MuRF: Unlocking the Multi-Scale Potential of Vision Foundation Models

Modern microscopy routinely produces gigapixel images that contain structures across multiple spatial scales, from fine cellular morphology to broader tissue organization. Many analysis tasks require combining these scales, yet most vision models operate at a single resolution or derive multi-scale features from one view, limiting their ability to exploit the inherently multi-resolution nature of microscopy data. We introduce MuViT, a transformer architecture built to fuse true multi-resolution observations from the same underlying image. MuViT embeds all patches into a shared world-coordinate system and extends rotary positional embeddings to these coordinates, enabling attention to integrate wide-field context with high-resolution detail within a single encoder. Across synthetic benchmarks, kidney histopathology, and high-resolution mouse-brain microscopy, MuViT delivers consistent improvements over strong ViT and CNN baselines. Multi-resolution MAE pretraining further produces scale-consistent representations that enhance downstream tasks. These results demonstrate that explicit world-coordinate modelling provides a simple yet powerful mechanism for leveraging multi-resolution information in large-scale microscopy analysis.

Recently, feature upsampling has gained increasing attention owing to its effectiveness in enhancing vision foundation models (VFMs) for pixel-level understanding tasks. Existing methods typically rely on high-resolution features from the same foundation model to achieve upsampling via self-reconstruction. However, relying solely on intra-model features forces the upsampler to overfit to the source model's inherent location misalignment and high-norm artifacts. To address this fundamental limitation, we propose DiveUp, a novel framework that breaks away from single-model dependency by introducing multi-VFM relational guidance. Instead of naive feature fusion, DiveUp leverages diverse VFMs as a panel of experts, utilizing their structural consensus to regularize the upsampler's learning process, effectively preventing the propagation of inaccurate spatial structures from the source model. To reconcile the unaligned feature spaces across different VFMs, we propose a universal relational feature representation, formulated as a local center-of-mass (COM) field, that extracts intrinsic geometric structures, enabling seamless cross-model interaction. Furthermore, we introduce a spikiness-aware selection strategy that evaluates the spatial reliability of each VFM, effectively filtering out high-norm artifacts to aggregate guidance from only the most reliable expert at each local region. DiveUp is a unified, encoder-agnostic framework; a jointly-trained model can universally upsample features from diverse VFMs without requiring per-model retraining. Extensive experiments demonstrate that DiveUp achieves state-of-the-art performance across various downstream dense prediction tasks, validating the efficacy of multi-expert relational guidance. Our code and models are available at: https://github.com/Xiaoqiong-Liu/DiveUp

Pre-trained Vision Foundation Models (VFMs) have become central to modern computer vision due to their powerful semantic representations and strong generalization ability. However, their patchified or pooled outputs are inherently low-resolution, limiting their effectiveness in tasks requiring fine-grained, pixel-level reasoning. Existing feature upsampling approaches either degrade semantic fidelity or rely on VFM-specific retraining and heavy architectures, hindering efficiency and scalability. To address these challenges, we propose RaysUp, an ultra-lightweight, task-agnostic, and VFM-agnostic feature upsampling framework that reconstructs high-resolution feature maps at arbitrary resolutions. Unlike conventional 2D interpolation or attention-based schemes, RaysUp lifts feature reconstruction into a geometry-aware ray domain. Specifically, we introduce a Spatially Decoupled Guidance Encoder for direction-aware guidance encoding, an Any-Resolution Cross-Attention mechanism for resolution-flexible reconstruction, and a novel Ray Positional Encoding (RayPE) that injects implicit 3D geometric priors via 6D Plucker ray coordinates. Finally, a Geometry-Aware Neighborhood Attention module further ensures content-adaptive bilateral aggregation while preserving geometric consistency. Extensive experiments across diverse dense prediction tasks demonstrate that RaysUp achieves state-of-the-art performance while using only 16% of the parameters of AnyUp and delivering approximately 7x faster inference. These results highlight a substantially improved accuracy-efficiency trade-off and establish RaysUp as a practical and scalable solution for universal feature upsampling. Code is available at https://github.com/MAP-RaysUp/RaysUp.