{"id":"https://openalex.org/W1941998953","doi":"https://doi.org/10.1111/jmi.12010","title":"Automated classification and visualization of fluorescent live cell microscopy images","display_name":"Automated classification and visualization of fluorescent live cell microscopy images","publication_year":2013,"publication_date":"2013-01-16","ids":{"openalex":"https://openalex.org/W1941998953","doi":"https://doi.org/10.1111/jmi.12010","mag":"1941998953","pmid":"https://pubmed.ncbi.nlm.nih.gov/23323688"},"language":"en","primary_location":{"id":"doi:10.1111/jmi.12010","doi":"https://doi.org/10.1111/jmi.12010","is_oa":false,"landing_page_url":"https://doi.org/10.1111/jmi.12010","pdf_url":null,"source":{"id":"https://openalex.org/S168975578","display_name":"Journal of Microscopy","issn_l":"0022-2720","issn":["0022-2720","1365-2818"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-d","jufo-1","ki-jl-1","medline","norway-1","poland-100","russia-white-list-2","vabb-shw"],"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Microscopy","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref","pubmed"],"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/A5084220653","display_name":"Kenneth L. Urish","orcid":"https://orcid.org/0000-0002-4511-1308","observed_orcids":["https://orcid.org/0000-0002-4511-1308"]},"institutions":[{"id":"https://openalex.org/I130769515","display_name":"Pennsylvania State University","ror":"https://ror.org/04p491231","country_code":"US","type":"education","lineage":["https://openalex.org/I130769515"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"K. L. URISH","raw_affiliation_strings":["Department of Orthopaedic Surgery and Rehabilitation, Division of Musculoskeletal Sciences, College of Medicine, The Pennsylvania State University, Hershey, Pennsylvania, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Orthopaedic Surgery and Rehabilitation, Division of Musculoskeletal Sciences, College of Medicine, The Pennsylvania State University, Hershey, Pennsylvania, USA","institution_ids":["https://openalex.org/I130769515"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002448467","display_name":"Bridget M. Deasy","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"B. M. DEASY","raw_affiliation_strings":["Department of Bioengineering, University of Pittsburgh, Pittsburgh, Pennsylvania, U.S.A","Stem Cell Research Center, University of Pittsburgh, Pennsylvania, U.S.A"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of Pittsburgh, Pittsburgh, Pennsylvania, U.S.A","institution_ids":["https://openalex.org/I170201317"]},{"raw_affiliation_string":"Stem Cell Research Center, University of Pittsburgh, Pennsylvania, U.S.A","institution_ids":["https://openalex.org/I170201317"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5103016781","display_name":"Johnny Huard","orcid":"https://orcid.org/0000-0003-1087-3342","observed_orcids":["https://orcid.org/0000-0003-1087-3342"]},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"J. HUARD","raw_affiliation_strings":["Department of Bioengineering, University of Pittsburgh, Pittsburgh, Pennsylvania, U.S.A","Department of Orthopaedic Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania, U.S.A","Stem Cell Research Center, University of Pittsburgh, Pennsylvania, U.S.A"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of Pittsburgh, Pittsburgh, Pennsylvania, U.S.A","institution_ids":["https://openalex.org/I170201317"]},{"raw_affiliation_string":"Department of Orthopaedic Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania, U.S.A","institution_ids":["https://openalex.org/I170201317"]},{"raw_affiliation_string":"Stem Cell Research Center, University of Pittsburgh, Pennsylvania, U.S.A","institution_ids":["https://openalex.org/I170201317"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5103016781"],"corresponding_institution_ids":["https://openalex.org/I170201317"],"apc_list":{"value":4760,"currency":"USD","value_usd":4760},"apc_paid":null,"fwci":0.4041,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.62874592,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"249","issue":"3","first_page":"206","last_page":"214"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":1.0,"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":1.0,"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/T12874","display_name":"Digital Imaging for Blood Diseases","score":0.0,"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"}},{"id":"https://openalex.org/T10540","display_name":"Advanced Fluorescence Microscopy