PlantDreamer: Achieving Realistic 3D Plant Models with Diffusion-Guided Gaussian Splatting

Recent years have seen substantial improvements in the ability to generate synthetic 3D objects using AI. However, generating complex 3D objects, such as plants, remains a considerable challenge. Current generative 3D models struggle with plant generation compared to general objects, limiting their usability in plant analysis tools, which require fine detail and accurate geometry. We introduce PlantDreamer, a novel approach to 3D synthetic plant generation, which can achieve greater levels of realism for complex plant geometry and textures than available text-to-3D models. To achieve this, our new generation pipeline leverages a depth ControlNet, fine-tuned Low-Rank Adaptation and an adaptable Gaussian culling algorithm, which directly improve textural realism and geometric integrity of generated 3D plant models. Additionally, PlantDreamer enables both purely synthetic plant generation, by leveraging L-System-generated meshes, and the enhancement of real-world plant point clouds by converting them into 3D Gaussian Splats. We evaluate our approach by comparing its outputs with state-of-the-art text-to-3D models, demonstrating that PlantDreamer outperforms existing methods in producing high-fidelity synthetic plants. Our results indicate that our approach not only advances synthetic plant generation, but also facilitates the upgrading of legacy point cloud datasets, making it a valuable tool for 3D phenotyping applications.

GrowSplat: Constructing Temporal Digital Twins of Plants with Gaussian Splats

Accurate temporal reconstructions of plant growth are essential for plant phenotyping and breeding, yet remain challenging due to complex geometries, occlusions, and non-rigid deformations of plants. We present a novel framework for building temporal digital twins of plants by combining 3D Gaussian Splatting with a robust sample alignment pipeline. Our method begins by reconstructing Gaussian Splats from multi-view camera data, then leverages a two-stage registration approach: coarse alignment through feature-based matching and Fast Global Registration, followed by fine alignment with Iterative Closest Point. This pipeline yields a consistent 4D model of plant development in discrete time steps. We evaluate the approach on data from the Netherlands Plant Eco-phenotyping Center, demonstrating detailed temporal reconstructions of Sequoia and Quinoa species. Videos and Images can be seen at https://berkeleyautomation.github.io/GrowSplat/

A Survey on 3D Reconstruction Techniques in Plant Phenotyping: From Classical Methods to Neural Radiance Fields (NeRF), 3D Gaussian Splatting (3DGS), and Beyond

Plant phenotyping plays a pivotal role in understanding plant traits and their interactions with the environment, making it crucial for advancing precision agriculture and crop improvement. 3D reconstruction technologies have emerged as powerful tools for capturing detailed plant morphology and structure, offering significant potential for accurate and automated phenotyping. This paper provides a comprehensive review of the 3D reconstruction techniques for plant phenotyping, covering classical reconstruction methods, emerging Neural Radiance Fields (NeRF), and the novel 3D Gaussian Splatting (3DGS) approach. Classical methods, which often rely on high-resolution sensors, are widely adopted due to their simplicity and flexibility in representing plant structures. However, they face challenges such as data density, noise, and scalability. NeRF, a recent advancement, enables high-quality, photorealistic 3D reconstructions from sparse viewpoints, but its computational cost and applicability in outdoor environments remain areas of active research. The emerging 3DGS technique introduces a new paradigm in reconstructing plant structures by representing geometry through Gaussian primitives, offering potential benefits in both efficiency and scalability. We review the methodologies, applications, and performance of these approaches in plant phenotyping and discuss their respective strengths, limitations, and future prospects (https://github.com/JiajiaLi04/3D-Reconstruction-Plants). Through this review, we aim to provide insights into how these diverse 3D reconstruction techniques can be effectively leveraged for automated and high-throughput plant phenotyping, contributing to the next generation of agricultural technology.

PhenoAssistant: A Conversational Multi-Agent AI System for Automated Plant Phenotyping

Plant phenotyping increasingly relies on (semi-)automated image-based analysis workflows to improve its accuracy and scalability. However, many existing solutions remain overly complex, difficult to reimplement and maintain, and pose high barriers for users without substantial computational expertise. To address these challenges, we introduce PhenoAssistant: a pioneering AI-driven system that streamlines plant phenotyping via intuitive natural language interaction. PhenoAssistant leverages a large language model to orchestrate a curated toolkit supporting tasks including automated phenotype extraction, data visualisation and automated model training. We validate PhenoAssistant through several representative case studies and a set of evaluation tasks. By significantly lowering technical hurdles, PhenoAssistant underscores the promise of AI-driven methodologies to democratising AI adoption in plant biology.

