{"id":"https://openalex.org/W4414450534","doi":"https://doi.org/10.3389/fninf.2025.1629388","title":"Software and pipelines for registration and analyses of rodent brain image data in reference atlas space","display_name":"Software and pipelines for registration and analyses of rodent brain image data in reference atlas space","publication_year":2025,"publication_date":"2025-09-24","ids":{"openalex":"https://openalex.org/W4414450534","doi":"https://doi.org/10.3389/fninf.2025.1629388","pmid":"https://pubmed.ncbi.nlm.nih.gov/41069395"},"language":"en","primary_location":{"id":"doi:10.3389/fninf.2025.1629388","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fninf.2025.1629388","pdf_url":"https://www.frontiersin.org/journals/neuroinformatics/articles/10.3389/fninf.2025.1629388/pdf","source":{"id":"https://openalex.org/S179816892","display_name":"Frontiers in Neuroinformatics","issn_l":"1662-5196","issn":["1662-5196"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Neuroinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.frontiersin.org/journals/neuroinformatics/articles/10.3389/fninf.2025.1629388/pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5069953798","display_name":"Maja Puchades","orcid":"https://orcid.org/0000-0002-4536-8197"},"institutions":[{"id":"https://openalex.org/I184942183","display_name":"University of Oslo","ror":"https://ror.org/01xtthb56","country_code":"NO","type":"education","lineage":["https://openalex.org/I184942183"]}],"countries":["NO"],"is_corresponding":true,"raw_author_name":"Maja A. Puchades","raw_affiliation_strings":["Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway","institution_ids":["https://openalex.org/I184942183"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026501693","display_name":"Sharon C. Yates","orcid":"https://orcid.org/0000-0002-3001-8725"},"institutions":[{"id":"https://openalex.org/I184942183","display_name":"University of Oslo","ror":"https://ror.org/01xtthb56","country_code":"NO","type":"education","lineage":["https://openalex.org/I184942183"]}],"countries":["NO"],"is_corresponding":false,"raw_author_name":"Sharon C. Yates","raw_affiliation_strings":["Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway","institution_ids":["https://openalex.org/I184942183"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039459350","display_name":"Gergely Csucs","orcid":"https://orcid.org/0000-0002-2093-6274"},"institutions":[{"id":"https://openalex.org/I184942183","display_name":"University of Oslo","ror":"https://ror.org/01xtthb56","country_code":"NO","type":"education","lineage":["https://openalex.org/I184942183"]}],"countries":["NO"],"is_corresponding":false,"raw_author_name":"Gergely Csucs","raw_affiliation_strings":["Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway","institution_ids":["https://openalex.org/I184942183"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091579055","display_name":"Harry Carey","orcid":"https://orcid.org/0000-0002-4111-6259"},"institutions":[{"id":"https://openalex.org/I184942183","display_name":"University of Oslo","ror":"https://ror.org/01xtthb56","country_code":"NO","type":"education","lineage":["https://openalex.org/I184942183"]}],"countries":["NO"],"is_corresponding":false,"raw_author_name":"Harry Carey","raw_affiliation_strings":["Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway","institution_ids":["https://openalex.org/I184942183"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5117382944","display_name":"Arda Balkir","orcid":null},"institutions":[{"id":"https://openalex.org/I184942183","display_name":"University of Oslo","ror":"https://ror.org/01xtthb56","country_code":"NO","type":"education","lineage":["https://openalex.org/I184942183"]}],"countries":["NO"],"is_corresponding":false,"raw_author_name":"Arda Balkir","raw_affiliation_strings":["Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway","institution_ids":["https://openalex.org/I184942183"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026824383","display_name":"Trygve B. Leergaard","orcid":"https://orcid.org/0000-0001-5965-8470"},"institutions":[{"id":"https://openalex.org/I184942183","display_name":"University of Oslo","ror":"https://ror.org/01xtthb56","country_code":"NO","type":"education","lineage":["https://openalex.org/I184942183"]}],"countries":["NO"],"is_corresponding":false,"raw_author_name":"Trygve B. Leergaard","raw_affiliation_strings":["Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway","institution_ids":["https://openalex.org/I184942183"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5035577948","display_name":"Jan G. Bjaalie","orcid":"https://orcid.org/0000-0001-7899-906X"},"institutions":[{"id":"https://openalex.org/I184942183","display_name":"University of Oslo","ror":"https://ror.org/01xtthb56","country_code":"NO","type":"education","lineage":["https://openalex.org/I184942183"]}],"countries":["NO"],"is_corresponding":false,"raw_author_name":"Jan