Plant Phenotyping

Cluster closure, defined as the progressive filling of gaps between the berries in a grape bunch, is a key trait in vineyard management, impacting disease risk. However, traditional visual scoring methods are labor-intensive, subjective, and lack temporal resolution. Existing datasets rarely support fine-grained berry-level analysis, limiting the development of robust deep learning models. In this work, we present ViViD-5k, a large-scale in-field Vineyard Vision Dataset containing 5,000 images with dense annotations, including over 648,000 berry centroids and cluster segmentation masks spanning 13 grape varieties. Building on this dataset, we introduce GrapeSAM, a two-stage visual pipeline that combines point-based berry localization with prompt-based segmentation using Segment Anything, followed by transformer-based cluster segmentation. The pipeline enables automated, in-field estimation of cluster closure with minimal supervision. Quantitative results demonstrate strong segmentation and counting accuracy across diverse conditions, while visualizations confirm robustness on both in-domain and out-of-domain samples. This work provides a scalable and objective alternative to manual compactness scoring and supports high-throughput grape phenotyping with enhanced spatial detail.

Accurate estimation of wheat spike volume is important for yield component analysis and stress resilience assessment, yet field-based measurement remains challenging. Active 3D sensing methods such as Light Detection and Ranging (LiDAR) or time-of-flight (ToF) are sensitive to plant motion or poorly suited to outdoor conditions, while 3D reconstructions are computationally expensive. Direct 2D image processing would offer computational advantages, but image-based models lack explicit geometric information. We therefore propose a hybrid 2D-3D approach with knowledge distillation during training while enabling efficient image-only inference. First, we train a rigid-invariant point cloud network using distance-based histogram features to obtain pose-robust geometric representations. We then combine the 3D model with a proposed multi-view image-based regulated Transformer (RT) in an ensemble architecture. Finally, we distill the ensemble knowledge into a purely image-based student model using either feature-based or label-based distillation. The two distilled RTs reduce the mean absolute error (MAE) from 654.31 mm$^3$ of the non-distilled RT to 639.93 mm$^3$ and 644.62 mm$^3$, and increase correlation from 0.76 to 0.77 and 0.82, respectively. At the same time, inference time is reduced from 160 ms to 1.4 ms per spike. Distillation further mitigates volume-dependent bias and reshapes the latent representation of the image model toward a geometry-aware shape. Our results demonstrate that 3D-informed training of a 2D Transformer allows for scalable and efficient spike volume estimation for high-throughput field phenotyping.

High-dimensional biological data often exhibit a severe mismatch between feature dimensionality and sample size, making reliable classification difficult in extremely small-data regimes. In these settings, kernel methods can lose discriminative power when latent compression fails to preserve class-separating structure. We study this problem in fine-grained plant phenomics and propose a hybrid workflow that compresses 1280-dimensional deep image embeddings into a 64-dimensional PCA space and then restructures them into an 11-dimensional supervised latent space using Linear Discriminant Analysis (LDA), followed by GPU-accelerated Quantum Kernel Alignment (QKA) on NVIDIA L40S hardware. Empirically, supervised latent restructuring substantially improves the geometric separability of the compressed representation, increasing the Silhouette coefficient from 0.003 in the raw embedding space and -0.006 in PCA-64 to 0.197 in the supervised LDA-11 space. However, downstream classical evaluation reveals a clear compression trade-off: Linear SVM and XGBoost improve in the restructured latent space, whereas RBF-SVM and Random Forest degrade under the same 11-dimensional bottleneck. Under a constrained optimization budget, QKA in this regime remains challenging, indicating that latent geometry alone is not sufficient for strong trainable quantum performance. These findings position representation geometry as a central design variable in small-data quantum learning and expose the practical difficulty of recovering nonlinear discriminative structure from aggressively compressed biological representations.

Accurate estimation of plant skeletal structures (e.g., branching structures) from images is essential for smart agriculture and plant science. Unlike human skeletons with fixed topology, plant skeleton estimation presents a unique challenge, i.e., estimating arbitrary tree graphs from images. To address this problem, we introduce PlantPose, a universal plant skeleton estimator via tree-constrained graph generation. PlantPose combines learning-based graph generation with traditional graph algorithms to enforce tree constraints during the training loop. To enhance the model's generalization capability, we curate a large and diverse dataset comprising real-world and synthetic plant images, along with simplified representations (e.g., sketches and abstract drawings). This dataset enables the generalized model to adapt to diverse input styles and categories of plant images while preserving topological consistency. Our approach demonstrates robust and accurate plant skeleton estimation across multiple domains, including previously unseen out-of-domain scenarios. Further analyses highlight the method's strengths and limitations in handling complex, heterogeneous data distributions. All implementations and datasets are available at https://github.com/huntorochi/PlantPose/.

High-throughput plant phenotyping, the quantitative measurement of observable plant traits, is critical for modern breeding but remains constrained by a "phenotyping bottleneck," where manual data collection is labor-intensive and prone to observer bias. Conventional closed-set computer vision systems fail to address this challenge, as they require extensive species-specific annotation and lack the flexibility to handle diverse breeding populations. To bridge this gap, we present CropVLM, a Vision-Language Model (VLM) adapted for the agricultural domain via Domain-Specific Semantic Alignment (DSSA). Trained on 52,987 manually selected image-caption pairs covering 37 species in natural field conditions, CropVLM effectively maps agronomic terminology to fine-grained visual features. We further introduce the Hybrid Open-Set Localization Network (HOS-Net), an architecture that integrates CropVLM to enable the detection of novel crops solely from natural language descriptions without retraining. By eliminating the reliance on species-specific training data, CropVLM provides a scalable solution for high-throughput phenotyping, accelerating genetic gain and facilitating large-scale biodiversity research essential for sustainable agriculture. The trained model weights and complete pipeline implementation are publicly available at: https://github.com/boudiafA/CropVLM. In comprehensive evaluations, CropVLM achieves 72.51% zero-shot classification accuracy, outperforming seven CLIP-style baselines. Our detection pipeline demonstrates superior zero-shot generalization to novel species, achieving 49.17 AP50 on our CVTCropDet benchmark and 50.73 AP50 on tropical fruit species, compared to 34.89 and 48.58 for the next-best method, respectively.

