J. Mason Earles

Devin A. Rippner, Pranav Raja, J. Mason Earles et al.

X-ray micro-computed tomography (X-ray microCT) has enabled the characterization of the properties and processes that take place in plants and soils at the micron scale. Despite the widespread use of this advanced technique, major limitations in both hardware and software limit the speed and accuracy of image processing and data analysis. Recent advances in machine learning, specifically the application of convolutional neural networks to image analysis, have enabled rapid and accurate segmentation of image data. Yet, challenges remain in applying convolutional neural networks to the analysis of environmentally and agriculturally relevant images. Specifically, there is a disconnect between the computer scientists and engineers, who build these AI/ML tools, and the potential end users in agricultural research, who may be unsure of how to apply these tools in their work. Additionally, the computing resources required for training and applying deep learning models are unique, more common to computer gaming systems or graphics design work, than to traditional computational systems. To navigate these challenges, we developed a modular workflow for applying convolutional neural networks to X-ray microCT images, using low-cost resources in Googles Colaboratory web application. Here we present the results of the workflow, illustrating how parameters can be optimized to achieve best results using example scans from walnut leaves, almond flower buds, and a soil aggregate. We expect that this framework will accelerate the adoption and use of emerging deep learning techniques within the plant and soil sciences.

Alexander G. Olenskyj, Brent S. Sams, Zhenghao Fei et al.

Yield estimation is a powerful tool in vineyard management, as it allows growers to fine-tune practices to optimize yield and quality. However, yield estimation is currently performed using manual sampling, which is time-consuming and imprecise. This study demonstrates the application of proximal imaging combined with deep learning for yield estimation in vineyards. Continuous data collection using a vehicle-mounted sensing kit combined with collection of ground truth yield data at harvest using a commercial yield monitor allowed for the generation of a large dataset of 23,581 yield points and 107,933 images. Moreover, this study was conducted in a mechanically managed commercial vineyard, representing a challenging environment for image analysis but a common set of conditions in the California Central Valley. Three model architectures were tested: object detection, CNN regression, and transformer models. The object detection model was trained on hand-labeled images to localize grape bunches, and either bunch count or pixel area was summed to correlate with grape yield. Conversely, regression models were trained end-to-end to predict grape yield from image data without the need for hand labeling. Results demonstrated that both a transformer as well as the object detection model with pixel area processing performed comparably, with a mean absolute percent error of 18% and 18.5%, respectively on a representative holdout dataset. Saliency mapping was used to demonstrate the attention of the CNN model was localized near the predicted location of grape bunches, as well as on the top of the grapevine canopy. Overall, the study showed the applicability of proximal imaging and deep learning for prediction of grapevine yield on a large scale. Additionally, the end-to-end modeling approach was able to perform comparably to the object detection approach while eliminating the need for hand-labeling.

Hamid Kamangir, Brent. S. Sams, Nick Dokoozlian et al.

Crop yield prediction is essential for agricultural planning but remains challenging due to the complex interactions between weather, climate, and management practices. To address these challenges, we introduce a deep learning-based multi-model called Climate-Management Aware Vision Transformer (CMAViT), designed for pixel-level vineyard yield predictions. CMAViT integrates both spatial and temporal data by leveraging remote sensing imagery and short-term meteorological data, capturing the effects of growing season variations. Additionally, it incorporates management practices, which are represented in text form, using a cross-attention encoder to model their interaction with time-series data. This innovative multi-modal transformer tested on a large dataset from 2016-2019 covering 2,200 hectares and eight grape cultivars including more than 5 million vines, outperforms traditional models like UNet-ConvLSTM, excelling in spatial variability capture and yield prediction, particularly for extreme values in vineyards. CMAViT achieved an R2 of 0.84 and a MAPE of 8.22% on an unseen test dataset. Masking specific modalities lowered performance: excluding management practices, climate data, and both reduced R2 to 0.73, 0.70, and 0.72, respectively, and raised MAPE to 11.92%, 12.66%, and 12.39%, highlighting each modality's importance for accurate yield prediction. Code is available at https://github.com/plant-ai-biophysics-lab/CMAViT.

Earl Ranario, Ismael Mayanja, Heesup Yun et al.

Accurate plant segmentation in thermal imagery remains a significant challenge for high throughput field phenotyping, particularly in outdoor environments where low contrast between plants and weeds and frequent occlusions hinder performance. To address this, we present a framework that leverages synthetic RGB imagery, a limited set of real annotations, and GAN-based cross-modality alignment to enhance semantic segmentation in thermal images. We trained models on 1,128 synthetic images containing complex mixtures of crop and weed plants in order to generate image segmentation masks for crop and weed plants. We additionally evaluated the benefit of integrating as few as five real, manually segmented field images within the training process using various sampling strategies. When combining all the synthetic images with a few labeled real images, we observed a maximum relative improvement of 22% for the weed class and 17% for the plant class compared to the full real-data baseline. Cross-modal alignment was enabled by translating RGB to thermal using CycleGAN-turbo, allowing robust template matching without calibration. Results demonstrated that combining synthetic data with limited manual annotations and cross-domain translation via generative models can significantly boost segmentation performance in complex field environments for multi-model imagery.