{"id":"https://openalex.org/W3014396133","doi":"https://doi.org/10.1371/journal.pcbi.1007756","title":"3D mesh processing using GAMer 2 to enable reaction-diffusion simulations in realistic cellular geometries","display_name":"3D mesh processing using GAMer 2 to enable reaction-diffusion simulations in realistic cellular geometries","publication_year":2020,"publication_date":"2020-04-06","ids":{"openalex":"https://openalex.org/W3014396133","doi":"https://doi.org/10.1371/journal.pcbi.1007756","mag":"3014396133","pmid":"https://pubmed.ncbi.nlm.nih.gov/32251448"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1007756","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1007756","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["arxiv","crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1371/journal.pcbi.1007756","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5085406263","display_name":"Christopher T. Lee","orcid":"https://orcid.org/0000-0002-0670-2308"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Christopher T. Lee","raw_affiliation_strings":["Department of Mechanical and Aerospace Engineering, University of California, San Diego, La Jolla, California, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Mechanical and Aerospace Engineering, University of California, San Diego, La Jolla, California, United States of America","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080784469","display_name":"Justin G. Laughlin","orcid":"https://orcid.org/0000-0001-8229-9760"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Justin G. Laughlin","raw_affiliation_strings":["Department of Mechanical and Aerospace Engineering, University of California, San Diego, La Jolla, California, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Mechanical and Aerospace Engineering, University of California, San Diego, La Jolla, California, United States of America","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017988202","display_name":"Nils Angliviel de La Beaumelle","orcid":"https://orcid.org/0000-0001-6052-2976"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nils Angliviel de La Beaumelle","raw_affiliation_strings":["Department of Mechanical and Aerospace Engineering, University of California, San Diego, La Jolla, California, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Mechanical and Aerospace Engineering, University of California, San Diego, La Jolla, California, United States of America","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081468273","display_name":"Rommie E. Amaro","orcid":"https://orcid.org/0000-0002-9275-9553"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rommie E. Amaro","raw_affiliation_strings":["Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, United States of America","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015837947","display_name":"J. Andrew McCammon","orcid":"https://orcid.org/0000-0003-3065-1456"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"J. Andrew McCammon","raw_affiliation_strings":["Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, United States of America","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034754633","display_name":"Ravi Ramamoorthi","orcid":"https://orcid.org/0000-0003-3993-5789"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ravi Ramamoorthi","raw_affiliation_strings":["Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California, United States of America","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080980271","display_name":"Michael Holst","orcid":"https://orcid.org/0000-0002-3064-4697"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michael Holst","raw_affiliation_strings":["Department of Mathematics, University of California, San Diego, La Jolla, California, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Mathematics, University of California, San Diego, La Jolla, California, United States of America","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5044701434","display_name":"Padmini Rangamani","orcid":"https://orcid.org/0000-0001-5953-4347"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Padmini Rangamani","raw_affiliation_strings":["Department of Mechanical and Aerospace Engineering, University of California, San Diego, La Jolla, California, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Mechanical and Aerospace Engineering, University of California, San Diego, La Jolla, California, United States of