{"id":"https://openalex.org/W4408084886","doi":"https://doi.org/10.1101/2025.02.26.640419","title":"Enhanced fluorescence lifetime imaging microscopy denoising via principal component analysis","display_name":"Enhanced fluorescence lifetime imaging microscopy denoising via principal component analysis","publication_year":2025,"publication_date":"2025-03-02","ids":{"openalex":"https://openalex.org/W4408084886","doi":"https://doi.org/10.1101/2025.02.26.640419","pmid":"https://pubmed.ncbi.nlm.nih.gov/40060483","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/11888454"},"language":"en","primary_location":{"id":"doi:10.1101/2025.02.26.640419","doi":"https://doi.org/10.1101/2025.02.26.640419","is_oa":true,"landing_page_url":"https://doi.org/10.1101/2025.02.26.640419","pdf_url":null,"source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nd","license_id":"https://openalex.org/licenses/cc-by-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.1101/2025.02.26.640419","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Soheil Soltani","orcid":"https://orcid.org/0000-0002-0859-2464","observed_orcids":["https://orcid.org/0000-0002-0859-2464"]},"institutions":[{"id":"https://openalex.org/I4405253461","display_name":"Ellison Medical Institute","ror":"https://ror.org/00pfj7a95","country_code":"US","type":"facility","lineage":["https://openalex.org/I4405253461"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Soheil Soltani","raw_affiliation_strings":["Ellison Medical Institute, Los Angeles, California 90064, USA","Ellison Medical Institute"],"raw_orcid":"https://orcid.org/0000-0002-0859-2464","affiliations":[{"raw_affiliation_string":"Ellison Medical Institute, Los Angeles, California 90064, USA","institution_ids":["https://openalex.org/I4405253461"]},{"raw_affiliation_string":"Ellison Medical Institute","institution_ids":["https://openalex.org/I4405253461"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066308151","display_name":"JN Paulson","orcid":"https://orcid.org/0000-0002-1889-0756","observed_orcids":["https://orcid.org/0000-0002-1889-0756"]},"institutions":[{"id":"https://openalex.org/I1174212","display_name":"University of Southern California","ror":"https://ror.org/03taz7m60","country_code":"US","type":"education","lineage":["https://openalex.org/I1174212"]},{"id":"https://openalex.org/I4405253461","display_name":"Ellison Medical Institute","ror":"https://ror.org/00pfj7a95","country_code":"US","type":"facility","lineage":["https://openalex.org/I4405253461"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jack G. Paulson","raw_affiliation_strings":["Ellison Medical Institute, Los Angeles, California 90064, USA","Mork Family Department of Chemical Engineering and Materials Science, Viterbi School of Engineering, University of Southern California, Los Angeles, California 90089, USA","Ellison Medical Institute"],"raw_orcid":"https://orcid.org/0000-0002-1889-0756","affiliations":[{"raw_affiliation_string":"Ellison Medical Institute, Los Angeles, California 90064, USA","institution_ids":["https://openalex.org/I4405253461"]},{"raw_affiliation_string":"Mork Family Department of Chemical Engineering and Materials Science, Viterbi School of Engineering, University of Southern California, Los Angeles, California 90089, USA","institution_ids":["https://openalex.org/I1174212"]},{"raw_affiliation_string":"Ellison Medical Institute","institution_ids":["https://openalex.org/I4405253461"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027968005","display_name":"Emma J. Fong","orcid":"https://orcid.org/0000-0001-6806-1959","observed_orcids":["https://orcid.org/0000-0001-6806-1959"]},"institutions":[{"id":"https://openalex.org/I4405253461","display_name":"Ellison Medical Institute","ror":"https://ror.org/00pfj7a95","country_code":"US","type":"facility","lineage":["https://openalex.org/I4405253461"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Emma J. Fong","raw_affiliation_strings":["Ellison Medical Institute, Los Angeles, California 90064, USA","Ellison Medical Institute"],"raw_orcid":"https://orcid.org/0000-0001-6806-1959","affiliations":[{"raw_affiliation_string":"Ellison Medical Institute, Los Angeles, California 90064, USA","institution_ids":["https://openalex.org/I4405253461"]},{"raw_affiliation_string":"Ellison