Scalable In-Domain Self-Supervised Foundation Model for Dense Representation Transfer in High-Resolution Plant Imaging

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.

Automated plant recognition plays a crucial role in biodiversity monitoring and conservation, yet current approaches rely heavily on supervised learning, which is limited by the availability of expert-labeled data. Self-supervised learning (SSL) offers a scalable alternative, but existing methods and training protocols are largely designed for coarse-grained visual tasks and may not transfer well to fine-grained domains such as plant species recognition. In this work, we investigate SSL for plant image representation learning. We show that commonly used augmentations in SSL pipelines - such as Gaussian blur, grayscale conversion, and solarization - are detrimental in the context of plant images, as they remove subtle discriminative cues essential for fine-grained recognition. We instead identify alternative transformations, including affine and posterization, that are better suited to this domain. We further demonstrate that training SimDINOv2 on the iNaturalist 2021 Plantae subset yields significantly stronger representations than training on ImageNet-1K, highlighting the importance of domain-specific data for SSL. Our findings are consistent across both ViT-Base and ViT-Large architectures. Moreover, our models achieve competitive performance and sometimes outperform strong supervised baselines Pl@ntCLEF and BioCLIP on downstream plant recognition tasks in few-shot settings. Overall, our results highlight the critical importance of domain-adapted augmentation strategies and dataset selection in self-supervised learning, and provide practical guidelines for building scalable models for biodiversity monitoring.

The use of accurate vision models for crop monitoring, disease diagnosis, and plant phenotyping in agriculture is hindered by the lack of expertly annotated data, especially in developing countries. We propose A100, an agricultural vision foundation model that is pre-trained using self-supervised learning on 3 million unlabeled images from fields covering more than 100 crop species. A100 uses a hybrid CNN-Transformer backbone that fuses MBConv stages for local feature extraction with Transformer stages for global contextual representation. A100 uses pre-training with the integration of DINO self-distillation, iBOT masked patch reconstruction, and KoLeo uniformity regularization, resulting in features that are better than ImageNet-12K supervised representations for agricultural applications without any fine-tuning. By utilizing a frozen backbone, the accuracy for crop classification of A100 is 95.37%, which is +2.56% better than ImageNet-12K, and reduces the leaf count error by 10.4% on the GroMo25 phenotyping benchmark, proving that the same backbone can be used for classification and regression tasks. After full fine-tuning, the performance of A100 is 99.90% on 32-class crop identification and 99.02% on 44-class disease detection. On the difficult PlantDoc dataset, A100 outperforms all baselines, such as CvT-13 (64.89% against 63.56%). Remarkably, A100 obtains 98.01% accuracy on plant classification using just 1% of the labelled data (about 284 images per category), showing great label efficiency for use cases with limited labeling. Under an identical protocol, A100 also outperforms the publicly released agricultural foundation models FoMo4Wheat and LeafVision by more than 14 points at 1% labels. We plan to publicly release our pretrained model to allow agricultural professionals to adapt A100 for various plant analysis applications using limited annotations.