America","institution_ids":["https://openalex.org/I36258959"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5044701434"],"corresponding_institution_ids":["https://openalex.org/I36258959"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":10.1702,"has_fulltext":false,"cited_by_count":71,"citation_normalized_percentile":{"value":0.98331539,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"16","issue":"4","first_page":"e1007756","last_page":"e1007756"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.9995999932289124,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.9995999932289124,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10540","display_name":"Advanced Fluorescence Microscopy Techniques","score":0.9969000220298767,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9962999820709229,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/polygon-mesh","display_name":"Polygon mesh","score":0.8602067232131958},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.608466386795044},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.57960444688797},{"id":"https://openalex.org/keywords/volume-mesh","display_name":"Volume mesh","score":0.5376046895980835},{"id":"https://openalex.org/keywords/finite-element-method","display_name":"Finite element method","score":0.5088698863983154},{"id":"https://openalex.org/keywords/computer-graphics","display_name":"Computer graphics (images)","score":0.4268329441547394},{"id":"https://openalex.org/keywords/mesh-generation","display_name":"Mesh generation","score":0.39882275462150574},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.18432331085205078}],"concepts":[{"id":"https://openalex.org/C31487907","wikidata":"https://www.wikidata.org/wiki/Q1154597","display_name":"Polygon mesh","level":2,"score":0.8602067232131958},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.608466386795044},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.57960444688797},{"id":"https://openalex.org/C170589453","wikidata":"https://www.wikidata.org/wiki/Q7940896","display_name":"Volume mesh","level":4,"score":0.5376046895980835},{"id":"https://openalex.org/C135628077","wikidata":"https://www.wikidata.org/wiki/Q220184","display_name":"Finite element method","level":2,"score":0.5088698863983154},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","level":1,"score":0.4268329441547394},{"id":"https://openalex.org/C181145010","wikidata":"https://www.wikidata.org/wiki/Q4418033","display_name":"Mesh generation","level":3,"score":0.39882275462150574},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.18432331085205078},{"id":"https://openalex.org/C97355855","wikidata":"https://www.wikidata.org/wiki/Q11473","display_name":"Thermodynamics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003712","descriptor_name":"Dendrites","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D003712","descriptor_name":"Dendrites","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D003712","descriptor_name":"Dendrites","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D003712","descriptor_name":"Dendrites","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D003712","descriptor_name":"Dendrites","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D003712","descriptor_name":"Dendrites","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D004058","descriptor_name":"Diffusion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004058","descriptor_name":"Diffusion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004058","descriptor_name":"Diffusion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004058","descriptor_name":"Diffusion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004058","descriptor_name":"Diffusion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004058","descriptor_name":"Diffusion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013526","descriptor_name":"Surgical Mesh","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013526","descriptor_name":"Surgical Mesh","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013526","descriptor_name":"Surgical Mesh","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013526","descriptor_name":"Surgical Mesh","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013526","descriptor_name":"Surgical Mesh","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013526","descriptor_name":"Surgical Mesh","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020342","descriptor_name":"Finite Element Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020342","descriptor_name":"Finite Element Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020342","descriptor_name":"Finite Element Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020342","descriptor_name":"Finite Element Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020342","descriptor_name":"Finite Element Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020342","descriptor_name":"Finite