{"id":"https://openalex.org/W4382893155","doi":"https://doi.org/10.1007/s12021-023-09638-2","title":"BrainLine: An Open Pipeline for Connectivity Analysis of Heterogeneous Whole-Brain Fluorescence Volumes","display_name":"BrainLine: An Open Pipeline for Connectivity Analysis of Heterogeneous Whole-Brain Fluorescence Volumes","publication_year":2023,"publication_date":"2023-07-02","ids":{"openalex":"https://openalex.org/W4382893155","doi":"https://doi.org/10.1007/s12021-023-09638-2","pmid":"https://pubmed.ncbi.nlm.nih.gov/37394568"},"language":"en","primary_location":{"id":"doi:10.1007/s12021-023-09638-2","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s12021-023-09638-2","pdf_url":"https://link.springer.com/content/pdf/10.1007/s12021-023-09638-2.pdf","source":{"id":"https://openalex.org/S3444786","display_name":"Neuroinformatics","issn_l":"1539-2791","issn":["1539-2791","1559-0089"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Neuroinformatics","raw_type":"journal-article"},"type":"letter","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://link.springer.com/content/pdf/10.1007/s12021-023-09638-2.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5056441901","display_name":"Thomas L. Athey","orcid":"https://orcid.org/0000-0002-8987-3486"},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]},{"id":"https://openalex.org/I2799853436","display_name":"Johns Hopkins Medicine","ror":"https://ror.org/037zgn354","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2799853436"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Thomas L. Athey","raw_affiliation_strings":["Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA. tathey1@jhu.edu","Institute of Computational Medicine, Johns Hopkins University, Baltimore, MD, USA. tathey1@jhu.edu","Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA. tathey1@jhu.edu","institution_ids":["https://openalex.org/I2799853436","https://openalex.org/I145311948"]},{"raw_affiliation_string":"Institute of Computational Medicine, Johns Hopkins University, Baltimore, MD, USA. tathey1@jhu.edu","institution_ids":["https://openalex.org/I2799853436","https://openalex.org/I145311948"]},{"raw_affiliation_string":"Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA","institution_ids":["https://openalex.org/I145311948"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101935888","display_name":"Matthew A. Wright","orcid":"https://orcid.org/0000-0001-7131-7492"},"institutions":[{"id":"https://openalex.org/I4387153466","display_name":"Weill Cornell Medicine","ror":"https://ror.org/02r109517","country_code":"US","type":"education","lineage":["https://openalex.org/I205783295","https://openalex.org/I4387153466"]},{"id":"https://openalex.org/I205783295","display_name":"Cornell University","ror":"https://ror.org/05bnh6r87","country_code":"US","type":"education","lineage":["https://openalex.org/I205783295"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Matthew A. Wright","raw_affiliation_strings":["Department of Psychiatry, Weill Cornell Medicine, New York, NY, USA"],"affiliations":[{"raw_affiliation_string":"Department of Psychiatry, Weill Cornell Medicine, New York, NY, USA","institution_ids":["https://openalex.org/I205783295","https://openalex.org/I4387153466"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108110877","display_name":"Marija Pavlovi\u0107","orcid":null},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Marija Pavlovic","raw_affiliation_strings":["Department of Bioengineering, Stanford University, Stanford, CA, USA"],"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, Stanford University, Stanford, CA, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012473250","display_name":"Vikram Chandrashekhar","orcid":"https://orcid.org/0000-0001-7478-5304"},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Vikram Chandrashekhar","raw_affiliation_strings":["Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA","institution_ids":["https://openalex.org/I145311948"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014360828","display_name":"Karl Deisseroth","orcid":"https://orcid.org/0000-0001-9440-3967"},"institutions":[{"id":"https://openalex.org/I1344073410","display_name":"Howard Hughes Medical Institute","ror":"https://ror.org/006w34k90","country_code":"US","type":"facility","lineage":["https://openalex.org/I1344073410"]},{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Karl Deisseroth","raw_affiliation_strings":["CNC Program, Stanford University, Stanford, CA, USA","Department of Bioengineering, Stanford University, Stanford, CA, USA","Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA","Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA"],"affiliations":[{"raw_affiliation_string":"CNC Program, Stanford University, Stanford, CA, USA","institution_ids":["https://openalex.org/I97018004"]},{"raw_affiliation_string":"Department of Bioengineering, Stanford