{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T11:43:10Z","timestamp":1753875790326,"version":"3.41.2"},"reference-count":43,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2024,8,12]],"date-time":"2024-08-12T00:00:00Z","timestamp":1723420800000},"content-version":"vor","delay-in-days":18,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Swiss Federal Institutes of Technology"},{"DOI":"10.13039\/501100004052","name":"King Abdullah University of Science and Technology","doi-asserted-by":"publisher","award":["OSR-2017-CRG6-3438"],"award-info":[{"award-number":["OSR-2017-CRG6-3438"]}],"id":[{"id":"10.13039\/501100004052","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,7,25]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Understanding the intracellular dynamics of brain cells entails performing three-dimensional molecular simulations incorporating ultrastructural models that can capture cellular membrane geometries at nanometer scales. While there is an abundance of neuronal morphologies available online, e.g. from NeuroMorpho.Org, converting those fairly abstract point-and-diameter representations into geometrically realistic and simulation-ready, i.e. watertight, manifolds is challenging. Many neuronal mesh reconstruction methods have been proposed; however, their resulting meshes are either biologically unplausible or non-watertight. We present an effective and unconditionally robust method capable of generating geometrically realistic and watertight surface manifolds of spiny cortical neurons from their morphological descriptions. The robustness of our method is assessed based on a mixed dataset of cortical neurons with a wide variety of morphological classes. The implementation is seamlessly extended and applied to synthetic astrocytic morphologies that are also plausibly biological in detail. Resulting meshes are ultimately used to create volumetric meshes with tetrahedral domains to perform scalable in silico reaction-diffusion simulations for revealing cellular structure\u2013function relationships. Availability and implementation: Our method is implemented in NeuroMorphoVis, a neuroscience-specific open source Blender add-on, making it freely accessible for neuroscience researchers.<\/jats:p>","DOI":"10.1093\/bib\/bbae393","type":"journal-article","created":{"date-parts":[[2024,8,12]],"date-time":"2024-08-12T05:29:22Z","timestamp":1723440562000},"source":"Crossref","is-referenced-by-count":0,"title":["Synthesis of geometrically realistic and watertight neuronal ultrastructure manifolds for <i>in silico<\/i> modeling"],"prefix":"10.1093","volume":"25","author":[{"given":"Marwan","family":"Abdellah","sequence":"first","affiliation":[{"name":"Blue Brain Project , \u00c9cole Polytecnique F\u00e9d\u00e9rale de Lausanne (EPFL), Campus Biotech, Chemin des Mines 9, Gen\u00e8ve 1202, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alessandro","family":"Foni","sequence":"additional","affiliation":[{"name":"Blue Brain Project , \u00c9cole Polytecnique F\u00e9d\u00e9rale de Lausanne (EPFL), Campus Biotech, Chemin des Mines 9, Gen\u00e8ve 1202, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Juan Jos\u00e9 Garc\u00eda","family":"Cantero","sequence":"additional","affiliation":[{"name":"Blue Brain Project , \u00c9cole Polytecnique F\u00e9d\u00e9rale de Lausanne (EPFL), Campus Biotech, Chemin des Mines 9, Gen\u00e8ve 1202, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nadir Rom\u00e1n","family":"Guerrero","sequence":"additional","affiliation":[{"name":"Blue Brain Project , \u00c9cole Polytecnique F\u00e9d\u00e9rale de Lausanne (EPFL), Campus Biotech, Chemin des Mines 9, Gen\u00e8ve 1202, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Elvis","family":"Boci","sequence":"additional","affiliation":[{"name":"Blue Brain Project , \u00c9cole Polytecnique F\u00e9d\u00e9rale de Lausanne (EPFL), Campus Biotech, Chemin des Mines 9, Gen\u00e8ve 1202, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Adrien","family":"Fleury","sequence":"additional","affiliation":[{"name":"Blue Brain Project , \u00c9cole Polytecnique F\u00e9d\u00e9rale de Lausanne (EPFL), Campus Biotech, Chemin des Mines 9, Gen\u00e8ve 1202, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jay S","family":"Coggan","sequence":"additional","affiliation":[{"name":"Blue Brain Project , \u00c9cole Polytecnique F\u00e9d\u00e9rale de Lausanne (EPFL), Campus Biotech, Chemin des Mines 9, Gen\u00e8ve 1202, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Daniel","family":"Keller","sequence":"additional","affiliation":[{"name":"Blue Brain Project , \u00c9cole Polytecnique F\u00e9d\u00e9rale de Lausanne (EPFL), Campus Biotech, Chemin des Mines 9, Gen\u00e8ve 1202, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Judit","family":"Planas","sequence":"additional","affiliation":[{"name":"Blue Brain Project , \u00c9cole Polytecnique F\u00e9d\u00e9rale de Lausanne (EPFL), Campus Biotech, Chemin des Mines 9, Gen\u00e8ve 1202, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jean-Denis","family":"Courcol","sequence":"additional","affiliation":[{"name":"Blue Brain Project , \u00c9cole Polytecnique F\u00e9d\u00e9rale de Lausanne (EPFL), Campus Biotech, Chemin des Mines 9, Gen\u00e8ve 1202, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Georges","family":"Khazen","sequence":"additional","affiliation":[{"name":"Blue Brain Project , \u00c9cole Polytecnique F\u00e9d\u00e9rale de Lausanne (EPFL), Campus Biotech, Chemin des Mines 9, Gen\u00e8ve 1202, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2024,8,12]]},"reference":[{"key":"2024081205275225500_ref1","doi-asserted-by":"crossref","first-page":"e2045","DOI":"10.1371\/journal.pone.0002045","article-title":"Calmodulin activation by calcium transients in the postsynaptic density of dendritic spines","volume":"3","author":"Keller","year":"2008","journal-title":"PloS One"},{"key":"2024081205275225500_ref2","doi-asserted-by":"crossref","first-page":"777","DOI":"10.1016\/j.tins.2022.06.007","article-title":"The quest for multiscale brain modeling","volume":"45","author":"D\u2019Angelo","year":"2022","journal-title":"Trends Neurosci"},{"key":"2024081205275225500_ref3","doi-asserted-by":"crossref","first-page":"527","DOI":"10.1038\/nature05127","article-title":"From in vivo to in silico biology and back","volume":"443","author":"Di 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