arXiv subjects

Brian N. Bailey

Publications and source records attributed to Brian N. Bailey.

14 recordsLinked to original sources

arXiv2026

Can Synthetic Data Overcome the Generalization Limits of AI-Based Flower and Pod Detection Across Cowpea Breeding Genotypes and Environments?

High-throughput phenotyping requires AI-enabled computer vision models that generalize across genotypes, locations, and growing seasons, yet such models often lose accuracy under new conditions. Annotating real imagery for every genotype-by-environment (G x E) combination a breeding program encounters is prohibitively expensive. We quantify how G x E shifts affect AI-based detection of cowpea flowers and pods across two California locations and two growing seasons. Flower detection mAP@50 fell from 76.3% to as low as 50.6% under unseen shifts, and pod detection was more sensitive. Feature-space and image-quality diagnostics confirmed these losses track measurable distributional shifts. Because closing this gap with real data alone is not practical, we test whether synthetic imagery, rendered from a procedural 3D cowpea model, can substitute for that annotation burden. Synthetic supervision alone improved over pretraining but remained limited by a domain gap driven by camera image formation, not scene content. A domain-gap-aware camera-realism augmentation strategy, optimized against measured real-image statistics via Wasserstein distance, narrowed this gap, and a linear HDR representation converted a smaller measured gap into a larger detection gain than an 8-bit representation. Optimized HDR synthetic data combined with as few as five real images matched or exceeded the real-data baseline for spatial generalization, and pod detection benefited most at the lowest shot counts, with more modest gains under temporal shift. These results show that synthetic data can overcome the generalization limits of AI-based flower and pod detection, but only when the domain gap is measured and optimized rather than assumed away.

cs.CV↗

arXiv2026

Does Your VFM Speak Plant? The Botanical Grammar of Vision Foundation Models for Object Detection

Vision foundation models (VFMs) offer the promise of zero-shot object detection without task-specific training data, yet their performance in complex agricultural scenes remains highly sensitive to text prompt construction. We present a systematic prompt optimization framework evaluating four open-vocabulary detectors -- YOLO World, SAM3, Grounding DINO, and OWLv2 -- for cowpea flower and pod detection across synthetic and real field imagery. We decompose prompts into eight axes and conduct one-factor-at-a-time analysis followed by combinatorial optimization, revealing that models respond divergently to prompt structure: conditions that optimize one architecture can collapse another. Applying model-specific combinatorial prompts yields substantial gains over a naive species-name baseline, including +0.357 mAP@0.5 for YOLO World and +0.362 mAP@0.5 for OWLv2 on synthetic cowpea flower data. To evaluate cross-task generalization, we use an LLM to translate the discovered axis structure to a morphologically distinct target -- cowpea pods -- and compare against prompting using the discovered optimal structures from synthetic flower data. Crucially, prompt structures optimized exclusively on synthetic data transfer effectively to real-world fields: synthetic-pipeline prompts match or exceed those discovered on labeled real data for the majority of model-object combinations (flower: 0.374 vs. 0.353 for YOLO World; pod: 0.429 vs. 0.371 for SAM3). Our findings demonstrate that prompt engineering can substantially close the gap between zero-shot VFMs and supervised detectors without requiring manual annotation, and that optimal prompts are model-specific, non-obvious, and transferable across domains.

cs.CV↗

arXiv2026

A Vision Language Model for Generating Procedural Plant Architecture Representations from Simulated Images

Three-dimensional (3D) procedural plant architecture models have emerged as an important tool for simulation-based studies of plant structure and function, extracting plant architectural parameters from field measurements, and for generating realistic plants in computer graphics. However, measuring the architectural parameters and nested structures for these models at the field scales remains prohibitively labor-intensive. We present a novel algorithm that generates a 3D plant architecture from an image, creating a functional structural plant model that reflects organ-level geometric and topological parameters and provides a more comprehensive representation of the plant's architecture. Instead of using 3D sensors or processing multi-view images with computer vision to obtain the 3D structure of plants, we proposed a method that generates token sequences that encode a procedural definition of plant architecture. This work used only synthetic images for training and testing, with exact architectural parameters known, allowing testing of the hypothesis that organ-level architectural parameters could be extracted from image data using a vision-language model (VLM). A synthetic dataset of cowpea plant images was generated using the Helios 3D plant simulator, with the detailed plant architecture encoded in XML files. We developed a plant architecture tokenizer for the XML file defining plant architecture, converting it into a token sequence that a language model can predict. The model achieved a token F1 score of 0.73 during teacher-forced training. Evaluation of the model was performed through autoregressive generation, achieving a BLEU-4 score of 94.00% and a ROUGE-L score of 0.5182. This led to the conclusion that such plant architecture model generation and parameter extraction were possible from synthetic images; thus, future work will extend the approach to real imagery data.

