$μ$Match: Foundation Models for Semi-supervised Learning and Domain Adaptation in EM

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.

MedicoSAM: Towards foundation models for medical image segmentation

Medical image segmentation is an important analysis task in clinical practice and research. Deep learning has massively advanced the field, but current approaches are mostly based on models trained for a specific task. Training such models or adapting them to a new condition is costly due to the need for (manually) labeled data. The emergence of vision foundation models, especially Segment Anything, offers a path to universal segmentation for medical images, overcoming these issues. Here, we study how to improve Segment Anything for medical images by comparing different finetuning strategies on a large and diverse dataset. We evaluate the finetuned models on a wide range of interactive and (automatic) semantic segmentation tasks. We find that the performance can be clearly improved for interactive segmentation. However, semantic segmentation does not benefit from pretraining on medical images. Our best model, MedicoSAM, is publicly available at https://github.com/computational-cell-analytics/medico-sam. We show that it is compatible with existing tools for data annotation and believe that it will be of great practical value.