{"id":"https://openalex.org/W2329635162","doi":"https://doi.org/10.1117/12.2216233","title":"An image registration pipeline for analysis of transsynaptic tracing in mice","display_name":"An image registration pipeline for analysis of transsynaptic tracing in mice","publication_year":2016,"publication_date":"2016-03-29","ids":{"openalex":"https://openalex.org/W2329635162","doi":"https://doi.org/10.1117/12.2216233","mag":"2329635162"},"language":"en","primary_location":{"id":"doi:10.1117/12.2216233","is_oa":false,"landing_page_url":"https://doi.org/10.1117/12.2216233","pdf_url":null,"source":{"id":"https://openalex.org/S183492911","display_name":"Proceedings of SPIE, the International Society for Optical Engineering/Proceedings of SPIE","issn_l":"0277-786X","issn":["0277-786X","1996-756X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310315543","host_organization_name":"SPIE","host_organization_lineage":["https://openalex.org/P4310315543"],"host_organization_lineage_names":["SPIE"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"SPIE Proceedings","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5007745285","display_name":"Kwame S. Kutten","orcid":"https://orcid.org/0000-0001-6735-1460"},"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":true,"raw_author_name":"Kwame S. Kutten","raw_affiliation_strings":["Johns Hopkins Univ. (United States)"],"affiliations":[{"raw_affiliation_string":"Johns Hopkins Univ. (United States)","institution_ids":["https://openalex.org/I145311948"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039159447","display_name":"Stephen Eacker","orcid":"https://orcid.org/0000-0002-9678-1192"},"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/I4210157164","display_name":"Orthopaedic Research Foundation","ror":"https://ror.org/05wxfpw56","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210157164"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Stephen M. Eacker","raw_affiliation_strings":["Diana Helis Henry Medical Research Foundation (United States)","Johns Hopkins Univ. (United States)"],"affiliations":[{"raw_affiliation_string":"Diana Helis Henry Medical Research Foundation (United States)","institution_ids":["https://openalex.org/I4210157164"]},{"raw_affiliation_string":"Johns Hopkins Univ. (United States)","institution_ids":["https://openalex.org/I145311948"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025568267","display_name":"Valina L. Dawson","orcid":"https://orcid.org/0000-0002-2915-3970"},"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/I4210157164","display_name":"Orthopaedic Research Foundation","ror":"https://ror.org/05wxfpw56","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210157164"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Valina L. Dawson","raw_affiliation_strings":["Diana Helis Henry Medical Research Foundation (United States)","Johns Hopkins Univ. (United States)"],"affiliations":[{"raw_affiliation_string":"Diana Helis Henry Medical Research Foundation (United States)","institution_ids":["https://openalex.org/I4210157164"]},{"raw_affiliation_string":"Johns Hopkins Univ. (United States)","institution_ids":["https://openalex.org/I145311948"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021759485","display_name":"Ted M. Dawson","orcid":"https://orcid.org/0000-0002-6459-0893"},"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/I4210157164","display_name":"Orthopaedic Research Foundation","ror":"https://ror.org/05wxfpw56","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210157164"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ted M. Dawson","raw_affiliation_strings":["Diana Helis Henry Medical Research Foundation (United States)","Johns Hopkins Univ. (United States)"],"affiliations":[{"raw_affiliation_string":"Diana Helis Henry Medical Research Foundation (United States)","institution_ids":["https://openalex.org/I4210157164"]},{"raw_affiliation_string":"Johns Hopkins Univ. (United States)","institution_ids":["https://openalex.org/I145311948"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085896998","display_name":"J. Tilak Ratnanather","orcid":"https://orcid.org/0000-0002-8631-489X"},"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":"Tilak Ratnanather","raw_affiliation_strings":["Johns Hopkins Univ. (United States)"],"affiliations":[{"raw_affiliation_string":"Johns Hopkins Univ. (United States)","institution_ids":["https://openalex.org/I145311948"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5033151214","display_name":"Michael I. Miller","orcid":"https://orcid.org/0000-0003-4689-3855"},"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":"Michael I. Miller","raw_affiliation_strings":["Johns Hopkins