{"id":"https://openalex.org/W2153582254","doi":"https://doi.org/10.1109/isbi.2009.5193229","title":"Automated analysis of Human Protein Atlas immunofluorescence images","display_name":"Automated analysis of Human Protein Atlas immunofluorescence images","publication_year":2009,"publication_date":"2009-06-01","ids":{"openalex":"https://openalex.org/W2153582254","doi":"https://doi.org/10.1109/isbi.2009.5193229","mag":"2153582254","pmid":"https://pubmed.ncbi.nlm.nih.gov/20628548"},"language":"en","primary_location":{"id":"doi:10.1109/isbi.2009.5193229","is_oa":false,"landing_page_url":"https://doi.org/10.1109/isbi.2009.5193229","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2009 IEEE International Symposium on Biomedical Imaging: From Nano to Macro","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2901900","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5026835151","display_name":"Justin Y. Newberg","orcid":"https://orcid.org/0000-0002-3764-4956"},"institutions":[{"id":"https://openalex.org/I74973139","display_name":"Carnegie Mellon University","ror":"https://ror.org/05x2bcf33","country_code":"US","type":"education","lineage":["https://openalex.org/I74973139"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Justin Y. Newberg","raw_affiliation_strings":["Center for Bioimage Informatics and Dept. of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA, USA","Center of Bioimage Informatics and Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA, USA"],"affiliations":[{"raw_affiliation_string":"Center for Bioimage Informatics and Dept. of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA, USA","institution_ids":["https://openalex.org/I74973139"]},{"raw_affiliation_string":"Center of Bioimage Informatics and Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA, USA","institution_ids":["https://openalex.org/I74973139"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090480371","display_name":"Jieyue Li","orcid":"https://orcid.org/0000-0002-0108-6657"},"institutions":[{"id":"https://openalex.org/I74973139","display_name":"Carnegie Mellon University","ror":"https://ror.org/05x2bcf33","country_code":"US","type":"education","lineage":["https://openalex.org/I74973139"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jieyue Li","raw_affiliation_strings":["Center of Bioimage Informatics and Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA, USA"],"affiliations":[{"raw_affiliation_string":"Center of Bioimage Informatics and Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA, USA","institution_ids":["https://openalex.org/I74973139"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103572065","display_name":"Arvind Rao","orcid":null},"institutions":[{"id":"https://openalex.org/I74973139","display_name":"Carnegie Mellon University","ror":"https://ror.org/05x2bcf33","country_code":"US","type":"education","lineage":["https://openalex.org/I74973139"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Arvind Rao","raw_affiliation_strings":["Lane Center of Computer Biology and Departments of Biological Sciences and Machine Learning, Carnegie Mellon University, Pittsburgh, PA, USA"],"affiliations":[{"raw_affiliation_string":"Lane Center of Computer Biology and Departments of Biological Sciences and Machine Learning, Carnegie Mellon University, Pittsburgh, PA, USA","institution_ids":["https://openalex.org/I74973139"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005639182","display_name":"Fredrik Pont\u00e9n","orcid":"https://orcid.org/0000-0003-0703-3940"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Fredrik Ponten","raw_affiliation_strings":["Department of Genetics and Pathology, Rudbeck Laboratory, Rudbeck Laboratory, Uppsala, Sweden"],"affiliations":[{"raw_affiliation_string":"Department of Genetics and Pathology, Rudbeck Laboratory, Rudbeck Laboratory, Uppsala, Sweden","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060241561","display_name":"Mathias Uhl\u00e9n","orcid":"https://orcid.org/0000-0002-4858-8056"},"institutions":[{"id":"https://openalex.org/I86987016","display_name":"KTH Royal Institute of Technology","ror":"https://ror.org/026vcq606","country_code":"SE","type":"education","lineage":["https://openalex.org/I86987016"]},{"id":"https://openalex.org/I4210135511","display_name":"AlbaNova","ror":"https://ror.org/044kkfr75","country_code":"SE","type":"facility","lineage":["https://openalex.org/I4210135511"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Mathias Uhlen","raw_affiliation_strings":["Department of Biotechnology, AlbaNova University Center Royal Institute of Technology, Stockholm, Sweden"],"affiliations":[{"raw_affiliation_string":"Department of Biotechnology, AlbaNova University Center Royal Institute of Technology, Stockholm, Sweden","institution_ids":["https://openalex.org/I86987016","https://openalex.org/I4210135511"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052101351","display_name":"Emma