{"id":"https://openalex.org/W2075405183","doi":"https://doi.org/10.1117/12.2043653","title":"Automatic registration of imaging mass spectrometry data to the Allen Brain Atlas transcriptome","display_name":"Automatic registration of imaging mass spectrometry data to the Allen Brain Atlas transcriptome","publication_year":2014,"publication_date":"2014-03-21","ids":{"openalex":"https://openalex.org/W2075405183","doi":"https://doi.org/10.1117/12.2043653","mag":"2075405183"},"language":"en","primary_location":{"id":"doi:10.1117/12.2043653","is_oa":false,"landing_page_url":"https://doi.org/10.1117/12.2043653","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/A5077410286","display_name":"Walid M. Abdelmoula","orcid":"https://orcid.org/0000-0003-3117-7389"},"institutions":[{"id":"https://openalex.org/I121797337","display_name":"Leiden University","ror":"https://ror.org/027bh9e22","country_code":"NL","type":"education","lineage":["https://openalex.org/I121797337"]}],"countries":["NL"],"is_corresponding":true,"raw_author_name":"Walid M. Abdelmoula","raw_affiliation_strings":["Leiden Univ. Medical Ctr. (Netherlands)","Leiden Univ. Medical Ctr., Netherlands"],"affiliations":[{"raw_affiliation_string":"Leiden Univ. Medical Ctr. (Netherlands)","institution_ids":["https://openalex.org/I121797337"]},{"raw_affiliation_string":"Leiden Univ. Medical Ctr., Netherlands","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102891233","display_name":"Ricardo J. Carreira","orcid":"https://orcid.org/0000-0002-7705-1354"},"institutions":[{"id":"https://openalex.org/I121797337","display_name":"Leiden University","ror":"https://ror.org/027bh9e22","country_code":"NL","type":"education","lineage":["https://openalex.org/I121797337"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Ricardo J. Carreira","raw_affiliation_strings":["Leiden Univ. Medical Ctr. (Netherlands)","Leiden Univ. Medical Ctr., Netherlands"],"affiliations":[{"raw_affiliation_string":"Leiden Univ. Medical Ctr. (Netherlands)","institution_ids":["https://openalex.org/I121797337"]},{"raw_affiliation_string":"Leiden Univ. Medical Ctr., Netherlands","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048475082","display_name":"Reinald Shyti","orcid":"https://orcid.org/0000-0002-1888-8656"},"institutions":[{"id":"https://openalex.org/I121797337","display_name":"Leiden University","ror":"https://ror.org/027bh9e22","country_code":"NL","type":"education","lineage":["https://openalex.org/I121797337"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Reinald Shyti","raw_affiliation_strings":["Leiden Univ. Medical Ctr. (Netherlands)","Leiden Univ. Medical Ctr., Netherlands"],"affiliations":[{"raw_affiliation_string":"Leiden Univ. Medical Ctr. (Netherlands)","institution_ids":["https://openalex.org/I121797337"]},{"raw_affiliation_string":"Leiden Univ. Medical Ctr., Netherlands","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010335172","display_name":"Benjamin Balluff","orcid":"https://orcid.org/0000-0003-0351-240X"},"institutions":[{"id":"https://openalex.org/I121797337","display_name":"Leiden University","ror":"https://ror.org/027bh9e22","country_code":"NL","type":"education","lineage":["https://openalex.org/I121797337"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Benjamin Balluff","raw_affiliation_strings":["Leiden Univ. Medical Ctr. (Netherlands)","Leiden Univ. Medical Ctr., Netherlands"],"affiliations":[{"raw_affiliation_string":"Leiden Univ. Medical Ctr. (Netherlands)","institution_ids":["https://openalex.org/I121797337"]},{"raw_affiliation_string":"Leiden Univ. Medical Ctr., Netherlands","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090031681","display_name":"Else A. Tolner","orcid":"https://orcid.org/0000-0002-6501-9971"},"institutions":[{"id":"https://openalex.org/I121797337","display_name":"Leiden University","ror":"https://ror.org/027bh9e22","country_code":"NL","type":"education","lineage":["https://openalex.org/I121797337"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Else Tolner","raw_affiliation_strings":["Leiden Univ. Medical Ctr. (Netherlands)","Leiden Univ. Medical Ctr., Netherlands"],"affiliations":[{"raw_affiliation_string":"Leiden Univ. Medical Ctr. (Netherlands)","institution_ids":["https://openalex.org/I121797337"]},{"raw_affiliation_string":"Leiden