Univ. (United States)"],"affiliations":[{"raw_affiliation_string":"Johns Hopkins Univ. (United States)","institution_ids":["https://openalex.org/I145311948"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5007745285"],"corresponding_institution_ids":["https://openalex.org/I145311948"],"apc_list":null,"apc_paid":null,"fwci":0.4821,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.83538012,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"9788","issue":null,"first_page":"978823","last_page":"978823"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.9987000226974487,"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":0.9987000226974487,"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":0.9951000213623047,"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/T10077","display_name":"Neuroscience and Neuropharmacology Research","score":0.993399977684021,"subfield":{"id":"https://openalex.org/subfields/2804","display_name":"Cellular and Molecular 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/substantia-nigra","display_name":"Substantia nigra","score":0.6663469076156616},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6165697574615479},{"id":"https://openalex.org/keywords/computer-vision","display_name":"Computer vision","score":0.6146149635314941},{"id":"https://openalex.org/keywords/tracing","display_name":"Tracing","score":0.5903341770172119},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5855344533920288},{"id":"https://openalex.org/keywords/image-registration","display_name":"Image registration","score":0.5409955978393555},{"id":"https://openalex.org/keywords/pars-compacta","display_name":"Pars compacta","score":0.5082942843437195},{"id":"https://openalex.org/keywords/locus-coeruleus","display_name":"Locus coeruleus","score":0.5010097026824951},{"id":"https://openalex.org/keywords/preprocessor","display_name":"Preprocessor","score":0.4962826371192932},{"id":"https://openalex.org/keywords/brain-atlas","display_name":"Brain atlas","score":0.4633638560771942},{"id":"https://openalex.org/keywords/neuroscience","display_name":"Neuroscience","score":0.4417320489883423},{"id":"https://openalex.org/keywords/putamen","display_name":"Putamen","score":0.4356832206249237},{"id":"https://openalex.org/keywords/neuroimaging","display_name":"Neuroimaging","score":0.415914386510849},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.3482714593410492},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.21412822604179382},{"id":"https://openalex.org/keywords/dopamine","display_name":"Dopamine","score":0.15436726808547974},{"id":"https://openalex.org/keywords/central-nervous-system","display_name":"Central nervous system","score":0.10989013314247131},{"id":"https://openalex.org/keywords/image","display_name":"Image (mathematics)","score":0.09086164832115173}],"concepts":[{"id":"https://openalex.org/C2780938664","wikidata":"https://www.wikidata.org/wiki/Q753278","display_name":"Substantia nigra","level":4,"score":0.6663469076156616},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6165697574615479},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.6146149635314941},{"id":"https://openalex.org/C138673069","wikidata":"https://www.wikidata.org/wiki/Q322229","display_name":"Tracing","level":2,"score":0.5903341770172119},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5855344533920288},{"id":"https://openalex.org/C166704113","wikidata":"https://www.wikidata.org/wiki/Q861092","display_name":"Image registration","level":3,"score":0.5409955978393555},{"id":"https://openalex.org/C2776773494","wikidata":"https://www.wikidata.org/wiki/Q3366041","display_name":"Pars compacta","level":5,"score":0.5082942843437195},{"id":"https://openalex.org/C2778468602","wikidata":"https://www.wikidata.org/wiki/Q1470452","display_name":"Locus coeruleus","level":3,"score":0.5010097026824951},{"id":"https://openalex.org/C34736171","wikidata":"https://www.wikidata.org/wiki/Q918333","display_name":"Preprocessor","level":2,"score":0.4962826371192932},{"id":"https://openalex.org/C2780972224","wikidata":"https://www.wikidata.org/wiki/Q17047956","display_name":"Brain atlas","level":2,"score":0.4633638560771942},{"id":"https://openalex.org/C169760540","wikidata":"https://www.wikidata.org/wiki/Q207011","display_name":"Neuroscience","level":1,"score":0.4417320489883423},{"id":"https://openalex.org/C2779714222","wikidata":"https://www.wikidata.org/wiki/Q550934","display_name":"Putamen","level":2,"score":0.4356832206249237},{"id":"https://openalex.org/C58693492","wikidata":"https://www.wikidata.org/wiki/Q551875","display_name":"Neuroimaging","level":2,"score":0.415914386510849},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3482714593410492},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.21412822604179382},{"id":"https://openalex.org/C513476851","wikidata":"https://www.wikidata.org/wiki/Q170304","display_name":"Dopamine","level":2,"score":0.15436726808547974},{"id":"https://openalex.org/C529278444","wikidata":"https://www.wikidata.org/wiki/Q47273","display_name":"Central