G. Bjaalie","raw_affiliation_strings":["Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway","institution_ids":["https://openalex.org/I184942183"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5069953798"],"corresponding_institution_ids":["https://openalex.org/I184942183"],"apc_list":{"value":2950,"currency":"USD","value_usd":2950},"apc_paid":{"value":2950,"currency":"USD","value_usd":2950},"fwci":2.7364,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.91549881,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":99},"biblio":{"volume":"19","issue":null,"first_page":"1629388","last_page":"1629388"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.9997000098228455,"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":0.9997000098228455,"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":0.9922000169754028,"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"}},{"id":"https://openalex.org/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.9907000064849854,"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/software","display_name":"Software","score":0.7239999771118164},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.7034000158309937},{"id":"https://openalex.org/keywords/atlas","display_name":"Atlas (anatomy)","score":0.583899974822998},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.545199990272522},{"id":"https://openalex.org/keywords/suite","display_name":"Suite","score":0.5192000269889832},{"id":"https://openalex.org/keywords/software-suite","display_name":"Software suite","score":0.43970000743865967},{"id":"https://openalex.org/keywords/brain-atlas","display_name":"Brain atlas","score":0.3953999876976013},{"id":"https://openalex.org/keywords/spatial-reference-system","display_name":"Spatial reference system","score":0.3935000002384186},{"id":"https://openalex.org/keywords/data-acquisition","display_name":"Data acquisition","score":0.39149999618530273}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7936000227928162},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.7239999771118164},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.7034000158309937},{"id":"https://openalex.org/C2776673561","wikidata":"https://www.wikidata.org/wiki/Q655357","display_name":"Atlas (anatomy)","level":2,"score":0.583899974822998},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.545199990272522},{"id":"https://openalex.org/C79581498","wikidata":"https://www.wikidata.org/wiki/Q1367530","display_name":"Suite","level":2,"score":0.5192000269889832},{"id":"https://openalex.org/C2778736646","wikidata":"https://www.wikidata.org/wiki/Q1143070","display_name":"Software suite","level":3,"score":0.43970000743865967},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.41100001335144043},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.40230000019073486},{"id":"https://openalex.org/C2780972224","wikidata":"https://www.wikidata.org/wiki/Q17047956","display_name":"Brain atlas","level":2,"score":0.3953999876976013},{"id":"https://openalex.org/C194226119","wikidata":"https://www.wikidata.org/wiki/Q161779","display_name":"Spatial reference system","level":2,"score":0.3935000002384186},{"id":"https://openalex.org/C163985040","wikidata":"https://www.wikidata.org/wiki/Q1172399","display_name":"Data acquisition","level":2,"score":0.39149999618530273},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.38370001316070557},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.3765999972820282},{"id":"https://openalex.org/C205427263","wikidata":"https://www.wikidata.org/wiki/Q1931480","display_name":"Neuroinformatics","level":2,"score":0.36489999294281006},{"id":"https://openalex.org/C166704113","wikidata":"https://www.wikidata.org/wiki/Q861092","display_name":"Image registration","level":3,"score":0.3361000120639801},{"id":"https://openalex.org/C159620131","wikidata":"https://www.wikidata.org/wiki/Q1938983","display_name":"Spatial analysis","level":2,"score":0.33329999446868896},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.33059999346733093},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.3224000036716461},{"id":"https://openalex.org/C172367668","wikidata":"https://www.wikidata.org/wiki/Q6504956","display_name":"Data visualization","level":3,"score":0.29339998960494995},{"id":"https://openalex.org/C60478076","wikidata":"https://www.wikidata.org/wiki/Q3036835","display_name":"Reference data","level":2,"score":0.2856999933719635},{"id":"https://openalex.org/C138958017","wikidata":"https://www.wikidata.org/wiki/Q190087","display_name":"Data type","level":2,"score":0.2851000130176544},{"id":"https://openalex.org/C64754055","wikidata":"https://www.wikidata.org/wiki/Q7574053","display_name":"Spatial contextual