Element Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D021621","descriptor_name":"Imaging, Three-Dimensional","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D021621","descriptor_name":"Imaging, Three-Dimensional","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D021621","descriptor_name":"Imaging, Three-Dimensional","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D021621","descriptor_name":"Imaging, Three-Dimensional","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D021621","descriptor_name":"Imaging, Three-Dimensional","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D021621","descriptor_name":"Imaging, Three-Dimensional","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":8,"locations":[{"id":"doi:10.1371/journal.pcbi.1007756","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1007756","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:32251448","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32251448","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:arXiv.org:1901.11008","is_oa":true,"landing_page_url":"http://arxiv.org/abs/1901.11008","pdf_url":"https://arxiv.org/pdf/1901.11008","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},{"id":"pmh:oai:RePEc:plo:pcbi00:1007756","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007756","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"},{"id":"pmh:oai:doaj.org/article:517c7c181edc4062a0f9f0441ddc7cdb","is_oa":true,"landing_page_url":"https://doaj.org/article/517c7c181edc4062a0f9f0441ddc7cdb","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 16, Iss 4, p e1007756 (2020)","raw_type":"article"},{"id":"pmh:oai:escholarship.org:ark:/13030/qt7b93501n","is_oa":false,"landing_page_url":"https://escholarship.org/uc/item/7b93501n","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLOS Computational Biology, vol 16, iss 4","raw_type":"article"},{"id":"pmh:oai:figshare.com:article/12088569","is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/3D_mesh_processing_using_GAMer_2_to_enable_reaction-diffusion_simulations_in_realistic_cellular_geometries/12088569","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Dataset"},{"id":"pmh:oai:pubmedcentral.nih.gov:7162555","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7162555","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1007756","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1007756","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1523888516","display_name":null,"funder_award_id":"FA9550-","funder_id":"https://openalex.org/F4320338279","funder_display_name":"Air Force Office of Scientific Research"},{"id":"https://openalex.org/G1594539231","display_name":null,"funder_award_id":"FA9550-18-1-0051","funder_id":"https://openalex.org/F4320338279","funder_display_name":"Air Force Office of Scientific Research"},{"id":"https://openalex.org/G2313822077","display_name":null,"funder_award_id":"GM008326","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G2864570036","display_name":null,"funder_award_id":"FA9550-18-1-0051","funder_id":"https://openalex.org/F4320333591","funder_display_name":"Multidisciplinary University Research Initiative"},{"id":"https://openalex.org/G2890344346","display_name":null,"funder_award_id":"GM31749","funder_id":"https://openalex.org/F4320332603","funder_display_name":"University of California, San Diego"},{"id":"https://openalex.org/G2978463324","display_name":null,"funder_award_id":"FA9550-18-1-00","funder_id":"https://openalex.org/F4320338279","funder_display_name":"Air Force Office of Scientific Research"},{"id":"https://openalex.org/G3084217198","display_name":null,"funder_award_id":"GM31749","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G343286159","display_name":null,"funder_award_id":"T32-GM008326","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G4383001364","display_name":null,"funder_award_id":"DMS-FRG1262982","funder_id":"https://openalex.org/F4320337380","funder_display_name":"Division of Mathematical Sciences"},{"id":"https://openalex.org/G4725541805","display_name":null,"funder_award_id":"GM31749","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G5809100787","display_name":null,"funder_award_id":"FA9550","funder_id":"https://openalex.org/F4320338279","funder_display_name":"Air Force Office of Scientific