{"id":"https://openalex.org/W4410296178","doi":"https://doi.org/10.1109/isbi60581.2025.10980913","title":"Diagnosis with Nanoscale Protein Distributions: Single-Molecule Fluorescence Localization Microscopy and Attention-Based Learning","display_name":"Diagnosis with Nanoscale Protein Distributions: Single-Molecule Fluorescence Localization Microscopy and Attention-Based Learning","publication_year":2025,"publication_date":"2025-04-14","ids":{"openalex":"https://openalex.org/W4410296178","doi":"https://doi.org/10.1109/isbi60581.2025.10980913"},"language":"en","primary_location":{"id":"doi:10.1109/isbi60581.2025.10980913","is_oa":false,"landing_page_url":"https://doi.org/10.1109/isbi60581.2025.10980913","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2025 IEEE 22nd International Symposium on Biomedical Imaging (ISBI)","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/A5012130837","display_name":"Alistair Curd","orcid":"https://orcid.org/0000-0002-3949-7523"},"institutions":[{"id":"https://openalex.org/I2801331674","display_name":"St James's University Hospital","ror":"https://ror.org/013s89d74","country_code":"GB","type":"healthcare","lineage":["https://openalex.org/I2799390153","https://openalex.org/I2801331674"]},{"id":"https://openalex.org/I130828816","display_name":"University of Leeds","ror":"https://ror.org/024mrxd33","country_code":"GB","type":"education","lineage":["https://openalex.org/I130828816"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Alistair Curd","raw_affiliation_strings":["Leeds Institute of Medical Research at St James's, School of Medicine, University of Leeds,UK"],"affiliations":[{"raw_affiliation_string":"Leeds Institute of Medical Research at St James's, School of Medicine, University of Leeds,UK","institution_ids":["https://openalex.org/I2801331674","https://openalex.org/I130828816"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066826618","display_name":"Hayley Slaney","orcid":null},"institutions":[{"id":"https://openalex.org/I130828816","display_name":"University of Leeds","ror":"https://ror.org/024mrxd33","country_code":"GB","type":"education","lineage":["https://openalex.org/I130828816"]},{"id":"https://openalex.org/I2801331674","display_name":"St James's University Hospital","ror":"https://ror.org/013s89d74","country_code":"GB","type":"healthcare","lineage":["https://openalex.org/I2799390153","https://openalex.org/I2801331674"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Hayley Slaney","raw_affiliation_strings":["Leeds Institute of Medical Research at St James's, School of Medicine, University of Leeds,UK"],"affiliations":[{"raw_affiliation_string":"Leeds Institute of Medical Research at St James's, School of Medicine, University of Leeds,UK","institution_ids":["https://openalex.org/I2801331674","https://openalex.org/I130828816"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044200654","display_name":"Scarlet Brockmoeller","orcid":"https://orcid.org/0000-0002-7452-5833"},"institutions":[{"id":"https://openalex.org/I130828816","display_name":"University of Leeds","ror":"https://ror.org/024mrxd33","country_code":"GB","type":"education","lineage":["https://openalex.org/I130828816"]},{"id":"https://openalex.org/I2801331674","display_name":"St James's University Hospital","ror":"https://ror.org/013s89d74","country_code":"GB","type":"healthcare","lineage":["https://openalex.org/I2799390153","https://openalex.org/I2801331674"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Scarlet Brockmoeller","raw_affiliation_strings":["Leeds Institute of Medical Research at St James's, School of Medicine, University of Leeds,UK"],"affiliations":[{"raw_affiliation_string":"Leeds Institute of Medical Research at St James's, School of Medicine, University of Leeds,UK","institution_ids":["https://openalex.org/I2801331674","https://openalex.org/I130828816"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050133572","display_name":"Andras-Gabor Miklosi","orcid":null},"institutions":[{"id":"https://openalex.org/I4210087780","display_name":"Oxford Nanoimaging (United Kingdom)","ror":"https://ror.org/002jmzw69","country_code":"GB","type":"company","lineage":["https://openalex.org/I4210087780"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Andras-Gabor Miklosi","raw_affiliation_strings":["ONI UK,Oxford,UK"],"affiliations":[{"raw_affiliation_string":"ONI UK,Oxford,UK","institution_ids":["https://openalex.org/I4210087780"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108647729","display_name":"Deep Arora","orcid":null},"institutions":[{"id":"https://openalex.org/I2801331674","display_name":"St James's University