cs.CV↗

arXiv2026

Using Vision Language Foundation Models to Generate Plant Simulation Configurations via In-Context Learning

This paper introduces a synthetic benchmark to evaluate the performance of vision language models (VLMs) in generating plant simulation configurations for digital twins. While functional-structural plant models (FSPMs) are useful tools for simulating biophysical processes in agricultural environments, their high complexity and low throughput create bottlenecks for deployment at scale. We propose a novel approach that leverages state-of-the-art open-source VLMs -- Gemma 3 and Qwen3-VL -- to directly generate simulation parameters in JSON format from drone-based remote sensing images. Using a synthetic cowpea plot dataset generated via the Helios 3D procedural plant generation library, we tested five in-context learning methods and evaluated the models across three categories: JSON integrity, geometric evaluations, and biophysical evaluations. Our results show that while VLMs can interpret structural metadata and estimate parameters like plant count and sun azimuth, they often exhibit performance degradation due to contextual bias or rely on dataset means when visual cues are insufficient. Validation on a real-world drone orthophoto dataset and an ablation study using a blind baseline further characterize the models' reasoning capabilities versus their reliance on contextual priors. To the best of our knowledge, this is the first study to utilize VLMs to generate structural JSON configurations for plant simulations, providing a scalable framework for reconstruction 3D plots for digital twin in agriculture.

cs.CV↗

arXiv2025

A generalized framework for procedural generation of three-dimensional static and dynamic plant model geometries

This work presents a new framework for procedural generation of dynamic 3D plant model geometries, which has been implemented in the Helios modeling system. Key goals of this work were to develop a model that 1) has a generalized set of parameters that are conserved across species, which are botanically-consistent and readily measurable; 2) significantly reduces the time and effort needed to create photorealistic, dynamically evolving plant models; 3) allows for encoding of the entire plant structure into a character-based representation that can integrated with machine learning models, and 4) includes realistic and computationally efficient collision physics. A model framework that satisfies these specifications is presented in this report. The model was implemented in the Helios C++ and PyHelios Python frameworks, which are open-source libraries that can be used to generate 3D plant geometries based on this model.

q-bio.OT↗

arXiv2025

Enabling Plant Phenotyping in Weedy Environments using Multi-Modal Imagery via Synthetic and Generated Training Data

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.

cs.CV↗

arXiv2025

AGILE: A Diffusion-Based Attention-Guided Image and Label Translation for Efficient Cross-Domain Plant Trait Identification

Semantically consistent cross-domain image translation facilitates the generation of training data by transferring labels across different domains, making it particularly useful for plant trait identification in agriculture. However, existing generative models struggle to maintain object-level accuracy when translating images between domains, especially when domain gaps are significant. In this work, we introduce AGILE (Attention-Guided Image and Label Translation for Efficient Cross-Domain Plant Trait Identification), a diffusion-based framework that leverages optimized text embeddings and attention guidance to semantically constrain image translation. AGILE utilizes pretrained diffusion models and publicly available agricultural datasets to improve the fidelity of translated images while preserving critical object semantics. Our approach optimizes text embeddings to strengthen the correspondence between source and target images and guides attention maps during the denoising process to control object placement. We evaluate AGILE on cross-domain plant datasets and demonstrate its effectiveness in generating semantically accurate translated images. Quantitative experiments show that AGILE enhances object detection performance in the target domain while maintaining realism and consistency. Compared to prior image translation methods, AGILE achieves superior semantic alignment, particularly in challenging cases where objects vary significantly or domain gaps are substantial.

cs.CV↗

arXiv2025

PhoTorch: A robust and generalized biochemical photosynthesis model fitting package based on PyTorch