Research"},{"id":"https://openalex.org/G5921281487","display_name":null,"funder_award_id":"number","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6068406125","display_name":null,"funder_award_id":"1262982","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6894402473","display_name":null,"funder_award_id":"Fellowship","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G7199578972","display_name":null,"funder_award_id":"GM103426","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7312852596","display_name":null,"funder_award_id":"T32-GM008326","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7908228807","display_name":null,"funder_award_id":"Molecular","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G7982897390","display_name":null,"funder_award_id":"P41-GM103426","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8251669355","display_name":null,"funder_award_id":"1620366","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G848032724","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G8993566740","display_name":null,"funder_award_id":"Postdoctoral Fellowship","funder_id":"https://openalex.org/F4320309331","funder_display_name":"Hartwell Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320309331","display_name":"Hartwell Foundation","ror":"https://ror.org/038cgyc59"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320332603","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48"},{"id":"https://openalex.org/F4320333591","display_name":"Multidisciplinary University Research Initiative","ror":null},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"},{"id":"https://openalex.org/F4320337380","display_name":"Division of Mathematical Sciences","ror":"https://ror.org/051fftw81"},{"id":"https://openalex.org/F4320338279","display_name":"Air Force Office of Scientific Research","ror":"https://ror.org/011e9bt93"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":139,"referenced_works":["https://openalex.org/W50490584","https://openalex.org/W74971858","https://openalex.org/W1480546554","https://openalex.org/W1505367476","https://openalex.org/W1513082520","https://openalex.org/W1542873368","https://openalex.org/W1549658690","https://openalex.org/W1568106481","https://openalex.org/W1569530544","https://openalex.org/W1587098034","https://openalex.org/W1589288858","https://openalex.org/W1591608973","https://openalex.org/W1626653188","https://openalex.org/W1965637518","https://openalex.org/W1967672419","https://openalex.org/W1984713107","https://openalex.org/W1986644591","https://openalex.org/W1987312063","https://openalex.org/W1987427622","https://openalex.org/W1992941642","https://openalex.org/W1996819948","https://openalex.org/W2000214666","https://openalex.org/W2001875460","https://openalex.org/W2004626802","https://openalex.org/W2007102247","https://openalex.org/W2012941040","https://openalex.org/W2015240388","https://openalex.org/W2018554421","https://openalex.org/W2024060242","https://openalex.org/W2024506048","https://openalex.org/W2025828073","https://openalex.org/W2029101220","https://openalex.org/W2031894851","https://openalex.org/W2034024171","https://openalex.org/W2034184519","https://openalex.org/W2038665424","https://openalex.org/W2043200611","https://openalex.org/W2043377185","https://openalex.org/W2049890302","https://openalex.org/W2050851932","https://openalex.org/W2052580196","https://openalex.org/W2052790699","https://openalex.org/W2052919172","https://openalex.org/W2053729608","https://openalex.org/W2062435050","https://openalex.org/W2063974361","https://openalex.org/W2065475665","https://openalex.org/W2066546878","https://openalex.org/W2067987159","https://openalex.org/W2069505635","https://openalex.org/W2069702026","https://openalex.org/W2071216784","https://openalex.org/W2077346271","https://openalex.org/W2079017595","https://openalex.org/W2082221311","https://openalex.org/W2092452774","https://openalex.org/W2100392179","https://openalex.org/W2103782445","https://openalex.org/W2109991971","https://openalex.org/W2112311198","https://openalex.org/W2113094198","https://openalex.org/W2122737923","https://openalex.org/W2130527887","https://openalex.org/W2131341034","https://openalex.org/W2132898564","https://openalex.org/W2134542242","https://openalex.org/W2137802747","https://openalex.org/W2140768702","https://openalex.org/W2143477348","https://openalex.org/W2147762902","https://openalex.org/W2150134853","https://openalex.org/W2151643303","https://openalex.org/W2154626303","https://openalex.org/W2158569910","https://openalex.org/W2159475546","https://openalex.org/W2160041854","https://openalex.org/W2161112329","https://openalex.org/W2161622851","https://openalex.org/W2161713570","https://openalex.org/W2164004277","https://openalex.org/W2168135619","https://openalex.org/W2169509065","https://openalex.org/W2190997232","https://openalex.org/W2212370034","https://openalex.org/W2235901111","https://openalex.org/W2237861927","https://openalex.org/W2247269323","https://openalex.org/W2409390176","https://openalex.org/W2412019936","https://openalex.org/W2480732292","https://openalex.org/W2517665947","https://openalex.org/W2531236954","https://openalex.org/W2541068854","https://openalex.org/W2554087130","