{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,9,12]],"date-time":"2024-09-12T17:59:06Z","timestamp":1726163946168},"reference-count":102,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2022,11,28]],"date-time":"2022-11-28T00:00:00Z","timestamp":1669593600000},"content-version":"vor","delay-in-days":2,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004052","name":"King Abdullah University of Science and Technology","doi-asserted-by":"publisher","award":["OSR-2017-CRG6-3438"],"id":[{"id":"10.13039\/501100004052","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001703","name":"Swiss Federal Institute of Technology Lausanne","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001703","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,1,19]]},"abstract":"Abstract<\/jats:title>\n \n \u00a0<\/jats:title>\n Ultraliser is a neuroscience-specific software framework capable of creating accurate and biologically realistic 3D models of complex neuroscientific structures at intracellular (e.g. mitochondria and endoplasmic reticula), cellular (e.g. neurons and glia) and even multicellular scales of resolution (e.g. cerebral vasculature and minicolumns). Resulting models are exported as triangulated surface meshes and annotated volumes for multiple applications in in silico neuroscience, allowing scalable supercomputer simulations that can unravel intricate cellular structure\u2013function relationships. Ultraliser implements a high-performance and unconditionally robust voxelization engine adapted to create optimized watertight surface meshes and annotated voxel grids from arbitrary non-watertight triangular soups, digitized morphological skeletons or binary volumetric masks. The framework represents a major leap forward in simulation-based neuroscience, making it possible to employ high-resolution 3D structural models for quantification of surface areas and volumes, which are of the utmost importance for cellular and system simulations. The power of Ultraliser is demonstrated with several use cases in which hundreds of models are created for potential application in diverse types of simulations. Ultraliser is publicly released under the GNU GPL3 license on GitHub (BlueBrain\/Ultraliser).<\/jats:p>\n <\/jats:sec>\n \n Significance<\/jats:title>\n There is crystal clear evidence on the impact of cell shape on its signaling mechanisms. Structural models can therefore be insightful to realize the function; the more realistic the structure can be, the further we get insights into the function. Creating realistic structural models from existing ones is challenging, particularly when needed for detailed subcellular simulations. We present Ultraliser, a neuroscience-dedicated framework capable of building these structural models with realistic and detailed cellular geometries that can be used for simulations.<\/jats:p>\n <\/jats:sec>","DOI":"10.1093\/bib\/bbac491","type":"journal-article","created":{"date-parts":[[2022,11,26]],"date-time":"2022-11-26T18:50:27Z","timestamp":1669488627000},"source":"Crossref","is-referenced-by-count":3,"title":["Ultraliser: a framework for creating multiscale, high-fidelity and geometrically realistic 3D models for in silico<\/i> neuroscience"],"prefix":"10.1093","volume":"24","author":[{"ORCID":"http:\/\/orcid.org\/0000-0002-7549-9657","authenticated-orcid":false,"given":"Marwan","family":"Abdellah","sequence":"first","affiliation":[{"name":"Blue Brain Project (BBP) \u00c9cole Polytecnique F\u00e9d\u00e9rale de Lausanne (EPFL) Geneva , Switzerland"}]},{"given":"Juan Jos\u00e9 Garc\u00eda","family":"Cantero","sequence":"additional","affiliation":[{"name":"Blue Brain Project (BBP) \u00c9cole Polytecnique F\u00e9d\u00e9rale de Lausanne (EPFL) Geneva , Switzerland"}]},{"given":"Nadir Rom\u00e1n","family":"Guerrero","sequence":"additional","affiliation":[{"name":"Blue Brain Project (BBP) \u00c9cole Polytecnique F\u00e9d\u00e9rale de Lausanne (EPFL) Geneva , Switzerland"}]},{"given":"Alessandro","family":"Foni","sequence":"additional","affiliation":[{"name":"Blue Brain Project (BBP) \u00c9cole Polytecnique F\u00e9d\u00e9rale de Lausanne (EPFL) Geneva , Switzerland"}]},{"given":"Jay S","family":"Coggan","sequence":"additional","affiliation":[{"name":"Blue Brain Project (BBP) \u00c9cole Polytecnique F\u00e9d\u00e9rale de Lausanne (EPFL) Geneva , Switzerland"}]},{"given":"Corrado","family":"Cal\u00ec","sequence":"additional","affiliation":[{"name":"Biological and Environmental Sciences and Engineering Division King Abdullah University of Science and Technology (KAUST) Thuwal , Saudi Arabia"},{"name":"Neuroscience Institute Cavalieri Ottolenghi (NICO) Orbassano , Italy"},{"name":"Department of Neuroscience, University of Torino Torino , Italy"}]},{"given":"Marco","family":"Agus","sequence":"additional","affiliation":[{"name":"Visual Computing Center King Abdullah University of Science and Technology (KAUST) Thuwal , Saudi Arabia"},{"name":"College of Science and Engineering Hamad Bin Khalifa University Doha , Qatar"}]},{"given":"Eleftherios","family":"Zisis","sequence":"additional","affiliation":[{"name":"Blue Brain Project (BBP) \u00c9cole Polytecnique F\u00e9d\u00e9rale de Lausanne (EPFL) Geneva , Switzerland"}]},{"given":"Daniel","family":"Keller","sequence":"additional","affiliation":[{"name":"Blue Brain Project (BBP) \u00c9cole Polytecnique F\u00e9d\u00e9rale de Lausanne (EPFL) Geneva , Switzerland"}]},{"given":"Markus","family":"Hadwiger","sequence":"additional","affiliation":[{"name":"Visual Computing Center King Abdullah University of Science and Technology (KAUST) Thuwal , Saudi Arabia"}]},{"given":"Pierre 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