Plant Phenotyping

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.

3D instance segmentation for laser scanning (LiDAR) point clouds remains a challenge in many remote sensing-related domains. Successful solutions typically rely on supervised deep learning and manual annotations, and consequently focus on objects that can be well delineated through visual inspection and manual labeling of point clouds. However, for tasks with more complex and cluttered scenes, such as in-field plant phenotyping in agriculture, such approaches are often infeasible. In this study, we tackle the task of in-field wheat head instance segmentation directly from terrestrial laser scanning (TLS) point clouds. To address the problem and circumvent the need for manual annotations, we propose a novel two-stage pipeline. To obtain the initial 3D instance proposals, the first stage uses 3D-to-2D multi-view projections, the Grounded SAM pipeline for zero-shot 2D object-centric segmentation, and multi-view label fusion. The second stage uses these initial proposals as noisy pseudo-labels to train a supervised 3D panoptic-style segmentation neural network. Our results demonstrate the feasibility of the proposed approach and show performance improvementsrelative to Wheat3DGS, a recent alternative solution for in-field wheat head instance segmentation without manual 3D annotations based on multi-view RGB images and 3D Gaussian Splatting, showcasing TLS as a competitive sensing alternative. Moreover, the results show that both stages of the proposed pipeline can deliver usable 3D instance segmentation without manual annotations, indicating promising, low-effort transferability to other comparable TLS-based point cloud segmentation tasks.

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.

Plant phenology, the study of cyclical events such as leafing out, flowering, or fruiting, has wide ecological impacts but is broadly understudied, especially in the tropics. Image analysis has greatly enhanced remote phenological monitoring, yet capturing phenology at the individual level remains challenging. In this project, we deployed low-cost, animal-triggered camera traps at the Pu'u Maka'ala Natural Area Reserve in Hawaii to simultaneously document shifts in plant phenology and flora-faunal interactions. Using a combination of foundation vision models and traditional computer vision methods, we measure phenological trends from images comparable to on-the-ground observations without relying on supervised learning techniques. These temporally fine-grained phenology measurements from camera-trap images uncover trends that coarser traditional sampling fails to detect. When combined with detailed visitation data detected from images, these trends can begin to elucidate drivers of both plant phenology and animal ecology.

Modeling plant growth dynamics plays a central role in modern agricultural research. However, learning robust predictors from multi-view plant imagery remains challenging due to strong viewpoint redundancy and viewpoint-dependent appearance changes. We propose a level-aware vision language framework that jointly predicts plant age and leaf count using a single multi-task model built on CLIP embeddings. Our method aggregates rotational views into angle-invariant representations and conditions visual features on lightweight text priors encoding viewpoint level for stable prediction under incomplete or unordered inputs. On the GroMo25 benchmark, our approach reduces mean age MAE from 7.74 to 3.91 and mean leaf-count MAE from 5.52 to 3.08 compared to the GroMo baseline, corresponding to improvements of 49.5% and 44.2%, respectively. The unified formulation simplifies the pipeline by replacing the conventional dual-model setup while improving robustness to missing views. The models and code is available at: https://github.com/SimonWarmers/CLIP-MVP

Intelligent forest tree breeding has advanced plant phenotyping, yet existing research largely focuses on large-leaf agricultural crops, with limited attention to fine-grained leaf analysis of sapling trees in open-field environments. Natural scenes introduce challenges including scale variation, illumination changes, and irregular leaf morphology. To address these issues, we collected UAV RGB imagery of field-grown saplings and constructed the Poplar-leaf dataset, containing 1,202 branches and 19,876 pixel-level annotated leaf instances. To our knowledge, this is the first instance segmentation dataset specifically designed for forestry leaves in open-field conditions. We propose LeafInst, a novel segmentation framework tailored for irregular and multi-scale leaf structures. The model integrates an Asymptotic Feature Pyramid Network (AFPN) for multi-scale perception, a Dynamic Asymmetric Spatial Perception (DASP) module for irregular shape modeling, and a dual-residual Dynamic Anomalous Regression Head (DARH) with Top-down Concatenation decoder Feature Fusion (TCFU) to improve detection and segmentation performance. On Poplar-leaf, LeafInst achieves 68.4 mAP, outperforming YOLOv11 by 7.1 percent and MaskDINO by 6.5 percent. On the public PhenoBench benchmark, it reaches 52.7 box mAP, exceeding MaskDINO by 3.4 percent. Additional experiments demonstrate strong generalization and practical utility for large-scale leaf phenotyping.

Precise localization and recognition of flowers are crucial for advancing automated agriculture, particularly in plant phenotyping, crop estimation, and yield monitoring. This paper benchmarks several YOLO architectures such as YOLOv5s, YOLOv8n/s/m, and YOLOv12n for flower object detection under two annotation regimes: single-image single-bounding box (SISBB) and single-image multiple-bounding box (SIMBB). The FloralSix dataset, comprising 2,816 high-resolution photos of six different flower species, is also introduced. It is annotated for both dense (clustered) and sparse (isolated) scenarios. The models were evaluated using Precision, Recall, and Mean Average Precision (mAP) at IoU thresholds of 0.5 ([email protected]) and 0.5-0.95 ([email protected]:0.95). In SISBB, YOLOv8m (SGD) achieved the best results with Precision 0.956, Recall 0.951, [email protected] 0.978, and [email protected]:0.95 0.865, illustrating strong accuracy in detecting isolated flowers. With [email protected] 0.934 and [email protected]:0.95 0.752, YOLOv12n (SGD) outperformed the more complicated SIMBB scenario, proving robustness in dense, multi-object detection. Results show how annotation density, IoU thresholds, and model size interact: recall-optimized models perform better in crowded environments, whereas precision-oriented models perform best in sparse scenarios. In both cases, the Stochastic Gradient Descent (SGD) optimizer consistently performed better than alternatives. These density-sensitive sensors are helpful for non-destructive crop analysis, growth tracking, robotic pollination, and stress evaluation.

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.