Lundberg","orcid":"https://orcid.org/0000-0001-7034-0850"},"institutions":[{"id":"https://openalex.org/I86987016","display_name":"KTH Royal Institute of Technology","ror":"https://ror.org/026vcq606","country_code":"SE","type":"education","lineage":["https://openalex.org/I86987016"]},{"id":"https://openalex.org/I4210135511","display_name":"AlbaNova","ror":"https://ror.org/044kkfr75","country_code":"SE","type":"facility","lineage":["https://openalex.org/I4210135511"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Emma Lundberg","raw_affiliation_strings":["Department of Biotechnology, AlbaNova University Center Royal Institute of Technology, Stockholm, Sweden"],"affiliations":[{"raw_affiliation_string":"Department of Biotechnology, AlbaNova University Center Royal Institute of Technology, Stockholm, Sweden","institution_ids":["https://openalex.org/I86987016","https://openalex.org/I4210135511"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5061773929","display_name":"Robert F. Murphy","orcid":"https://orcid.org/0000-0003-0358-901X"},"institutions":[{"id":"https://openalex.org/I74973139","display_name":"Carnegie Mellon University","ror":"https://ror.org/05x2bcf33","country_code":"US","type":"education","lineage":["https://openalex.org/I74973139"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Robert F. Murphy","raw_affiliation_strings":["Center of Bioimage Informatics and Department of Biomedical Engineering, Lane Center of Computer Biol. and Departments of Biological Sciences and Machine Learning, Carnegie Mellon University, Pittsburgh, PA, USA"],"affiliations":[{"raw_affiliation_string":"Center of Bioimage Informatics and Department of Biomedical Engineering, Lane Center of Computer Biol. and Departments of Biological Sciences and Machine Learning, Carnegie Mellon University, Pittsburgh, PA, USA","institution_ids":["https://openalex.org/I74973139"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5026835151"],"corresponding_institution_ids":["https://openalex.org/I74973139"],"apc_list":null,"apc_paid":null,"fwci":4.9875,"has_fulltext":false,"cited_by_count":28,"citation_normalized_percentile":{"value":0.94305787,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"5193229","issue":null,"first_page":"1023","last_page":"1026"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.9998999834060669,"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":0.9998999834060669,"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/T13114","display_name":"Image Processing Techniques and Applications","score":0.9914000034332275,"subfield":{"id":"https://openalex.org/subfields/2214","display_name":"Media Technology"},"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/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.9896000027656555,"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/atlas","display_name":"Atlas (anatomy)","score":0.8663827776908875},{"id":"https://openalex.org/keywords/human-protein-atlas","display_name":"Human Protein Atlas","score":0.8124864101409912},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.712148904800415},{"id":"https://openalex.org/keywords/random-forest","display_name":"Random forest","score":0.6717467308044434},{"id":"https://openalex.org/keywords/support-vector-machine","display_name":"Support vector machine","score":0.6679973602294922},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.6199445724487305},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.5089735984802246},{"id":"https://openalex.org/keywords/contextual-image-classification","display_name":"Contextual image classification","score":0.4279515743255615},{"id":"https://openalex.org/keywords/human-proteins","display_name":"Human proteins","score":0.4128419756889343},{"id":"https://openalex.org/keywords/proteomics","display_name":"Proteomics","score":0.41201210021972656},{"id":"https://openalex.org/keywords/protein-expression","display_name":"Protein expression","score":0.1665293574333191},{"id":"https://openalex.org/keywords/image","display_name":"Image (mathematics)","score":0.16286316514015198},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.07943561673164368}],"concepts":[{"id":"https://openalex.org/C2776673561","wikidata":"https://www.wikidata.org/wiki/Q655357","display_name":"Atlas (anatomy)","level":2,"score":0.8663827776908875},{"id":"https://openalex.org/C158163496","wikidata":"https://www.wikidata.org/wiki/Q5937310","display_name":"Human Protein Atlas","level":4,"score":0.8124864101409912},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.712148904800415},{"id":"https://openalex.org/C169258074","wikidata":"https://www.wikidata.org/wiki/Q245748","display_name":"Random forest","level":2,"score":0.6717467308044434},{"id":"https://openalex.org/C12267149","wikidata":"https://www.wikidata.org/wiki/Q282453","display_name":"Support vector machine","level":2,"score":0.6679973602294922},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6199445724487305},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.5089735984802246},{"id":"https://openalex.org/C75294576","wikidata":"https://www.wikidata.org/wiki/Q5165192","display_name":"Contextual