Advancements in artificial intelligence (AI) have greatly benefited plant phenotyping and predictive modeling. However, unrealized opportunities exist in leveraging AI advancements in model parameter optimization for parameter fitting in complex biophysical models. This work developed novel software, PhoTorch, for fitting parameters of the Farquhar, von Caemmerer, and Berry (FvCB) biochemical photosynthesis model based the parameter optimization components of the popular AI framework PyTorch. The primary novelty of the software lies in its computational efficiency, robustness of parameter estimation, and flexibility in handling different types of response curves and sub-model functional forms. PhoTorch can fit both steady-state and non-steady-state gas exchange data with high efficiency and accuracy. Its flexibility allows for optional fitting of temperature and light response parameters, and can simultaneously fit light response curves and standard A/Ci curves. These features are not available within presently available A/Ci curve fitting packages. Results illustrated the robustness and efficiency of PhoTorch in fitting A/Ci curves with high variability and some level of artifacts and noise. PhoTorch is more than four times faster than benchmark software, which may be relevant when processing many non-steady-state A/Ci curves with hundreds of data points per curve. PhoTorch provides researchers from various fields with a reliable and efficient tool for analyzing photosynthetic data. The Python package is openly accessible from the repository: https://github.com/GEMINI-Breeding/photorch.

cs.CE↗

arXiv2024

Fusion-Driven Tree Reconstruction and Fruit Localization: Advancing Precision in Agriculture

Fruit distribution is pivotal in shaping the future of both agriculture and agricultural robotics, paving the way for a streamlined supply chain. This study introduces an innovative methodology that harnesses the synergy of RGB imagery, LiDAR, and IMU data, to achieve intricate tree reconstructions and the pinpoint localization of fruits. Such integration not only offers insights into the fruit distribution, which enhances the precision of guidance for agricultural robotics and automation systems, but also sets the stage for simulating synthetic fruit patterns across varied tree architectures. To validate this approach, experiments have been carried out in both a controlled environment and an actual peach orchard. The results underscore the robustness and efficacy of this fusion-driven methodology, highlighting its potential as a transformative tool for future agricultural robotics and precision farming.

cs.RO↗

arXiv2024

DAVIS-Ag: A Synthetic Plant Dataset for Prototyping Domain-Inspired Active Vision in Agricultural Robots

In agricultural environments, viewpoint planning can be a critical functionality for a robot with visual sensors to obtain informative observations of objects of interest (e.g., fruits) from complex structures of plant with random occlusions. Although recent studies on active vision have shown some potential for agricultural tasks, each model has been designed and validated on a unique environment that would not easily be replicated for benchmarking novel methods being developed later. In this paper, we introduce a dataset, so-called DAVIS-Ag, for promoting more extensive research on Domain-inspired Active VISion in Agriculture. To be specific, we leveraged our open-source "AgML" framework and 3D plant simulator of "Helios" to produce 502K RGB images from 30K densely sampled spatial locations in 632 synthetic orchards. Moreover, plant environments of strawberries, tomatoes, and grapes are considered at two different scales (i.e., Single-Plant and Multi-Plant). Useful labels are also provided for each image, including (1) bounding boxes and (2) instance segmentation masks for all identifiable fruits, and also (3) pointers to other images of the viewpoints that are reachable by an execution of action so as to simulate active viewpoint selections at each time step. Using DAVIS-Ag, we visualize motivating examples where fruit visibility can dramatically change depending on the pose of the camera view primarily due to occlusions by other components, such as leaves. Furthermore, we present several baseline models with experiment results for benchmarking in the task of target visibility maximization. Transferability to real strawberry environments is also investigated to demonstrate the feasibility of using the dataset for prototyping real-world solutions. For future research, our dataset is made publicly available online: https://github.com/ctyeong/DAVIS-Ag.

cs.RO↗

arXiv2024

VisTA-SR: Improving the Accuracy and Resolution of Low-Cost Thermal Imaging Cameras for Agriculture