https://openalex.org/W2587288333","https://openalex.org/W2588088434","https://openalex.org/W2613629789","https://openalex.org/W2618988158","https://openalex.org/W2809944305","https://openalex.org/W2810169789","https://openalex.org/W2887091285","https://openalex.org/W2896075424","https://openalex.org/W2898655452","https://openalex.org/W2901563685","https://openalex.org/W2908553168","https://openalex.org/W2911967907","https://openalex.org/W2913772345","https://openalex.org/W2949808130","https://openalex.org/W2963263954","https://openalex.org/W2963306246","https://openalex.org/W2963381503","https://openalex.org/W2963652100","https://openalex.org/W2963969994","https://openalex.org/W2967980310","https://openalex.org/W2973537857","https://openalex.org/W2979293455","https://openalex.org/W2980686459","https://openalex.org/W2982268628","https://openalex.org/W2998590421","https://openalex.org/W3002581259","https://openalex.org/W3084381186","https://openalex.org/W3084409310","https://openalex.org/W3093598461","https://openalex.org/W3098433950","https://openalex.org/W3098455240","https://openalex.org/W3100597379","https://openalex.org/W3103476862","https://openalex.org/W3105118431","https://openalex.org/W4206796399","https://openalex.org/W4236451756","https://openalex.org/W4239375937","https://openalex.org/W4242723867","https://openalex.org/W4245317623","https://openalex.org/W4385483120","https://openalex.org/W4385489877","https://openalex.org/W6683021576","https://openalex.org/W6738012370","https://openalex.org/W6752768766","https://openalex.org/W6996289242"],"related_works":["https://openalex.org/W2784995402","https://openalex.org/W2050851932","https://openalex.org/W2601611040","https://openalex.org/W2184057547","https://openalex.org/W4210950568","https://openalex.org/W2048163432","https://openalex.org/W2381018316","https://openalex.org/W156011255","https://openalex.org/W1740070153","https://openalex.org/W2369809820"],"abstract_inverted_index":{"Recent":[0],"advances":[1],"in":[2,12,23,161,166],"electron":[3,44,124],"microscopy":[4],"have":[5],"enabled":[6],"the":[7,27,55,68,77,90,112,139,190,204],"imaging":[8],"of":[9,43,57,60,79,114,123,126,158,192,206],"single":[10,210],"cells":[11],"3D":[13,48],"at":[14,131,189,203],"nanometer":[15],"length":[16,134,173],"scale":[17,174],"resolutions.":[18],"An":[19],"uncharted":[20],"frontier":[21,202],"for":[22,144],"silico":[24],"biology":[25,212],"is":[26,150,213],"ability":[28],"to":[29,88,120,168],"simulate":[30,171],"cellular":[31,172,195],"processes":[32,62,160],"using":[33,63,117],"these":[34],"observed":[35],"geometries.":[36],"Enabling":[37],"such":[38,61,66],"simulations":[39,59,157],"requires":[40],"watertight":[41],"meshing":[42],"micrograph":[45],"images":[46],"into":[47],"volume":[49],"meshes,":[50],"which":[51,105],"can":[52],"then":[53],"form":[54],"basis":[56],"computer":[58],"numerical":[64],"techniques":[65],"as":[67],"finite":[69,145],"element":[70,146],"method.":[71],"In":[72],"this":[73],"paper,":[74],"we":[75],"describe":[76],"use":[78],"our":[80],"recently":[81],"rewritten":[82],"mesh":[83],"processing":[84],"software,":[85],"GAMer":[86,118],"2,":[87],"bridge":[89],"gap":[91],"between":[92],"poorly":[93],"conditioned":[94],"meshes":[95,104,141],"generated":[96],"from":[97],"segmented":[98],"micrographs":[99,125],"and":[100,136,170,186,194,209],"boundary":[101],"marked":[102],"tetrahedral":[103],"are":[106,142],"compatible":[107],"with":[108],"simulation.":[109],"We":[110,197],"demonstrate":[111],"application":[113],"a":[115,121,200],"workflow":[116],"2":[119],"series":[122],"neuronal":[127],"dendrite":[128],"morphology":[129],"explored":[130],"three":[132],"different":[133],"scales":[135],"show":[137],"that":[138,199],"resulting":[140],"suitable":[143],"simulations.":[147],"This":[148],"work":[149],"an":[151],"important":[152],"step":[153],"towards":[154],"making":[155],"physical":[156,184],"biological":[159],"realistic":[162,183],"geometries":[163],"routine.":[164],"Innovations":[165],"algorithms":[167],"reconstruct":[169],"phenomena":[175],"based":[176],"on":[177],"emerging":[178],"structural":[179],"data":[180],"will":[181],"enable":[182],"models":[185],"advance":[187],"discovery":[188],"interface":[191],"geometry":[193],"processes.":[196],"posit":[198],"new":[201],"intersection":[205],"computational":[207],"technologies":[208],"cell":[211],"now":[214],"open.":[215]},"counts_by_year":[{"year":2025,"cited_by_count":13},{"year":2024,"cited_by_count":11},{"year":2023,"cited_by_count":9},{"year":2022,"cited_by_count":14},{"year":2021,"cited_by_count":16},{"year":2020,"cited_by_count":5},{"year":2019,"cited_by_count":2},{"year":2017,"cited_by_count":1}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
