{"id":"https://openalex.org/W2795106634","doi":"https://doi.org/10.1186/s12859-018-2087-4","title":"Assessing microscope image focus quality with deep learning","display_name":"Assessing microscope image focus quality with deep learning","publication_year":2018,"publication_date":"2018-03-02","ids":{"openalex":"https://openalex.org/W2795106634","doi":"https://doi.org/10.1186/s12859-018-2087-4","mag":"2795106634","pmid":"https://pubmed.ncbi.nlm.nih.gov/29540156"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-018-2087-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-018-2087-4","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-018-2087-4","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","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":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-018-2087-4","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5090108597","display_name":"Samuel Yang","orcid":"https://orcid.org/0000-0003-2460-6456"},"institutions":[{"id":"https://openalex.org/I1291425158","display_name":"Google (United States)","ror":"https://ror.org/00njsd438","country_code":"US","type":"company","lineage":["https://openalex.org/I1291425158","https://openalex.org/I4210128969"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Samuel J. Yang","raw_affiliation_strings":["Google Inc, Mountain View, CA, USA. samuely@google.com","Google Inc, Mountain View, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Google Inc, Mountain View, CA, USA. samuely@google.com","institution_ids":[]},{"raw_affiliation_string":"Google Inc, Mountain View, CA, USA","institution_ids":["https://openalex.org/I1291425158"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050107108","display_name":"Marc Berndl","orcid":"https://orcid.org/0000-0001-6750-5861"},"institutions":[{"id":"https://openalex.org/I1291425158","display_name":"Google (United States)","ror":"https://ror.org/00njsd438","country_code":"US","type":"company","lineage":["https://openalex.org/I1291425158","https://openalex.org/I4210128969"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Marc Berndl","raw_affiliation_strings":["Google Inc, Mountain View, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Google Inc, Mountain View, CA, USA","institution_ids":["https://openalex.org/I1291425158"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050136303","display_name":"D. Michael Ando","orcid":"https://orcid.org/0000-0001-9022-8444"},"institutions":[{"id":"https://openalex.org/I1291425158","display_name":"Google (United States)","ror":"https://ror.org/00njsd438","country_code":"US","type":"company","lineage":["https://openalex.org/I1291425158","https://openalex.org/I4210128969"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"D. Michael Ando","raw_affiliation_strings":["Google Inc, Mountain View, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Google Inc, Mountain View, CA, USA","institution_ids":["https://openalex.org/I1291425158"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112270288","display_name":"Mariya Barch","orcid":null},"institutions":[{"id":"https://openalex.org/I4210152820","display_name":"Taube Koret Center","ror":"https://ror.org/05j1wft12","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210152820"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mariya Barch","raw_affiliation_strings":["Taube/Koret Center for Neurodegenerative Disease Research and DaedalusBio, Gladstone, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Taube/Koret Center for Neurodegenerative Disease Research and DaedalusBio, Gladstone, USA","institution_ids":["https://openalex.org/I4210152820"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065263704","display_name":"Arunachalam Narayanaswamy","orcid":"https://orcid.org/0000-0002-0775-4070"},"institutions":[{"id":"https://openalex.org/I1291425158","display_name":"Google (United States)","ror":"https://ror.org/00njsd438","country_code":"US","type":"company","lineage":["https://openalex.org/I1291425158","https://openalex.org/I4210128969"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Arunachalam Narayanaswamy","raw_affiliation_strings":["Google Inc, Mountain View, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Google Inc, Mountain View, CA, USA","institution_ids":["https://openalex.org/I1291425158"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004253857","display_name":"Eric Christiansen","orcid":null},"institutions":[{"id":"https://openalex.org/I1291425158","display_name":"Google (United States)","ror":"https://ror.org/00njsd438","country_code":"US","type":"company","lineage":["https://openalex.org/I1291425158","https://openalex.org/I4210128969"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Eric Christiansen","raw_affiliation_strings":["Google Inc, Mountain View, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Google Inc, Mountain View, CA, USA","institution_ids":["https://openalex.org/I1291425158"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070161680","display_name":"Stephan