Medical Institute","institution_ids":["https://openalex.org/I4405253461"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079254926","display_name":"Shannon M. Mumenthaler","orcid":"https://orcid.org/0000-0003-2687-3769","observed_orcids":["https://orcid.org/0000-0003-2687-3769"]},"institutions":[{"id":"https://openalex.org/I1174212","display_name":"University of Southern California","ror":"https://ror.org/03taz7m60","country_code":"US","type":"education","lineage":["https://openalex.org/I1174212"]},{"id":"https://openalex.org/I4405253461","display_name":"Ellison Medical Institute","ror":"https://ror.org/00pfj7a95","country_code":"US","type":"facility","lineage":["https://openalex.org/I4405253461"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shannon M. Mumenthaler","raw_affiliation_strings":["Alfred E. Mann Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, California 90089, USA","Ellison Medical Institute, Los Angeles, California 90064, USA","Keck School of Medicine of USC, University of Southern California, Los Angeles, California 90033, USA","Ellison Medical Institute"],"raw_orcid":"https://orcid.org/0000-0003-2687-3769","affiliations":[{"raw_affiliation_string":"Alfred E. Mann Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, California 90089, USA","institution_ids":["https://openalex.org/I1174212"]},{"raw_affiliation_string":"Ellison Medical Institute, Los Angeles, California 90064, USA","institution_ids":["https://openalex.org/I4405253461"]},{"raw_affiliation_string":"Keck School of Medicine of USC, University of Southern California, Los Angeles, California 90033, USA","institution_ids":["https://openalex.org/I1174212"]},{"raw_affiliation_string":"Ellison Medical Institute","institution_ids":["https://openalex.org/I4405253461"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101679309","display_name":"Andrea M. Armani","orcid":"https://orcid.org/0000-0001-9890-5104","observed_orcids":["https://orcid.org/0000-0001-9890-5104"]},"institutions":[{"id":"https://openalex.org/I1174212","display_name":"University of Southern California","ror":"https://ror.org/03taz7m60","country_code":"US","type":"education","lineage":["https://openalex.org/I1174212"]},{"id":"https://openalex.org/I4405253461","display_name":"Ellison Medical Institute","ror":"https://ror.org/00pfj7a95","country_code":"US","type":"facility","lineage":["https://openalex.org/I4405253461"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Andrea M. Armani","raw_affiliation_strings":["Alfred E. Mann Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, California 90089, USA","Ellison Medical Institute, Los Angeles, California 90064, USA","Ming Hsieh Department of Electrical and Computer Engineering \u2013 Electrophysics, Viterbi School of Engineering, University of Southern California, Los Angeles, California 90089, USA","Mork Family Department of Chemical Engineering and Materials Science, Viterbi School of Engineering, University of Southern California, Los Angeles, California 90089, USA","Ellison Medical Institute"],"raw_orcid":"https://orcid.org/0000-0001-9890-5104","affiliations":[{"raw_affiliation_string":"Alfred E. Mann Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, California 90089, USA","institution_ids":["https://openalex.org/I1174212"]},{"raw_affiliation_string":"Ellison Medical Institute, Los Angeles, California 90064, USA","institution_ids":["https://openalex.org/I4405253461"]},{"raw_affiliation_string":"Ming Hsieh Department of Electrical and Computer Engineering \u2013 Electrophysics, Viterbi School of Engineering, University of Southern California, Los Angeles, California 90089, USA","institution_ids":["https://openalex.org/I1174212"]},{"raw_affiliation_string":"Mork Family Department of Chemical Engineering and Materials Science, Viterbi School of Engineering, University of Southern California, Los Angeles, California 90089, USA","institution_ids":["https://openalex.org/I1174212"]},{"raw_affiliation_string":"Ellison Medical Institute","institution_ids":["https://openalex.org/I4405253461"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I4405253461"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10540","display_name":"Advanced Fluorescence Microscopy