{"id":"https://openalex.org/W4391679929","doi":"https://doi.org/10.3389/fbinf.2024.1336257","title":"A perspective on FAIR quality control in multiplexed imaging data processing","display_name":"A perspective on FAIR quality control in multiplexed imaging data processing","publication_year":2024,"publication_date":"2024-02-09","ids":{"openalex":"https://openalex.org/W4391679929","doi":"https://doi.org/10.3389/fbinf.2024.1336257","pmid":"https://pubmed.ncbi.nlm.nih.gov/38405548"},"language":"en","primary_location":{"id":"doi:10.3389/fbinf.2024.1336257","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2024.1336257","pdf_url":"https://www.frontiersin.org/articles/10.3389/fbinf.2024.1336257/pdf?isPublishedV2=False","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.frontiersin.org/articles/10.3389/fbinf.2024.1336257/pdf?isPublishedV2=False","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5093896899","display_name":"Wouter-Michiel Vierdag","orcid":"https://orcid.org/0000-0003-1666-5421"},"institutions":[{"id":"https://openalex.org/I4210138560","display_name":"European Molecular Biology Laboratory","ror":"https://ror.org/03mstc592","country_code":"DE","type":"government","lineage":["https://openalex.org/I4210138560"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Wouter-Michiel A. M. Vierdag","raw_affiliation_strings":["Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany"],"affiliations":[{"raw_affiliation_string":"Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany","institution_ids":["https://openalex.org/I4210138560"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5067094283","display_name":"Sinem K. Saka","orcid":"https://orcid.org/0000-0002-5017-379X"},"institutions":[{"id":"https://openalex.org/I4210138560","display_name":"European Molecular Biology Laboratory","ror":"https://ror.org/03mstc592","country_code":"DE","type":"government","lineage":["https://openalex.org/I4210138560"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Sinem K. Saka","raw_affiliation_strings":["Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany"],"affiliations":[{"raw_affiliation_string":"Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany","institution_ids":["https://openalex.org/I4210138560"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5093896899"],"corresponding_institution_ids":["https://openalex.org/I4210138560"],"apc_list":{"value":1900,"currency":"USD","value_usd":1900},"apc_paid":{"value":1900,"currency":"USD","value_usd":1900},"fwci":5.975,"has_fulltext":true,"cited_by_count":7,"citation_normalized_percentile":{"value":0.95929132,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"4","issue":null,"first_page":"1336257","last_page":"1336257"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.9968000054359436,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},"topics":[{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.9968000054359436,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9961000084877014,"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.9958999752998352,"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/computer-science","display_name":"Computer science","score":0.7988708019256592},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.790107250213623},{"id":"https://openalex.org/keywords/multiplexing","display_name":"Multiplexing","score":0.6343992948532104},{"id":"https://openalex.org/keywords/image-processing","display_name":"Image processing","score":0.568567156791687},{"id":"https://openalex.org/keywords/data-processing","display_name":"Data processing","score":0.5494264960289001},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5451270341873169},{"id":"https://openalex.org/keywords/pipeline-transport","display_name":"Pipeline transport","score":0.5320336222648621},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.5093423128128052},{"id":"https://openalex.org/keywords/image-quality","display_name":"Image quality","score":0.4998152256011963},{"id":"https://openalex.org/keywords/quality","display_name":"Quality (philosophy)","score":0.47031369805336},{"id":"https://openalex.org/keywords/perspective","display_name":"Perspective (graphical)","score":0.4622957110404968},{"id":"https://openalex.org/keywords/data-quality","display_name":"Data quality","score":0.439410924911499},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4025675654411316},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3898223340511322},{"id":"https://openalex.org/keywords/computer-vision","display_name":"Computer