of using terrestrial lidar to monitor 3D maize phenotypes under drought stress in the field and may provide new insights on identifying the key phenotypes and growth stages influenced by drought stress.

Deep Learning: Individual Maize Segmentation From Terrestrial Lidar Data Using Faster R-CNN and Regional Growth Algorithms.

The rapid development of light detection and ranging (Lidar) provides a promising way to obtain three-dimensional (3D) phenotype traits with its high ability of recording accurate 3D laser points. Recently, Lidar has been widely used to obtain phenotype data in the greenhouse and field with along other sensors. Individual maize segmentation is the prerequisite for high throughput phenotype data extraction at individual crop or leaf level, which is still a huge challenge. Deep learning, a state-of-the-art machine learning method, has shown high performance in object detection, classification, and segmentation. In this study, we proposed a method to combine deep leaning and regional growth algorithms to segment individual maize from terrestrial Lidar data. The scanned 3D points of the training site were sliced row and row with a fixed 3D window. Points within the window were compressed into deep images, which were used to train the Faster R-CNN (region-based convolutional neural network) model to learn the ability of detecting maize stem. Three sites of different planting densities were used to test the method. Each site was also sliced into many 3D windows, and the testing deep images were generated. The detected stem in the testing images can be mapped into 3D points, which were used as seed points for the regional growth algorithm to grow individual maize from bottom to up. The results showed that the method combing deep leaning and regional growth algorithms was promising in individual maize segmentation, and the values of r, p, and F of the three testing sites with different planting density were all over 0.9. Moreover, the height of the truly segmented maize was highly correlated to the manually measured height (R2> 0.9). This work shows the possibility of using deep leaning to solve the individual maize segmentation problem from Lidar data.