{"id":"https://openalex.org/W4321002108","doi":"https://doi.org/10.1186/s12859-023-05168-5","title":"petiteFinder: an automated computer vision tool to compute Petite colony frequencies in baker\u2019s yeast","display_name":"petiteFinder: an automated computer vision tool to compute Petite colony frequencies in baker\u2019s yeast","publication_year":2023,"publication_date":"2023-02-15","ids":{"openalex":"https://openalex.org/W4321002108","doi":"https://doi.org/10.1186/s12859-023-05168-5","pmid":"https://pubmed.ncbi.nlm.nih.gov/36793007"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-023-05168-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-023-05168-5","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-023-05168-5","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/counter/pdf/10.1186/s12859-023-05168-5","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5082435763","display_name":"Christopher J. Nunn","orcid":"https://orcid.org/0000-0002-9598-1045"},"institutions":[{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Christopher J. Nunn","raw_affiliation_strings":["Department of Physics, University of Toronto, Toronto, ON, M5S 2W9, Canada. chris.nunn@utoronto.ca","Department of Physics, University of Toronto, Toronto, ON, M5S 2W9, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Physics, University of Toronto, Toronto, ON, M5S 2W9, Canada. chris.nunn@utoronto.ca","institution_ids":["https://openalex.org/I185261750"]},{"raw_affiliation_string":"Department of Physics, University of Toronto, Toronto, ON, M5S 2W9, Canada","institution_ids":["https://openalex.org/I185261750"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023257622","display_name":"Eugene Klyshko","orcid":"https://orcid.org/0000-0002-7895-8636"},"institutions":[{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Eugene Klyshko","raw_affiliation_strings":["Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON, L5L 1C6, Canada","Department of Physics, University of Toronto, Toronto, ON, M5S 2W9, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON, L5L 1C6, Canada","institution_ids":["https://openalex.org/I185261750"]},{"raw_affiliation_string":"Department of Physics, University of Toronto, Toronto, ON, M5S 2W9, Canada","institution_ids":["https://openalex.org/I185261750"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5061121742","display_name":"Sidhartha Goyal","orcid":"https://orcid.org/0000-0002-7452-892X"},"institutions":[{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Sidhartha Goyal","raw_affiliation_strings":["Department of Physics, University of Toronto, Toronto, ON, M5S 2W9, Canada","IBBME, University of Toronto, Toronto, ON, M5S 3G9, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Physics, University of Toronto, Toronto, ON, M5S 2W9, Canada","institution_ids":["https://openalex.org/I185261750"]},{"raw_affiliation_string":"IBBME, University of Toronto, Toronto, ON, M5S 3G9, Canada","institution_ids":["https://openalex.org/I185261750"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5082435763"],"corresponding_institution_ids":["https://openalex.org/I185261750"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.6756,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.79984995,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":95},"biblio":{"volume":"24","issue":"1","first_page":"50","last_page":"50"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.2207999974489212,"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":0.2207999974489212,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.22020000219345093,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.07620000094175339,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"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/biology","display_name":"Biology","score":0.5825754404067993},{"id":"https://openalex.org/keywords/yeast","display_name":"Yeast","score":0.5821692943572998},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.45241355895996094},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4486069679260254},{"id":"https://openalex.org/keywords/object-detection","display_name":"Object detection","score":0.4256516396999359},{"id":"https://openalex.org/keywords/object","display_name":"Object (grammar)","score":0.42421165108680725},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.401394248008728},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.3277878761291504},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.19941288232803345}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5825754404067993},{"id":"https://openalex.org/C2779222958","wikidata":"https://www.wikidata.org/wiki/Q45422","display_name":"Yeast","level":2,"score":0.5821692943572998},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.45241355895996094},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4486069679260254},{"id":"https://openalex.org/C2776151529","wikidata":"https://www.wikidata.org/wiki/Q3045304","display_name":"Object detection","level":3,"score":0.4256516396999359},{"id":"https://openalex.org/C2781238097","wikidata":"https://www.wikidata.org/wiki/Q175026","display_name":"Object (grammar)","level":2,"score":0.42421165108680725},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.401394248008728},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3277878761291504},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.19941288232803345}],"mesh":[{"descriptor_ui":"D005285","descriptor_name":"Fermentation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005285","descriptor_name":"Fermentation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005285","descriptor_name":"Fermentation","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":"D008928","descriptor_name":"Mitochondria","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008928","descriptor_name":"Mitochondria","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008928","descriptor_name":"Mitochondria","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-023-05168-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-023-05168-5","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-023-05168-5","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:36793007","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36793007","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:pubmedcentral.nih.gov:9930278","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9930278","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC9930278/pdf/12859_2023_Article_5168.pdf","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"},{"id":"pmh:oai:doaj.org/article:8894275d15d549faa12a1e7a0fd51e65","is_oa":true,"landing_page_url":"https://doaj.org/article/8894275d15d549faa12a1e7a0fd51e65","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 