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

arXiv: https://arxiv.org/abs/2609.32183 · HTML: https://mlsanity.com/paper/2609.32183/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 18 of its 23 references that are in the map.
- First posted on arXiv 26 Sep 2026.

## Builds on (most cited first, 18 of 18)

- [A Simple Framework for Contrastive Learning of Visual Representations](https://mlsanity.com/paper/2002.05709/) (2020)
- [DINOv2: Learning Robust Visual Features without Supervision](https://mlsanity.com/paper/2304.07193/) (2023)
- [Momentum Contrast for Unsupervised Visual Representation Learning](https://mlsanity.com/paper/1911.05722/) (2019)
- [Masked Autoencoders Are Scalable Vision Learners](https://mlsanity.com/paper/2111.06377/) (2021)
- [Emerging Properties in Self-Supervised Vision Transformers](https://mlsanity.com/paper/2104.14294/) (2021)
- [BEiT: BERT Pre-Training of Image Transformers](https://mlsanity.com/paper/2106.08254/) (2021)
- [DINOv3](https://mlsanity.com/paper/2508.10104/) (2025)
- [iBOT: Image BERT Pre-Training with Online Tokenizer](https://mlsanity.com/paper/2111.07832/) (2021)
- [SatMAE: Pre-training Transformers for Temporal and Multi-Spectral Satellite Imagery](https://mlsanity.com/paper/2207.08051/) (2022)
- [Learning Pixel-level Semantic Affinity with Image-level Supervision for Weakly Supervised Semantic Segmentation](https://mlsanity.com/paper/1803.10464/) (2018)
- [Scale-MAE: A Scale-Aware Masked Autoencoder for Multiscale Geospatial Representation Learning](https://mlsanity.com/paper/2212.14532/) (2022)
- [Prithvi-EO-2.0: A Versatile Multi-Temporal Foundation Model for Earth Observation Applications](https://mlsanity.com/paper/2412.02732/) (2024)
- [Virchow: A Million-Slide Digital Pathology Foundation Model](https://mlsanity.com/paper/2309.07778/) (2023)
- [Vision Foundation Models in Remote Sensing: A Survey](https://mlsanity.com/paper/2408.03464/) (2024)
- [ASIGN: An Anatomy-aware Spatial Imputation Graphic Network for 3D Spatial Transcriptomics](https://mlsanity.com/paper/2412.03026/) (2024)
- [ORBIT-2: Scaling Exascale Vision Foundation Models for Weather and Climate Downscaling](https://mlsanity.com/paper/2505.04802/) (2025)
- [Evaluating Cell AI Foundation Models in Kidney Pathology with Human-in-the-Loop Enrichment](https://mlsanity.com/paper/2411.00078/) (2024)
- [DeepAndes: A Self-Supervised Vision Foundation Model for Multi-Spectral Remote Sensing Imagery of the Andes](https://mlsanity.com/paper/2504.20303/) (2025)

## Abstract (arXiv)

High-resolution plant imaging enables detailed characterization of plant morphology, but dense scientific analysis remains limited by costly pixel-level annotations, large image pixel dimensions, and substantial variation in imaging conditions. This work proposes a scalable in-domain self-supervised pretrained foundation model for high-resolution, high-pixel-dimension multi-species plant imagery. A masked autoencoder with a ViT backbone is pretrained on more than 10 million multi-view plant image tiles using distributed training. Following scalable pretraining, the learned foundation-model representations are comprehensively benchmarked across fine-grained dense prediction and coarse global feature recognition, with particular emphasis on limited supervision and realistic downstream imaging conditions. This work focuses on the domain gap of existing foundation models in dense feature representation and transfer. Through extensive experiments involving limited annotations, cross-view variation, and resolution degradation, the in-domain FM achieves a Mean Dice of 0.8686 and a Pooled Dice of 0.8959, outperforming an MAE counterpart pretrained on large-scale natural-image data by 0.0694 and 0.0613, respectively. The results further indicate that increasing pretraining scale produces consistent improvements in dense feature transfer. Overall, these findings suggest that scaling in-domain self-supervised pretraining can reduce the domain gap and improve transferable dense representations for high-pixel-dimension scientific imaging.