{"id":"https://openalex.org/W4410493213","doi":"https://doi.org/10.1371/journal.pcbi.1013087","title":"Optical Neuroimage Studio (OptiNiSt): Intuitive, scalable, extendable framework for optical neuroimage data analysis","display_name":"Optical Neuroimage Studio (OptiNiSt): Intuitive, scalable, extendable framework for optical neuroimage data analysis","publication_year":2025,"publication_date":"2025-05-19","ids":{"openalex":"https://openalex.org/W4410493213","doi":"https://doi.org/10.1371/journal.pcbi.1013087","pmid":"https://pubmed.ncbi.nlm.nih.gov/40388494"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1013087","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1013087","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":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1371/journal.pcbi.1013087","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5063504337","display_name":"Y. Yamane","orcid":"https://orcid.org/0000-0002-3348-1942"},"institutions":[{"id":"https://openalex.org/I142637625","display_name":"Okinawa Institute of Science and Technology Graduate University","ror":"https://ror.org/02qg15b79","country_code":"JP","type":"education","lineage":["https://openalex.org/I142637625"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Yukako Yamane","raw_affiliation_strings":["Neural Computation Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan"],"raw_orcid":"https://orcid.org/0000-0002-3348-1942","affiliations":[{"raw_affiliation_string":"Neural Computation Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan","institution_ids":["https://openalex.org/I142637625"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073297477","display_name":"Yuzhe Li","orcid":"https://orcid.org/0000-0002-6282-1600"},"institutions":[{"id":"https://openalex.org/I142637625","display_name":"Okinawa Institute of Science and Technology Graduate University","ror":"https://ror.org/02qg15b79","country_code":"JP","type":"education","lineage":["https://openalex.org/I142637625"]},{"id":"https://openalex.org/I75917431","display_name":"Nara Institute of Science and Technology","ror":"https://ror.org/05bhada84","country_code":"JP","type":"education","lineage":["https://openalex.org/I75917431"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Yuzhe Li","raw_affiliation_strings":["Mathmatical Informatics Lab, Nara Institute of Science and Technology, Nara, Japan","Neural Computation Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Mathmatical Informatics Lab, Nara Institute of Science and Technology, Nara, Japan","institution_ids":["https://openalex.org/I75917431"]},{"raw_affiliation_string":"Neural Computation Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan","institution_ids":["https://openalex.org/I142637625"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013134800","display_name":"Keita Matsumoto","orcid":"https://orcid.org/0000-0002-0527-7418"},"institutions":[{"id":"https://openalex.org/I68926175","display_name":"Hoya (Japan)","ror":"https://ror.org/049vpfq31","country_code":"JP","type":"company","lineage":["https://openalex.org/I68926175"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Keita Matsumoto","raw_affiliation_strings":["Araya Inc., Tokyo, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Araya Inc., Tokyo, Japan","institution_ids":["https://openalex.org/I68926175"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5107419148","display_name":"Ryota Kanai","orcid":null},"institutions":[{"id":"https://openalex.org/I68926175","display_name":"Hoya (Japan)","ror":"https://ror.org/049vpfq31","country_code":"JP","type":"company","lineage":["https://openalex.org/I68926175"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Ryota Kanai","raw_affiliation_strings":["Araya Inc., Tokyo, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Araya Inc., Tokyo, Japan","institution_ids":["https://openalex.org/I68926175"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5107402568","display_name":"Miles Desforges","orcid":null},"institutions":[{"id":"https://openalex.org/I142637625","display_name":"Okinawa Institute of Science and Technology Graduate University","ror":"https://ror.org/02qg15b79","country_code":"JP","type":"education","lineage":["https://openalex.org/I142637625"]},{"id":"https://openalex.org/I68926175","display_name":"Hoya (Japan)","ror":"https://ror.org/049vpfq31","country_code":"JP","type":"company","lineage":["https://openalex.org/I68926175"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Miles Desforges","raw_affiliation_strings":["Araya Inc., Tokyo, Japan","Neural Computation Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan"],"raw_orcid":"https://orcid.org/0000-0003-3631-0580","affiliations":[{"raw_affiliation_string":"Araya Inc., Tokyo, Japan","institution_ids":["https://openalex.org/I68926175"]},{"raw_affiliation_string":"Neural Computation Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan","institution_ids":["https://openalex.org/I142637625"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062858756","display_name":"Carlos