{"id":"https://openalex.org/W7151216605","doi":"https://doi.org/10.1109/icmla66185.2025.00207","title":"Background-Aware Instance Segmentation for Early Detection of E. coli and Salmonella in Time-Stamped Microscopy Images","display_name":"Background-Aware Instance Segmentation for Early Detection of E. coli and Salmonella in Time-Stamped Microscopy Images","publication_year":2025,"publication_date":"2025-12-03","ids":{"openalex":"https://openalex.org/W7151216605","doi":"https://doi.org/10.1109/icmla66185.2025.00207"},"language":null,"primary_location":{"id":"doi:10.1109/icmla66185.2025.00207","is_oa":false,"landing_page_url":"https://doi.org/10.1109/icmla66185.2025.00207","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2025 International Conference on Machine Learning and Applications (ICMLA)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"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/A5133101098","display_name":"Bibek Koirala","orcid":null},"institutions":[{"id":"https://openalex.org/I110378019","display_name":"Southern Illinois University Carbondale","ror":"https://ror.org/049kefs16","country_code":"US","type":"education","lineage":["https://openalex.org/I110378019","https://openalex.org/I2801502357"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Bibek Koirala","raw_affiliation_strings":["Southern Illinois University Carbondale (SIUC),School of Computing,Department of Computer Science,Carbondale,IL,USA"],"affiliations":[{"raw_affiliation_string":"Southern Illinois University Carbondale (SIUC),School of Computing,Department of Computer Science,Carbondale,IL,USA","institution_ids":["https://openalex.org/I110378019"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5133089736","display_name":"Anas M. Alsobeh","orcid":null},"institutions":[{"id":"https://openalex.org/I110378019","display_name":"Southern Illinois University Carbondale","ror":"https://ror.org/049kefs16","country_code":"US","type":"education","lineage":["https://openalex.org/I110378019","https://openalex.org/I2801502357"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Anas M. Alsobeh","raw_affiliation_strings":["Southern Illinois University Carbondale (SIUC),School of Computing,Department of Information Technology,Carbondale,IL,USA"],"affiliations":[{"raw_affiliation_string":"Southern Illinois University Carbondale (SIUC),School of Computing,Department of Information Technology,Carbondale,IL,USA","institution_ids":["https://openalex.org/I110378019"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040584477","display_name":"Namariq Dhahir","orcid":"https://orcid.org/0000-0002-9403-4433"},"institutions":[{"id":"https://openalex.org/I110378019","display_name":"Southern Illinois University Carbondale","ror":"https://ror.org/049kefs16","country_code":"US","type":"education","lineage":["https://openalex.org/I110378019","https://openalex.org/I2801502357"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Namariq Dhahir","raw_affiliation_strings":["Southern Illinois University Carbondale (SIUC),School of Agricultural Sciences,Carbondale,IL,USA"],"affiliations":[{"raw_affiliation_string":"Southern Illinois University Carbondale (SIUC),School of Agricultural Sciences,Carbondale,IL,USA","institution_ids":["https://openalex.org/I110378019"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5019065958","display_name":"Amer AbuGhazaleh","orcid":"https://orcid.org/0000-0003-1589-2358"},"institutions":[{"id":"https://openalex.org/I110378019","display_name":"Southern Illinois University Carbondale","ror":"https://ror.org/049kefs16","country_code":"US","type":"education","lineage":["https://openalex.org/I110378019","https://openalex.org/I2801502357"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Amer AbuGhazaleh","raw_affiliation_strings":["Southern Illinois University Carbondale (SIUC),School of Agricultural Sciences,Carbondale,IL,USA"],"affiliations":[{"raw_affiliation_string":"Southern Illinois University Carbondale (SIUC),School of