vision","score":0.3599448800086975},{"id":"https://openalex.org/keywords/image","display_name":"Image (mathematics)","score":0.30195730924606323},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.14596202969551086},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.08552658557891846}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7988708019256592},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.790107250213623},{"id":"https://openalex.org/C19275194","wikidata":"https://www.wikidata.org/wiki/Q222903","display_name":"Multiplexing","level":2,"score":0.6343992948532104},{"id":"https://openalex.org/C9417928","wikidata":"https://www.wikidata.org/wiki/Q1070689","display_name":"Image processing","level":3,"score":0.568567156791687},{"id":"https://openalex.org/C138827492","wikidata":"https://www.wikidata.org/wiki/Q6661985","display_name":"Data processing","level":2,"score":0.5494264960289001},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5451270341873169},{"id":"https://openalex.org/C175309249","wikidata":"https://www.wikidata.org/wiki/Q725864","display_name":"Pipeline transport","level":2,"score":0.5320336222648621},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.5093423128128052},{"id":"https://openalex.org/C55020928","wikidata":"https://www.wikidata.org/wiki/Q3813865","display_name":"Image quality","level":3,"score":0.4998152256011963},{"id":"https://openalex.org/C2779530757","wikidata":"https://www.wikidata.org/wiki/Q1207505","display_name":"Quality (philosophy)","level":2,"score":0.47031369805336},{"id":"https://openalex.org/C12713177","wikidata":"https://www.wikidata.org/wiki/Q1900281","display_name":"Perspective (graphical)","level":2,"score":0.4622957110404968},{"id":"https://openalex.org/C24756922","wikidata":"https://www.wikidata.org/wiki/Q1757694","display_name":"Data quality","level":3,"score":0.439410924911499},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4025675654411316},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3898223340511322},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.3599448800086975},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.30195730924606323},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.14596202969551086},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.08552658557891846},{"id":"https://openalex.org/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","level":1,"score":0.0},{"id":"https://openalex.org/C21547014","wikidata":"https://www.wikidata.org/wiki/Q1423657","display_name":"Operations management","level":1,"score":0.0},{"id":"https://openalex.org/C176217482","wikidata":"https://www.wikidata.org/wiki/Q860554","display_name":"Metric (unit)","level":2,"score":0.0},{"id":"https://openalex.org/C87717796","wikidata":"https://www.wikidata.org/wiki/Q146326","display_name":"Environmental engineering","level":1,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.3389/fbinf.2024.1336257","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2024.1336257","pdf_url":"https://www.frontiersin.org/articles/10.3389/fbinf.2024.1336257/pdf?isPublishedV2=False","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38405548","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38405548","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":"Frontiers in bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10885342","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10885342","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10885342/pdf/fbinf-04-1336257.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":"Front Bioinform","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:b9f0482d56394deca88d5cb36a8ae6f4","is_oa":true,"landing_page_url":"https://doaj.org/article/b9f0482d56394deca88d5cb36a8ae6f4","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Frontiers in Bioinformatics, Vol 4 (2024)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.3389/fbinf.2024.1336257","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2024.1336257","pdf_url":"https://www.frontiersin.org/articles/10.3389/fbinf.2024.1336257/pdf?isPublishedV2=False","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure","score":0.5799999833106995}],"awards":[],"funders":[{"id":"https://openalex.org/F4320314023","display_name":"European Molecular Biology