Hospital","ror":"https://ror.org/013s89d74","country_code":"GB","type":"healthcare","lineage":["https://openalex.org/I2799390153","https://openalex.org/I2801331674"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Deep Arora","raw_affiliation_strings":["Bexley Wing, St James's University Hospital,Department of Histopathology,Leeds,UK"],"affiliations":[{"raw_affiliation_string":"Bexley Wing, St James's University Hospital,Department of Histopathology,Leeds,UK","institution_ids":["https://openalex.org/I2801331674"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054911826","display_name":"Andrew Lewington","orcid":"https://orcid.org/0000-0001-5504-0120"},"institutions":[{"id":"https://openalex.org/I2801331674","display_name":"St James's University Hospital","ror":"https://ror.org/013s89d74","country_code":"GB","type":"healthcare","lineage":["https://openalex.org/I2799390153","https://openalex.org/I2801331674"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Andrew Lewington","raw_affiliation_strings":["St. James's University Hospital,Renal Department,Leeds,UK"],"affiliations":[{"raw_affiliation_string":"St. James's University Hospital,Renal Department,Leeds,UK","institution_ids":["https://openalex.org/I2801331674"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049755145","display_name":"James H. Felce","orcid":"https://orcid.org/0000-0001-5531-9244"},"institutions":[{"id":"https://openalex.org/I4210087780","display_name":"Oxford Nanoimaging (United Kingdom)","ror":"https://ror.org/002jmzw69","country_code":"GB","type":"company","lineage":["https://openalex.org/I4210087780"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"James H. Felce","raw_affiliation_strings":["ONI UK,Oxford,UK"],"affiliations":[{"raw_affiliation_string":"ONI UK,Oxford,UK","institution_ids":["https://openalex.org/I4210087780"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074325740","display_name":"Omar S. M. El Nahhas","orcid":"https://orcid.org/0000-0002-2542-2117"},"institutions":[{"id":"https://openalex.org/I4210108778","display_name":"Fresenius (Germany)","ror":"https://ror.org/01v376g59","country_code":"DE","type":"company","lineage":["https://openalex.org/I4210108778"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Omar S.M. El Nahhas","raw_affiliation_strings":["Else Kroener Fresenius Center for Digital Health, Technical University Dresden,Dresden,Germany"],"affiliations":[{"raw_affiliation_string":"Else Kroener Fresenius Center for Digital Health, Technical University Dresden,Dresden,Germany","institution_ids":["https://openalex.org/I4210108778"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034336361","display_name":"Marko van Treeck","orcid":null},"institutions":[{"id":"https://openalex.org/I4210108778","display_name":"Fresenius (Germany)","ror":"https://ror.org/01v376g59","country_code":"DE","type":"company","lineage":["https://openalex.org/I4210108778"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Marko van Treeck","raw_affiliation_strings":["Else Kroener Fresenius Center for Digital Health, Technical University Dresden,Dresden,Germany"],"affiliations":[{"raw_affiliation_string":"Else Kroener Fresenius Center for Digital Health, Technical University Dresden,Dresden,Germany","institution_ids":["https://openalex.org/I4210108778"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073483894","display_name":"Jakob Nikolas Kather","orcid":"https://orcid.org/0000-0002-3730-5348"},"institutions":[{"id":"https://openalex.org/I4210108778","display_name":"Fresenius (Germany)","ror":"https://ror.org/01v376g59","country_code":"DE","type":"company","lineage":["https://openalex.org/I4210108778"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Jakob Kather","raw_affiliation_strings":["Else Kroener Fresenius Center for Digital Health, Technical University Dresden,Dresden,Germany"],"affiliations":[{"raw_affiliation_string":"Else Kroener Fresenius Center for Digital Health, Technical University Dresden,Dresden,Germany","institution_ids":["https://openalex.org/I4210108778"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5056121788","display_name":"Philip Quirke","orcid":"https://orcid.org/0000-0002-3597-5444"},"institutions":[{"id":"https://openalex.org/I130828816","display_name":"University of Leeds","ror":"https://ror.org/024mrxd33","country_code":"GB","type":"education","lineage":["https://openalex.org/I130828816"]},{"id":"https://openalex.org/I2801331674","display_name":"St James's University Hospital","ror":"https://ror.org/013s89d74","country_code":"GB","type":"healthcare","lineage":["https://openalex.org/I2799390153","https://openalex.org/I2801331674"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Phil