A Multimodal 3D Foundation Model for Light Sheet Fluorescence Microscopy Enables Few-Shot Segmentation, Classification, and Deblurring

Deep learning underlies most modern approaches and tools in computer vision, including biomedical imaging. However, for interactive semantic segmentation (often called pixel classification in this context) and interactive object-level classification (object classification), feature-based shallow learning remains widely used. This is due to the diversity of data in this domain, the lack of large pretraining datasets, and the need for computational and label efficiency. In contrast, state-of-the-art tools for many other vision tasks in microscopy - most notably cellular instance segmentation - already rely on deep learning and have recently benefited substantially from vision foundation models (VFMs), particularly SAM. Here, we investigate whether VFMs can also improve pixel and object classification compared to current approaches. To this end, we evaluate several VFMs, including general-purpose models (SAM, SAM2, SAM3, DINOv3) and domain-specific ones ($μ$SAM, PathoSAM, KRONOS), in combination with shallow learning and attentive probing on five diverse and challenging datasets. Our results demonstrate consistent improvements over hand-crafted features and provide a clear pathway toward practical improvements. Furthermore, our study establishes a benchmark for VFMs in microscopy and informs future developments in this area.

Single-cell light microscopy images have become an important data source for characterizing cell phenotypes, but their complexity and heterogeneity pose challenges to high-throughput automated analysis. Existing representation learning methods mostly rely on task-oriented modeling, which is limited by specific datasets and predefined tasks, making them difficult to generalize across different cell types and microscopy modalities, and experimental conditions. Although general-purpose methods have improved the generalization ability of image representation in recent years, their limited utilization of experimental background and biological context information still poses challenges in complex phenotypic analysis. Here, we propose scMIR, a vision-language foundation model for single-cell light microscopy image representation. By synergistically combining self-supervised image reconstruction with text-guided cross-modal alignment, scMIR can simultaneously encode morphological and biological semantic information in a unified representation space. scMIR is pre-trained on 207,957 image-text pairs, covering various cell types, microscopy modalities, and perturbation conditions. scMIR outperforms existing general models and task-oriented methods as systematically evaluated on various complex tasks using 16 benchmark datasets, including cell classification, clustering, phenotype inference, and batch effect correction tasks. Furthermore, scMIR shows a strong generalization ability across various tasks without requiring task-specific fine-tuning. With its unique advantages, we envision scMIR may promote the standardization and automation of high-throughput phenotyping workflows through supporting various downstream analysis tasks.

We investigate volumetric reconstruction for compressive sensing light-sheet microscopy (CS-LSM), where fast volumetric imaging is achieved by encoding multiple axial planes into each camera exposure. To recover the underlying volume from highly multiplexed measurements, we propose a plug-and-play (PnP) framework that flexibly incorporates any user-specified denoiser into the reconstruction process. Building on a slice-based formulation, we further introduce an axial-coupled model that exploits correlations between adjacent slices to improve volumetric continuity. For efficient computation, we derive a Woodbury-based update for the data-consistency step in both the slice-based and axial-coupled formulations, and employ a Gauss-Seidel sweep for the denoising step in the axial-coupled model. Under a weakly convex regularization assumption, we establish subsequential convergence of the proposed algorithm. Experiments on synthetic and real zebrafish-heart data demonstrate that the proposed framework successfully recovers cellular structures from compressed measurements, and provide practical insights into the comparative performance of commonly used denoisers within the PnP framework under the CS-LSM setup.