University, Stanford, CA, USA","institution_ids":["https://openalex.org/I97018004"]},{"raw_affiliation_string":"Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA","institution_ids":["https://openalex.org/I97018004"]},{"raw_affiliation_string":"Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA","institution_ids":["https://openalex.org/I1344073410","https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033151214","display_name":"Michael I. Miller","orcid":"https://orcid.org/0000-0003-4689-3855"},"institutions":[{"id":"https://openalex.org/I2799424032","display_name":"Discovery Institute","ror":"https://ror.org/05t8s3y29","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I2799424032"]},{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michael I. Miller","raw_affiliation_strings":["Center for Imaging Science, Johns Hopkins University, Baltimore, MD, USA","Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA","Institute of Computational Medicine, Johns Hopkins University, Baltimore, MD, USA","Kavli Neuroscience Discovery Institute, Johns Hopkins University, Baltimore, MD, USA"],"affiliations":[{"raw_affiliation_string":"Center for Imaging Science, Johns Hopkins University, Baltimore, MD, USA","institution_ids":["https://openalex.org/I145311948"]},{"raw_affiliation_string":"Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA","institution_ids":["https://openalex.org/I145311948"]},{"raw_affiliation_string":"Institute of Computational Medicine, Johns Hopkins University, Baltimore, MD, USA","institution_ids":["https://openalex.org/I145311948"]},{"raw_affiliation_string":"Kavli Neuroscience Discovery Institute, Johns Hopkins University, Baltimore, MD, USA","institution_ids":["https://openalex.org/I2799424032","https://openalex.org/I145311948"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5065441417","display_name":"Joshua T Vogelstein","orcid":"https://orcid.org/0000-0003-2487-6237"},"institutions":[{"id":"https://openalex.org/I2799424032","display_name":"Discovery Institute","ror":"https://ror.org/05t8s3y29","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I2799424032"]},{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Joshua T. Vogelstein","raw_affiliation_strings":["Center for Imaging Science, Johns Hopkins University, Baltimore, MD, USA","Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA","Institute of Computational Medicine, Johns Hopkins University, Baltimore, MD, USA","Kavli Neuroscience Discovery Institute, Johns Hopkins University, Baltimore, MD, USA"],"affiliations":[{"raw_affiliation_string":"Center for Imaging Science, Johns Hopkins University, Baltimore, MD, USA","institution_ids":["https://openalex.org/I145311948"]},{"raw_affiliation_string":"Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA","institution_ids":["https://openalex.org/I145311948"]},{"raw_affiliation_string":"Institute of Computational Medicine, Johns Hopkins University, Baltimore, MD, USA","institution_ids":["https://openalex.org/I145311948"]},{"raw_affiliation_string":"Kavli Neuroscience Discovery Institute, Johns Hopkins University, Baltimore, MD, USA","institution_ids":["https://openalex.org/I2799424032","https://openalex.org/I145311948"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5056441901"],"corresponding_institution_ids":["https://openalex.org/I145311948","https://openalex.org/I2799853436"],"apc_list":{"value":3190,"currency":"EUR","value_usd":4190},"apc_paid":{"value":3190,"currency":"EUR","value_usd":4190},"fwci":0.3538,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.76412748,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"21","issue":"4","first_page":"637","last_page":"639"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.9998000264167786,"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":0.9998000264167786,"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":0.9973999857902527,"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/T10241","display_name":"Functional Brain Connectivity Studies","score":0.9776999950408936,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.6438962817192078},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5466240048408508},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3817312717437744},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.18735387921333313}],"concepts":[{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.6438962817192078},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5466240048408508},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3817312717437744},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.18735387921333313}],"mesh":[{"descriptor_ui":"D001921","descriptor_name":"Brain","qualifier_ui":"Q000000981","qualifier_name":"diagnostic imaging","is_major_topic":true},{"descriptor_ui":"D001921","descriptor_name":"Brain","qualifier_ui":"Q000000981","qualifier_name":"diagnostic