awareness","level":2,"score":0.28439998626708984},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.2784999907016754},{"id":"https://openalex.org/C2778464652","wikidata":"https://www.wikidata.org/wiki/Q309849","display_name":"Open research","level":2,"score":0.2757999897003174},{"id":"https://openalex.org/C9417928","wikidata":"https://www.wikidata.org/wiki/Q1070689","display_name":"Image processing","level":3,"score":0.26759999990463257},{"id":"https://openalex.org/C107457646","wikidata":"https://www.wikidata.org/wiki/Q207434","display_name":"Human\u2013computer interaction","level":1,"score":0.2660999894142151},{"id":"https://openalex.org/C175309249","wikidata":"https://www.wikidata.org/wiki/Q725864","display_name":"Pipeline transport","level":2,"score":0.25609999895095825},{"id":"https://openalex.org/C76518257","wikidata":"https://www.wikidata.org/wiki/Q271680","display_name":"Software framework","level":5,"score":0.2547000050544739},{"id":"https://openalex.org/C2993059035","wikidata":"https://www.wikidata.org/wiki/Q1073","display_name":"Brain research","level":2,"score":0.25429999828338623}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.3389/fninf.2025.1629388","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fninf.2025.1629388","pdf_url":"https://www.frontiersin.org/journals/neuroinformatics/articles/10.3389/fninf.2025.1629388/pdf","source":{"id":"https://openalex.org/S179816892","display_name":"Frontiers in Neuroinformatics","issn_l":"1662-5196","issn":["1662-5196"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Neuroinformatics","raw_type":"journal-article"},{"id":"pmid:41069395","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41069395","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":"Frontiers in neuroinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:d67615dc72cc42778e4ea69a45c1cb9d","is_oa":true,"landing_page_url":"https://doaj.org/article/d67615dc72cc42778e4ea69a45c1cb9d","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":"Frontiers in Neuroinformatics, Vol 19 (2025)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:11312271","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12504246","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":null,"raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:12504246","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12504246/","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":"Front Neuroinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.3389/fninf.2025.1629388","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fninf.2025.1629388","pdf_url":"https://www.frontiersin.org/journals/neuroinformatics/articles/10.3389/fninf.2025.1629388/pdf","source":{"id":"https://openalex.org/S179816892","display_name":"Frontiers in Neuroinformatics","issn_l":"1662-5196","issn":["1662-5196"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Neuroinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1765773415","display_name":null,"funder_award_id":"269774","funder_id":"https://openalex.org/F4320323299","funder_display_name":"Norges Forskningsr\u00e5d"},{"id":"https://openalex.org/G2789362503","display_name":null,"funder_award_id":"945539","funder_id":"https://openalex.org/F4320334322","funder_display_name":"HORIZON EUROPE Framework Programme"},{"id":"https://openalex.org/G3551564797","display_name":null,"funder_award_id":"101147319","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G4649087444","display_name":null,"funder_award_id":"785907","funder_id":"https://openalex.org/F4320334322","funder_display_name":"HORIZON EUROPE Framework Programme"},{"id":"https://openalex.org/G5766349579","display_name":null,"funder_award_id":"785907","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G6167187853","display_name":null,"funder_award_id":"2022-2027","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G8163049627","display_name":"Digital Archive for the Study of pre-Islamic Arabian Inscriptions","funder_award_id":"269774","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G8301431789","display_name":null,"funder_award_id":"101147319","funder_id":"https://openalex.org/F4320334322","funder_display_name":"HORIZON EUROPE Framework Programme"},{"id":"https://openalex.org/G8767435255","display_name":null,"funder_award_id":"945539","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"}],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320323299","display_name":"Norges Forskningsr\u00e5d","ror":"https://ror.org/00epmv149"},{"id":"https://openalex.org/F4320334322","display_name":"HORIZON EUROPE Framework