Hoyer","orcid":"https://orcid.org/0000-0002-5207-0380"},"institutions":[{"id":"https://openalex.org/I1291425158","display_name":"Google (United States)","ror":"https://ror.org/00njsd438","country_code":"US","type":"company","lineage":["https://openalex.org/I1291425158","https://openalex.org/I4210128969"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Stephan Hoyer","raw_affiliation_strings":["Google Inc, Mountain View, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Google Inc, Mountain View, CA, USA","institution_ids":["https://openalex.org/I1291425158"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5105776175","display_name":"C. Roat","orcid":"https://orcid.org/0000-0001-8020-6401"},"institutions":[{"id":"https://openalex.org/I1291425158","display_name":"Google (United States)","ror":"https://ror.org/00njsd438","country_code":"US","type":"company","lineage":["https://openalex.org/I1291425158","https://openalex.org/I4210128969"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chris Roat","raw_affiliation_strings":["Google Inc, Mountain View, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Google Inc, Mountain View, CA, USA","institution_ids":["https://openalex.org/I1291425158"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102106282","display_name":"Jane Hung","orcid":null},"institutions":[{"id":"https://openalex.org/I107606265","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142","country_code":"US","type":"funder","lineage":["https://openalex.org/I107606265"]},{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jane Hung","raw_affiliation_strings":["Department of Chemical Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA","Imaging Platform, Broad Institute of Harvard and MIT, Cambridge, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemical Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA","institution_ids":["https://openalex.org/I63966007"]},{"raw_affiliation_string":"Imaging Platform, Broad Institute of Harvard and MIT, Cambridge, MA, USA","institution_ids":["https://openalex.org/I107606265"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078540488","display_name":"Curtis Rueden","orcid":"https://orcid.org/0000-0001-7055-6707"},"institutions":[{"id":"https://openalex.org/I135310074","display_name":"University of Wisconsin\u2013Madison","ror":"https://ror.org/01y2jtd41","country_code":"US","type":"education","lineage":["https://openalex.org/I135310074"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Curtis T. Rueden","raw_affiliation_strings":["Laboratory for Optical and Computational Instrumentation, University of Wisconsin at Madison, Madison, WI, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory for Optical and Computational Instrumentation, University of Wisconsin at Madison, Madison, WI, USA","institution_ids":["https://openalex.org/I135310074"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073029842","display_name":"Asim Shankar","orcid":null},"institutions":[{"id":"https://openalex.org/I1291425158","display_name":"Google (United States)","ror":"https://ror.org/00njsd438","country_code":"US","type":"company","lineage":["https://openalex.org/I1291425158","https://openalex.org/I4210128969"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Asim Shankar","raw_affiliation_strings":["Google Inc, Mountain View, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Google Inc, Mountain View, CA, USA","institution_ids":["https://openalex.org/I1291425158"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064983402","display_name":"Steven Finkbeiner","orcid":"https://orcid.org/0000-0002-3480-394X"},"institutions":[{"id":"https://openalex.org/I4210152820","display_name":"Taube Koret Center","ror":"https://ror.org/05j1wft12","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210152820"]},{"id":"https://openalex.org/I180670191","display_name":"University of California, San Francisco","ror":"https://ror.org/043mz5j54","country_code":"US","type":"education","lineage":["https://openalex.org/I180670191"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Steven Finkbeiner","raw_affiliation_strings":["Departments of Neurology and Physiology, University of California, San Francisco, CA, USA","Taube/Koret Center for Neurodegenerative Disease Research and DaedalusBio, Gladstone, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Departments of Neurology and Physiology, University of California, San Francisco, CA, USA","institution_ids":["https://openalex.org/I180670191"]},{"raw_affiliation_string":"Taube/Koret Center for Neurodegenerative Disease Research and DaedalusBio, Gladstone, USA","institution_ids":["https://openalex.org/I4210152820"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5091446023","display_name":"Philip Nelson","orcid":"https://orcid.org/0000-0002-1782-3076"},"institutions":[{"id":"https://openalex.org/I1291425158","display_name":"Google (United States)","ror":"https://ror.org/00njsd438","country_code":"US","type":"company","lineage":["https://openalex.org/I1291425158","https://openalex.org/I4210128969"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Philip