{"id":"https://openalex.org/W2970563515","doi":"https://doi.org/10.1093/bioinformatics/btz674","title":"Semi-blind sparse affine spectral unmixing of autofluorescence-contaminated micrographs","display_name":"Semi-blind sparse affine spectral unmixing of autofluorescence-contaminated micrographs","publication_year":2019,"publication_date":"2019-08-28","ids":{"openalex":"https://openalex.org/W2970563515","doi":"https://doi.org/10.1093/bioinformatics/btz674","mag":"2970563515","pmid":"https://pubmed.ncbi.nlm.nih.gov/31504202"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btz674","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz674","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","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/A5029856761","display_name":"Blair J. Rossetti","orcid":"https://orcid.org/0000-0003-2405-4209"},"institutions":[{"id":"https://openalex.org/I150468666","display_name":"Emory University","ror":"https://ror.org/03czfpz43","country_code":"US","type":"education","lineage":["https://openalex.org/I150468666"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Blair J Rossetti","raw_affiliation_strings":["Department of Computer Science, Emory University , Atlanta, GA 30322, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Emory University , Atlanta, GA 30322, USA","institution_ids":["https://openalex.org/I150468666"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034561548","display_name":"Steven A. Wilbert","orcid":"https://orcid.org/0009-0008-4409-8974"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Steven A Wilbert","raw_affiliation_strings":["Department of Microbiology, Forsyth Institute , Cambridge, MA 02142, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Microbiology, Forsyth Institute , Cambridge, MA 02142, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044247683","display_name":"Jessica L. Mark Welch","orcid":"https://orcid.org/0000-0003-0696-2334"},"institutions":[{"id":"https://openalex.org/I1338920048","display_name":"Marine Biological Laboratory","ror":"https://ror.org/046dg4z72","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1338920048"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jessica L Mark Welch","raw_affiliation_strings":["Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory , Woods Hole, MA 02543, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory , Woods Hole, MA 02543, USA","institution_ids":["https://openalex.org/I1338920048"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002316771","display_name":"Gary G. Borisy","orcid":"https://orcid.org/0000-0002-0266-8018"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Gary G Borisy","raw_affiliation_strings":["Department of Microbiology, Forsyth Institute , Cambridge, MA 02142, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Microbiology, Forsyth Institute , Cambridge, MA 02142, USA","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5045326873","display_name":"James G. Nagy","orcid":"https://orcid.org/0000-0002-0451-3853"},"institutions":[{"id":"https://openalex.org/I150468666","display_name":"Emory University","ror":"https://ror.org/03czfpz43","country_code":"US","type":"education","lineage":["https://openalex.org/I150468666"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"James G Nagy","raw_affiliation_strings":["Department of Mathematics, Emory University , Atlanta, GA 30322, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mathematics, Emory University , Atlanta, GA 30322, USA","institution_ids":["https://openalex.org/I150468666"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.7255,"has_fulltext":false,"cited_by_count":17,"citation_normalized_percentile":{"value":0.75184052,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"36","issue":"3","first_page":"910","last_page":"917"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11659","display_name":"Advanced Image Fusion Techniques","score":0.3880000114440918,"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/T11659","display_name":"Advanced Image Fusion Techniques","score":0.3880000114440918,"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/T10689","display_name":"Remote-Sensing Image Classification","score":0.10700000077486038,"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/T10640","display_name":"Spectroscopy and Chemometric