{"id":"https://openalex.org/W4416620171","doi":"https://doi.org/10.2478/rrlm-2025-0027","title":"Using deep learning methods to automatically interpret blood culture Gram stains","display_name":"Using deep learning methods to automatically interpret blood culture Gram stains","publication_year":2025,"publication_date":"2025-10-01","ids":{"openalex":"https://openalex.org/W4416620171","doi":"https://doi.org/10.2478/rrlm-2025-0027"},"language":"en","primary_location":{"id":"doi:10.2478/rrlm-2025-0027","doi":"https://doi.org/10.2478/rrlm-2025-0027","is_oa":true,"landing_page_url":"https://doi.org/10.2478/rrlm-2025-0027","pdf_url":"https://reference-global.com/2/v2/download/article/10.2478/rrlm-2025-0027.pdf","source":{"id":"https://openalex.org/S2738061079","display_name":"Revista rom\u00e2n\u0103 de medicin\u0103 de laborator","issn_l":"1841-6624","issn":["1841-6624","2284-5623"],"is_oa":true,"is_in_doaj":true,"is_core":false,"listed_in":["doaj","poland-20","vabb-shw"],"host_organization":"https://openalex.org/P4310320322","host_organization_name":"De Gruyter Open","host_organization_lineage":["https://openalex.org/P4310320322","https://openalex.org/P4310313990"],"host_organization_lineage_names":["De Gruyter Open","De Gruyter"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Revista Romana de Medicina de Laborator","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://reference-global.com/2/v2/download/article/10.2478/rrlm-2025-0027.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5004565432","display_name":"Reyhan Yi\u015f","orcid":"https://orcid.org/0000-0001-5774-0315","observed_orcids":["https://orcid.org/0000-0001-5774-0315"]},"institutions":[{"id":"https://openalex.org/I4387152504","display_name":"Bak\u0131r\u00e7ay \u00dcniversitesi","ror":"https://ror.org/017v96566","country_code":null,"type":"education","lineage":["https://openalex.org/I4387152504"]}],"countries":[],"is_corresponding":false,"raw_author_name":"Reyhan Yi\u015f","raw_affiliation_strings":["Department of Medical Microbiology , \u0130zmir Bak\u0131r\u00e7ay University , Turkey"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Medical Microbiology , \u0130zmir Bak\u0131r\u00e7ay University , Turkey","institution_ids":["https://openalex.org/I4387152504"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034491818","display_name":"Kenan Kocadurdu","orcid":"https://orcid.org/0000-0003-4274-6188","observed_orcids":["https://orcid.org/0000-0003-4274-6188"]},"institutions":[{"id":"https://openalex.org/I4387152504","display_name":"Bak\u0131r\u00e7ay \u00dcniversitesi","ror":"https://ror.org/017v96566","country_code":null,"type":"education","lineage":["https://openalex.org/I4387152504"]}],"countries":[],"is_corresponding":false,"raw_author_name":"Kenan Kocadurdu","raw_affiliation_strings":["\u00c7i\u011fli Training and Research Hospital , \u0130zmir Bak\u0131r\u00e7ay University , Turkey"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"\u00c7i\u011fli Training and Research Hospital , \u0130zmir Bak\u0131r\u00e7ay University , Turkey","institution_ids":["https://openalex.org/I4387152504"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5035182904","display_name":"Mustafa Berkta\u015f","orcid":"https://orcid.org/0000-0002-4413-0435","observed_orcids":["https://orcid.org/0000-0002-4413-0435"]},"institutions":[{"id":"https://openalex.org/I4387152504","display_name":"Bak\u0131r\u00e7ay \u00dcniversitesi","ror":"https://ror.org/017v96566","country_code":null,"type":"education","lineage":["https://openalex.org/I4387152504"]}],"countries":[],"is_corresponding":false,"raw_author_name":"Mustafa Berkta\u015f","raw_affiliation_strings":["Department of Medical Microbiology , \u0130zmir Bak\u0131r\u00e7ay University , Turkey"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Medical Microbiology , \u0130zmir Bak\u0131r\u00e7ay University , Turkey","institution_ids":["https://openalex.org/I4387152504"]}]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I4387152504"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.25095871,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"33","issue":"4","first_page":"259","last_page":"266"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12874","display_name":"Digital Imaging for Blood Diseases","score":0.353300005197525,"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"}},"topics":[{"id":"https://openalex.org/T12874","display_name":"Digital Imaging for Blood Diseases","score":0.353300005197525,"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.2295999974012375,"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/T12167","display_name":"Bacterial Identification and Susceptibility Testing","score":0.2134999930858612,"subfield":{"id":"https://openalex.org/subfields/1308","display_name":"Clinical