24, Iss 1, Pp 1-16 (2023)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s12859-023-05168-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-023-05168-5","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-023-05168-5","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":[],"awards":[{"id":"https://openalex.org/G3500906978","display_name":null,"funder_award_id":"326844","funder_id":"https://openalex.org/F4320306164","funder_display_name":"Simons Foundation"},{"id":"https://openalex.org/G560051739","display_name":null,"funder_award_id":"RGPIN-2015","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"},{"id":"https://openalex.org/G5881564744","display_name":null,"funder_award_id":"RGPIN-2015-0","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"}],"funders":[{"id":"https://openalex.org/F4320306164","display_name":"Simons Foundation","ror":"https://ror.org/01cmst727"},{"id":"https://openalex.org/F4320322015","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087"},{"id":"https://openalex.org/F4320334593","display_name":"Natural Sciences and Engineering Research Council of Canada","ror":"https://ror.org/01h531d29"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4321002108.pdf"},"referenced_works_count":30,"referenced_works":["https://openalex.org/W639708223","https://openalex.org/W1861492603","https://openalex.org/W1895943017","https://openalex.org/W1971045545","https://openalex.org/W2011605550","https://openalex.org/W2039202014","https://openalex.org/W2072383593","https://openalex.org/W2079497959","https://openalex.org/W2101926813","https://openalex.org/W2110616752","https://openalex.org/W2110764733","https://openalex.org/W2112796928","https://openalex.org/W2133059825","https://openalex.org/W2136271342","https://openalex.org/W2151596071","https://openalex.org/W2194775991","https://openalex.org/W2552422090","https://openalex.org/W2565639579","https://openalex.org/W2588991035","https://openalex.org/W2807098876","https://openalex.org/W2900215683","https://openalex.org/W2927453739","https://openalex.org/W2963179609","https://openalex.org/W3031591112","https://openalex.org/W3034745255","https://openalex.org/W3096088707","https://openalex.org/W4225270153","https://openalex.org/W4225385469","https://openalex.org/W4307411363","https://openalex.org/W4366071607"],"related_works":["https://openalex.org/W261727187","https://openalex.org/W4240624121","https://openalex.org/W2124768480","https://openalex.org/W1985900993","https://openalex.org/W2385199909","https://openalex.org/W4234489124","https://openalex.org/W191878457","https://openalex.org/W2017288326","https://openalex.org/W2544770378","https://openalex.org/W4292830139"],"abstract_inverted_index":{"BACKGROUND:":[0],"Mitochondrial":[1],"respiration":[2,16,92],"is":[3,17],"central":[4],"to":[5,40,86,166,172,201,293],"cellular":[6],"and":[7,80,117,148,151,177,240,255,273],"organismal":[8],"health":[9],"in":[10,93,225,236,243,245,253,297],"eukaryotes.":[11],"In":[12],"baker's":[13,53],"yeast,":[14],"however,":[15],"dispensable":[18],"under":[19],"fermentation":[20],"conditions.":[21],"Because":[22],"yeast":[23,30,54],"are":[24,31,67,73],"tolerant":[25],"of":[26,44,49,69,90,95,100,136,159,257,276],"this":[27,194,203,271,281],"mitochondrial":[28,50,91,295],"dysfunction,":[29],"widely":[32],"used":[33,85],"by":[34],"biologists":[35],"as":[36,198,213],"a":[37,42,57,126,199,214,246],"model":[38],"organism":[39],"ask":[41],"variety":[43],"questions":[45],"about":[46],"the":[47,88,98,134,137,175,186,258],"integrity":[48,89],"respiration.":[51,70],"Fortunately,":[52],"also":[55],"display":[56],"visually":[58],"identifiable":[59],"Petite":[60,71,101,138,149,153,210,239,259,290],"colony":[61,102,109,154,181,211,260,267,291],"phenotype":[62],"that":[63,132,287],"indicates":[64],"when":[65],"cells":[66],"incapable":[68],"colonies":[72,150],"smaller":[74],"than":[75],"their":[76,81],"Grande":[77,147,241],"(wild-type)":[78],"counterparts,":[79],"frequency":[82,139],"can":[83,196],"be":[84],"infer":[87,294],"populations":[94],"cells.":[96],"Unfortunately,":[97],"computation":[99],"frequencies":[103,155,292],"currently":[104,263],"relies":[105,264],"on":[106,208,265,289],"laborious":[107],"manual":[108,266],"counting":[110],"methods":[111],"which":[112,262],"limit":[113],"both":[114],"experimental":[115,188,277],"throughput":[116,135],"reproducibility.":[118],"RESULTS:":[119],"To":[120],"address":[121],"these":[122],"problems,":[123],"we":[124,190,192,206,279],"introduce":[125],"deep":[127],"learning":[128],"enabled":[129],"tool,":[130],"petiteFinder,":[131],"increases":[133],"assay.":[140,204],"This":[141],"automated":[142,248],"computer":[143,215],"vision":[144,216],"tool":[145,272],"detects":[146],"computes":[152],"from":[156],"scanned":[157],"images":[158,244],"Petri":[160],"dishes.":[161],"It":[162,250],"achieves":[163],"accuracy":[164,238],"comparable":[165],"human":[167],"annotation":[168],"but":[169],"at":[170],"up":[171],"100":[173],"times":[174],"speed":[176],"outperforms":[178],"semi-supervised":[179],"Grande/Petite":[180],"classification":[182],"approaches.":[183],"Combined":[184],"with":[185,221,233],"detailed":[187],"protocols":[189],"provide,":[191],"believe":[193],"study":[195,282],"serve":[197],"foundation":[200],"standardize":[202],"Finally,":[205],"comment":[207],"how":[209],"detection":[212,224,228,232,242],"problem":[217],"highlights":[218],"ongoing":[219],"difficulties":[220],"small":[222],"object":[223,227],"existing":[226],"architectures.":[229],"CONCLUSION:":[230],"Colony":[231],"petiteFinder":[234],"results":[235],"high":[237],"completely":[247],"fashion.":[249],"addresses":[251],"issues":[252],"scalability":[254],"reproducibility":[256],"assay":[261],"counting.":[268],"By":[269],"constructing":[270],"providing":[274],"details":[275],"conditions,":[278],"hope":[280],"will":[283],"enable":[284],"larger-scale":[285],"experiments":[286],"rely":[288],"function":[296],"yeast.":[298]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