Quirke","raw_affiliation_strings":["Leeds Institute of Medical Research at St James's, School of Medicine, University of Leeds,UK"],"affiliations":[{"raw_affiliation_string":"Leeds Institute of Medical Research at St James's, School of Medicine, University of Leeds,UK","institution_ids":["https://openalex.org/I2801331674","https://openalex.org/I130828816"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":11,"corresponding_author_ids":["https://openalex.org/A5012130837"],"corresponding_institution_ids":["https://openalex.org/I130828816","https://openalex.org/I2801331674"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.04230007,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"5"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10857","display_name":"Advanced Electron Microscopy Techniques and Applications","score":0.9807000160217285,"subfield":{"id":"https://openalex.org/subfields/1315","display_name":"Structural 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"}},"topics":[{"id":"https://openalex.org/T10857","display_name":"Advanced Electron Microscopy Techniques and Applications","score":0.9807000160217285,"subfield":{"id":"https://openalex.org/subfields/1315","display_name":"Structural 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/T10540","display_name":"Advanced Fluorescence Microscopy Techniques","score":0.9004999995231628,"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/nanoscopic-scale","display_name":"Nanoscopic scale","score":0.78633052110672},{"id":"https://openalex.org/keywords/microscopy","display_name":"Microscopy","score":0.6631448268890381},{"id":"https://openalex.org/keywords/fluorescence","display_name":"Fluorescence","score":0.6146524548530579},{"id":"https://openalex.org/keywords/fluorescence-microscope","display_name":"Fluorescence microscope","score":0.5964985489845276},{"id":"https://openalex.org/keywords/materials-science","display_name":"Materials science","score":0.5323486924171448},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.4702569246292114},{"id":"https://openalex.org/keywords/nanotechnology","display_name":"Nanotechnology","score":0.46086299419403076},{"id":"https://openalex.org/keywords/biophysics","display_name":"Biophysics","score":0.3476508855819702},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.25656288862228394},{"id":"https://openalex.org/keywords/optics","display_name":"Optics","score":0.23602783679962158},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.15861257910728455},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.08282768726348877}],"concepts":[{"id":"https://openalex.org/C45206210","wikidata":"https://www.wikidata.org/wiki/Q2415817","display_name":"Nanoscopic scale","level":2,"score":0.78633052110672},{"id":"https://openalex.org/C147080431","wikidata":"https://www.wikidata.org/wiki/Q1074953","display_name":"Microscopy","level":2,"score":0.6631448268890381},{"id":"https://openalex.org/C91881484","wikidata":"https://www.wikidata.org/wiki/Q191807","display_name":"Fluorescence","level":2,"score":0.6146524548530579},{"id":"https://openalex.org/C169274487","wikidata":"https://www.wikidata.org/wiki/Q840211","display_name":"Fluorescence microscope","level":3,"score":0.5964985489845276},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.5323486924171448},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.4702569246292114},{"id":"https://openalex.org/C171250308","wikidata":"https://www.wikidata.org/wiki/Q11468","display_name":"Nanotechnology","level":1,"score":0.46086299419403076},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.3476508855819702},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.25656288862228394},{"id":"https://openalex.org/C120665830","wikidata":"https://www.wikidata.org/wiki/Q14620","display_name":"Optics","level":1,"score":0.23602783679962158},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.15861257910728455},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.08282768726348877},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/isbi60581.2025.10980913","is_oa":false,"landing_page_url":"https://doi.org/10.1109/isbi60581.2025.10980913","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2025 IEEE 22nd International Symposium on Biomedical Imaging (ISBI)","raw_type":"proceedings-article"},{"id":"pmh:oai:eprints.whiterose.ac.uk:225595","is_oa":false,"landing_page_url":"https://orcid.org/0000-0002-3949-7523>,","pdf_url":null,"source":{"id":"https://openalex.org/S4306400854","display_name":"White Rose Research Online (University of Leeds, The University of Sheffield, University