Biochemistry"},"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/blood-culture","display_name":"blood culture","score":0.9319999814033508},{"id":"https://openalex.org/keywords/gram-stain","display_name":"Gram staining","score":0.8040000200271606},{"id":"https://openalex.org/keywords/deep-learning","display_name":"deep learning","score":0.7770000100135803},{"id":"https://openalex.org/keywords/convolutional-neural-networks","display_name":"convolutional neural networks","score":0.8159999847412109},{"id":"https://openalex.org/keywords/slide-scanning","display_name":"slide scanning","score":0.4129999876022339},{"id":"https://openalex.org/keywords/automated-blood-culture-systems","display_name":"automated blood culture systems","score":0.531000018119812},{"id":"https://openalex.org/keywords/antimicrobial-stewardship","display_name":"antimicrobial stewardship","score":0.8960000276565552}],"concepts":[{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.6685000061988831},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6370000243186951},{"id":"https://openalex.org/C205501099","wikidata":"https://www.wikidata.org/wiki/Q188990","display_name":"Gram staining","level":3,"score":0.5699999928474426},{"id":"https://openalex.org/C2779473907","wikidata":"https://www.wikidata.org/wiki/Q886695","display_name":"Blood culture","level":3,"score":0.5388000011444092},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.41929998993873596},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.41830000281333923},{"id":"https://openalex.org/C2776040555","wikidata":"https://www.wikidata.org/wiki/Q19903321","display_name":"Antimicrobial stewardship","level":4,"score":0.366100013256073},{"id":"https://openalex.org/C19527891","wikidata":"https://www.wikidata.org/wiki/Q1120908","display_name":"Medical physics","level":1,"score":0.3652999997138977},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.3562999963760376},{"id":"https://openalex.org/C3017819844","wikidata":"https://www.wikidata.org/wiki/Q886475","display_name":"Blood smear","level":3,"score":0.3431999981403351},{"id":"https://openalex.org/C2777267654","wikidata":"https://www.wikidata.org/wiki/Q3519023","display_name":"Test (biology)","level":2,"score":0.3402999937534332},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.33880001306533813},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3176000118255615},{"id":"https://openalex.org/C2777950569","wikidata":"https://www.wikidata.org/wiki/Q17021836","display_name":"Stewardship (theology)","level":3,"score":0.30239999294281006},{"id":"https://openalex.org/C169903167","wikidata":"https://www.wikidata.org/wiki/Q3985153","display_name":"Test set","level":2,"score":0.27300000190734863},{"id":"https://openalex.org/C9417928","wikidata":"https://www.wikidata.org/wiki/Q1070689","display_name":"Image processing","level":3,"score":0.2635999917984009},{"id":"https://openalex.org/C136229726","wikidata":"https://www.wikidata.org/wiki/Q327092","display_name":"Biomedical engineering","level":1,"score":0.26159998774528503},{"id":"https://openalex.org/C74864618","wikidata":"https://www.wikidata.org/wiki/Q2332446","display_name":"Staining","level":2,"score":0.25619998574256897}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.2478/rrlm-2025-0027","doi":"https://doi.org/10.2478/rrlm-2025-0027","is_oa":true,"landing_page_url":"https://doi.org/10.2478/rrlm-2025-0027","pdf_url":"https://reference-global.com/2/v2/download/article/10.2478/rrlm-2025-0027.pdf","source":{"id":"https://openalex.org/S2738061079","display_name":"Revista rom\u00e2n\u0103 de medicin\u0103 de laborator","issn_l":"1841-6624","issn":["1841-6624","2284-5623"],"is_oa":true,"is_in_doaj":true,"is_core":false,"listed_in":["doaj","poland-20","vabb-shw"],"host_organization":"https://openalex.org/P4310320322","host_organization_name":"De Gruyter Open","host_organization_lineage":["https://openalex.org/P4310320322","https://openalex.org/P4310313990"],"host_organization_lineage_names":["De Gruyter Open","De Gruyter"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Revista Romana de Medicina de Laborator","raw_type":"journal-article"},{"id":"pmh:oai:doaj.org/article:0a1ca971ce7f4191a8dad4c7971ecbe1","doi":null,"is_oa":true,"landing_page_url":"https://doaj.org/article/0a1ca971ce7f4191a8dad4c7971ecbe1","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,"listed_in":[],"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":"Romanian Journal of Laboratory Medicine, Vol 33, Iss 4, Pp 259-266 (2025)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.2478/rrlm-2025-0027","doi":"https://doi.org/10.2478/rrlm-2025-0027","is_oa":true,"landing_page_url":"https://doi.org/10.2478/rrlm-2025-0027","pdf_url":"https://reference-global.com/2/v2/download/article/10.2478/rrlm-2025-0027.pdf","source":{"id":"https://openalex.org/S2738061079","display_name":"Revista