Light-microscopy-based connectomic reconstruction of mammalian brain tissue

• Published in: Nature (London) Vol. 642; no. 8067; pp. 398 - 410
• Main Authors: Tavakoli, Mojtaba R., Lyudchik, Julia, Januszewski, Michał, Vistunou, Vitali, Agudelo Dueñas, Nathalie, Vorlaufer, Jakob, Sommer, Christoph, Kreuzinger, Caroline, Oliveira, Bárbara, Cenameri, Alban, Novarino, Gaia, Jain, Viren, Danzl, Johann G.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 12.06.2025
• Subjects: 13/1; 13/51; 14/19; 14/34; 14/63; 631/1647/245/2221; 631/1647/328/2238; 631/378/3920; 631/378/87; 639/624/1107/328/1978; 64/110; 64/60; Animals; Brain - anatomy & histology; Brain - cytology; Brain - diagnostic imaging; Connectome - methods; Deep Learning; Female; Humanities and Social Sciences; Hydrogels - chemistry; Male; Mice; Microscopy - methods; multidisciplinary; Neurons - cytology; Science; Science (multidisciplinary); Synapses - metabolism
• ISSN: 0028-0836; 1476-4687; 1476-4687
• DOI: 10.1038/s41586-025-08985-1

The information-processing capability of the brain’s cellular network depends on the physical wiring pattern between neurons and their molecular and functional characteristics. Mapping neurons and resolving their individual synaptic connections can be achieved by volumetric imaging at nanoscale resolution 1 , 2 with dense cellular labelling. Light microscopy is uniquely positioned to visualize specific molecules, but dense, synapse-level circuit reconstruction by light microscopy has been out of reach, owing to limitations in resolution, contrast and volumetric imaging capability. Here we describe light-microscopy-based connectomics (LICONN). We integrated specifically engineered hydrogel embedding and expansion with comprehensive deep-learning-based segmentation and analysis of connectivity, thereby directly incorporating molecular information into synapse-level reconstructions of brain tissue. LICONN will allow synapse-level phenotyping of brain tissue in biological experiments in a readily adoptable manner. A technique called LICONN (light-microscopy-based connectomics) allows mapping of brain tissue at synapse level and simultaneous measurement of molecular information, thus enabling quantification of cellular properties and multimodal analysis of brain tissue.