Evaluating Vision Foundation Models for Pixel and Object Classification in Microscopy

Cell segmentation is critical for computational pathology and biomedical discovery. While recent Vision Foundation Models (VFMs) have demonstrated remarkable universal feature representations, unlocking their full potential for cellular imaging is currently bottlenecked by resource-intensive adaptation paradigms. Existing methods typically rely on fine-tuning heavy visual encoders, leading to extensive computational overhead and a dependency on large-scale annotations. To address this, we propose the EffiCell-Seg framework for highly efficient cell segmentation without re-training the visual encoder. Our core insight is that pretrained VFMs intrinsically encode complementary structural priors: global saliency for localizing potential cells, and local morphological patterns for delineating cellular structures. To harness these priors, we devise a Cell Structure Prompt Encoder (CSP-Encoder) that synthesizes semantic-aware saliency and principal morphological features from frozen VFM representations into explicit structural prior maps. Moreover, we propose a Synergistic Mask Decoder (SM-Decoder) that enforces contextual consistency by jointly predicting geometric distance fields and semantic maps via mutual cross-guidance. Extensive experiments demonstrate that EffiCell-Seg outperforms state-of-the-art methods across diverse cell imaging modalities while requiring only ~5M trainable parameters, over 130x fewer than fully fine-tuned VFM counterparts. The code is available at https://github.com/xq141839/EffiCell-Seg.

Vision foundation models have substantially advanced computer vision, enabling state-of-the-art performance in zero- and few-shot settings. They have been successfully applied to biomedical imaging tasks ranging from organ segmentation in computed tomography to cell segmentation in light microscopy. Electron microscopy (EM) is a central modality for analyzing cellular ultrastructure due to its nanometer-scale resolution. However, the application of foundation models in EM has so far been limited to specific organelles, such as mitochondria, largely due to the diversity of segmentation tasks and the scarcity of comprehensively annotated data. As a result, EM segmentation still predominantly relies on supervised learning, requiring extensive manual annotation and limiting ultrastructural analysis. To address this gap, we propose $μ$Match, a framework for semi-supervised learning and domain adaptation that leverages foundation models. We implement state-of-the-art student-teacher-based methods and evaluate multiple foundation models (SAM, SAM2, $μ$SAM, DINOv2/v3) on challenging EM tasks, including mitochondrion, nucleus, and neurite segmentation. Our results demonstrate consistent improvements over strong baselines and highlight a path toward substantially reducing the annotation effort in EM.

Although large-scale visual foundation models (VFMs) achieve remarkable performance in semantic understanding, they still underperform in instance-aware dense prediction tasks. They exhibit different biases in representation: for instance, promptable segmentation models (e.g., SAM2) focus on fine-grained region boundaries, while self-supervised models (e.g., DINOv3) emphasize object-level structure. This observation highlights the potential of combining complementary features from different VFMs to enhance downstream dense prediction tasks. However, naive multi-VFM fusion seldom leads to reliable gains, and interpretable principles for leveraging their complementary features are still underexplored. In this work, we propose a metric-guided approach that effectively selects and aggregates complementary features from different VFMs based on explicit assessment scores. Specifically, we design a suite of label-free metrics in feature space across two aspects, Structural Coherence and Edge Fidelity, to assess features of VFM encoders. Guided by these scores, we identify complementary edge-strong and structure-strong encoder pairs, and integrate them via a master-auxiliary fusion scheme. This feature fusion requires no complex architectural changes and is trained only in a single stage. Our model shows consistent performance gains across multiple dense prediction tasks compared with the baselines, with better object-level semantics and more accurately localized boundaries. The code is available at {https://github.com/gyc-code/metric-guided-fusion}.