{"id":"https://openalex.org/W2982830820","doi":"https://doi.org/10.1021/acs.jcim.9b00734","title":"ImageDataExtractor: A Tool To Extract and Quantify Data from Microscopy Images","display_name":"ImageDataExtractor: A Tool To Extract and Quantify Data from Microscopy Images","publication_year":2019,"publication_date":"2019-11-12","ids":{"openalex":"https://openalex.org/W2982830820","doi":"https://doi.org/10.1021/acs.jcim.9b00734","mag":"2982830820","pmid":"https://pubmed.ncbi.nlm.nih.gov/31714792"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.9b00734","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.9b00734","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"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/A5000726701","display_name":"Karim T. Mukaddem","orcid":null},"institutions":[{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Karim T. Mukaddem","raw_affiliation_strings":["Cavendish Laboratory, Department of Physics, University of Cambridge, J. J. Thomson Avenue, Cambridge CB3 0HE, U.K"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Cavendish Laboratory, Department of Physics, University of Cambridge, J. J. Thomson Avenue, Cambridge CB3 0HE, U.K","institution_ids":["https://openalex.org/I241749"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037756990","display_name":"Edward J. Beard","orcid":"https://orcid.org/0000-0003-2546-3899"},"institutions":[{"id":"https://openalex.org/I1286704778","display_name":"Rutherford Appleton Laboratory","ror":"https://ror.org/03gq8fr08","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1286704778","https://openalex.org/I162524378","https://openalex.org/I4210087105"]},{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Edward J. Beard","raw_affiliation_strings":["Cavendish Laboratory, Department of Physics, University of Cambridge, J. J. Thomson Avenue, Cambridge CB3 0HE, U.K","ISIS Neutron and Muon Source, STFC Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0QX, U.K"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Cavendish Laboratory, Department of Physics, University of Cambridge, J. J. Thomson Avenue, Cambridge CB3 0HE, U.K","institution_ids":["https://openalex.org/I241749"]},{"raw_affiliation_string":"ISIS Neutron and Muon Source, STFC Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0QX, U.K","institution_ids":["https://openalex.org/I1286704778"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077251431","display_name":"Batuhan Yildirim","orcid":"https://orcid.org/0000-0001-7741-0516"},"institutions":[{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Batuhan Yildirim","raw_affiliation_strings":["Cavendish Laboratory, Department of Physics, University of Cambridge, J. J. Thomson Avenue, Cambridge CB3 0HE, U.K"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Cavendish Laboratory, Department of Physics, University of Cambridge, J. J. Thomson Avenue, Cambridge CB3 0HE, U.K","institution_ids":["https://openalex.org/I241749"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5068607578","display_name":"Jacqueline M. Cole","orcid":"https://orcid.org/0000-0002-1552-8743"},"institutions":[{"id":"https://openalex.org/I1286704778","display_name":"Rutherford Appleton Laboratory","ror":"https://ror.org/03gq8fr08","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1286704778","https://openalex.org/I162524378","https://openalex.org/I4210087105"]},{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Jacqueline M. Cole","raw_affiliation_strings":["Cavendish Laboratory, Department of Physics, University of Cambridge, J. J. Thomson Avenue, Cambridge CB3 0HE, U.K","Department of Chemical Engineering and Biotechnology, University of Cambridge, West Cambridge Site, Philippa Fawcett Drive, Cambridge CB3 0AS, U.K","ISIS Neutron and Muon Source, STFC Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0QX, U.K"],"raw_orcid":"https://orcid.org/0000-0002-1552-8743","affiliations":[{"raw_affiliation_string":"Cavendish Laboratory, Department of Physics, University of Cambridge, J. J. Thomson Avenue, Cambridge CB3 0HE, U.K","institution_ids":["https://openalex.org/I241749"]},{"raw_affiliation_string":"Department of Chemical Engineering and Biotechnology, University of Cambridge, West Cambridge Site, Philippa Fawcett Drive, Cambridge CB3 0AS, U.K","institution_ids":["https://openalex.org/I241749"]},{"raw_affiliation_string":"ISIS Neutron and Muon Source, STFC Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0QX, U.K","institution_ids":["https://openalex.org/I1286704778"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5068607578"],"corresponding_institution_ids":["https://openalex.org/I1286704778","https://openalex.org/I241749"],"apc_list":null,"apc_paid":null,"fwci":5.3991,"has_fulltext":false,"cited_by_count":62,"citation_normalized_percentile":{"value":0.9621931,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"60","issue":"5","first_page":"2492","last_page":"2509"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9926999807357788,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9926999807357788,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"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/T11948","display_name":"Machine