{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,26]],"date-time":"2026-06-26T22:25:27Z","timestamp":1782512727912,"version":"3.54.5"},"reference-count":69,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2025,9,29]],"date-time":"2025-09-29T00:00:00Z","timestamp":1759104000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Neuroinform."],"abstract":"<jats:p>In recent years, advances in microscopy and the development of novel fluorescent probes have significantly improved neuronal imaging. Many neuropsychiatric disorders are characterized by alterations in neuronal arborization, neuronal loss\u2014as seen in Parkinson\u2019s disease\u2014or synaptic loss, as in Alzheimer\u2019s disease. Neurodevelopmental disorders can also impact dendritic spine morphogenesis, as observed in autism spectrum disorders and schizophrenia. In this review, we provide an overview of the various labeling and microscopy techniques available to visualize neuronal structure, including dendritic spines and synapses. Particular attention is given to available fluorescent probes, recent technological advances in super-resolution microscopy (SIM, STED, STORM, MINFLUX), and segmentation methods. Aimed at biologists, this review presents both classical segmentation approaches and recent tools based on deep learning methods, with the goal of remaining accessible to readers without programming expertise.<\/jats:p>","DOI":"10.3389\/fninf.2025.1630133","type":"journal-article","created":{"date-parts":[[2025,9,29]],"date-time":"2025-09-29T05:26:30Z","timestamp":1759123590000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":1,"title":["Super-resolution microscopy and deep learning methods: what can they bring to neuroscience: from neuron to 3D spine segmentation"],"prefix":"10.3389","volume":"19","author":[{"given":"Paul","family":"Nazac","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shengyan","family":"Xu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Victor","family":"Breton","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David","family":"Boulet","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lydia","family":"Danglot","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2025,9,29]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"12405","DOI":"10.1038\/s41598-022-16137-y","article-title":"An interactive time series image analysis software for dendritic spines","volume":"12","author":"Argun\u015fah","year":"2022","journal-title":"Sci. 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