Programme","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4414450534.pdf","grobid_xml":"https://content.openalex.org/works/W4414450534.grobid-xml"},"referenced_works_count":66,"referenced_works":["https://openalex.org/W1514624092","https://openalex.org/W1682263115","https://openalex.org/W2020688250","https://openalex.org/W2167279371","https://openalex.org/W2302501749","https://openalex.org/W2342477170","https://openalex.org/W2462878378","https://openalex.org/W2563079618","https://openalex.org/W2773247831","https://openalex.org/W2899304965","https://openalex.org/W2914654471","https://openalex.org/W2946652954","https://openalex.org/W2947461179","https://openalex.org/W2952481429","https://openalex.org/W2964777970","https://openalex.org/W2966999298","https://openalex.org/W2975634117","https://openalex.org/W2977175469","https://openalex.org/W2985746287","https://openalex.org/W2991741056","https://openalex.org/W3005972569","https://openalex.org/W3021105102","https://openalex.org/W3030923655","https://openalex.org/W3080801996","https://openalex.org/W3092644694","https://openalex.org/W3092695059","https://openalex.org/W3111449295","https://openalex.org/W3118418851","https://openalex.org/W3157335290","https://openalex.org/W3165457844","https://openalex.org/W3180424009","https://openalex.org/W4206584351","https://openalex.org/W4220716820","https://openalex.org/W4223598649","https://openalex.org/W4223901815","https://openalex.org/W4224247597","https://openalex.org/W4283321589","https://openalex.org/W4297373464","https://openalex.org/W4306173528","https://openalex.org/W4306776548","https://openalex.org/W4307836742","https://openalex.org/W4308361273","https://openalex.org/W4377024525","https://openalex.org/W4385617550","https://openalex.org/W4386511958","https://openalex.org/W4386923319","https://openalex.org/W4386935584","https://openalex.org/W4387252449","https://openalex.org/W4387845470","https://openalex.org/W4392375298","https://openalex.org/W4392963971","https://openalex.org/W4398141685","https://openalex.org/W4402053377","https://openalex.org/W4403701747","https://openalex.org/W4404285560","https://openalex.org/W4404287847","https://openalex.org/W4404516898","https://openalex.org/W4410569787","https://openalex.org/W4411537777","https://openalex.org/W4412202444","https://openalex.org/W4413817451","https://openalex.org/W6889246178","https://openalex.org/W6907801676","https://openalex.org/W6907827205","https://openalex.org/W6963926464","https://openalex.org/W6964249581"],"related_works":[],"abstract_inverted_index":{"Advancements":[0],"in":[1,28,55,132,151,167],"methodologies":[2],"for":[3,17,36,41,109,128,182,204],"efficient":[4],"large-scale":[5],"acquisition":[6],"of":[7,20,46,74,83,91,105,111],"high-resolution":[8],"serial":[9,112],"microscopy":[10],"image":[11],"data":[12,130,177],"have":[13,101],"opened":[14],"new":[15],"possibilities":[16],"experimental":[18],"studies":[19,61],"cellular":[21],"and":[22,39,52,57,70,86,107,125,127,144,172,200],"subcellular":[23],"features":[24],"across":[25,93],"whole":[26],"brains":[27],"animal":[29],"models.":[30],"There":[31],"is":[32],"a":[33,63,103,133],"high":[34],"demand":[35],"open-source":[37],"software":[38,147,191],"workflows":[40],"automated":[42],"or":[43],"semi-automated":[44],"analysis":[45,131],"such":[47],"data,":[48],"facilitating":[49],"anatomical,":[50],"functional,":[51],"molecular":[53],"mapping":[54],"healthy":[56],"diseased":[58],"brains.":[59],"These":[60],"share":[62],"common":[64],"need":[65],"to":[66,116,159,174],"consistently":[67],"identify,":[68],"visualize,":[69],"quantify":[71],"the":[72,168,175,180,197],"location":[73],"observations":[75],"within":[76],"anatomically":[77],"defined":[78],"regions,":[79],"ensuring":[80],"reproducible":[81],"interpretation":[82],"anatomical":[84],"locations,":[85],"thereby":[87],"allowing":[88],"meaningful":[89],"comparisons":[90],"results":[92],"multiple":[94],"independent":[95],"studies.":[96],"Addressing":[97],"this":[98],"need,":[99],"we":[100],"developed":[102],"suite":[104],"desktop":[106],"web-applications":[108,164],"registration":[110],"brain":[113,118],"section":[114],"images":[115],"three-dimensional":[117],"reference":[119],"atlases":[120],"(QuickNII,":[121],"VisuAlign,":[122],"WebAlign,":[123],"WebWarp,":[124],"DeepSlice)":[126],"performing":[129],"spatial":[134],"context":[135],"provided":[136],"by":[137,196],"an":[138,183],"atlas":[139],"(Nutil,":[140],"QCAlign,":[141],"SeriesZoom,":[142],"LocaliZoom,":[143],"MeshView).":[145],"The":[146,163],"can":[148],"be":[149],"utilized":[150],"various":[152],"combinations,":[153],"creating":[154],"customized":[155],"analytical":[156,185],"pipelines":[157],"suited":[158],"specific":[160],"research":[161,170,198],"needs.":[162],"are":[165],"integrated":[166],"EBRAINS":[169,176],"infrastructure":[171],"coupled":[173],"platform,":[178],"establishing":[179],"foundation":[181],"online":[184],"workbench.":[186],"We":[187],"here":[188],"present":[189],"our":[190],"ecosystem,":[192],"exemplify":[193],"its":[194],"use":[195],"community,":[199],"discuss":[201],"possible":[202],"directions":[203],"future":[205],"developments.":[206]},"counts_by_year":[{"year":2026,"cited_by_count":2}],"updated_date":"2026-05-08T15:41:06.802602","created_date":"2025-10-10T00:00:00"}