imaging","is_major_topic":true},{"descriptor_ui":"D001921","descriptor_name":"Brain","qualifier_ui":"Q000000981","qualifier_name":"diagnostic imaging","is_major_topic":true},{"descriptor_ui":"D001921","descriptor_name":"Brain","qualifier_ui":"Q000000981","qualifier_name":"diagnostic imaging","is_major_topic":true},{"descriptor_ui":"D001921","descriptor_name":"Brain","qualifier_ui":"Q000000981","qualifier_name":"diagnostic imaging","is_major_topic":true},{"descriptor_ui":"D005453","descriptor_name":"Fluorescence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005453","descriptor_name":"Fluorescence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005453","descriptor_name":"Fluorescence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005453","descriptor_name":"Fluorescence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005453","descriptor_name":"Fluorescence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008279","descriptor_name":"Magnetic Resonance Imaging","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008279","descriptor_name":"Magnetic Resonance Imaging","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008279","descriptor_name":"Magnetic Resonance Imaging","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008279","descriptor_name":"Magnetic Resonance Imaging","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008279","descriptor_name":"Magnetic Resonance Imaging","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1007/s12021-023-09638-2","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s12021-023-09638-2","pdf_url":"https://link.springer.com/content/pdf/10.1007/s12021-023-09638-2.pdf","source":{"id":"https://openalex.org/S3444786","display_name":"Neuroinformatics","issn_l":"1539-2791","issn":["1539-2791","1559-0089"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Neuroinformatics","raw_type":"journal-article"},{"id":"pmid:37394568","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37394568","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":"Neuroinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10582119","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10582119","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10582119/pdf/12021_2023_Article_9638.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":"Neuroinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1007/s12021-023-09638-2","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s12021-023-09638-2","pdf_url":"https://link.springer.com/content/pdf/10.1007/s12021-023-09638-2.pdf","source":{"id":"https://openalex.org/S3444786","display_name":"Neuroinformatics","issn_l":"1539-2791","issn":["1539-2791","1559-0089"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Neuroinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3664711276","display_name":null,"funder_award_id":"2031985","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"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/G6446039348","display_name":null,"funder_award_id":"RO1AG066184-01","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6474092033","display_name":null,"funder_award_id":"U19AG033655","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6552646818","display_name":null,"funder_award_id":"RF1MH121539","funder_id":"https://openalex.org/F4320337346","funder_display_name":"National Institute of Mental Health"},{"id":"https://openalex.org/G6671297155","display_name":null,"funder_award_id":"CAREER","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6755165505","display_name":null,"funder_award_id":"award","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6816467790","display_name":null,"funder_award_id":"K08MH113039","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7291171672","display_name":null,"funder_award_id":"RF1MH121539","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G848032724","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320325162","display_name":"NOMIS Stiftung","ror":"https://ror.org/01zkd3118"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337346","display_name":"National Institute of Mental Health","ror":"https://ror.org/04xeg9z08"},{"id":"https://openalex.org/F4320337347","display_name":"National Institute on Drug Abuse","ror":"https://ror.org/00fq5cm18"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4382893155.pdf"},"referenced_works_count":8,"referenced_works":["https://openalex.org/W1593532658","https://openalex.org/W2975634117","https://openalex.org/W3021105102","https://openalex.org/W3022214373","https://openalex.org/W3138257762","https://openalex.org/W3180424009","https://openalex.org/W3181631423","https://openalex.org/W3199687289"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W4391913857","https://openalex.org/W2350741829","https://openalex.org/W2530322880"],"abstract_inverted_index":null,"counts_by_year":[{"year":2023,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