A Novel WaveInst-based Network for Tree Trunk Structure Extraction and Pattern Analysis in Forest Inventory

The pattern analysis of tree structure holds significant scientific value for genetic breeding and forestry management. The current trunk and branch extraction technologies are mainly LiDAR-based or UAV-based. The former approaches obtain high-precision 3D data, but its equipment cost is high and the three-dimensional (3D) data processing is complex. The latter approaches efficiently capture canopy information, but they miss the 3-D structure of trees. In order to deal with the branch information extraction from the complex background interference and occlusion, this work proposes a novel WaveInst instance segmentation framework, involving a discrete wavelet transform, to enhance multi-scale edge information for accurately improving tree structure extraction. Experimental results of the proposed model show superior performance on SynthTree43k, CaneTree100, Urban Street and our PoplarDataset. Moreover, we present a new Phenotypic dataset PoplarDataset, which is dedicated to extract tree structure and pattern analysis from artificial forest. The proposed method achieves a mean average precision of 49.6 and 24.3 for the structure extraction of mature and juvenile trees, respectively, surpassing the existing state-of-the-art method by 9.9. Furthermore, by in tegrating the segmentation model within the regression model, we accurately achieve significant tree grown parameters, such as the location of trees, the diameter-at-breast-height of individual trees, and the plant height, from 2D images directly. This study provides a scientific and plenty of data for tree structure analysis in related to the phenotype research, offering a platform for the significant applications in precision forestry, ecological monitoring, and intelligent breeding.

A Low-Cost Photogrammetry System for 3D Plant Modeling and Phenotyping

We present an open-source, low-cost photogrammetry system for 3D plant modeling and phenotyping. The system uses a structure-from-motion approach to reconstruct 3D representations of the plants via point clouds. Using wheat as an example, we demonstrate how various phenotypic traits can be computed easily from the point clouds. These include standard measurements such as plant height and radius, as well as features that would be more cumbersome to measure by hand, such as leaf angles and convex hull. We further demonstrate the utility of the system through the investigation of specific metrics that may yield objective classifications of erectophile versus planophile wheat canopy architectures.

ChronoRoot 2.0: An Open AI-Powered Platform for 2D Temporal Plant Phenotyping

The analysis of plant developmental plasticity, including root system architecture, is fundamental to understanding plant adaptability and development, particularly in the context of climate change and agricultural sustainability. While significant advances have been made in plant phenotyping technologies, comprehensive temporal analysis of root development remains challenging, with most existing solutions providing either limited throughput or restricted structural analysis capabilities. Here, we present ChronoRoot 2.0, an integrated open-source platform that combines affordable hardware with advanced artificial intelligence to enable sophisticated temporal plant phenotyping. The system introduces several major advances, offering an integral perspective of seedling development: (i) simultaneous multi-organ tracking of six distinct plant structures, (ii) quality control through real-time validation, (iii) comprehensive architectural measurements including novel gravitropic response parameters, and (iv) dual specialized user interfaces for both architectural analysis and high-throughput screening. We demonstrate the system's capabilities through three use cases for Arabidopsis thaliana: characterization of circadian growth patterns under different light conditions, detailed analysis of gravitropic responses in transgenic plants, and high-throughput screening of etiolation responses across multiple genotypes. ChronoRoot 2.0 maintains its predecessor's advantages of low cost and modularity while significantly expanding its capabilities, making sophisticated temporal phenotyping more accessible to the broader plant science community. The system's open-source nature, combined with extensive documentation and containerized deployment options, ensures reproducibility and enables community-driven development of new analytical capabilities.

