Text-conditioned Segmentation for Tomato Phenotyping via Procedural Synthetic Data
Authors: Samy Mounir, Mikolaj Cieslak, Najmeddine Dhieb, Hakim Ghazzai, Jonathan Klein, Katja Froehlich, Soeren Pirk, Wojciech Palubicki, +3 more
Organizations: Computer, Electrical and Mathematical Sciences and Engineering Division, KAUST, KSA · Department of Computer Science, University of Calgary, Canada · Department of Computer Science, Kiel University, Germany · Department of Artificial Intelligence, Adam Mickiewicz University, Poland · Department of Electronics and Telecommunications, Polytechnic University of Turin, Italy
Abstract
Vision-based automation is an excellent candidate for reducing manual labor in greenhouse crop production and phenotyping. However, progress is constrained by the lack of annotated training data. Recent advances in vision-based foundational models have shown promising results in zero-shot generalization to novel domains, but their performance drops in complex agricultural environments. In this work, we present a sim-to-real framework for tomato plant segmentation that combines synthetic data generation with fine-tuning of a foundation model. We model a commercial cherry tomato greenhouse and use it to generate a large-scale synthetic dataset under diverse viewpoints, lighting conditions, and plant morphology. Subsequently, we fine-tune the Segment Anything Model 3 (SAM 3) on the synthetic dataset, specializing its text-conditioned segmentation behavior for greenhouse crop organs while retaining the general visual prior that makes zero-shot transfer possible. By evaluating our framework on multiple real-world greenhouse datasets, we demonstrate that combining synthetic data with SAM 3 fine-tuning significantly improves segmentation performance and model confidence. To support community benchmarking, we publicly release the procedural model, the generated synthetic dataset, and our fine-tuned SAM 3 weights.
Driven by rapid advances in large-scale generative models, synthetic data has emerged as a promising solution for visual understanding. While modern diffusion models achieve remarkable photorealistic image synthesis, their potential in complex visual segmentation tasks remains underexplored. In this work, we conduct a systematic analysis of synthetic images from state-of-the-art diffusion models to uncover the factors governing their utility. In particular, synthetic images characterized by dense scene composition and fine instance fidelity demonstrate distinctive benefits, yielding significantly more discriminative spatial representations. Building on these insights, we propose SENSE, a unified framework that leverages flexible and scalable synthetic data to substantially enhance segmentation performance. Notably, SENSE is model-agnostic, compatible with diverse architectures (e.g., DPT and Mask2Former), and scales effectively across models with varying parameter capacities. Extensive experiments on Cityscapes, COCO, and ADE20K validate the effectiveness and generalization capability of our approach. Code is available at https://github.com/zhang0jhon/SENSE.
In this manuscript we release two datasets for visual sensing of tomato plants grown in commercial-like settings and acquired using a robot. The first is BUTom21 which consists of still images and manual annotations. The second is BUTom-ST21 which consists of video-based data and semi-automated annotations through AI-based methods, referred to as pseudo-labels. In both cases, we provide pixel-level labels for the ripeness of the fruit. The aim is to provide the research community a challenging set of real-world imagery to explore methods to sense and estimate the state of tomato plants and their fruit, which is an important horticultural crop. Importantly, the spatial-temporal dataset provides individual fruit count and ripeness information enabling researchers to push the boundaries of field-based phenotyping.
Accurate 3D plant organ segmentation is fundamental to automated phenotyping. Existing approaches rely on annotated training data or species-specific model configurations. We present an annotation-free pipeline for 3D plant organ segmentation, combining text-prompted SAM3 segmentation with semantic neural radiance fields (NeRFs). Given only multi-view RGB images and a list of class names, our zero-shot pipeline produces semantically labeled 3D point clouds without manual annotation, per-species fine-tuning, or domain-specific preprocessing. Multi-view NeRF fusion acts as effective implicit consensus mechanism that lifts imperfect per-frame masks into accurate 3D labels. On a controlled Begonia maculata testbed the SAM3 pipeline achieves 92.6% mIoU, reaching 95.9% of the oracle upper bound established with perfect ground-truth masks. The pipeline was further evaluated on a new dataset spanning ten diverse plant point clouds reaching an average 0.856 mIoU, with leaf and pot IoU above 0.91 and 0.90 for every species, respectively. These results demonstrate that annotation-free 3D plant organ segmentation is now feasible and approaching the range of supervised methods.