Univ. Medical Ctr., Netherlands","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050164405","display_name":"Anouk den Braber","orcid":"https://orcid.org/0000-0002-3377-2627"},"institutions":[{"id":"https://openalex.org/I121797337","display_name":"Leiden University","ror":"https://ror.org/027bh9e22","country_code":"NL","type":"education","lineage":["https://openalex.org/I121797337"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Arn M. J. M. van den Maagdenberg","raw_affiliation_strings":["Leiden Univ. Medical Ctr. (Netherlands)","Leiden Univ. Medical Ctr., Netherlands"],"affiliations":[{"raw_affiliation_string":"Leiden Univ. Medical Ctr. (Netherlands)","institution_ids":["https://openalex.org/I121797337"]},{"raw_affiliation_string":"Leiden Univ. Medical Ctr., Netherlands","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019003563","display_name":"Boudewijn P. F. Lelieveldt","orcid":"https://orcid.org/0000-0001-8269-7603"},"institutions":[{"id":"https://openalex.org/I121797337","display_name":"Leiden University","ror":"https://ror.org/027bh9e22","country_code":"NL","type":"education","lineage":["https://openalex.org/I121797337"]},{"id":"https://openalex.org/I98358874","display_name":"Delft University of Technology","ror":"https://ror.org/02e2c7k09","country_code":"NL","type":"education","lineage":["https://openalex.org/I98358874"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"B. P. F. Lelieveldt","raw_affiliation_strings":["Delft Univ. of Technology (Netherlands)","Leiden Univ. Medical Ctr. (Netherlands)"],"affiliations":[{"raw_affiliation_string":"Delft Univ. of Technology (Netherlands)","institution_ids":["https://openalex.org/I98358874"]},{"raw_affiliation_string":"Leiden Univ. Medical Ctr. (Netherlands)","institution_ids":["https://openalex.org/I121797337"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087234831","display_name":"Liam A. McDonnell","orcid":"https://orcid.org/0000-0003-0595-9491"},"institutions":[{"id":"https://openalex.org/I121797337","display_name":"Leiden University","ror":"https://ror.org/027bh9e22","country_code":"NL","type":"education","lineage":["https://openalex.org/I121797337"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Liam McDonnell","raw_affiliation_strings":["Leiden Univ. Medical Ctr. (Netherlands)","Leiden Univ. Medical Ctr., Netherlands"],"affiliations":[{"raw_affiliation_string":"Leiden Univ. Medical Ctr. (Netherlands)","institution_ids":["https://openalex.org/I121797337"]},{"raw_affiliation_string":"Leiden Univ. Medical Ctr., Netherlands","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5003711050","display_name":"Jouke Dijkstra","orcid":"https://orcid.org/0000-0002-8666-3731"},"institutions":[{"id":"https://openalex.org/I121797337","display_name":"Leiden University","ror":"https://ror.org/027bh9e22","country_code":"NL","type":"education","lineage":["https://openalex.org/I121797337"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Jouke Dijkstra","raw_affiliation_strings":["Leiden Univ. Medical Ctr. (Netherlands)","Leiden Univ. Medical Ctr., Netherlands"],"affiliations":[{"raw_affiliation_string":"Leiden Univ. Medical Ctr. (Netherlands)","institution_ids":["https://openalex.org/I121797337"]},{"raw_affiliation_string":"Leiden Univ. Medical Ctr., Netherlands","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5077410286"],"corresponding_institution_ids":["https://openalex.org/I121797337"],"apc_list":null,"apc_paid":null,"fwci":0.2789,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.59208268,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"9034","issue":null,"first_page":"90343M","last_page":"90343M"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.9891999959945679,"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"}},"topics":[{"id":"https://openalex.org/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.9891999959945679,"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.9890999794006348,"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/T10627","display_name":"Advanced Image and Video Retrieval Techniques","score":0.9879000186920166,"subfield":{"id":"https://openalex.org/subfields/1707","display_name":"Computer Vision and Pattern Recognition"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/mass-spectrometry-imaging","display_name":"Mass