Thermal cameras are an important tool for agricultural research because they allow for non-invasive measurement of plant temperature, which relates to important photochemical, hydraulic, and agronomic traits. Utilizing low-cost thermal cameras can lower the barrier to introducing thermal imaging in agricultural research and production. This paper presents an approach to improve the temperature accuracy and image quality of low-cost thermal imaging cameras for agricultural applications. Leveraging advancements in computer vision techniques, particularly deep learning networks, we propose a method, called $\textbf{VisTA-SR}$ ($\textbf{Vis}$ual \& $\textbf{T}$hermal $\textbf{A}$lignment and $\textbf{S}$uper-$\textbf{R}$esolution Enhancement) that combines RGB and thermal images to enhance the capabilities of low-resolution thermal cameras. The research includes calibration and validation of temperature measurements, acquisition of paired image datasets, and the development of a deep learning network tailored for agricultural thermal imaging. Our study addresses the challenges of image enhancement in the agricultural domain and explores the potential of low-cost thermal cameras to replace high-resolution industrial cameras. Experimental results demonstrate the effectiveness of our approach in enhancing temperature accuracy and image sharpness, paving the way for more accessible and efficient thermal imaging solutions in agriculture.

cs.CV↗

arXiv2024

A text-based, generative deep learning model for soil reflectance spectrum simulation in the VIS-NIR (400-2499 nm) bands

Simulating soil reflectance spectra is invaluable for soil-plant radiative modeling and training machine learning models, yet it is difficult as the intricate relationships between soil structure and its constituents. To address this, a fully data-driven soil optics generative model (SOGM) for simulation of soil reflectance spectra based on soil property inputs was developed. The model is trained on an extensive dataset comprising nearly 180,000 soil spectra-property pairs from 17 datasets. It generates soil reflectance spectra from text-based inputs describing soil properties and their values rather than only numerical values and labels in binary vector format. The generative model can simulate output spectra based on an incomplete set of input properties. SOGM is based on the denoising diffusion probabilistic model (DDPM). Two additional sub-models were also built to complement the SOGM: a spectral padding model that can fill in the gaps for spectra shorter than the full visible-near-infrared range (VIS-NIR; 400 to 2499 nm), and a wet soil spectra model that can estimate the effects of water content on soil reflectance spectra given the dry spectrum predicted by the SOGM. The SOGM was up-scaled by coupling with the Helios 3D plant modeling software, which allowed for generation of synthetic aerial images of simulated soil and plant scenes. It can also be easily integrated with soil-plant radiation model used for remote sensin research like PROSAIL. The testing results of the SOGM on new datasets that not included in model training proved that the model can generate reasonable soil reflectance spectra based on available property inputs. The presented models are openly accessible on: https://github.com/GEMINI-Breeding/SOGM_soil_spectra_simulation.

cs.LG↗

arXiv2023

Walnut Detection Through Deep Learning Enhanced by Multispectral Synthetic Images

The accurate identification of walnuts within orchards brings forth a plethora of advantages, profoundly amplifying the efficiency and productivity of walnut orchard management. Nevertheless, the unique characteristics of walnut trees, characterized by their closely resembling shapes, colors, and textures between the walnuts and leaves, present a formidable challenge in precisely distinguishing between them during the annotation process. In this study, we present a novel approach to improve walnut detection efficiency, utilizing YOLOv5 trained on an enriched image set that incorporates both real and synthetic RGB and NIR images. Our analysis comparing results from our original and augmented datasets shows clear improvements in detection when using the synthetic images.

cs.CV↗

arXiv2021

Enlisting 3D Crop Models and GANs for More Data Efficient and Generalizable Fruit Detection

Training real-world neural network models to achieve high performance and generalizability typically requires a substantial amount of labeled data, spanning a broad range of variation. This data-labeling process can be both labor and cost intensive. To achieve desirable predictive performance, a trained model is typically applied into a domain where the data distribution is similar to the training dataset. However, for many agricultural machine learning problems, training datasets are collected at a specific location, during a specific period in time of the growing season. Since agricultural systems exhibit substantial variability in terms of crop type, cultivar, management, seasonal growth dynamics, lighting condition, sensor type, etc, a model trained from one dataset often does not generalize well across domains. To enable more data efficient and generalizable neural network models in agriculture, we propose a method that generates photorealistic agricultural images from a synthetic 3D crop model domain into real world crop domains. The method uses a semantically constrained GAN (generative adversarial network) to preserve the fruit position and geometry. We observe that a baseline CycleGAN method generates visually realistic target domain images but does not preserve fruit position information while our method maintains fruit positions well. Image generation results in vineyard grape day and night images show the visual outputs of our network are much better compared to a baseline network. Incremental training experiments in vineyard grape detection tasks show that the images generated from our method can significantly speed the domain adaption process, increase performance for a given number of labeled images (i.e. data efficiency), and decrease labeling requirements.

cs.CV↗