Techniques","score":0.0,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/automatic-image-classification","display_name":"automated image classification","score":0.7559999823570251},{"id":"https://openalex.org/keywords/live-cell-imaging","display_name":"live-cell imaging","score":0.6850000023841858},{"id":"https://openalex.org/keywords/high-throughput-microscopy","display_name":"high-throughput imaging","score":0.8299999833106995},{"id":"https://openalex.org/keywords/image-segmentation","display_name":"image segmentation","score":0.49399998784065247},{"id":"https://openalex.org/keywords/gating","display_name":"gating","score":0.6000000238418579},{"id":"https://openalex.org/keywords/fluorescence-intensity","display_name":"fluorescence intensity","score":0.722000002861023},{"id":"https://openalex.org/keywords/apoptosis","display_name":"apoptosis","score":0.625},{"id":"https://openalex.org/keywords/staurosporine","display_name":"staurosporine","score":0.9660000205039978},{"id":"https://openalex.org/keywords/myoblasts","display_name":"myoblasts","score":0.7799999713897705},{"id":"https://openalex.org/keywords/open-source-image-analysis-software","display_name":"open-source image analysis software","score":0.7329999804496765},{"id":"https://openalex.org/keywords/small-molecule-screening","display_name":"small molecule screening","score":0.6140000224113464}],"concepts":[{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.641381561756134},{"id":"https://openalex.org/C553184892","wikidata":"https://www.wikidata.org/wiki/Q1141429","display_name":"Flow cytometry","level":2,"score":0.6348135471343994},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6107065081596375},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.6005668044090271},{"id":"https://openalex.org/C147080431","wikidata":"https://www.wikidata.org/wiki/Q1074953","display_name":"Microscopy","level":2,"score":0.5855575799942017},{"id":"https://openalex.org/C169274487","wikidata":"https://www.wikidata.org/wiki/Q840211","display_name":"Fluorescence microscope","level":3,"score":0.5391734838485718},{"id":"https://openalex.org/C2780339063","wikidata":"https://www.wikidata.org/wiki/Q5201367","display_name":"Cytometry","level":3,"score":0.5085951089859009},{"id":"https://openalex.org/C157764524","wikidata":"https://www.wikidata.org/wiki/Q1383412","display_name":"Throughput","level":3,"score":0.4786168932914734},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4465668499469757},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.4265679121017456},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.37057167291641235},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.3491423428058624},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.32041746377944946},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2678728997707367},{"id":"https://openalex.org/C91881484","wikidata":"https://www.wikidata.org/wiki/Q191807","display_name":"Fluorescence","level":2,"score":0.2644047141075134},{"id":"https://openalex.org/C153911025","wikidata":"https://www.wikidata.org/wiki/Q7202","display_name":"Molecular biology","level":1,"score":0.1552978754043579},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.13579681515693665},{"id":"https://openalex.org/C120665830","wikidata":"https://www.wikidata.org/wiki/Q14620","display_name":"Optics","level":1,"score":0.07727402448654175},{"id":"https://openalex.org/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","level":1,"score":0.0},{"id":"https://openalex.org/C555944384","wikidata":"https://www.wikidata.org/wiki/Q249","display_name":"Wireless","level":2,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001331","descriptor_name":"Automation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D002478","descriptor_name":"Cells, Cultured","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003584","descriptor_name":"Cytological Techniques","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D008856","descriptor_name":"Microscopy, Fluorescence","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017209","descriptor_name":"Apoptosis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019311","descriptor_name":"Staurosporine","qualifier_ui":"Q000633","qualifier_name":"toxicity","is_major_topic":false},{"descriptor_ui":"D032446","descriptor_name":"Myoblasts","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1111/jmi.12010","doi":"https://doi.org/10.1111/jmi.12010","is_oa":false,"landing_page_url":"https://doi.org/10.1111/jmi.12010","pdf_url":null,"source":{"id":"https://openalex.org/S168975578","display_name":"Journal