spectrometry imaging","score":0.7536367177963257},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7446295022964478},{"id":"https://openalex.org/keywords/brain-atlas","display_name":"Brain atlas","score":0.6843017339706421},{"id":"https://openalex.org/keywords/atlas","display_name":"Atlas (anatomy)","score":0.6727168560028076},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.6358771324157715},{"id":"https://openalex.org/keywords/image-registration","display_name":"Image registration","score":0.6210371255874634},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.6024664044380188},{"id":"https://openalex.org/keywords/pixel","display_name":"Pixel","score":0.5011322498321533},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.47029921412467957},{"id":"https://openalex.org/keywords/neuroimaging","display_name":"Neuroimaging","score":0.46587488055229187},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.45404282212257385},{"id":"https://openalex.org/keywords/human-protein-atlas","display_name":"Human Protein Atlas","score":0.4194454550743103},{"id":"https://openalex.org/keywords/computer-vision","display_name":"Computer vision","score":0.4006612002849579},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3656327724456787},{"id":"https://openalex.org/keywords/mass-spectrometry","display_name":"Mass spectrometry","score":0.19799286127090454},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.17079535126686096},{"id":"https://openalex.org/keywords/protein-expression","display_name":"Protein expression","score":0.16340109705924988},{"id":"https://openalex.org/keywords/neuroscience","display_name":"Neuroscience","score":0.15414530038833618},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.14914441108703613},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.14325052499771118},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.1243409514427185},{"id":"https://openalex.org/keywords/anatomy","display_name":"Anatomy","score":0.10538512468338013},{"id":"https://openalex.org/keywords/image","display_name":"Image (mathematics)","score":0.08527633547782898}],"concepts":[{"id":"https://openalex.org/C24066741","wikidata":"https://www.wikidata.org/wiki/Q3796564","display_name":"Mass spectrometry imaging","level":3,"score":0.7536367177963257},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7446295022964478},{"id":"https://openalex.org/C2780972224","wikidata":"https://www.wikidata.org/wiki/Q17047956","display_name":"Brain atlas","level":2,"score":0.6843017339706421},{"id":"https://openalex.org/C2776673561","wikidata":"https://www.wikidata.org/wiki/Q655357","display_name":"Atlas (anatomy)","level":2,"score":0.6727168560028076},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.6358771324157715},{"id":"https://openalex.org/C166704113","wikidata":"https://www.wikidata.org/wiki/Q861092","display_name":"Image registration","level":3,"score":0.6210371255874634},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6024664044380188},{"id":"https://openalex.org/C160633673","wikidata":"https://www.wikidata.org/wiki/Q355198","display_name":"Pixel","level":2,"score":0.5011322498321533},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.47029921412467957},{"id":"https://openalex.org/C58693492","wikidata":"https://www.wikidata.org/wiki/Q551875","display_name":"Neuroimaging","level":2,"score":0.46587488055229187},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.45404282212257385},{"id":"https://openalex.org/C158163496","wikidata":"https://www.wikidata.org/wiki/Q5937310","display_name":"Human Protein Atlas","level":4,"score":0.4194454550743103},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.4006612002849579},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3656327724456787},{"id":"https://openalex.org/C162356407","wikidata":"https://www.wikidata.org/wiki/Q180809","display_name":"Mass spectrometry","level":2,"score":0.19799286127090454},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.17079535126686096},{"id":"https://openalex.org/C6856738","wikidata":"https://www.wikidata.org/wiki/Q331672","display_name":"Protein