Enrique Gutierrez","orcid":"https://orcid.org/0000-0001-5202-4969"},"institutions":[{"id":"https://openalex.org/I142637625","display_name":"Okinawa Institute of Science and Technology Graduate University","ror":"https://ror.org/02qg15b79","country_code":"JP","type":"education","lineage":["https://openalex.org/I142637625"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Carlos Enrique Gutierrez","raw_affiliation_strings":["Neural Computation Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan"],"raw_orcid":"https://orcid.org/0000-0001-5202-4969","affiliations":[{"raw_affiliation_string":"Neural Computation Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan","institution_ids":["https://openalex.org/I142637625"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5004840638","display_name":"Kenji Doya","orcid":"https://orcid.org/0000-0002-2446-6820"},"institutions":[{"id":"https://openalex.org/I142637625","display_name":"Okinawa Institute of Science and Technology Graduate University","ror":"https://ror.org/02qg15b79","country_code":"JP","type":"education","lineage":["https://openalex.org/I142637625"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Kenji Doya","raw_affiliation_strings":["Neural Computation Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan"],"raw_orcid":"https://orcid.org/0000-0002-2446-6820","affiliations":[{"raw_affiliation_string":"Neural Computation Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan","institution_ids":["https://openalex.org/I142637625"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5063504337"],"corresponding_institution_ids":["https://openalex.org/I142637625"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.07892084,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"21","issue":"5","first_page":"e1013087","last_page":"e1013087"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.9965999722480774,"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":0.9965999722480774,"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/T11992","display_name":"CCD and CMOS Imaging Sensors","score":0.9764000177383423,"subfield":{"id":"https://openalex.org/subfields/2208","display_name":"Electrical and Electronic Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10540","display_name":"Advanced Fluorescence Microscopy Techniques","score":0.9677000045776367,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6182498335838318},{"id":"https://openalex.org/keywords/studio","display_name":"Studio","score":0.49196478724479675},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.43348583579063416},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.34122806787490845}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6182498335838318},{"id":"https://openalex.org/C45012715","wikidata":"https://www.wikidata.org/wiki/Q746628","display_name":"Studio","level":2,"score":0.49196478724479675},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.43348583579063416},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.34122806787490845},{"id":"https://openalex.org/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","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":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001921","descriptor_name":"Brain","qualifier_ui":"Q000000981","qualifier_name":"diagnostic imaging","is_major_topic":false},{"descriptor_ui":"D001921","descriptor_name":"Brain","qualifier_ui":"Q000000981","qualifier_name":"diagnostic imaging","is_major_topic":false},{"descriptor_ui":"D001921","descriptor_name":"Brain","qualifier_ui":"Q000000981","qualifier_name":"diagnostic imaging","is_major_topic":false},{"descriptor_ui":"D001921","descriptor_name":"Brain","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D001921","descriptor_name":"Brain","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D001921","descriptor_name":"Brain","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D002118","descriptor_name":"Calcium","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D002118","descriptor_name":"Calcium","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D002118","descriptor_name":"Calcium","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":true},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059906","descriptor_name":"Neuroimaging","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059906","descriptor_name":"Neuroimaging","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059906","descriptor_name":"Neuroimaging","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1371/journal.pcbi.1013087","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1013087","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:40388494","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40388494","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:RePEc:plo:pcbi00:1013087","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1013087","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:1706485303b543bc99c968557f4c7324","is_oa":true,"landing_page_url":"https://doaj.org/article/1706485303b543bc99c968557f4c7324","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"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 