A Vision Language Model for Generating Procedural Plant Architecture Representations from Simulated Images
Authors: Heesup Yun, Isaac Kazuo Uyehara, Ioannis Droutsas, Earl Ranario, Christine H. Diepenbrock, Brian N. Bailey, J. Mason Earles
Organizations: Biological and Agricultural Engineering, One Shields Avenue, Davis, 95616, CA, USA · Department of Plant Sciences, One Shields Avenue, Davis, 95616, CA, USA · Wageningen University & Research, P.O. Box 9101, 6700 HB Wageningen, The Netherlands · Viticulture and Enology, One Shields Avenue, Davis, 95616, CA, USA
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.
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.
Editable 3D models of field-grown crops support high-throughput phenotyping and in silico breeding trials, but building them from scanned point clouds requires organ-level segmentation and fitting. Procedural generators can turn an organ-level parameter set into an analysis-suitable 3D model, but obtaining that set requires hours of manual tuning per plant or segmentation models trained on species-specific labels. We present an automated pipeline that reconstructs procedural maize models from raw 3D point clouds without manual tuning or species-specific training data. A multimodal vision-language model (VLM) annotates leaf midlines in rendered orthographic views. Deterministic geometric algorithms back-project the annotations onto the point cloud, merge them into 3D leaves by cross-view consensus, and grow the midlines to full blades on an orientation-weighted surface graph. Measured organ parameters populate a plant descriptor for a Non-Uniform Rational B-Spline (NURBS)-based procedural model generator. Each leaf surface is then refined against its scan points by differentiable NURBS fitting. The pipeline reached a median whole-plant Chamfer distance of 5.4 mm on 100 genotypically diverse field-grown maize plants from the MaizeField3D dataset. The reconstructions were closer to the scans than those of an earlier semi-automated pipeline based on manual annotations. The pipeline recovered 1,017 of 1,023 (99.4%) curated reference leaves at an intersection-over-union of at least 0.5 without using those labels as input. These results show that VLM annotations become usable organ-level measurements when downstream geometric stages can correct them. This makes automated generation of editable 3D plant assets feasible at the scale of modern phenotyping experiments.
Mozhgan Hadadi, Talukder Z. Jubery, Adarsh Krishnamurthy +1
Autoregressive rigging models such as UniRig and SkinTokens perform well on articulated characters, but their ability to generalize to plant structures remains largely unexplored, since plant topologies exhibit highly variable, non-canonical branching patterns that challenge learned skeletal priors. We evaluate these models for plant skeletal reconstruction using synthetic L-system-generated trees and real scanned data spanning monopodial, sympodial, whorled, and vine-like archetypes. Preliminary testing showed UniRig collapsing complex branching into near-linear chains, while SkinTokens preserved topology better but over-segmented branches and produced an unstable output space, so we focused on UniRig for its greater stability. Diagnosis traced the collapse to sampling-level suppression of branch tokens, and further analysis showed the frozen mesh encoder had limited sensitivity to structural variation, pointing to a geometric bottleneck in the tokenization pipeline rather than a purely learned bias. Building on these findings, we applied multi-round fine-tuning over multiple procedurally generated synthetic datasets. Across rounds, the model progressively recovered accurate branching topology and generalized beyond branch-only structures to plants with foliage, a harder case given the zero-thickness, mesh-normal-dependent geometry of leaves. The resulting model generalized well across diverse plant forms without leaf-specific architectural changes, indicating that targeted fine-tuning can substantially close the domain gap between character-rigging priors and plant skeletal structure. As such, our work points toward a viable path for automated plant rigging across both branch topology and foliage type, even those not considered in our findings.
Nathan Hu, Yang Yang, Fumio Okura
Mathematics, UCLA, Los Angeles, CA, United States of America · Computer Science, University of Osaka, Osaka, Japan