{"id":"https://openalex.org/W4377565316","doi":"https://doi.org/10.1093/bioinformatics/btad568","title":"VoDEx: a Python library for time annotation and management of volumetric functional imaging data","display_name":"VoDEx: a Python library for time annotation and management of volumetric functional imaging data","publication_year":2023,"publication_date":"2023-09-01","ids":{"openalex":"https://openalex.org/W4377565316","doi":"https://doi.org/10.1093/bioinformatics/btad568","pmid":"https://pubmed.ncbi.nlm.nih.gov/37214133"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btad568","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad568","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad568/51529667/btad568.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad568/51529667/btad568.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5066007908","display_name":"Anna Nadtochiy","orcid":"https://orcid.org/0000-0002-5520-2289"},"institutions":[{"id":"https://openalex.org/I1174212","display_name":"University of Southern California","ror":"https://ror.org/03taz7m60","country_code":"US","type":"education","lineage":["https://openalex.org/I1174212"]},{"id":"https://openalex.org/I4210166946","display_name":"Imaging Center","ror":"https://ror.org/05hsqsk33","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210166946"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Anna Nadtochiy","raw_affiliation_strings":["Department of Quantitative and Computational Biology, University of Southern California , Los Angeles, CA 90089, United States","Translational Imaging Center, University of Southern California , Los Angeles, CA 90089, United States"],"affiliations":[{"raw_affiliation_string":"Department of Quantitative and Computational Biology, University of Southern California , Los Angeles, CA 90089, United States","institution_ids":["https://openalex.org/I1174212"]},{"raw_affiliation_string":"Translational Imaging Center, University of Southern California , Los Angeles, CA 90089, United States","institution_ids":["https://openalex.org/I4210166946","https://openalex.org/I1174212"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063629404","display_name":"Peter Luu","orcid":"https://orcid.org/0000-0002-5319-9848"},"institutions":[{"id":"https://openalex.org/I1174212","display_name":"University of Southern California","ror":"https://ror.org/03taz7m60","country_code":"US","type":"education","lineage":["https://openalex.org/I1174212"]},{"id":"https://openalex.org/I4210166946","display_name":"Imaging Center","ror":"https://ror.org/05hsqsk33","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210166946"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Peter Luu","raw_affiliation_strings":["Division of Molecular and Computational Biology, Department of Biological Sciences, University of Southern California , Los Angeles, CA 90089, United States","Translational Imaging Center, University of Southern California , Los Angeles, CA 90089, United States"],"affiliations":[{"raw_affiliation_string":"Division of Molecular and Computational Biology, Department of Biological Sciences, University of Southern California , Los Angeles, CA 90089, United States","institution_ids":["https://openalex.org/I1174212"]},{"raw_affiliation_string":"Translational Imaging Center, University of Southern California , Los Angeles, CA 90089, United States","institution_ids":["https://openalex.org/I4210166946","https://openalex.org/I1174212"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047064481","display_name":"Scott E. Fraser","orcid":"https://orcid.org/0000-0002-5377-0223"},"institutions":[{"id":"https://openalex.org/I1174212","display_name":"University of Southern California","ror":"https://ror.org/03taz7m60","country_code":"US","type":"education","lineage":["https://openalex.org/I1174212"]},{"id":"https://openalex.org/I4210166946","display_name":"Imaging Center","ror":"https://ror.org/05hsqsk33","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210166946"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Scott E Fraser","raw_affiliation_strings":["Department of Quantitative and Computational Biology, University of Southern California , Los Angeles, CA 90089, United States","Division of Molecular and Computational Biology, Department of Biological Sciences, University of Southern California , Los Angeles, CA 90089, United States","Translational Imaging Center, University of Southern California , Los Angeles, CA 90089, United States"],"affiliations":[{"raw_affiliation_string":"Department of Quantitative and Computational Biology, University of Southern California , Los Angeles, CA 90089, United States","institution_ids":["https://openalex.org/I1174212"]},{"raw_affiliation_string":"Division of Molecular and Computational Biology, Department of Biological Sciences, University of Southern California , Los Angeles, CA 90089, United States","institution_ids":["https://openalex.org/I1174212"]},{"raw_affiliation_string":"Translational Imaging Center, University of Southern California , Los Angeles, CA 90089, United States","institution_ids":["https://openalex.org/I4210166946","https://openalex.org/I1174212"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5053981034","display_name":"Thai V. Truong","orcid":"https://orcid.org/0000-0001-6475-8935"},"institutions":[{"id":"https://openalex.org/I1174212","display_name":"University of Southern