Nelson","raw_affiliation_strings":["Google Inc, Mountain View, CA, USA. pqnelson@google.com","Google Inc, Mountain View, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Google Inc, Mountain View, CA, USA. pqnelson@google.com","institution_ids":[]},{"raw_affiliation_string":"Google Inc, Mountain View, CA, USA","institution_ids":["https://openalex.org/I1291425158"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":13,"corresponding_author_ids":["https://openalex.org/A5090108597"],"corresponding_institution_ids":["https://openalex.org/I1291425158"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":19.2451,"has_fulltext":true,"cited_by_count":158,"citation_normalized_percentile":{"value":0.99345959,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":100},"biblio":{"volume":"19","issue":"1","first_page":"77","last_page":"77"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T13114","display_name":"Image Processing Techniques and Applications","score":0.8080999851226807,"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"}},"topics":[{"id":"https://openalex.org/T13114","display_name":"Image Processing Techniques and Applications","score":0.8080999851226807,"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.1607999950647354,"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":0.01119999960064888,"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/artificial-intelligence","display_name":"Artificial intelligence","score":0.8036870956420898},{"id":"https://openalex.org/keywords/focus","display_name":"Focus (optics)","score":0.7276597619056702},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7010939121246338},{"id":"https://openalex.org/keywords/image-quality","display_name":"Image quality","score":0.5640009045600891},{"id":"https://openalex.org/keywords/computer-vision","display_name":"Computer vision","score":0.5514692068099976},{"id":"https://openalex.org/keywords/autofocus","display_name":"Autofocus","score":0.5288668274879456},{"id":"https://openalex.org/keywords/pixel","display_name":"Pixel","score":0.5001187324523926},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.49800610542297363},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.48355624079704285},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.44017666578292847},{"id":"https://openalex.org/keywords/binary-image","display_name":"Binary image","score":0.42079412937164307},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.41163599491119385},{"id":"https://openalex.org/keywords/image-processing","display_name":"Image processing","score":0.3866141736507416},{"id":"https://openalex.org/keywords/image","display_name":"Image (mathematics)","score":0.3665764629840851},{"id":"https://openalex.org/keywords/optics","display_name":"Optics","score":0.11216539144515991},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.0740821361541748}],"concepts":[{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.8036870956420898},{"id":"https://openalex.org/C192209626","wikidata":"https://www.wikidata.org/wiki/Q190909","display_name":"Focus (optics)","level":2,"score":0.7276597619056702},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7010939121246338},{"id":"https://openalex.org/C55020928","wikidata":"https://www.wikidata.org/wiki/Q3813865","display_name":"Image quality","level":3,"score":0.5640009045600891},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.5514692068099976},{"id":"https://openalex.org/C103764139","wikidata":"https://www.wikidata.org/wiki/Q210008","display_name":"Autofocus","level":3,"score":0.5288668274879456},{"id":"https://openalex.org/C160633673","wikidata":"https://www.wikidata.org/wiki/Q355198","display_name":"Pixel","level":2,"score":0.5001187324523926},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.49800610542297363},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.48355624079704285},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.44017666578292847},{"id":"https://openalex.org/C193828747","wikidata":"https://www.wikidata.org/wiki/Q864118","display_name":"Binary image","level":4,"score":0.42079412937164307},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.41163599491119385},{"id":"https://openalex.org/C9417928","wikidata":"https://www.wikidata.org/wiki/Q1070689","display_name":"Image processing","level":3,"score":0.3866141736507416},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.3665764629840851},{"id":"https://openalex.org/C120665830","wikidata":"https://www.wikidata.org/wiki/Q14620","display_name":"Optics","level":1,"score":0.11216539144515991},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0740821361541748},{"id":"https://openalex.org/C187736073","wikidata":"https://www.wikidata.org/wiki/Q2920921","display_name":"Management","level":1,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001859","descriptor_name":"Bone Neoplasms","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":false},{"descriptor_ui":"D001859","descriptor_name":"Bone Neoplasms","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":false},{"descriptor_ui":"D001859","descriptor_name":"Bone