expression","level":3,"score":0.16340109705924988},{"id":"https://openalex.org/C169760540","wikidata":"https://www.wikidata.org/wiki/Q207011","display_name":"Neuroscience","level":1,"score":0.15414530038833618},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.14914441108703613},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.14325052499771118},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.1243409514427185},{"id":"https://openalex.org/C105702510","wikidata":"https://www.wikidata.org/wiki/Q514","display_name":"Anatomy","level":1,"score":0.10538512468338013},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.08527633547782898},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1117/12.2043653","is_oa":false,"landing_page_url":"https://doi.org/10.1117/12.2043653","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":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":9,"referenced_works":["https://openalex.org/W2003410902","https://openalex.org/W2034432063","https://openalex.org/W2055974891","https://openalex.org/W2072645055","https://openalex.org/W2131184257","https://openalex.org/W2133287637","https://openalex.org/W2147950119","https://openalex.org/W2153475143","https://openalex.org/W4230102617"],"related_works":["https://openalex.org/W3214912135","https://openalex.org/W4387252449","https://openalex.org/W2012519212","https://openalex.org/W4249039539","https://openalex.org/W1523541591","https://openalex.org/W2592984741","https://openalex.org/W2582837249","https://openalex.org/W1967068856","https://openalex.org/W1592689442","https://openalex.org/W2055554484"],"abstract_inverted_index":{"Imaging":[0],"Mass":[1],"Spectrometry":[2],"(IMS)":[3],"is":[4,129,170],"an":[5],"emerging":[6],"molecular":[7,24],"imaging":[8],"technology":[9],"that":[10],"provides":[11],"spatially":[12,55,97],"resolved":[13,56],"information":[14],"on":[15,40,141,210],"biomolecular":[16,42],"structures;":[17],"each":[18],"image":[19],"pixel":[20],"effectively":[21],"represents":[22],"a":[23,112,148,195],"mass":[25],"spectrum.":[26],"By":[27],"combining":[28],"the":[29,61,67,102,127,130,133,138,153,163,173,182,186,199,204,223,233],"histological":[30,156],"images":[31],"and":[32,79,86,177],"IMS-images,":[33],"neuroanatomical":[34],"structures":[35],"can":[36],"be":[37,93],"distinguished":[38],"based":[39,140],"their":[41],"features":[43],"as":[44,64],"opposed":[45],"to":[46,96,101,117,121,158,172,184,203],"morphological":[47],"features.":[48],"The":[49,206],"combination":[50],"of":[51,60,76,126,132,198,225],"IMS":[52,99,201],"data":[53],"with":[54,232],"gene":[57,80],"expression":[58,81],"maps":[59],"mouse":[62,216],"brain,":[63],"provided":[65],"by":[66],"Allen":[68,103],"Mouse":[69],"Brain":[70,104],"atlas,":[71],"would":[72,92],"enable":[73],"comparative":[74],"studies":[75],"spatial":[77],"metabolic":[78],"patterns":[82],"in":[83,181],"life-sciences":[84],"research":[85],"biomarker":[87],"discovery.":[88],"As":[89],"such,":[90],"it":[91,161],"highly":[94],"desirable":[95],"register":[98,118],"slices":[100],"Atlas":[105],"(ABA).":[106],"In":[107],"this":[108],"paper,":[109],"we":[110,146],"propose":[111],"multi-step":[113],"automatic":[114],"registration":[115,169,193],"pipeline":[116,207],"ABA":[119,164,183,235],"histology":[120,143],"IMS-":[122],"images.":[123],"Key":[124],"novelty":[125],"method":[128],"selection":[131],"best":[134],"reference":[135,189],"section":[136,157,176],"from":[137,152,214,229],"ABA,":[139],"pre-processed":[142],"sections.":[144,165],"First,":[145],"extracted":[147],"hippocampus-specific":[149],"geometrical":[150],"feature":[151],"given":[154],"experimental":[155,200],"initially":[159,174],"localize":[160],"among":[162],"Then,":[166],"feature-based":[167],"linear":[168],"applied":[171,209],"localized":[175],"its":[178],"two":[179,215],"neighbors":[180],"select":[185],"most":[187],"similar":[188],"section.":[190],"A":[191],"non-rigid":[192],"yields":[194],"one-to-one":[196],"mapping":[197],"slice":[202],"ABA.":[205],"was":[208],"6":[211],"coronal":[212],"sections":[213],"brains,":[217],"showing":[218],"high":[219],"anatomical":[220],"correspondence,":[221],"demonstrating":[222],"feasibility":[224],"complementing":[226],"biomolecule":[227],"distributions":[228],"individual":[230],"mice":[231],"genome-wide":[234],"transcriptome.":[236]},"counts_by_year":[{"year":2016,"cited_by_count":1},{"year":2014,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
