Near-earth hyperspectral big data present both huge opportunities and challenges for spurring developments in agriculture and high-throughput plant phenotyping and breeding. In this article, we present data-driven approaches to address the calibration challenges for utilizing near-earth hyperspectral data for agriculture. A data-driven, fully automated calibration workflow that includes a suite of robust algorithms for radiometric calibration, bidirectional reflectance distribution function (BRDF) correction and reflectance normalization, soil and shadow masking, and image quality assessments was developed. An empirical method that utilizes predetermined models between camera photon counts (digital numbers) and downwelling irradiance measurements for each spectral band was established to perform radiometric calibration. A kernel-driven semiempirical BRDF correction method based on the Ross Thick-Li Sparse (RTLS) model was used to normalize the data for both changes in solar elevation and sensor view angle differences attributed to pixel location within the field of view. Following rigorous radiometric and BRDF corrections, novel rule-based methods were developed to conduct automatic soil removal; and a newly proposed approach was used for image quality assessment; additionally, shadow masking and plot-level feature extraction were carried out. Our results show that the automated calibration, processing, storage, and analysis pipeline developed in this work can effectively handle massive amounts of hyperspectral data and address the urgent challenges related to the production of sustainable bioenergy and food crops, targeting methods to accelerate plant breeding for improving yield and biomass traits.

We explore the use of deep convolutional neural networks (CNNs) trained on overhead imagery of biomass sorghum to ascertain the relationship between single nucleotide polymorphisms (SNPs), or groups of related SNPs, and the phenotypes they control. We consider both CNNs trained explicitly on the classification task of predicting whether an image shows a plant with a reference or alternate version of various SNPs as well as CNNs trained to create data-driven features based on learning features so that images from the same plot are more similar than images from different plots, and then using the features this network learns for genetic marker classification. We characterize how efficient both approaches are at predicting the presence or absence of a genetic markers, and visualize what parts of the images are most important for those predictions. We find that the data-driven approaches give somewhat higher prediction performance, but have visualizations that are harder to interpret; and we give suggestions of potential future machine learning research and discuss the possibilities of using this approach to uncover unknown genotype × phenotype relationships.

Wheat is a globally cultivated cereal crop with substantial protein content present in its seeds. This research aimed to develop robust methods for predicting seed protein concentration in wheat seeds using bench-top hyperspectral imaging in the visible, near-infrared (VNIR), and shortwave infrared (SWIR) regions. To fully utilize the spectral and texture features of the full VNIR and SWIR spectral domains, a computer-vision-aided image co-registration methodology was implemented to seamlessly align the VNIR and SWIR bands. Sensitivity analyses were also conducted to identify the most sensitive bands for seed protein estimation. Convolutional neural networks (CNNs) with attention mechanisms were proposed along with traditional machine learning models based on feature engineering including Random Forest (RF) and Support Vector Machine (SVM) regression for comparative analysis. Additionally, the CNN classification approach was used to estimate low, medium, and high protein concentrations because this type of classification is more applicable for breeding efforts. Our results showed that the proposed CNN with attention mechanisms predicted wheat protein content with R² values of 0.70 and 0.65 for ventral and dorsal seed orientations, respectively. Although, the R² of the CNN approach was lower than of the best performing feature-based method, RF (R² of 0.77), end-to-end prediction capabilities with CNN hold great promise for the automation of wheat protein estimation for breeding. The CNN model achieved better classification of protein concentrations between low, medium, and high protein contents, with an R² of 0.82. This study’s findings highlight the significant potential of hyperspectral imaging and machine learning techniques for advancing precision breeding practices, optimizing seed sorting processes, and enabling targeted agricultural input applications.

A core objective of the TERRA-REF project was to generate an open-access reference dataset for the evaluation of sensing technologies to study plants under field conditions. The TERRA-REF program deployed a suite of high-resolution, cutting edge technology sensors on a gantry system with the aim of scanning 1 hectare (10 ⁴ m) at around 1 mm ² spatial resolution multiple times per week. The system contains co-located sensors including a stereo-pair RGB camera, a thermal imager, a laser scanner to capture 3D structure, and two hyperspectral cameras covering wavelengths of 300-2500nm. This sensor data is provided alongside over sixty types of traditional plant phenotype measurements that can be used to train new machine learning models. Associated weather and environmental measurements, information about agronomic management and experimental design, and the genomic sequences of hundreds of plant varieties have been collected and are available alongside the sensor and plant phenotype data.Over the course of four years and ten growing seasons, the TERRA-REF system generated over 1 PB of sensor data and almost 45 million files. The subset that has been released to the public domain accounts for two seasons and about half of the total data volume. This provides an unprecedented opportunity for investigations far beyond the core biological scope of the project.The focus of this paper is to provide the Computer Vision and Machine Learning communities an overview of the available data and some potential applications of this one of a kind data.

Geospatial Artificial Intelligence (GeoAI) and data processing techniques have significantly advanced object detection, prediction, and classification tasks. However, the availability of machine learning-ready, labeled data for specific applications such as plant disease detection remains the major challenge for the broader adoption of GeoAI. For instance, collecting temporal UAV imagery of agricultural crops to track disease emergence and progress requires substantial human labor and resources, which is often limited to a small spatial scale. Recognizing the pivotal role of temporal data in pattern recognition, object detection, and scene reconstruction, we introduce an innovative approach to augment multispectral temporal datasets: the Geospatial Time Machine. Our proposed methodology combines Graph Neural Network (GNN) and Generative Adversarial Network (GAN) architectures to generate comprehensive synthetic temporal data encompassing multivariate time series. The results demonstrate that imagery generated through backcasting can enhance the accuracy of downstream classification tasks by up to 53% in plant disease detection, particularly in the initial stages of analyzing a crop growth using multispectral and multitemporal datasets.

Triplet loss is an extremely common approach to distance metric learning. Representations of images from the same class are optimized to be mapped closer together in an embedding space than representations of images from different classes. Much work on triplet losses focuses on selecting the most useful triplets of images to consider, with strategies that select dissimilar examples from the same class or similar examples from different classes. The consensus of previous research is that optimizing with the \textit{hardest} negative examples leads to bad training behavior. That's a problem -- these hardest negatives are literally the cases where the distance metric fails to capture semantic similarity. In this paper, we characterize the space of triplets and derive why hard negatives make triplet loss training fail. We offer a simple fix to the loss function and show that, with this fix, optimizing with hard negative examples becomes feasible. This leads to more generalizable features, and image retrieval results that outperform state of the art for datasets with high intra-class variance.