California","ror":"https://ror.org/03taz7m60","country_code":"US","type":"education","lineage":["https://openalex.org/I1174212"]},{"id":"https://openalex.org/I4210166946","display_name":"Imaging Center","ror":"https://ror.org/05hsqsk33","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210166946"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Thai V Truong","raw_affiliation_strings":["Division of Molecular and Computational Biology, Department of Biological Sciences, University of Southern California , Los Angeles, CA 90089, United States","Translational Imaging Center, University of Southern California , Los Angeles, CA 90089, United States"],"affiliations":[{"raw_affiliation_string":"Division of Molecular and Computational Biology, Department of Biological Sciences, University of Southern California , Los Angeles, CA 90089, United States","institution_ids":["https://openalex.org/I1174212"]},{"raw_affiliation_string":"Translational Imaging Center, University of Southern California , Los Angeles, CA 90089, United States","institution_ids":["https://openalex.org/I4210166946","https://openalex.org/I1174212"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5066007908"],"corresponding_institution_ids":["https://openalex.org/I1174212","https://openalex.org/I4210166946"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.1742,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.46417978,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"39","issue":"9","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10241","display_name":"Functional Brain Connectivity Studies","score":0.9934999942779541,"subfield":{"id":"https://openalex.org/subfields/2805","display_name":"Cognitive Neuroscience"},"field":{"id":"https://openalex.org/fields/28","display_name":"Neuroscience"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10241","display_name":"Functional Brain Connectivity Studies","score":0.9934999942779541,"subfield":{"id":"https://openalex.org/subfields/2805","display_name":"Cognitive Neuroscience"},"field":{"id":"https://openalex.org/fields/28","display_name":"Neuroscience"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10581","display_name":"Neural dynamics and brain function","score":0.9746999740600586,"subfield":{"id":"https://openalex.org/subfields/2805","display_name":"Cognitive Neuroscience"},"field":{"id":"https://openalex.org/fields/28","display_name":"Neuroscience"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10778","display_name":"Philosophy and History of Science","score":0.9605000019073486,"subfield":{"id":"https://openalex.org/subfields/1207","display_name":"History and Philosophy of Science"},"field":{"id":"https://openalex.org/fields/12","display_name":"Arts and Humanities"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.871471107006073},{"id":"https://openalex.org/keywords/plug-in","display_name":"Plug-in","score":0.8583282232284546},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8434900045394897},{"id":"https://openalex.org/keywords/timeline","display_name":"Timeline","score":0.8012257814407349},{"id":"https://openalex.org/keywords/mit-license","display_name":"MIT License","score":0.7587363719940186},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.6527017951011658},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5815688371658325},{"id":"https://openalex.org/keywords/open-source","display_name":"Open source","score":0.5749278664588928},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.49031832814216614},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.340279221534729},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.3297531008720398},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.3255046606063843},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.25985240936279297}],"concepts":[{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.871471107006073},{"id":"https://openalex.org/C4924752","wikidata":"https://www.wikidata.org/wiki/Q184148","display_name":"Plug-in","level":2,"score":0.8583282232284546},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8434900045394897},{"id":"https://openalex.org/C4438859","wikidata":"https://www.wikidata.org/wiki/Q186117","display_name":"Timeline","level":2,"score":0.8012257814407349},{"id":"https://openalex.org/C174183944","wikidata":"https://www.wikidata.org/wiki/Q334661","display_name":"MIT License","level":3,"score":0.7587363719940186},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.6527017951011658},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5815688371658325},{"id":"https://openalex.org/C3018397939","wikidata":"https://www.wikidata.org/wiki/Q3644502","display_name":"Open source","level":3,"score":0.5749278664588928},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.49031832814216614},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.340279221534729},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.3297531008720398},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.3255046606063843},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.25985240936279297},{"id":"https://openalex.org/C166957645","wikidata":"https://www.wikidata.org/wiki/Q23498","display_name":"Archaeology","level":1,"score":0.0},{"id":"https://openalex.org/C95457728","wikidata":"https://www.wikidata.org/wiki/Q309","display_name":"History","level":0,"score":0.0}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/btad568","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad568","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad568/51529667/btad568.