MicroscopyMatching: Towards a Ready-to-use Framework for Microscopy Image Analysis in Diverse Conditions
Authors: Xiaofei Hui, Haoxuan Qu, Hossein Rahmani, Shuohong Wang, Jeff W. Lichtman, Jun Liu
Organizations: School of Computing and Communications, Lancaster University, Lancaster, LA1 4WA, UK. · Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA. · Department of Molecular and Cellular Biology, Center for Brain Science, Harvard University, Cambridge, MA 02138, USA.
Abstract
Analyzing microscopy images to extract biological object properties (e.g., their morphological organization, temporal dynamics, and population density) is fundamental to various biomedical research. Yet conducting this manually is costly and time-consuming. Though deep learning-based approaches have been explored to automate this process, the substantial diversity of microscopy analysis settings in practice (including variations of biological object types, sample processing protocols, imaging equipment, and analysis tasks, etc.) often renders them ineffective. As a result, these approaches typically require extensive adaptation for different settings, which, however, can impose burdens that are often practically unsustainable for laboratories, forcing biomedical researchers to still commonly rely on manual analysis, thereby severely bottlenecking the pace of biomedical research progress. This situation has created a pressing and long-standing need for a reliable and broadly applicable microscopy image analysis tool, yet such a tool is still missing. To address this gap, we present the first ready-to-use microscopy image analysis framework, MicroscopyMatching, that can reliably perform key analysis tasks (including segmentation, tracking, and counting) across diverse microscopy analysis settings. From a fundamentally different perspective, MicroscopyMatching reformulates diverse microscopy image analysis tasks as a unified matching problem, effectively handling this problem by exploiting the robust matching capability from pre-trained latent diffusion models.
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 (μSAM, 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.
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 μMatch, 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, μSAM, 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.
High-throughput microfluidic live-cell imaging generates rich single-cell data. Yet semi-automated procedures for locating regions of interest (RoIs), each containing one cell population, and removing surrounding microfluidic structures from recorded images, scale with the number of RoIs. This prevents real-time image analysis and delays time-to-insight by hours to days. We introduce the Design-Aware and Real-Time capable (DART) paradigm for microfluidic cultivation chips, which aligns the CAD blueprint with the physical chip and thereby enables throughput-independent localization of all RoIs and fully automated image processing across diverse RoI geometries and chip layouts. DART establishes this alignment through embedded fiducial markers and deep-learning-based marker detection. We validate DART using the Swiss Army Knife chip, which combines eight structurally distinct RoI designs across 1164 RoI locations. DART localizes all RoIs in five minutes, removes microfluidic structures from raw microscopy images in 40 ms, and performs fully automated image analysis, including cell segmentation, in under 1.1 s per image. Together, these capabilities establish DART as an end-to-end hardware-software paradigm with real-time-capable analysis that paves the way toward closed-loop and outcome-driven smart microscopy.
Johannes Seiffarth, Matthias Pesch, Lukas Scholtes +3