Agricultural Sciences,Carbondale,IL,USA","institution_ids":["https://openalex.org/I110378019"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5133101098"],"corresponding_institution_ids":["https://openalex.org/I110378019"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.74872716,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"1354","last_page":"1361"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T13114","display_name":"Image Processing Techniques and Applications","score":0.48649999499320984,"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":0.48649999499320984,"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":0.4083999991416931,"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/T11393","display_name":"Biosensors and Analytical Detection","score":0.01549999974668026,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical 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/segmentation","display_name":"Segmentation","score":0.5196999907493591},{"id":"https://openalex.org/keywords/microscopy","display_name":"Microscopy","score":0.49149999022483826},{"id":"https://openalex.org/keywords/image-segmentation","display_name":"Image segmentation","score":0.42980000376701355},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.4171000123023987},{"id":"https://openalex.org/keywords/salmonella","display_name":"Salmonella","score":0.3691999912261963},{"id":"https://openalex.org/keywords/enterobacteriaceae","display_name":"Enterobacteriaceae","score":0.3012000024318695}],"concepts":[{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5390999913215637},{"id":"https://openalex.org/C89600930","wikidata":"https://www.wikidata.org/wiki/Q1423946","display_name":"Segmentation","level":2,"score":0.5196999907493591},{"id":"https://openalex.org/C147080431","wikidata":"https://www.wikidata.org/wiki/Q1074953","display_name":"Microscopy","level":2,"score":0.49149999022483826},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.48399999737739563},{"id":"https://openalex.org/C124504099","wikidata":"https://www.wikidata.org/wiki/Q56933","display_name":"Image segmentation","level":3,"score":0.42980000376701355},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.4171000123023987},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.40290001034736633},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.37400001287460327},{"id":"https://openalex.org/C2781065037","wikidata":"https://www.wikidata.org/wiki/Q150839","display_name":"Salmonella","level":3,"score":0.3691999912261963},{"id":"https://openalex.org/C2778910516","wikidata":"https://www.wikidata.org/wiki/Q380136","display_name":"Enterobacteriaceae","level":4,"score":0.3012000024318695},{"id":"https://openalex.org/C9417928","wikidata":"https://www.wikidata.org/wiki/Q1070689","display_name":"Image processing","level":3,"score":0.2840999960899353},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.2786000072956085},{"id":"https://openalex.org/C547475151","wikidata":"https://www.wikidata.org/wiki/Q25419","display_name":"Escherichia coli","level":3,"score":0.275299996137619},{"id":"https://openalex.org/C523546767","wikidata":"https://www.wikidata.org/wiki/Q10876","display_name":"Bacteria","level":2,"score":0.27320000529289246}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/icmla66185.2025.00207","is_oa":false,"landing_page_url":"https://doi.org/10.1109/icmla66185.2025.00207","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2025 International Conference on Machine Learning and Applications (ICMLA)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320306114","display_name":"U.S. Department of Agriculture","ror":"https://ror.org/01na82s61"},{"id":"https://openalex.org/F4320332299","display_name":"National Institute of Food and