Neoplasms","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":false},{"descriptor_ui":"D001859","descriptor_name":"Bone Neoplasms","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":false},{"descriptor_ui":"D003952","descriptor_name":"Diagnostic Imaging","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D003952","descriptor_name":"Diagnostic Imaging","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D003952","descriptor_name":"Diagnostic Imaging","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D003952","descriptor_name":"Diagnostic Imaging","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D008853","descriptor_name":"Microscopy","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D008853","descriptor_name":"Microscopy","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D008853","descriptor_name":"Microscopy","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D008853","descriptor_name":"Microscopy","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D012516","descriptor_name":"Osteosarcoma","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":false},{"descriptor_ui":"D012516","descriptor_name":"Osteosarcoma","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":false},{"descriptor_ui":"D012516","descriptor_name":"Osteosarcoma","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":false},{"descriptor_ui":"D012516","descriptor_name":"Osteosarcoma","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014407","descriptor_name":"Tumor Cells, Cultured","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014407","descriptor_name":"Tumor Cells, Cultured","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014407","descriptor_name":"Tumor Cells, Cultured","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014407","descriptor_name":"Tumor Cells, Cultured","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1186/s12859-018-2087-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-018-2087-4","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-018-2087-4","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","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":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:29540156","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29540156","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:5d2ce73d279747d2bfbef81a96bfc6be","is_oa":true,"landing_page_url":"https://doaj.org/article/5d2ce73d279747d2bfbef81a96bfc6be","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 19, Iss 1, Pp 1-9 (2018)","raw_type":"article"},{"id":"pmh:oai:escholarship.org:ark:/13030/qt0bn6n707","is_oa":true,"landing_page_url":"https://escholarship.org/uc/item/0bn6n707","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"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":"BMC Bioinformatics, vol 19, iss 1","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:5853029","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5853029","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-018-2087-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-018-2087-4","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-018-2087-4","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","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":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Industry, innovation and infrastructure","score":0.5199999809265137,"id":"https://metadata.un.org/sdg/9"}],"awards":[{"id":"https://openalex.org/G2659049673","display_name":null,"funder_award_id":"U54 HG008105","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3147500668","display_name":null,"funder_award_id":"U54 NS091046","funder_id":"https://openalex.org/F4320337359","funder_display_name":"National Institute of Neurological Disorders and Stroke"},{"id":"https://openalex.org/G4209298178","display_name":null,"funder_award_id":"RF1 AG058476","funder_id":"https://openalex.org/F4320337337","funder_display_name":"National Institute on Aging"},{"id":"https://openalex.org/G5950577451","display_name":null,"funder_award_id":"NIH U54","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G674720239","display_name":null,"funder_award_id":"R01 NS083390","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7037629968","display_name":null,"funder_award_id":"R01 NS083390","funder_id":"https://openalex.org/F4320337359","funder_display_name":"National Institute of Neurological Disorders and Stroke"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337337","display_name":"National Institute on Aging","ror":"https://ror.org/049v75w11"},{"id":"https://openalex.org/F4320337359","display_name":"National Institute of Neurological Disorders and