Laboratory","ror":"https://ror.org/050589e39"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4391679929.pdf"},"referenced_works_count":49,"referenced_works":["https://openalex.org/W1998614190","https://openalex.org/W2167279371","https://openalex.org/W2173763791","https://openalex.org/W2302501749","https://openalex.org/W2641905542","https://openalex.org/W2895259663","https://openalex.org/W2922020904","https://openalex.org/W2952481429","https://openalex.org/W3016787828","https://openalex.org/W3047081808","https://openalex.org/W3083230937","https://openalex.org/W3099559583","https://openalex.org/W3099978069","https://openalex.org/W3160059695","https://openalex.org/W3160476106","https://openalex.org/W3173096232","https://openalex.org/W3194189918","https://openalex.org/W3194359278","https://openalex.org/W3209378804","https://openalex.org/W3214596602","https://openalex.org/W3215069361","https://openalex.org/W3215932031","https://openalex.org/W3217102738","https://openalex.org/W4210583065","https://openalex.org/W4212959882","https://openalex.org/W4225678977","https://openalex.org/W4229557751","https://openalex.org/W4253933889","https://openalex.org/W4280560433","https://openalex.org/W4286005528","https://openalex.org/W4308361273","https://openalex.org/W4321373707","https://openalex.org/W4366134602","https://openalex.org/W4375852635","https://openalex.org/W4377233165","https://openalex.org/W4381684985","https://openalex.org/W4383710649","https://openalex.org/W4385174515","https://openalex.org/W4386623320","https://openalex.org/W4387494379","https://openalex.org/W4387660860","https://openalex.org/W4388069610","https://openalex.org/W4388228824","https://openalex.org/W4389040937","https://openalex.org/W4390839439","https://openalex.org/W4393004135","https://openalex.org/W4401685352","https://openalex.org/W4402926830","https://openalex.org/W6968973386"],"related_works":["https://openalex.org/W1995889332","https://openalex.org/W3104163240","https://openalex.org/W3008693296","https://openalex.org/W2890791469","https://openalex.org/W4312283151","https://openalex.org/W2381158465","https://openalex.org/W4251457771","https://openalex.org/W2078091825","https://openalex.org/W2617721340","https://openalex.org/W4386427058"],"abstract_inverted_index":{"Multiplexed":[0],"imaging":[1,8,15,161,183,193],"approaches":[2],"are":[3],"getting":[4],"increasingly":[5],"adopted":[6],"for":[7,131,142,180,200],"of":[9,20,23,28,37,54,61,68,80,90,117,121,127,137,146,159,169,176,191,217],"large":[10,181],"tissue":[11],"areas,":[12],"yielding":[13],"big":[14],"datasets":[16,39,162],"both":[17,130],"in":[18,203,220],"terms":[19],"the":[21,26,59,77,88,91,108,122,132,138,144,147,160,164,170,186,197],"number":[22,53],"samples":[24],"and":[25,35,47,94,106,135,141,155,163,189],"size":[27,188],"image":[29,123,204],"data":[30],"per":[31],"sample.":[32],"The":[33],"processing":[34,82,124],"analysis":[36,60,134,139,165,205],"these":[38,75,118],"is":[40,84,126],"complex":[41],"owing":[42],"to":[43],"frequent":[44],"technical":[45],"artifacts":[46],"heterogeneous":[48],"profiles":[49],"from":[50,96],"a":[51],"high":[52],"stained":[55],"targets":[56],"To":[57],"streamline":[58],"multiplexed":[62,182,192],"images,":[63],"automated":[64],"pipelines":[65,206],"making":[66],"use":[67],"state-of-the-art":[69],"algorithms":[70],"have":[71],"been":[72],"developed.":[73],"In":[74],"pipelines,":[76],"output":[78,89],"quality":[79,112],"one":[81],"step":[83,93],"typically":[85],"dependent":[86],"on":[87,215],"previous":[92],"errors":[95],"each":[97,116],"step,":[98],"even":[99],"when":[100],"they":[101],"appear":[102],"minor,":[103],"can":[104],"propagate":[105],"confound":[107],"results.":[109],"Thus,":[110],"rigorous":[111],"control":[113],"(QC)":[114],"at":[115],"different":[119,198],"steps":[120],"pipeline":[125],"paramount":[128],"importance":[129],"proper":[133],"interpretation":[136],"results":[140],"ensuring":[143],"reusability":[145],"data.":[148,184],"Ideally,":[149],"QC":[150,178,202],"should":[151],"become":[152],"an":[153],"integral":[154],"easily":[156],"retrievable":[157],"part":[158],"process.":[166],"Yet,":[167],"limitations":[168],"currently":[171],"available":[172],"frameworks":[173],"make":[174],"integration":[175],"interactive":[177],"difficult":[179],"Given":[185],"increasing":[187],"complexity":[190],"datasets,":[194],"we":[195],"present":[196],"challenges":[199],"integrating":[201],"as":[207,209],"well":[208],"suggest":[210],"possible":[211],"solutions":[212],"that":[213],"build":[214],"top":[216],"recent":[218],"advances":[219],"bioimage":[221],"analysis.":[222]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":2},{"year":2022,"cited_by_count":1}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}