image classification","level":3,"score":0.4279515743255615},{"id":"https://openalex.org/C2911029443","wikidata":"https://www.wikidata.org/wiki/Q21296145","display_name":"Human proteins","level":3,"score":0.4128419756889343},{"id":"https://openalex.org/C46111723","wikidata":"https://www.wikidata.org/wiki/Q471857","display_name":"Proteomics","level":3,"score":0.41201210021972656},{"id":"https://openalex.org/C6856738","wikidata":"https://www.wikidata.org/wiki/Q331672","display_name":"Protein expression","level":3,"score":0.1665293574333191},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.16286316514015198},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.07943561673164368},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","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":4,"locations":[{"id":"doi:10.1109/isbi.2009.5193229","is_oa":false,"landing_page_url":"https://doi.org/10.1109/isbi.2009.5193229","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2009 IEEE International Symposium on Biomedical Imaging: From Nano to Macro","raw_type":"proceedings-article"},{"id":"pmid:20628548","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20628548","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":"Proceedings. IEEE International Symposium on Biomedical Imaging","raw_type":null},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.655.8932","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.655.8932","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2901900/pdf/nihms212411.pdf","raw_type":"text"},{"id":"pmh:oai:pubmedcentral.nih.gov:2901900","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2901900","pdf_url":null,"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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Proc IEEE Int Symp Biomed Imaging","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:2901900","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2901900","pdf_url":null,"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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Proc IEEE Int Symp Biomed Imaging","raw_type":"Text"},"sustainable_development_goals":[{"score":0.7599999904632568,"id":"https://metadata.un.org/sdg/15","display_name":"Life in Land"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337401","display_name":"Division of Emerging Frontiers","ror":"https://ror.org/01tnvpc68"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":12,"referenced_works":["https://openalex.org/W1890677866","https://openalex.org/W1984643873","https://openalex.org/W2000266578","https://openalex.org/W2007737306","https://openalex.org/W2106876831","https://openalex.org/W2113846729","https://openalex.org/W2116633773","https://openalex.org/W2123762916","https://openalex.org/W2135565251","https://openalex.org/W2145752049","https://openalex.org/W2153944330","https://openalex.org/W2911964244"],"related_works":["https://openalex.org/W3095316811","https://openalex.org/W2012758140","https://openalex.org/W2090672107","https://openalex.org/W2182694331","https://openalex.org/W2112224076","https://openalex.org/W2001939488","https://openalex.org/W2084348622","https://openalex.org/W1601898704","https://openalex.org/W2177273497","https://openalex.org/W2122863289"],"abstract_inverted_index":{"The":[0],"Human":[1],"Protein":[2],"Atlas":[3,29,55],"is":[4],"a":[5,58],"rich":[6],"source":[7],"of":[8,61,68,91],"location":[9],"proteomics":[10],"data.":[11],"In":[12],"this":[13],"work,":[14],"we":[15,50,81,103],"present":[16],"an":[17],"automated":[18,118],"approach":[19],"for":[20,66],"processing":[21],"and":[22,41,71,100],"classifying":[23],"major":[24],"subcellular":[25,48],"patterns":[26],"in":[27,77,89,117],"the":[28,69,86,106,109],"images.":[30],"We":[31],"demonstrate":[32],"that":[33,105],"two":[34],"different":[35],"classification":[36,79],"frameworks":[37,93],"(support":[38],"vector":[39],"machine":[40],"random":[42],"forest)":[43],"are":[44,82,94,114],"effective":[45],"at":[46],"determining":[47],"locations;":[49],"can":[51],"analyze":[52],"over":[53],"3500":[54],"images":[56],"with":[57],"high":[59],"degree":[60],"accuracy,":[62],"up":[63],"to":[64,96,111],"87.5%":[65],"all":[67],"samples":[70,76],"98.5%":[72],"when":[73],"only":[74],"considering":[75],"whose":[78],"assignments":[80],"most":[83],"confident.":[84],"Moreover,":[85],"features":[87,107],"obtained":[88],"both":[90],"these":[92],"observed":[95],"be":[97],"highly":[98],"consistent":[99],"generalizable.":[101],"Additionally,":[102],"observe":[104],"relating":[108],"proteins":[110],"cell":[112],"markers":[113],"especially":[115],"important":[116],"learning":[119],"approaches.":[120]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":4},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":4}],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2025-10-10T00:00:00"}