Agriculture","ror":"https://ror.org/05qx3fv49"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":14,"referenced_works":["https://openalex.org/W2194775991","https://openalex.org/W2963150697","https://openalex.org/W3004173949","https://openalex.org/W3005887317","https://openalex.org/W3095812427","https://openalex.org/W4225264236","https://openalex.org/W4284670866","https://openalex.org/W4311935231","https://openalex.org/W4385245566","https://openalex.org/W4393132084","https://openalex.org/W4405087766","https://openalex.org/W4407474975","https://openalex.org/W4411565511","https://openalex.org/W7116328676"],"related_works":[],"abstract_inverted_index":{"Rapid":[0],"detection":[1,43,248],"of":[2,46,70,89,110,273],"bacterial":[3,151,251,254],"contamination":[4],"in":[5,52,127,162,179,290],"food":[6,287],"supply":[7],"chains":[8],"is":[9],"essential":[10],"to":[11,63,104,158,166],"prevent":[12],"outbreaks":[13],"and":[14,24,29,44,49,80,112,145,209,224,234,239,241,253],"protect":[15],"public":[16],"health.":[17],"Traditional":[18],"microbiological":[19],"methods,":[20],"such":[21],"as":[22],"culture":[23,134],"biochemical":[25],"testing,":[26],"are":[27],"slow":[28],"can":[30],"delay":[31],"necessary":[32],"interventions.":[33],"This":[34,282],"study":[35],"presents":[36],"deep":[37],"learning\u2013based":[38],"approaches":[39],"for":[40,143,148,169,193,236,243,275],"the":[41,99,215,219],"early":[42],"classification":[45,149],"Escherichia":[47],"coli":[48],"Salmonella":[50],"Typhimurium":[51],"microscopy":[53,266],"images":[54],"captured":[55],"during":[56],"incubation":[57,217],"periods":[58],"ranging":[59],"from":[60,98],"1.5":[61,102],"hours":[62,280],"4":[64,105],"hours,":[65],"with":[66,115],"a":[67,77,87,108,146,170],"step":[68],"size":[69],"30":[71],"min,":[72],"under":[73,95,174],"two":[74],"different":[75],"conditions:":[76],"plain":[78],"background":[79,263],"an":[81,163,188,271],"onion":[82],"mixture":[83],"background.":[84],"We":[85],"annotated":[86,123],"dataset":[88,121],"2,200":[90],"high-resolution":[91],"(2160\u00d71620)":[92],"images,":[93],"collected":[94],"60\u00d7":[96],"magnification":[97],"time":[100],"frame":[101],"h":[103],"h,":[106],"using":[107,124],"combination":[109],"manual":[111,119],"semi-automated":[113],"techniques":[114],"Mask":[116,190,196,259],"R-CNN.":[117],"For":[118,129],"annotation,":[120],"was":[122,156],"tkinter":[125],"framework":[126],"python.":[128],"model":[130,192],"training,":[131],"only":[132],"pure":[133],"data":[135],"were":[136,232],"used.":[137],"The":[138],"initial":[139],"pipeline":[140],"employed":[141],"Cellpose":[142,155],"segmentation":[144],"ViT":[147],"across":[150,211,250],"growth":[152,212,255],"stages.":[153,213],"However,":[154],"unable":[157],"segment":[159],"all":[160],"instances":[161],"image":[164],"due":[165],"its":[167],"requirement":[168],"diameter":[171],"parameter,":[172],"which,":[173],"variable":[175],"colony":[176],"sizes,":[177],"resulted":[178],"partial":[180],"segmentation.":[181,195],"To":[182],"overcome":[183],"these":[184],"challenges,":[185],"we":[186],"adopted":[187],"end-to-end":[189],"R-CNN":[191,197,260],"instance":[194],"achieved":[198],"consistently":[199],"strong":[200],"mean":[201,220],"Intersection":[202],"over":[203],"Union":[204],"(mIoU)":[205],"scores":[206],"between":[207],"0.91":[208],"0.98":[210],"Over":[214],"full":[216],"period,":[218],"Average":[221,225],"Precision":[222],"(AP)":[223],"Recall":[226],"(AR)":[227],"at":[228,278],"IoU":[229],"threshold":[230],"0.5":[231],"0.93":[233],"0.96":[235],"E.":[237],"coli,":[238],"0.945":[240],"0.975":[242],"Salmonella,":[244],"respectively,":[245],"indicating":[246],"robust":[247],"performance":[249],"types":[252],"period.":[256],"Using":[257],"fine-tuned":[258],"trained":[261],"on":[262,285],"aware":[264],"time-stamped":[265],"datasets,":[267],"our":[268],"method":[269],"achieves":[270],"mAP@0.5":[272],"0.95":[274],"colonies":[276],"cultured":[277],"2":[279],"timepoint.":[281],"work":[283],"focuses":[284],"proactive":[286],"safety":[288],"monitoring":[289],"agricultural":[291],"pipelines.":[292]},"counts_by_year":[],"updated_date":"2026-04-09T06:08:40.794217","created_date":"2026-04-08T00:00:00"}