of Microscopy","issn_l":"0022-2720","issn":["0022-2720","1365-2818"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-d","jufo-1","ki-jl-1","medline","norway-1","poland-100","russia-white-list-2","vabb-shw"],"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Microscopy","raw_type":"journal-article"},{"id":"pmid:23323688","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23323688","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,"listed_in":[],"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":"Journal of microscopy","raw_type":"Journal Article"},{"id":"pmh:oai:d-scholarship.pitt.edu:20803","doi":null,"is_oa":false,"landing_page_url":"http://d-scholarship.pitt.edu/20803/1/licence.txt","pdf_url":null,"source":{"id":"https://openalex.org/S4306402372","display_name":"D-Scholarship@Pitt (University of Pittsburgh)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I170201317","host_organization_name":"University of Pittsburgh","host_organization_lineage":["https://openalex.org/I170201317"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"","raw_type":"Article"}],"best_oa_location":null,"sustainable_development_goals":[],"sustainable_development_goals_aurora":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":28,"referenced_works":["https://openalex.org/W1486369662","https://openalex.org/W1558633536","https://openalex.org/W1969761972","https://openalex.org/W1993669821","https://openalex.org/W1994481920","https://openalex.org/W2032481416","https://openalex.org/W2036595842","https://openalex.org/W2036925553","https://openalex.org/W2037586865","https://openalex.org/W2062867597","https://openalex.org/W2075275335","https://openalex.org/W2086944387","https://openalex.org/W2091784906","https://openalex.org/W2100383758","https://openalex.org/W2108694034","https://openalex.org/W2119291330","https://openalex.org/W2124426078","https://openalex.org/W2129224689","https://openalex.org/W2133059825","https://openalex.org/W2134300204","https://openalex.org/W2147385427","https://openalex.org/W2162245111","https://openalex.org/W2176834306","https://openalex.org/W2265188304","https://openalex.org/W4229810054","https://openalex.org/W4232265030","https://openalex.org/W4232676535","https://openalex.org/W4242738252"],"related_works":["https://openalex.org/W4280640171","https://openalex.org/W7099466088","https://openalex.org/W1487944143","https://openalex.org/W7098261817","https://openalex.org/W2148927885","https://openalex.org/W2072422078","https://openalex.org/W2891902316","https://openalex.org/W2138625292","https://openalex.org/W2148971795","https://openalex.org/W1984360622"],"abstract_inverted_index":{"Robotic,":[0],"high-throughput":[1,69],"microscopy":[2,70],"is":[3,25,87,100,119],"a":[4,35,46,76,92,144],"powerful":[5],"tool":[6],"for":[7],"small":[8],"molecule":[9],"screening":[10],"and":[11,16,29,91,104,112,124,154],"classifying":[12],"cell":[13,83,148],"phenotype,":[14],"proteomic":[15],"genomic":[17],"data.":[18],"An":[19],"important":[20],"hurdle":[21],"in":[22,75,143],"the":[23,26,53,106,128,133,139],"field":[24],"automated":[27],"classification":[28],"visualization":[30],"of":[31,38,40,42,55,94,108,114,132,141],"results":[32,157],"collected":[33],"from":[34,52],"data":[36,71],"set":[37],"tens":[39],"thousands":[41],"images.":[43],"We":[44],"present":[45],"method":[47,118],"that":[48,67,126],"approaches":[49],"these":[50,156],"problems":[51],"perspective":[54],"flow":[56,80,98,159],"cytometry":[57,99],"with":[58,121],"supporting":[59],"open-source":[60,122],"code.":[61],"Image":[62],"analysis":[63],"software":[64,123,134],"was":[65,135],"created":[66],"allowed":[68],"to":[72,97,102,152,158],"be":[73],"analysed":[74],"similar":[77,96],"manner":[78],"as":[79],"cytometry.":[81,160],"Each":[82],"on":[84],"an":[85,89],"image":[86],"considered":[88],"object":[90],"series":[93],"gates":[95],"used":[101],"classify":[103],"quantify":[105],"properties":[107],"cells":[109],"including":[110],"size":[111],"level":[113],"fluorescent":[115],"intensity.":[116],"This":[117],"released":[120],"code":[125],"demonstrates":[127],"method's":[129],"implementation.":[130],"Accuracy":[131],"determined":[136],"by":[137],"measuring":[138],"levels":[140],"apoptosis":[142],"primary":[145],"murine":[146],"myoblast":[147],"line":[149],"after":[150],"exposure":[151],"staurosporine":[153],"comparing":[155]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2013,"cited_by_count":1}],"updated_date":"2026-10-31T12:09:11.096373","created_date":"2016-06-24T00:00:00"}