21, Iss 5, p e1013087 (2025)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:12124740","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12124740","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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.1013087","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1013087","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":[{"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9","score":0.5099999904632568}],"awards":[{"id":"https://openalex.org/G7041379740","display_name":null,"funder_award_id":"JP19dm0207001, JP23wm0625001","funder_id":"https://openalex.org/F4320311405","funder_display_name":"Japan Agency for Medical Research and Development"}],"funders":[{"id":"https://openalex.org/F4320311405","display_name":"Japan Agency for Medical Research and Development","ror":"https://ror.org/004rtk039"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":26,"referenced_works":["https://openalex.org/W2131938193","https://openalex.org/W2302501749","https://openalex.org/W2469581795","https://openalex.org/W2522169164","https://openalex.org/W2536349837","https://openalex.org/W2805271873","https://openalex.org/W2950205567","https://openalex.org/W2983005665","https://openalex.org/W3087419153","https://openalex.org/W3119242117","https://openalex.org/W3122109253","https://openalex.org/W3149302371","https://openalex.org/W3154637644","https://openalex.org/W3213475423","https://openalex.org/W3214659141","https://openalex.org/W4210644165","https://openalex.org/W4210730450","https://openalex.org/W4212917819","https://openalex.org/W4213028935","https://openalex.org/W4220740615","https://openalex.org/W4225957438","https://openalex.org/W4286513803","https://openalex.org/W4300716329","https://openalex.org/W4303418847","https://openalex.org/W4367857023","https://openalex.org/W4383033802"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W392621609","https://openalex.org/W2537599345","https://openalex.org/W3016102847","https://openalex.org/W2049507953","https://openalex.org/W2389938625","https://openalex.org/W1555246577","https://openalex.org/W4386493544"],"abstract_inverted_index":{"Advancements":[0],"in":[1,13,36,147,181,202,213,233],"calcium":[2,111],"indicators":[3],"and":[4,28,45,55,66,82,91,106,135,177,190,208],"optical":[5,9,235],"techniques":[6],"have":[7],"made":[8],"neural":[10,30,236],"recording":[11,76],"common":[12],"neuroscience.":[14],"As":[15],"data":[16,41,47,86,89,112,201,220,223,237],"volumes":[17],"grow,":[18],"streamlining":[19],"the":[20,117,137,171,187,210],"analysis":[21,37,78,113,125,158,211,238],"pipelines":[22,126],"for":[23,80,88,109,222],"image":[24,200],"preprocessing,":[25],"signal":[26],"extraction,":[27],"subsequent":[29],"activity":[31],"analyses":[32],"becomes":[33],"essential.":[34],"Challenges":[35],"includes":[38,116],"1)":[39,120],"ensuring":[40],"quality":[42],"of":[43,205],"original":[44],"processed":[46],"at":[48,139],"each":[49,61,77,140],"step,":[50],"2)":[51,151],"selecting":[52,128],"optimal":[53],"algorithms":[54,159],"their":[56,133],"parameters":[57,178],"from":[58],"numerous":[59],"options,":[60],"with":[62,174],"its":[63,175],"own":[64],"pros":[65],"cons,":[67],"by":[68,127],"implementing":[69],"or":[70],"installing":[71],"them":[72],"manually,":[73],"3)":[74,164],"systematically":[75],"step":[79,141],"reproducibility,":[81],"4)":[83,196],"adopting":[84],"standard":[85,219],"formats":[87,207],"sharing":[90],"meta-analyses.":[92],"To":[93],"address":[94],"these":[95],"challenges,":[96],"we":[97],"developed":[98],"Optical":[99],"Neuroimage":[100],"Studio":[101],"(OptiNiSt),":[102],"a":[103,143,148,166,182,203,218],"scalable,":[104],"extendable,":[105],"reproducible":[107,189],"framework":[108,229],"creating":[110],"pipelines.":[114],"OptiNiSt":[115,197],"following":[118],"features.":[119],"Researchers":[121],"can":[122,160,198],"easily":[123,162],"create":[124],"multiple":[129],"processing":[130,167],"modules,":[131],"tuning":[132],"parameters,":[134],"visualizing":[136],"results":[138,212],"through":[142],"graphic":[144],"user":[145],"interface":[146],"web":[149],"browser.":[150],"In":[152],"addition":[153],"to":[154],"pre-installed":[155],"tools,":[156],"new":[157],"be":[161,231],"added.":[163],"Once":[165],"pipeline":[168,188],"is":[169],"designed,":[170],"entire":[172],"workflow":[173],"modules":[176],"are":[179],"stored":[180],"YAML":[183],"file,":[184],"which":[185],"makes":[186],"deployable":[191],"on":[192],"high-performance":[193],"computing":[194],"clusters.":[195],"read":[199],"variety":[204],"file":[206],"store":[209],"NWB":[214],"(Neurodata":[215],"Without":[216],"Borders),":[217],"format":[221],"sharing.":[224],"We":[225],"expect":[226],"that":[227],"this":[228],"will":[230],"helpful":[232],"standardizing":[234],"protocols.":[239]},"counts_by_year":[],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
