SynapseNet: Deep learning for automatic synapse reconstruction
Electron microscopy is an important technique for the study of synaptic morphology and its relation to synaptic function. The data analysis for this task requires the segmentation of the relevant synaptic structures, such as synaptic vesicles (SV), active zones, mitochondria, presynaptic densities, synaptic ribbons, and synaptic compartments. Previous studies were predominantly based on manual segmentation, which is very time-consuming and prevented the systematic analysis of large datasets. Here, we introduce SynapseNet, a tool for the automatic segmentation and analysis of synapses in electron micrographs. It can reliably segment SVs and other synaptic structures in a wide range of electron microscopy approaches, thanks to a large annotated dataset, which we assembled, and domain adaptation functionality we developed. We demonstrated its capability for (semi-)automatic biological analysis in two applications and made it available as an easy-to-use tool to enable novel data-driven insights into synapse organization and function.
Authors
- J. Bahr (ORCID: https://orcid.org/0009-0005-1348-8839)
- Valentin Schwarze (ORCID: https://orcid.org/0000-0001-9277-0122)
- Arsen Petrović (ORCID: https://orcid.org/0000-0003-4448-4230)
- Cordelia Imig (ORCID: https://orcid.org/0000-0001-7351-8706)
- Frederieke Moschref
- Kirsten Weyand
- Susann Michanski (ORCID: https://orcid.org/0000-0001-5893-1981)
- Constantin Pape (ORCID: https://orcid.org/0000-0001-6562-7187)
- Anika Hintze (ORCID: https://orcid.org/0000-0001-8823-6672)
- Benjamin H. Cooper (ORCID: https://orcid.org/0000-0003-2374-9922)
- Rubén Fernández‐Busnadiego (ORCID: https://orcid.org/0000-0002-8366-7622)
- Silvio O. Rizzoli (ORCID: https://orcid.org/0000-0002-1667-7839)
- Tobias Moser (ORCID: https://orcid.org/0000-0001-7145-0533)
- Lydia Maus
- Nils Brose (ORCID: https://orcid.org/0000-0003-0938-8534)
- Carolin Wichmann (ORCID: https://orcid.org/0000-0001-8868-8716)
- Anwai Archit (ORCID: https://orcid.org/0009-0002-9533-8620)
- Thanh Thao (ORCID: https://orcid.org/0009-0004-2374-5803)
- Sarah Muth
- Luca Freckmann
- Sophia Mutschall
- Ines Hojas-Garcia-Plaza
Institutions
- Novo Nordisk (Denmark) (DK)
- Novo Nordisk Foundation (DK)
- Bernstein Center for Computational Neuroscience Göttingen (DE)
- Universitätsmedizin Göttingen (DE)
- European Neuroscience Institute Göttingen (DE)
- Max Planck Institute of Experimental Medicine (DE)
- Max Planck Institute for Multidisciplinary Sciences (DE)
- University of Göttingen (DE)
Publication Details
- Journal
- Molecular Biology of the Cell
- Published
- 2025-08-28
- DOI
- https://doi.org/10.1091/mbc.e24-11-0519
- Citations
- 6
- Primary Topic
- Advanced Electron Microscopy Techniques and Applications
- Type
- article
- Field-Weighted Citation Impact
- 15.29
Funders
- Universitätsmedizin Göttingen
- European Commission
- Deutsche Forschungsgemeinschaft
- European Regional Development Fund