Learning in Materials Science","score":0.9907000064849854,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12282","display_name":"Mineral Processing and Grinding","score":0.9843999743461609,"subfield":{"id":"https://openalex.org/subfields/2210","display_name":"Mechanical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6790448427200317},{"id":"https://openalex.org/keywords/property","display_name":"Property (philosophy)","score":0.6184125542640686},{"id":"https://openalex.org/keywords/thresholding","display_name":"Thresholding","score":0.6009414792060852},{"id":"https://openalex.org/keywords/microscopy","display_name":"Microscopy","score":0.5239149332046509},{"id":"https://openalex.org/keywords/convolutional-neural-network","display_name":"Convolutional neural network","score":0.5168319344520569},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5008060932159424},{"id":"https://openalex.org/keywords/segmentation","display_name":"Segmentation","score":0.4911913573741913},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.3341318368911743},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.33357954025268555},{"id":"https://openalex.org/keywords/image","display_name":"Image (mathematics)","score":0.30637890100479126},{"id":"https://openalex.org/keywords/optics","display_name":"Optics","score":0.09476786851882935},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.09385746717453003}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6790448427200317},{"id":"https://openalex.org/C189950617","wikidata":"https://www.wikidata.org/wiki/Q937228","display_name":"Property (philosophy)","level":2,"score":0.6184125542640686},{"id":"https://openalex.org/C191178318","wikidata":"https://www.wikidata.org/wiki/Q2256906","display_name":"Thresholding","level":3,"score":0.6009414792060852},{"id":"https://openalex.org/C147080431","wikidata":"https://www.wikidata.org/wiki/Q1074953","display_name":"Microscopy","level":2,"score":0.5239149332046509},{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.5168319344520569},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5008060932159424},{"id":"https://openalex.org/C89600930","wikidata":"https://www.wikidata.org/wiki/Q1423946","display_name":"Segmentation","level":2,"score":0.4911913573741913},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3341318368911743},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.33357954025268555},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.30637890100479126},{"id":"https://openalex.org/C120665830","wikidata":"https://www.wikidata.org/wiki/Q14620","display_name":"Optics","level":1,"score":0.09476786851882935},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.09385746717453003},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008853","descriptor_name":"Microscopy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008853","descriptor_name":"Microscopy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008853","descriptor_name":"Microscopy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1021/acs.jcim.9b00734","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.9b00734","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:31714792","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31714792","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":"Journal of chemical information and modeling","raw_type":null},{"id":"pmh:oai:purl.org/net/epubs:work/44703564","is_oa":false,"landing_page_url":"http://purl.org/net/epubs/work/44703564","pdf_url":null,"source":{"id":"https://openalex.org/S4306400600","display_name":"ePubs (Science and Technology Facilities Council, Research Councils UK)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I162524378","host_organization_name":"Science and Technology Facilities Council","host_organization_lineage":["https://openalex.org/I162524378"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9","score":0.4399999976158142}],"awards":[{"id":"https://openalex.org/G1531024995","display_name":null,"funder_award_id":"RCSRF1819\\7\\10","funder_id":"https://openalex.org/F4320320005","funder_display_name":"Royal Academy of Engineering"}],"funders":[{"id":"https://openalex.org/F4320307790","display_name":"BASF","ror":"https://ror.org/01q8f6705"},{"id":"https://openalex.org/F4320320005","display_name":"Royal Academy of Engineering","ror":"https://ror.org/0526snb40"},{"id":"https://openalex.org/F4320334632","display_name":"Science and Technology Facilities