Stroke","ror":"https://ror.org/01s5ya894"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2795106634.pdf","grobid_xml":"https://content.openalex.org/works/W2795106634.grobid-xml"},"referenced_works_count":24,"referenced_works":["https://openalex.org/W569478347","https://openalex.org/W1555447043","https://openalex.org/W1966401971","https://openalex.org/W1998614190","https://openalex.org/W1999085806","https://openalex.org/W2019062120","https://openalex.org/W2037586865","https://openalex.org/W2041404167","https://openalex.org/W2060807102","https://openalex.org/W2097117768","https://openalex.org/W2099540110","https://openalex.org/W2143805215","https://openalex.org/W2167279371","https://openalex.org/W2170947705","https://openalex.org/W2222445509","https://openalex.org/W2271840356","https://openalex.org/W2302517508","https://openalex.org/W2312404985","https://openalex.org/W2411833100","https://openalex.org/W2468160901","https://openalex.org/W2618245351","https://openalex.org/W2728842897","https://openalex.org/W2797749376","https://openalex.org/W2964121744"],"related_works":["https://openalex.org/W3186605777","https://openalex.org/W3107295340","https://openalex.org/W2574769845","https://openalex.org/W2164349598","https://openalex.org/W146855993","https://openalex.org/W2220864757","https://openalex.org/W153415493","https://openalex.org/W2801208768","https://openalex.org/W3080815883","https://openalex.org/W2794758705"],"abstract_inverted_index":{"BACKGROUND:":[0],"Large":[1],"image":[2,30,42,51,106,111,179,312,322],"datasets":[3],"acquired":[4,258],"on":[5,108,140,169,208,259],"automated":[6,29],"microscopes":[7],"typically":[8],"have":[9],"some":[10],"fraction":[11],"of":[12,20,25,60,73,89,100,105,130,148,157,217,251,270,293],"low":[13],"quality,":[14],"out-of-focus":[15,271],"images,":[16,61,83,175],"despite":[17,226],"the":[18,48,74,122,177,202,241,298,332],"use":[19,292,339],"hardware":[21],"autofocus":[22],"systems.":[23],"Identification":[24],"these":[26],"images":[27,147,215,233,273,296],"using":[28],"analysis":[31],"with":[32,192,274],"high":[33],"accuracy":[34,277],"is":[35,47,54,324,335],"important":[36],"for":[37,300,318,337],"obtaining":[38],"a":[39,64,71,94,109,128,196,260,301,327],"clean,":[40],"unbiased":[41],"dataset.":[43,305],"Complicating":[44],"this":[45],"task":[46],"fact":[49],"that":[50,240],"focus":[52,107,180,287],"quality":[53,78],"only":[55,69,141,227],"well-defined":[56],"in":[57,77,112,340],"foreground":[58],"regions":[59],"and":[62,125,211,219,224,249,278,288,313,321,331,343],"as":[63,326],"result,":[65],"most":[66],"previous":[67,206,282],"approaches":[68,207,283],"enable":[70],"computation":[72],"relative":[75],"difference":[76],"between":[79],"two":[80,245],"or":[81],"more":[82],"rather":[84],"than":[85,281],"an":[86,102,252],"absolute":[87,103,159,178],"measure":[88,104,129],"quality.":[90],"RESULTS:":[91],"We":[92],"present":[93],"deep":[95,265],"neural":[96,266],"network":[97,267],"model":[98,119,137,166,204,242,307,319,334],"capable":[99],"predicting":[101],"single":[110],"isolation,":[113],"without":[114],"any":[115],"user-specified":[116],"parameters.":[117],"The":[118,136,164,291,306,316],"operates":[120],"at":[121],"image-patch":[123],"level,":[124],"also":[126,308],"outputs":[127],"prediction":[131,323],"certainty,":[132],"enabling":[133],"interpretable":[134,285],"predictions.":[135,290],"was":[138],"trained":[139,165,203],"384":[142],"in-focus":[143],"Hoechst":[144,173,210,231,248],"(nuclei)":[145],"stain":[146,174,214,232],"U2OS":[149],"cells,":[150],"which":[151],"were":[152],"synthetically":[153,294],"defocused":[154,295],"to":[155,181,244,310],"one":[156,183],"11":[158],"defocus":[160,184],"levels":[161],"during":[162,234],"training.":[163,235],"can":[167],"generalize":[168],"previously":[170],"unseen":[171,253],"real":[172],"identifying":[176],"within":[182],"level":[185],"(approximately":[186],"3":[187],"pixel":[188],"blur":[189],"diameter":[190],"difference)":[191],"95%":[193],"accuracy.":[194],"On":[195],"simpler":[197],"binary":[198],"in/out-of-focus":[199],"classification":[200,269],"task,":[201],"outperforms":[205],"both":[209,275],"Phalloidin":[212],"(actin)":[213],"(F-scores":[216],"0.89":[218],"0.86,":[220],"respectively":[221],"over":[222],"0.84":[223],"0.83),":[225],"having":[228],"been":[229],"presented":[230],"Lastly,":[236],"we":[237],"observe":[238],"qualitatively":[239],"generalizes":[243,309],"additional":[246],"stains,":[247],"Tubulin,":[250],"cell":[254,314],"type":[255],"(Human":[256],"MCF-7)":[257],"different":[261,311],"instrument.":[262],"CONCLUSIONS:":[263],"Our":[264],"enables":[268],"microscope":[272],"higher":[276],"greater":[279],"precision":[280],"via":[284],"patch-level":[286],"certainty":[289],"precludes":[297],"need":[299],"manually":[302],"annotated":[303],"training":[304,320],"types.":[315],"framework":[317],"available":[325,336],"free":[328],"software":[329],"library":[330],"pre-trained":[333],"immediate":[338],"Fiji":[341],"(ImageJ)":[342],"CellProfiler.":[344]},"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2025,"cited_by_count":12},{"year":2024,"cited_by_count":14},{"year":2023,"cited_by_count":20},{"year":2022,"cited_by_count":19},{"year":2021,"cited_by_count":33},{"year":2020,"cited_by_count":31},{"year":2019,"cited_by_count":20},{"year":2018,"cited_by_count":4}],"updated_date":"2026-06-24T13:16:06.693445","created_date":"2025-10-10T00:00:00"}