of York)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2800616092","host_organization_name":"White Rose University Consortium","host_organization_lineage":["https://openalex.org/I2800616092"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"NonPeerReviewed"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3284872871","display_name":null,"funder_award_id":"204825/Z/16/Z","funder_id":"https://openalex.org/F4320307874","funder_display_name":"Wellcome"},{"id":"https://openalex.org/G5372446471","display_name":null,"funder_award_id":"NIHR203331","funder_id":"https://openalex.org/F4320315071","funder_display_name":"NIHR Biomedical Research Centre, Royal Marsden NHS Foundation Trust/Institute of Cancer Research"},{"id":"https://openalex.org/G5927828031","display_name":null,"funder_award_id":"NIHR201643","funder_id":"https://openalex.org/F4320309229","funder_display_name":"National Institute on Handicapped Research"}],"funders":[{"id":"https://openalex.org/F4320307874","display_name":"Wellcome","ror":"https://ror.org/029chgv08"},{"id":"https://openalex.org/F4320309229","display_name":"National Institute on Handicapped Research","ror":null},{"id":"https://openalex.org/F4320315071","display_name":"NIHR Biomedical Research Centre, Royal Marsden NHS Foundation Trust/Institute of Cancer Research","ror":"https://ror.org/0187kwz08"},{"id":"https://openalex.org/F4320320298","display_name":"University of Leeds","ror":"https://ror.org/024mrxd33"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":15,"referenced_works":["https://openalex.org/W2106316394","https://openalex.org/W3035233969","https://openalex.org/W3107935094","https://openalex.org/W3135547872","https://openalex.org/W3167557279","https://openalex.org/W4210283200","https://openalex.org/W4287510106","https://openalex.org/W4361215239","https://openalex.org/W4386303561","https://openalex.org/W4391722054","https://openalex.org/W4392947521","https://openalex.org/W4394764020","https://openalex.org/W4402415665","https://openalex.org/W4402581324","https://openalex.org/W6747701563"],"related_works":["https://openalex.org/W4211107619","https://openalex.org/W2161433272","https://openalex.org/W2894139091","https://openalex.org/W1637909","https://openalex.org/W1983780159","https://openalex.org/W659245948","https://openalex.org/W2793462084","https://openalex.org/W2094643072","https://openalex.org/W4251922430","https://openalex.org/W4206210906"],"abstract_inverted_index":{"Single-molecule":[0],"(fluorescence)":[1],"localization":[2],"microscopy":[3,31],"(SMLM)":[4],"finds":[5],"the":[6,103,144],"position":[7],"of":[8,19,26,67,84,108,115,134],"markers":[9],"for":[10,58,163],"target":[11],"proteins":[12],"at":[13,126],"approx.":[14],"10":[15],"nm":[16],"precision.":[17],"Diagnosis":[18],"some":[20],"diseases":[21,90],"currently":[22],"relies":[23],"on":[24],"inspection":[25],"nanoscale":[27,166],"morphology":[28],"by":[29,132],"electron":[30],"(EM),":[32],"an":[33],"expensive":[34],"and":[35,48,52,112,140,151],"slow":[36],"test":[37],"with":[38,87,98,154,156],"limited":[39],"sample":[40,158],"coverage.":[41],"Nanoscale":[42],"biological":[43],"processes":[44],"also":[45],"underlie":[46],"health":[47],"disease":[49,170],"in":[50,110,168],"general,":[51],"so":[53],"there":[54],"is":[55],"a":[56,99],"need":[57],"more":[59],"efficient":[60],"diagnostic":[61],"methods.":[62],"We":[63,81,117],"demonstrate":[64],"that":[65],"SMLM":[66,139],"routine":[68],"biopsy":[69],"samples":[70],"can":[71],"be":[72],"used":[73],"to":[74,146,149],"assist":[75],"diagnosis":[76,83,150],"via":[77],"data":[78],"classification":[79],"models.":[80,138],"predict":[82],"20":[85],"patients":[86],"chronic":[88],"renal":[89],"(focal":[91],"segmental":[92],"glomerulosclerosis":[93],"or":[94],"minimal":[95],"change":[96],"disease)":[97],"mean":[100],"area":[101],"under":[102],"receiver":[104],"operating":[105],"characteristic":[106],"curve":[107],"0.97":[109],"cross-validation,":[111],"balanced":[113],"accuracy":[114],"90%.":[116],"tested":[118],"state-of-the-art":[119],"pretrained":[120],"feature":[121],"extraction":[122],"from":[123],"image":[124],"tiles":[125],"0.045":[127],"microns":[128],"per":[129],"pixel,":[130],"followed":[131],"training":[133],"weakly":[135],"supervised,":[136],"attention-based":[137],"automated":[141],"analysis":[142],"has":[143],"potential":[145],"save":[147],"time":[148],"costs":[152],"compared":[153],"EM,":[155],"greater":[157],"coverage,":[159],"as":[160,162],"well":[161],"finding":[164],"new":[165],"biomarkers":[167],"other":[169],"areas.":[171]},"counts_by_year":[],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}