Council","ror":"https://ror.org/057g20z61"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":43,"referenced_works":["https://openalex.org/W1665214252","https://openalex.org/W1885185971","https://openalex.org/W1964869106","https://openalex.org/W1981934656","https://openalex.org/W1992985800","https://openalex.org/W2012100460","https://openalex.org/W2023752928","https://openalex.org/W2065429801","https://openalex.org/W2091346776","https://openalex.org/W2095374961","https://openalex.org/W2109738979","https://openalex.org/W2121076213","https://openalex.org/W2133003941","https://openalex.org/W2147800946","https://openalex.org/W2155912251","https://openalex.org/W2159498975","https://openalex.org/W2268990527","https://openalex.org/W2316351572","https://openalex.org/W2319902168","https://openalex.org/W2344149869","https://openalex.org/W2344382642","https://openalex.org/W2519301945","https://openalex.org/W2523785361","https://openalex.org/W2529996553","https://openalex.org/W2531274738","https://openalex.org/W2669881333","https://openalex.org/W2755202310","https://openalex.org/W2758586798","https://openalex.org/W2766362701","https://openalex.org/W2770164889","https://openalex.org/W2793842878","https://openalex.org/W2803232390","https://openalex.org/W2808304511","https://openalex.org/W2904992191","https://openalex.org/W2910302825","https://openalex.org/W2953641512","https://openalex.org/W2971847579","https://openalex.org/W2992302948","https://openalex.org/W3098269892","https://openalex.org/W3099859964","https://openalex.org/W3100230575","https://openalex.org/W3100990679","https://openalex.org/W3210232381"],"related_works":["https://openalex.org/W1542224353","https://openalex.org/W1661087619","https://openalex.org/W2116854923","https://openalex.org/W2750730210","https://openalex.org/W2236974868","https://openalex.org/W4312766348","https://openalex.org/W4233939244","https://openalex.org/W2730764323","https://openalex.org/W3123806511","https://openalex.org/W1976727107"],"abstract_inverted_index":{"The":[0,53,225,274],"rise":[1],"of":[2,55,65,102,107,120,151,229,241,260],"data":[3,21,63,105],"science":[4],"is":[5,58,78,188,267,277,284],"leading":[6],"to":[7,47,73,81,174,237,286],"new":[8],"paradigms":[9],"in":[10,32,86,140],"data-driven":[11,245],"materials":[12,246],"discovery.":[13,247],"This":[14],"carries":[15],"an":[16],"essential":[17],"notion":[18],"that":[19,35,42,159,232],"large":[20,62],"sources":[22,64,106,240],"containing":[23],"chemical":[24,66,83],"structure":[25,67],"and":[26,37,68,100,138,161,179,213,221,251,265,283],"property":[27,69],"information":[28,70,109,181,195,243],"can":[29,44,234],"be":[30,45,116,235],"mined":[31],"a":[33,49,74,135,141,149],"fashion":[34,143],"detects":[36],"exploits":[38],"structure-property":[39],"relationships,":[40],"such":[41,88],"chemicals":[43],"predicted":[46],"suit":[48],"given":[50],"material":[51,56,92],"application.":[52,76],"success":[54],"predictions":[57],"predicated":[59],"on":[60,97],"these":[61],"being":[71],"suited":[72],"target":[75],"Microscopy":[77],"commonly":[79],"used":[80,236],"characterize":[82],"structure,":[84],"especially":[85],"fields":[87],"as":[89],"nanotechnology":[90],"where":[91,207],"properties":[93],"are":[94,211,253],"highly":[95,117],"dependent":[96],"the":[98,129,156,258,261,280],"size":[99,178],"shape":[101,180],"nanoparticles.":[103],"Large":[104],"nanoparticle":[108],"stemming":[110],"from":[111,165,202,288],"microscopy":[112,121,163],"images":[113,122,164],"would":[114],"thus":[115],"beneficial.":[118],"Millions":[119],"exist,":[123],"but":[124],"they":[125,147],"lie":[126],"fragmented":[127],"across":[128],"literature,":[130],"typically":[131],"presented":[132],"individually":[133],"within":[134],"paper":[136],"article":[137],"usually":[139],"qualitative":[142],"therein,":[144],"even":[145],"though":[146],"harbor":[148],"wealth":[150],"numeric":[152],"information.":[153],"We":[154],"present":[155],"ImageDataExtractor":[157,230,275],"toolkit":[158],"autoidentifies":[160],"autoextracts":[162],"scientific":[166],"documents,":[167],"whereupon":[168],"it":[169,233],"autonomously":[170],"analyzes":[171],"each":[172],"image":[173,187,262],"produce":[175],"quantitative":[176],"particle":[177,242],"about":[182],"its":[183,192],"subject":[184],"material.":[185],"Each":[186],"quantified":[189],"by":[190],"decoding":[191],"scale":[193],"bar":[194],"using":[196,215],"optical":[197],"character":[198],"recognition,":[199],"with":[200],"help":[201],"super-resolution":[203],"convolutional":[204],"neural":[205],"networks":[206],"required.":[208],"Individual":[209],"particles":[210],"detected":[212],"profiled":[214],"various":[216],"thresholding,":[217],"segmentation,":[218],"polygon":[219],"fitting,":[220],"edge":[222],"correction":[223],"routines.":[224],"high-throughput":[226],"operational":[227],"capability":[228],"means":[231],"generate":[238],"large-data":[239],"for":[244,257,270],"Evaluation":[248],"metrics,":[249],"precision":[250,266],"recall,":[252],"greater":[254],"than":[255],"80%":[256,269],"majority":[259],"processing":[263],"steps,":[264],"above":[268],"all":[271],"critical":[272],"steps.":[273],"tool":[276],"released":[278],"under":[279],"MIT":[281],"license":[282],"available":[285],"download":[287],"http://www.imagedataextractor.org.":[289]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":14},{"year":2024,"cited_by_count":10},{"year":2023,"cited_by_count":10},{"year":2022,"cited_by_count":9},{"year":2021,"cited_by_count":14},{"year":2020,"cited_by_count":4}],"updated_date":"2026-04-24T08:23:43.765630","created_date":"2025-10-10T00:00:00"}