Techniques","score":0.9907000064849854,"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/T10540","display_name":"Advanced Fluorescence Microscopy Techniques","score":0.9907000064849854,"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/T10688","display_name":"Image and Signal Denoising Methods","score":0.006599999964237213,"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":0.0008999999845400453,"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/fluorescence-lifetime-imaging-microscopy","display_name":"fluorescence lifetime imaging","score":0.9980000257492065},{"id":"https://openalex.org/keywords/noise-reduction","display_name":"noise reduction","score":0.8050000071525574},{"id":"https://openalex.org/keywords/principal-component-analysis","display_name":"principal component analysis","score":0.9789999723434448},{"id":"https://openalex.org/keywords/autofluorescence-lifetime","display_name":"autofluorescence lifetime","score":0.8730000257492065},{"id":"https://openalex.org/keywords/cellular-metabolism","display_name":"cellular metabolism","score":0.652999997138977},{"id":"https://openalex.org/keywords/colorectal-cancer-organoids","display_name":"colorectal cancer organoids","score":0.9639999866485596},{"id":"https://openalex.org/keywords/treatment-response","display_name":"treatment response","score":0.6470000147819519},{"id":"https://openalex.org/keywords/metabolic-heterogeneity","display_name":"metabolic heterogeneity","score":0.7160000205039978},{"id":"https://openalex.org/keywords/image-denoising","display_name":"image denoising","score":0.746999979019165}],"concepts":[{"id":"https://openalex.org/C27438332","wikidata":"https://www.wikidata.org/wiki/Q2873","display_name":"Principal component analysis","level":2,"score":0.7910687923431396},{"id":"https://openalex.org/C179687394","wikidata":"https://www.wikidata.org/wiki/Q4826281","display_name":"Autofluorescence","level":3,"score":0.707680344581604},{"id":"https://openalex.org/C3770464","wikidata":"https://www.wikidata.org/wiki/Q775963","display_name":"Smoothing","level":2,"score":0.604103147983551},{"id":"https://openalex.org/C191178318","wikidata":"https://www.wikidata.org/wiki/Q2256906","display_name":"Thresholding","level":3,"score":0.5839486718177795},{"id":"https://openalex.org/C163294075","wikidata":"https://www.wikidata.org/wiki/Q581861","display_name":"Noise reduction","level":2,"score":0.5766255259513855},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5513762831687927},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5438221096992493},{"id":"https://openalex.org/C51432778","wikidata":"https://www.wikidata.org/wiki/Q1259145","display_name":"Independent component analysis","level":2,"score":0.5387306213378906},{"id":"https://openalex.org/C57477423","wikidata":"https://www.wikidata.org/wiki/Q1434196","display_name":"Fluorescence-lifetime imaging microscopy","level":3,"score":0.5354201197624207},{"id":"https://openalex.org/C99498987","wikidata":"https://www.wikidata.org/wiki/Q2210247","display_name":"Noise (video)","level":3,"score":0.487548291683197},{"id":"https://openalex.org/C147080431","wikidata":"https://www.wikidata.org/wiki/Q1074953","display_name":"Microscopy","level":2,"score":0.4829356372356415},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.45583346486091614},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.346097856760025},{"id":"https://openalex.org/C91881484","wikidata":"https://www.wikidata.org/wiki/Q191807","display_name":"Fluorescence","level":2,"score":0.28772538900375366},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.27262628078460693},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.18492832779884338},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.15374669432640076},{"id":"https://openalex.org/C120665830","wikidata":"https://www.wikidata.org/wiki/Q14620","display_name":"Optics","level":1,"score":0.1462232768535614},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.13979268074035645},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.13508471846580505},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.08476507663726807}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1101/2025.02.26.640419","doi":"https://doi.org/10.1101/2025.02.26.640419","is_oa":true,"landing_page_url":"https://doi.org/10.1101/2025.02.26.640419","pdf_url":null,"source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nd","license_id":"https://openalex.org/licenses/cc-by-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},{"id":"pmid:40060483","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40060483","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,"listed_in":[],"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":"bioRxiv : the preprint server for biology","raw_type":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:11888454","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11888454","pdf_url":null,"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,"listed_in":[],"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-nd","license_id":"https://openalex.org/licenses/cc-by-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1101/2025.02.26.640419","doi":"https://doi.org/10.1101/2025.02.26.640419","is_oa":true,"landing_page_url":"https://doi.org/10.1101/2025.02.26.640419","pdf_url":null,"source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nd","license_id":"https://openalex.org/licenses/cc-by-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","score":0.428600013256073,"display_name":"Good health and well-being"}],"sustainable_development_goals_aurora":[{"id":"https://metadata.un.org/sdg/3","score":0.7200000286102295,"display_name":"Good health and well-being"}],"study_designs":[],"awards":[{"id":"https://openalex.org/G2789349153","display_name":"Multiscale systems biology modeling to exploit tumor-stromal metabolic crosstalk in colorectal cancer","funder_award_id":"U01CA232137","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G9000910363","display_name":"University of Southern California Norris Comprehensive Cancer Center Support Grant (CCSG)","funder_award_id":"P30CA014089","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"}],"funders":[{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W4416291689","https://openalex.org/W2565773229","https://openalex.org/W7133506156","https://openalex.org/W4390111530","https://openalex.org/W6964467282","https://openalex.org/W2077363074","https://openalex.org/W4408605713","https://openalex.org/W3114821321","https://openalex.org/W2152003580","https://openalex.org/W7168427496"],"abstract_inverted_index":{"Fluorescence":[0],"Lifetime":[1],"Imaging":[2],"Microscopy":[3],"(FLIM)":[4],"quantifies":[5],"the":[6,25,28,68,77,107],"autofluorescence":[7],"lifetime":[8],"to":[9,94,110,114,144],"measure":[10],"cellular":[11],"metabolism,":[12],"therapeutic":[13],"efficacy,":[14],"and":[15,38,51,75],"disease":[16],"progression.":[17],"These":[18,45],"dynamic":[19],"processes":[20],"are":[21,43],"intrinsically":[22],"heterogeneous,":[23],"increasing":[24],"complexity":[26],"of":[27,70,85,88,97],"signal":[29,69],"analysis.":[30],"Often":[31],"noise":[32],"reduction":[33],"strategies":[34],"that":[35,104,129],"combine":[36],"thresholding":[37],"non-selective":[39],"data":[40,52,119,125],"smoothing":[41],"filters":[42],"applied.":[44],"can":[46],"result":[47],"in":[48,112],"error":[49],"introduction":[50],"loss.":[53,120],"To":[54,79],"mitigate":[55],"these":[56],"issues,":[57],"we":[58,102,127],"develop":[59],"noise-corrected":[60],"principal":[61],"component":[62],"analysis":[63,84,116,147],"(NC-PCA).":[64],"This":[65],"approach":[66],"isolates":[67],"interest":[71],"by":[72],"selectively":[73],"identifying":[74],"removing":[76],"noise.":[78],"validate":[80],"NC-PCA,":[81,130],"a":[82,95,123],"secondary":[83],"FLIM":[86,146],"images":[87],"patient-derived":[89],"colorectal":[90],"cancer":[91],"organoids":[92],"exposed":[93],"range":[96],"therapeutics":[98],"was":[99],"performed.":[100],"First,":[101],"demonstrate":[103],"NC-PCA":[105,139],"decreases":[106],"uncertainty":[108],"up":[109],"4-fold":[111],"comparison":[113],"conventional":[115,132],"with":[117],"no":[118],"Then,":[121],"using":[122],"merged":[124],"set,":[126],"show":[128],"unlike":[131],"methods,":[133],"identifies":[134],"multiple":[135],"metabolic":[136],"states.":[137],"Thus,":[138],"provides":[140],"an":[141],"enabling":[142],"tool":[143],"advance":[145],"across":[148],"fields.":[149]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-10-30T12:39:25.321706","created_date":"2025-03-03T00:00:00"}