Analyses","score":0.08709999918937683,"subfield":{"id":"https://openalex.org/subfields/1602","display_name":"Analytical Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/autofluorescence","display_name":"Autofluorescence","score":0.7431694865226746},{"id":"https://openalex.org/keywords/affine-transformation","display_name":"Affine transformation","score":0.6538717150688171},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5484737157821655},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5248020887374878},{"id":"https://openalex.org/keywords/endmember","display_name":"Endmember","score":0.48733410239219666},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.464804083108902},{"id":"https://openalex.org/keywords/hyperspectral-imaging","display_name":"Hyperspectral imaging","score":0.42686212062835693},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.3871946632862091},{"id":"https://openalex.org/keywords/fluorescence","display_name":"Fluorescence","score":0.3410458564758301},{"id":"https://openalex.org/keywords/optics","display_name":"Optics","score":0.12762320041656494},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.1256410777568817}],"concepts":[{"id":"https://openalex.org/C179687394","wikidata":"https://www.wikidata.org/wiki/Q4826281","display_name":"Autofluorescence","level":3,"score":0.7431694865226746},{"id":"https://openalex.org/C92757383","wikidata":"https://www.wikidata.org/wiki/Q382497","display_name":"Affine transformation","level":2,"score":0.6538717150688171},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5484737157821655},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5248020887374878},{"id":"https://openalex.org/C58237817","wikidata":"https://www.wikidata.org/wiki/Q5376204","display_name":"Endmember","level":3,"score":0.48733410239219666},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.464804083108902},{"id":"https://openalex.org/C159078339","wikidata":"https://www.wikidata.org/wiki/Q959005","display_name":"Hyperspectral imaging","level":2,"score":0.42686212062835693},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.3871946632862091},{"id":"https://openalex.org/C91881484","wikidata":"https://www.wikidata.org/wiki/Q191807","display_name":"Fluorescence","level":2,"score":0.3410458564758301},{"id":"https://openalex.org/C120665830","wikidata":"https://www.wikidata.org/wiki/Q14620","display_name":"Optics","level":1,"score":0.12762320041656494},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.1256410777568817},{"id":"https://openalex.org/C202444582","wikidata":"https://www.wikidata.org/wiki/Q837863","display_name":"Pure mathematics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005456","descriptor_name":"Fluorescent Dyes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005456","descriptor_name":"Fluorescent Dyes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005456","descriptor_name":"Fluorescent Dyes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005456","descriptor_name":"Fluorescent Dyes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008856","descriptor_name":"Microscopy, Fluorescence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008856","descriptor_name":"Microscopy, Fluorescence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008856","descriptor_name":"Microscopy, Fluorescence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008856","descriptor_name":"Microscopy, Fluorescence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btz674","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz674","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:31504202","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31504202","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":"Bioinformatics (Oxford, England)","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G5649142708","display_name":null,"funder_award_id":"R01DE022586","funder_id":"https://openalex.org/F4320337365","funder_display_name":"National Institute of Dental and Craniofacial Research"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337365","display_name":"National Institute of Dental and Craniofacial