nervous system","level":2,"score":0.10989013314247131},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.09086164832115173},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C137183658","wikidata":"https://www.wikidata.org/wiki/Q461076","display_name":"Dopaminergic","level":3,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1117/12.2216233","is_oa":false,"landing_page_url":"https://doi.org/10.1117/12.2216233","pdf_url":null,"source":{"id":"https://openalex.org/S183492911","display_name":"Proceedings of SPIE, the International Society for Optical Engineering/Proceedings of SPIE","issn_l":"0277-786X","issn":["0277-786X","1996-756X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310315543","host_organization_name":"SPIE","host_organization_lineage":["https://openalex.org/P4310315543"],"host_organization_lineage_names":["SPIE"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"SPIE Proceedings","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3","score":0.6299999952316284}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":21,"referenced_works":["https://openalex.org/W1970928383","https://openalex.org/W1975379532","https://openalex.org/W1982535961","https://openalex.org/W1997128521","https://openalex.org/W2002506451","https://openalex.org/W2006896953","https://openalex.org/W2020230579","https://openalex.org/W2024524081","https://openalex.org/W2026892575","https://openalex.org/W2054870083","https://openalex.org/W2102099319","https://openalex.org/W2104612543","https://openalex.org/W2123491442","https://openalex.org/W2156875677","https://openalex.org/W2164826784","https://openalex.org/W2170167891","https://openalex.org/W4240271001","https://openalex.org/W6643071648","https://openalex.org/W6647375556","https://openalex.org/W6655546516","https://openalex.org/W6684167227"],"related_works":["https://openalex.org/W2178039548","https://openalex.org/W2359931691","https://openalex.org/W3049065873","https://openalex.org/W154169386","https://openalex.org/W2884144427","https://openalex.org/W4248431072","https://openalex.org/W2035149159","https://openalex.org/W2383678931","https://openalex.org/W2067317860","https://openalex.org/W1974898145"],"abstract_inverted_index":{"Parkinson's":[0],"Disease":[1],"(PD)":[2],"is":[3],"a":[4,51,70,88,109,158],"movement":[5],"disorder":[6],"characterized":[7],"by":[8,162],"the":[9,15,25,32,36,40,79,85,93,106,115,129,172,175],"loss":[10],"of":[11,34,39,81,101,157,171],"dopamine":[12],"neurons":[13,23,38,83],"in":[14,24,48,84],"substantia":[16],"nigra":[17],"pars":[18],"compacta":[19],"(SNpc)":[20],"and":[21,42,57,69],"norepinephrine":[22],"locus":[26],"coeruleus":[27],"(LC).":[28],"To":[29],"further":[30],"understand":[31],"pathophysiology":[33],"PD,":[35],"input":[37,82],"SNpc":[41],"LC":[43],"will":[44],"be":[45,74,180],"transsynapticly":[46],"traced":[47],"mice":[49],"using":[50,59,119,131],"fluorescent":[52],"recombinant":[53],"rabies":[54],"virus":[55,165],"(RbV)":[56],"imaged":[58],"serial":[60],"two-photon":[61],"tomography":[62],"(STP).":[63],"A":[64],"mapping":[65],"between":[66,146],"these":[67,99],"images":[68,102,118],"brain":[71,110,160],"atlas":[72],"must":[73],"found":[75,178],"to":[76,91,98,128,179],"accurately":[77],"determine":[78],"locations":[80],"brain.":[86],"Therefore":[87],"registration":[89,173],"pipeline":[90,149,176],"align":[92],"Allen":[94],"Reference":[95],"Atlas":[96],"(ARA)":[97],"types":[100],"was":[103,112,150,177],"developed.":[104],"In":[105],"preprocessing":[107],"step,":[108],"mask":[111],"generated":[113],"from":[114],"transsynaptic":[116,185],"tracing":[117],"simple":[120],"morphological":[121],"operators.":[122],"The":[123,148],"masks":[124],"were":[125],"then":[126,151],"registered":[127],"ARA":[130],"Large":[132],"Deformation":[133],"Diffeomorphic":[134],"Metric":[135],"Mapping":[136],"(LDDMM),":[137],"an":[138,154,163],"algorithm":[139],"specialized":[140],"for":[141,182],"calculating":[142],"anatomically":[143],"realistic":[144],"transforms":[145],"images.":[147],"tested":[152],"on":[153,168],"STP":[155],"scan":[156],"mouse":[159],"labeled":[161],"adeno-associated":[164],"(AAV).":[166],"Based":[167],"qualitative":[169],"evaluation":[170],"results,":[174],"sufficient":[181],"use":[183],"with":[184],"RbV":[186],"tracing.":[187]},"counts_by_year":[{"year":2016,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