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:37214133","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37214133","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":"ArXiv","raw_type":null},{"id":"pmid:37699009","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37699009","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10197724","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10197724","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10197724/pdf/nihpp-2305.07438v1.pdf","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":"ArXiv","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:10562951","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10562951","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10562951/pdf/btad568.pdf","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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btad568","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad568","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad568/51529667/btad568.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2460454746","display_name":null,"funder_award_id":"1U01NS126562-01","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3388672947","display_name":null,"funder_award_id":"1U01NS122082-01","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6345853531","display_name":null,"funder_award_id":"unknown","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7414692163","display_name":null,"funder_award_id":"RPG0008/2017","funder_id":"https://openalex.org/F4320307846","funder_display_name":"Human Frontier Science Program"},{"id":"https://openalex.org/G7983688560","display_name":null,"funder_award_id":"08/2017","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320307846","display_name":"Human Frontier Science Program","ror":"https://ror.org/02ebx7v45"},{"id":"https://openalex.org/F4320308668","display_name":"University of Southern California","ror":"https://ror.org/03taz7m60"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4377565316.pdf"},"referenced_works_count":26,"referenced_works":["https://openalex.org/W1965333862","https://openalex.org/W2015159529","https://openalex.org/W2136145485","https://openalex.org/W2302501749","https://openalex.org/W2519489054","https://openalex.org/W2805271873","https://openalex.org/W2887114371","https://openalex.org/W2889412653","https://openalex.org/W2903368869","https://openalex.org/W2913606428","https://openalex.org/W2951103577","https://openalex.org/W3003257820","https://openalex.org/W3035965352","https://openalex.org/W3099878876","https://openalex.org/W3103145119","https://openalex.org/W3135427297","https://openalex.org/W3152449813","https://openalex.org/W4205122060","https://openalex.org/W4205560034","https://openalex.org/W4206967482","https://openalex.org/W4220851883","https://openalex.org/W4225756840","https://openalex.org/W4285388124","https://openalex.org/W4288052974","https://openalex.org/W4292202382","https://openalex.org/W6841483637"],"related_works":["https://openalex.org/W4320062235","https://openalex.org/W4386041260","https://openalex.org/W4298269242","https://openalex.org/W4298401663","https://openalex.org/W4300787769","https://openalex.org/W4302475558","https://openalex.org/W4301355831","https://openalex.org/W4298345637","https://openalex.org/W2113128227","https://openalex.org/W4311938462"],"abstract_inverted_index":{"In":[0],"functional":[1,59],"imaging":[2,17,36,60,75,91],"studies,":[3],"accurately":[4],"synchronizing":[5],"the":[6,33,53,64,84,115,150,162],"time":[7],"course":[8],"of":[9,32,58,90],"experimental":[10,34,65,99],"manipulations":[11],"and":[12,35,41,56,67,82,87,97,102,110,126],"stimulus":[13],"presentations":[14],"with":[15,74],"resulting":[16],"data":[18,54,92],"is":[19,39,105,120,130,139,165],"crucial":[20],"for":[21,80,161],"analysis.":[22],"Current":[23],"software":[24],"tools":[25,79],"lack":[26],"such":[27],"functionality,":[28],"requiring":[29],"manual":[30],"processing":[31],"data,":[37],"which":[38,145],"error-prone":[40],"potentially":[42],"non-reproducible.":[43],"We":[44],"present":[45],"VoDEx,":[46],"an":[47,106],"open-source":[48,107],"Python":[49,108],"library":[50,109],"that":[51],"streamlines":[52],"management":[55],"analysis":[57],"data.":[61,76],"VoDEx":[62,77,104],"synchronizes":[63],"timeline":[66,85],"events":[68],"(eg.":[69],"presented":[70],"stimuli,":[71],"recorded":[72],"behavior)":[73],"provides":[78],"logging":[81],"storing":[83],"annotation,":[86],"enables":[88],"retrieval":[89],"based":[93],"on":[94,133,167],"specific":[95],"time-based":[96],"manipulation-based":[98],"conditions.":[100],"Availability":[101],"Implementation:":[103],"can":[111,146],"be":[112,147],"installed":[113,148],"via":[114],"\"pip":[116,156],"install\"":[117],"command.":[118],"It":[119],"released":[121],"under":[122],"a":[123,142],"BSD":[124],"license,":[125],"its":[127],"source":[128,159],"code":[129,160],"publicly":[131],"accessible":[132],"GitHub":[134,168],"https://github.com/LemonJust/vodex.":[135],"A":[136],"graphical":[137],"interface":[138],"available":[140,166],"as":[141],"napari-vodex":[143],"plugin,":[144],"through":[149],"napari":[151,163],"plugins":[152],"menu":[153],"or":[154],"using":[155],"install.\"":[157],"The":[158],"plugin":[164],"https://github.com/LemonJust/napari-vodex.":[169]},"counts_by_year":[{"year":2024,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2023-05-24T00:00:00"}