Research","ror":"https://ror.org/004a2wv92"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":50,"referenced_works":["https://openalex.org/W77632492","https://openalex.org/W1246381107","https://openalex.org/W1483193883","https://openalex.org/W1963659868","https://openalex.org/W1964570608","https://openalex.org/W1971941671","https://openalex.org/W1988386267","https://openalex.org/W2036247241","https://openalex.org/W2037328426","https://openalex.org/W2043079694","https://openalex.org/W2053830048","https://openalex.org/W2058187222","https://openalex.org/W2058549613","https://openalex.org/W2063790512","https://openalex.org/W2075665712","https://openalex.org/W2078200937","https://openalex.org/W2094808655","https://openalex.org/W2107003353","https://openalex.org/W2107120407","https://openalex.org/W2126032703","https://openalex.org/W2133362850","https://openalex.org/W2141201649","https://openalex.org/W2163727866","https://openalex.org/W2163886442","https://openalex.org/W2170249894","https://openalex.org/W2213984952","https://openalex.org/W2252298505","https://openalex.org/W2295820431","https://openalex.org/W2296544499","https://openalex.org/W2394629425","https://openalex.org/W2401639901","https://openalex.org/W2404400936","https://openalex.org/W2415282303","https://openalex.org/W2418731786","https://openalex.org/W2465777910","https://openalex.org/W2476124783","https://openalex.org/W2490201121","https://openalex.org/W2560690681","https://openalex.org/W2571462224","https://openalex.org/W2594777858","https://openalex.org/W2595741664","https://openalex.org/W2748313021","https://openalex.org/W2803631955","https://openalex.org/W2887422961","https://openalex.org/W2999905431","https://openalex.org/W4230665766","https://openalex.org/W4233760599","https://openalex.org/W4234514769","https://openalex.org/W6664980779","https://openalex.org/W6675750237"],"related_works":["https://openalex.org/W2037328426","https://openalex.org/W1990914742","https://openalex.org/W2891033441","https://openalex.org/W2006559622","https://openalex.org/W2315521504","https://openalex.org/W3106536224","https://openalex.org/W2890371384","https://openalex.org/W2773863718","https://openalex.org/W2563324120","https://openalex.org/W2040756827"],"abstract_inverted_index":{"MOTIVATION:":[0],"Spectral":[1],"unmixing":[2,56,125,148],"methods":[3,44,164],"attempt":[4],"to":[5,59,101,135,162],"determine":[6],"the":[7,80,85,99,132,137,189],"concentrations":[8],"of":[9,24,79,131],"different":[10],"fluorophores":[11,61],"present":[12],"at":[13,192],"each":[14],"pixel":[15],"location":[16],"in":[17,183],"an":[18,55,103],"image":[19],"by":[20,68,153],"analyzing":[21],"a":[22,77,120,144,166],"set":[23],"measured":[25],"emission":[26,64],"spectra.":[27],"Unmixing":[28],"algorithms":[29],"have":[30],"shown":[31],"great":[32],"promise":[33],"for":[34,93,109,165,178],"applications":[35],"where":[36],"samples":[37],"contain":[38],"many":[39],"fluorescent":[40],"labels;":[41],"however,":[42],"existing":[43,163],"perform":[45],"poorly":[46],"when":[47],"confronted":[48],"with":[49,62,188],"autofluorescence-contaminated":[50],"images.":[51,116],"RESULTS:":[52],"We":[53],"propose":[54,119],"algorithm":[57,127],"designed":[58],"separate":[60],"overlapping":[63],"spectra":[65,113,142],"from":[66,114],"contamination":[67],"autofluorescence":[69,138],"and":[70,139,185],"background":[71,94,140],"fluorescence.":[72,95],"First,":[73],"we":[74,97,118],"formally":[75],"define":[76],"generalization":[78],"linear":[81],"mixing":[82],"model,":[83],"called":[84],"affine":[86,104,123],"mixture":[87],"model":[88],"(AMM),":[89],"that":[90,128],"specifically":[91],"accounts":[92],"Second,":[96],"use":[98],"AMM":[100],"derive":[102],"nonnegative":[105],"matrix":[106],"factorization":[107],"method":[108],"estimating":[110],"fluorophore":[111],"endmember":[112],"reference":[115],"Lastly,":[117],"semi-blind":[121],"sparse":[122],"spectral":[124,150],"(SSASU)":[126],"uses":[129],"knowledge":[130],"estimated":[133],"endmembers":[134],"learn":[136],"fluorescence":[141],"on":[143],"per-image":[145],"basis.":[146],"When":[147],"real-world":[149],"images":[151],"contaminated":[152],"autofluorescence,":[154],"SSASU":[155],"greatly":[156],"improved":[157],"proportion":[158],"indeterminacy":[159],"as":[160],"compared":[161],"given":[167],"relative":[168],"reconstruction":[169],"error.":[170],"AVAILABILITY":[171],"AND":[172],"IMPLEMENTATION:":[173],"The":[174],"source":[175],"code":[176],"used":[177],"this":[179],"paper":[180],"was":[181],"written":[182],"Julia":[184],"is":[186],"available":[187],"test":[190],"data":[191],"https://github.com/brossetti/ssasu.":[193]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1}],"updated_date":"2026-08-01T09:00:35.917206","created_date":"2025-10-10T00:00:00"}