rom\u00e2n\u0103 de medicin\u0103 de laborator","issn_l":"1841-6624","issn":["1841-6624","2284-5623"],"is_oa":true,"is_in_doaj":true,"is_core":false,"listed_in":["doaj","poland-20","vabb-shw"],"host_organization":"https://openalex.org/P4310320322","host_organization_name":"De Gruyter Open","host_organization_lineage":["https://openalex.org/P4310320322","https://openalex.org/P4310313990"],"host_organization_lineage_names":["De Gruyter Open","De Gruyter"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Revista Romana de Medicina de Laborator","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Good health and well-being","score":0.428600013256073,"id":"https://metadata.un.org/sdg/3"}],"sustainable_development_goals_aurora":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4416620171.pdf","grobid_xml":"https://content.openalex.org/works/W4416620171.grobid-xml"},"referenced_works_count":30,"referenced_works":["https://openalex.org/W1789064953","https://openalex.org/W1985889629","https://openalex.org/W2002773042","https://openalex.org/W2154007902","https://openalex.org/W2163605009","https://openalex.org/W2171155970","https://openalex.org/W2186773111","https://openalex.org/W2194775991","https://openalex.org/W2478394825","https://openalex.org/W2549139847","https://openalex.org/W2560540564","https://openalex.org/W2768412660","https://openalex.org/W2783699776","https://openalex.org/W2808662277","https://openalex.org/W2895763047","https://openalex.org/W2919115771","https://openalex.org/W2944779197","https://openalex.org/W2947792531","https://openalex.org/W2963268748","https://openalex.org/W2963855133","https://openalex.org/W3006436762","https://openalex.org/W3012661213","https://openalex.org/W3015938277","https://openalex.org/W3084139975","https://openalex.org/W3158631502","https://openalex.org/W4211061854","https://openalex.org/W4245594042","https://openalex.org/W4249027830","https://openalex.org/W4285019461","https://openalex.org/W4294186675"],"related_works":[],"abstract_inverted_index":{"Abstract":[0],"Background":[1],"Gram":[2,114,206],"staining":[3,115,207],"of":[4,26,43,48,58,129],"the":[5,11,28,33,37,49,56,69,85,91,97,130,133,141,153,159,165,231],"smear":[6],"prepared":[7,95],"as":[8,10],"soon":[9],"growth":[12,104],"signal":[13],"is":[14,21,46,209],"received":[15],"in":[16,24,132],"automated":[17,113,203],"blood":[18,70,185,246],"culture":[19,186,247],"systems":[20],"very":[22],"important":[23],"terms":[25],"providing":[27],"first":[29,241],"critical":[30],"information":[31],"for":[32,65,205,211,235],"clinician":[34],"to":[35,73,182,226,238],"plan":[36],"appropriate":[38],"treatment.":[39],"However,":[40],"microscopic":[41],"interpretation":[42,208],"Gram-stained":[44],"smears":[45,89,107],"one":[47],"most":[50],"time-intensive":[51],"processes.":[52],"At":[53],"this":[54],"stage,":[55],"use":[57],"deep":[59,149,166,192],"learning":[60,150,167,193],"techniques":[61],"will":[62,223],"be":[63,180],"beneficial":[64],"us.":[66],"Methods":[67],"In":[68],"cultures":[71],"sent":[72],"\u0130zmir":[74],"Bak\u0131r\u00e7ay":[75],"University":[76],"\u00c7i\u011fli":[77],"Training":[78],"and":[79,117,123,147,152,172,218],"Research":[80],"Hospital":[81],"Microbiology":[82],"Laboratory":[83],"during":[84,217],"project":[86],"period,":[87],"two":[88],"with":[90,96,102,119],"same":[92,98],"thickness":[93],"were":[94,108,156],"technique":[99],"from":[100],"those":[101],"positive":[103,245],"signals.":[105],"The":[106,174],"stained":[109],"on":[110,140],"a":[111,120,184,191,236,244],"fully":[112],"device":[116],"digitized":[118],"slide":[121,187],"scanning":[122],"imaging":[124],"device.":[125],"After":[126],"manual":[127],"labeling":[128],"micro-organisms":[131],"images":[134],"obtained,":[135],"work":[136],"was":[137],"carried":[138],"out":[139],"training":[142],"set":[143],"using":[144,190],"image":[145],"processing":[146],"current":[148],"techniques,":[151],"analysis":[154],"results":[155,175],"supported":[157],"by":[158,229],"test":[160],"set.":[161],"Results":[162],"We":[163],"used":[164],"models":[168],"xresnet50,":[169],"resnet50,":[170],"xresnext50,":[171],"mobilenetV3.":[173],"indicate":[176],"that":[177],"it":[178,233],"may":[179],"possible":[181],"develop":[183],"evaluation":[188],"system":[189,204],"model,":[194],"particularly":[195],"outside":[196,219],"laboratory":[197,214,237],"working":[198,220],"hours.":[199,221],"Conclusions":[200],"Developing":[201],"an":[202],"crucial":[210],"ensuring":[212],"uninterrupted":[213],"operations":[215],"both":[216],"This":[222],"also":[224],"contribute":[225],"antimicrobial":[227],"stewardship":[228],"reducing":[230],"time":[232],"takes":[234],"issue":[239],"its":[240],"report":[242],"after":[243],"signal.":[248]},"counts_by_year":[],"updated_date":"2026-10-14T16:39:01.820549","created_date":"2025-11-25T00:00:00"}