{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,29]],"date-time":"2026-10-29T07:02:47Z","timestamp":1793257367338,"version":"4.5.0"},"reference-count":46,"publisher":"Oxford University Press (OUP)","issue":"Supplement_1","license":[{"start":{"date-parts":[[2021,7,12]],"date-time":"2021-07-12T00:00:00Z","timestamp":1626048000000},"content-version":"vor","delay-in-days":11,"URL":"http:\/\/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","id":[{"id":"10.13039\/501100004052","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Office of Sponsored Research","award":["OSR-2017-CRG6-3438"],"award-info":[{"award-number":["OSR-2017-CRG6-3438"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,8,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Astrocytes, the most abundant glial cells in the mammalian brain, have an instrumental role in developing neuronal circuits. They contribute to the physical structuring of the brain, modulating synaptic activity and maintaining the blood\u2013brain barrier in addition to other significant aspects that impact brain function. Biophysically, detailed astrocytic models are key to unraveling their functional mechanisms via molecular simulations at microscopic scales. Detailed, and complete, biological reconstructions of astrocytic cells are sparse. Nonetheless, data-driven digital reconstruction of astroglial morphologies that are statistically identical to biological counterparts are becoming available. We use those synthetic morphologies to generate astrocytic meshes with realistic geometries, making it possible to perform these simulations.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We present an unconditionally robust method capable of reconstructing high fidelity polygonal meshes of astroglial cells from algorithmically-synthesized morphologies. Our method uses implicit surfaces, or metaballs, to skin the different structural components of astrocytes and then blend them in a seamless fashion. We also provide an end-to-end pipeline to produce optimized two- and three-dimensional meshes for visual analytics and simulations, respectively. The performance of our pipeline has been assessed with a group of 5000 astroglial morphologies and the geometric metrics of the resulting meshes are evaluated. The usability of the meshes is then demonstrated with different use cases.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Our metaball skinning algorithm is implemented in Blender 2.82 relying on its Python API (Application Programming Interface). To make it accessible to computational biologists and neuroscientists, the implementation has been integrated into NeuroMorphoVis, an open source and domain specific package that is primarily designed for neuronal morphology visualization and meshing.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab280","type":"journal-article","created":{"date-parts":[[2021,4,23]],"date-time":"2021-04-23T13:07:48Z","timestamp":1619183268000},"page":"i426-i433","source":"Crossref","is-referenced-by-count":12,"title":["Metaball skinning of synthetic astroglial morphologies into realistic mesh models for <i>in silico<\/i> simulations and visual analytics"],"prefix":"10.1093","volume":"37","author":[{"given":"Marwan","family":"Abdellah","sequence":"first","affiliation":[{"name":"Blue Brain Project (BBP), \u00c9cole polytechnique f\u00e9d\u00e9rale de Lausanne (EPFL) , Geneva 1202, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alessandro","family":"Foni","sequence":"additional","affiliation":[{"name":"Blue Brain Project (BBP), \u00c9cole polytechnique f\u00e9d\u00e9rale de Lausanne (EPFL) , Geneva 1202, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eleftherios","family":"Zisis","sequence":"additional","affiliation":[{"name":"Blue Brain Project (BBP), \u00c9cole polytechnique f\u00e9d\u00e9rale de Lausanne (EPFL) , Geneva 1202, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nadir Rom\u00e1n","family":"Guerrero","sequence":"additional","affiliation":[{"name":"Blue Brain Project (BBP), \u00c9cole polytechnique f\u00e9d\u00e9rale de Lausanne (EPFL) , Geneva 1202, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Samuel","family":"Lapere","sequence":"additional","affiliation":[{"name":"Blue Brain Project (BBP), \u00c9cole polytechnique f\u00e9d\u00e9rale de Lausanne (EPFL) , Geneva 1202, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jay S","family":"Coggan","sequence":"additional","affiliation":[{"name":"Blue Brain Project (BBP), \u00c9cole polytechnique f\u00e9d\u00e9rale de Lausanne (EPFL) , Geneva 1202, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel","family":"Keller","sequence":"additional","affiliation":[{"name":"Blue Brain Project (BBP), \u00c9cole polytechnique f\u00e9d\u00e9rale de Lausanne (EPFL) , Geneva 1202, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Henry","family":"Markram","sequence":"additional","affiliation":[{"name":"Blue Brain Project (BBP), \u00c9cole polytechnique f\u00e9d\u00e9rale de Lausanne (EPFL) , Geneva 1202, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Felix","family":"Sch\u00fcrmann","sequence":"additional","affiliation":[{"name":"Blue Brain Project (BBP), \u00c9cole polytechnique f\u00e9d\u00e9rale de Lausanne (EPFL) , Geneva 1202, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2021,7,12]]},"reference":[{"key":"2023062410175916400_btab280-B1","doi-asserted-by":"crossref","first-page":"402","DOI":"10.1186\/s12859-017-1788-4","article-title":"Reconstruction and visualization of large-scale volumetric models of neocortical circuits for physically-plausible in silico optical studies","volume":"18","author":"Abdellah","year":"2017","journal-title":"BMC Bioinformatics"},{"key":"2023062410175916400_btab280-B2","doi-asserted-by":"crossref","first-page":"i574","DOI":"10.1093\/bioinformatics\/bty231","article-title":"Neuromorphovis: a collaborative framework for analysis and visualization of neuronal morphology skeletons reconstructed from microscopy stacks","volume":"34","author":"Abdellah","year":"2018","journal-title":"Bioinformatics"},{"key":"2023062410175916400_btab280-B4","doi-asserted-by":"crossref","first-page":"i534","DOI":"10.1093\/bioinformatics\/btaa461","article-title":"Interactive visualization and analysis of morphological skeletons of brain vasculature networks with vessmorphovis","volume":"36","author":"Abdellah","year":"2020","journal-title":"Bioinformatics"},{"key":"2023062410175916400_btab280-B5","doi-asserted-by":"crossref","first-page":"9247","DOI":"10.1523\/JNEUROSCI.2055-07.2007","article-title":"Neuromorpho. org: a central resource for neuronal morphologies","volume":"27","author":"Ascoli","year":"2007","journal-title":"J. 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