Wheat3DGS: In-field 3D Reconstruction, Instance Segmentation and Phenotyping of Wheat Heads with Gaussian Splatting

Automated extraction of plant morphological traits is crucial for supporting crop breeding and agricultural management through high-throughput field phenotyping (HTFP). Solutions based on multi-view RGB images are attractive due to their scalability and affordability, enabling volumetric measurements that 2D approaches cannot directly capture. While advanced methods like Neural Radiance Fields (NeRFs) have shown promise, their application has been limited to counting or extracting traits from only a few plants or organs. Furthermore, accurately measuring complex structures like individual wheat heads-essential for studying crop yields-remains particularly challenging due to occlusions and the dense arrangement of crop canopies in field conditions. The recent development of 3D Gaussian Splatting (3DGS) offers a promising alternative for HTFP due to its high-quality reconstructions and explicit point-based representation. In this paper, we present Wheat3DGS, a novel approach that leverages 3DGS and the Segment Anything Model (SAM) for precise 3D instance segmentation and morphological measurement of hundreds of wheat heads automatically, representing the first application of 3DGS to HTFP. We validate the accuracy of wheat head extraction against high-resolution laser scan data, obtaining per-instance mean absolute percentage errors of 15.1%, 18.3%, and 40.2% for length, width, and volume. We provide additional comparisons to NeRF-based approaches and traditional Muti-View Stereo (MVS), demonstrating superior results. Our approach enables rapid, non-destructive measurements of key yield-related traits at scale, with significant implications for accelerating crop breeding and improving our understanding of wheat development.

NeRF-based Point Cloud Reconstruction using a Stationary Camera for Agricultural Applications

This paper presents a NeRF-based framework for point cloud (PCD) reconstruction, specifically designed for indoor high-throughput plant phenotyping facilities. Traditional NeRF-based reconstruction methods require cameras to move around stationary objects, but this approach is impractical for high-throughput environments where objects are rapidly imaged while moving on conveyors or rotating pedestals. To address this limitation, we develop a variant of NeRF-based PCD reconstruction that uses a single stationary camera to capture images as the object rotates on a pedestal. Our workflow comprises COLMAP-based pose estimation, a straightforward pose transformation to simulate camera movement, and subsequent standard NeRF training. A defined Region of Interest (ROI) excludes irrelevant scene data, enabling the generation of high-resolution point clouds (10M points). Experimental results demonstrate excellent reconstruction fidelity, with precision-recall analyses yielding an F-score close to 100.00 across all evaluated plant objects. Although pose estimation remains computationally intensive with a stationary camera setup, overall training and reconstruction times are competitive, validating the method's feasibility for practical high-throughput indoor phenotyping applications. Our findings indicate that high-quality NeRF-based 3D reconstructions are achievable using a stationary camera, eliminating the need for complex camera motion or costly imaging equipment. This approach is especially beneficial when employing expensive and delicate instruments, such as hyperspectral cameras, for 3D plant phenotyping. Future work will focus on optimizing pose estimation techniques and further streamlining the methodology to facilitate seamless integration into automated, high-throughput 3D phenotyping pipelines.

Multimodal Data Integration for Sustainable Indoor Gardening: Tracking Anyplant with Time Series Foundation Model

Indoor gardening within sustainable buildings offers a transformative solution to urban food security and environmental sustainability. By 2030, urban farming, including Controlled Environment Agriculture (CEA) and vertical farming, is expected to grow at a compound annual growth rate (CAGR) of 13.2% from 2024 to 2030, according to market reports. This growth is fueled by advancements in Internet of Things (IoT) technologies, sustainable innovations such as smart growing systems, and the rising interest in green interior design. This paper presents a novel framework that integrates computer vision, machine learning (ML), and environmental sensing for the automated monitoring of plant health and growth. Unlike previous approaches, this framework combines RGB imagery, plant phenotyping data, and environmental factors such as temperature and humidity, to predict plant water stress in a controlled growth environment. The system utilizes high-resolution cameras to extract phenotypic features, such as RGB, plant area, height, and width while employing the Lag-Llama time series model to analyze and predict water stress. Experimental results demonstrate that integrating RGB, size ratios, and environmental data significantly enhances predictive accuracy, with the Fine-tuned model achieving the lowest errors (MSE = 0.420777, MAE = 0.595428) and reduced uncertainty. These findings highlight the potential of multimodal data and intelligent systems to automate plant care, optimize resource consumption, and align indoor gardening with sustainable building management practices, paving the way for resilient, green urban spaces.