Stomata play a crucial role in regulating plant physiological processes and reflecting environmental responses. However, accurate and high-throughput stomatal phenotyping remains challenging, as conventional approaches rely on destructive sampling and manual annotation, restricting large-scale and field deployment. To overcome these limitations, a noninvasive restoration-detection integrated framework, termed StomaD2, is developed to achieve accurate and fast stomatal phenotyping under complex imaging conditions. The framework incorporates a diffusion-based restoration module to recover degraded images and a specialized rotated object detection network tailored to the small, dense, and cluttered characteristics of stomata. The proposed network enhances feature representation through three key innovations: a column-wise structure for global feature interaction, context-aware resampling and reweighting mechanism to improve multi-scale consistency, and a feature reassembly module to boost discrimination against complex backgrounds. In extensive comparisons, StomaD2 demonstrated state-of-the-art performance. On public Maize and Wheat datasets, it achieved accuracies of 0.994 and 0.992, respectively, significantly outperforming existing benchmarks. When benchmarked against ten other advanced models, including Oriented Former and YOLOv12, StomaD2 achieved a top-tier F1-score/mAP of 0.989. The framework is integrated into a user-friendly, field-operable system that supports the fast extraction of eight stomatal phenotypes, such as density and conductance. Validated on more than 130 plant species, StomaD2's results highlight its strong generalizability and potential for large-scale phenotyping, plant physiology analysis, and precision agriculture applications.

Image-based plant phenotyping depends on dense structural understanding of crops, yet pixel-level annotation remains expensive across species, organs, growth stages, and field conditions. General-purpose vision foundation models offer a natural route to label efficiency, but their web-scale pretraining objectives transfer weakly to agricultural imagery, where semantics are often determined by fine organ geometry inside repetitive, texture-dominated scenes. We introduce SPROUT, a diffusion foundation model for multi-crop plant phenotyping. SPROUT learns from 2.6 million unlabeled open-field images (MCD-2.6M) using a pixel-space Diffusion Transformer, and selects transferable features with a label-free effective-rank criterion over denoising timesteps. This design shifts pretraining from crop-based invariance to structure-preserving denoising, making the representation better aligned with dense phenotyping tasks. We evaluate SPROUT across dense phenotyping tasks, including organ segmentation, crop-weed parsing, depth estimation, and counting. SPROUT consistently improves over strong web-pretrained baselines, with the largest gains on dense structural prediction, and shows favorable label and compute efficiency compared with general-purpose and crop-specific foundation models. The source code and MCD-2.6M dataset are publicly available.

This paper introduces a benchmark for evaluating whether vision-language models (VLMs) can generate plant simulation configurations from imagery using in-context learning. We study this benchmark for cowpea plot reconstruction for plant simulations, where the VLM needs to generate structured JSON configurations that include field and plant information. Open-source multimodal models from Gemma 4 and Qwen3.5 families are evaluated on a synthetic cowpea dataset with known JSON ground truth and on a real drone orthophoto dataset with field-collected JSON. Five in-context learning methods are used, from format restriction instruction to few-shot image examples with auxiliary grounding information. The results show that VLMs can generate valid JSON outputs, can generally estimate days after planting (DAP), plant counts, plant locations, sun angles, and leaf chlorophyll content, and can render approximate simulations of cowpea plots. Error metrics fluctuate across model families and often remain worse than dataset baselines, particularly when VLMs' pretrained knowledge dominates over weak visual evidence. These results position image-to-simulation JSON generation as a promising but currently challenging task, and establish a benchmark for studying how multimodal reasoning, prompt design, and the sim-to-real domain gap affect plant phenotyping tasks.

High-resolution phenotyping at the level of individual leaves offers fine-grained insights into plant development and stress responses. However, the full potential of accurate leaf tracking over time remains largely unexplored due to the absence of robust tracking methods, particularly for structurally complex crops such as canola. Existing plant-specific tracking methods are typically limited to small-scale species or rely on constrained imaging conditions. In contrast, generic multi-object tracking (MOT) methods are not designed for dynamic biological scenes. Progress in the development of accurate leaf tracking models has also been hindered by a lack of large-scale datasets captured under realistic conditions. In this work, we introduce CanolaTrack, a new benchmark dataset comprising 5704 RGB images with 31,840 annotated leaf instances collected from 184 canola plants during their early growth stages. To enable accurate leaf tracking over time, we introduce LeafTrackNet, an efficient framework that combines a YOLOv10-based leaf detector with a MobileNetV3-based embedding network. During inference, leaf identities are maintained over time through an embedding-based memory association strategy. When trained directly on each target dataset without prior CanolaTrack fine-tuning, LeafTrackNet achieves HOTA scores of 88.03, 87.33, and 74.20 on CanolaTrack, KOMATSUNA, and MSU-PID, respectively, outperforming the corresponding second-best methods by 8.35, 4.94, and 1.62 HOTA points. This work provides a new benchmark for leaf-level tracking under realistic conditions and introduces CanolaTrack, which, to the best of our knowledge, is the largest leaf-tracking dataset for agricultural crops. Our code and dataset are publicly available at GitHub.