{"id":"https://openalex.org/W3164482086","doi":"https://doi.org/10.1109/isbi48211.2021.9433951","title":"A Robust and Versatile Framework to Compare Spike Detection Methods in Calcium Imaging of Neuronal Activity","display_name":"A Robust and Versatile Framework to Compare Spike Detection Methods in Calcium Imaging of Neuronal Activity","publication_year":2021,"publication_date":"2021-04-13","ids":{"openalex":"https://openalex.org/W3164482086","doi":"https://doi.org/10.1109/isbi48211.2021.9433951","mag":"3164482086"},"language":"en","primary_location":{"id":"doi:10.1109/isbi48211.2021.9433951","is_oa":false,"landing_page_url":"https://doi.org/10.1109/isbi48211.2021.9433951","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2021 IEEE 18th International Symposium on Biomedical Imaging (ISBI)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://pasteur.hal.science/pasteur-03699904/document","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5011334130","display_name":"Samuel Kubler","orcid":null},"institutions":[{"id":"https://openalex.org/I157536573","display_name":"Institut Pasteur","ror":"https://ror.org/0495fxg12","country_code":"FR","type":"funder","lineage":["https://openalex.org/I157536573"]},{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"funder","lineage":["https://openalex.org/I1294671590"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Samuel Kubler","raw_affiliation_strings":["Institut Pasteur, BioImage Analysis Unit, CNRS UMR 3691. 25 rue du docteur Roux, Paris, France"],"affiliations":[{"raw_affiliation_string":"Institut Pasteur, BioImage Analysis Unit, CNRS UMR 3691. 25 rue du docteur Roux, Paris, France","institution_ids":["https://openalex.org/I157536573","https://openalex.org/I1294671590"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076283372","display_name":"Suvadip Mukherjee","orcid":"https://orcid.org/0000-0002-2842-6527"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"funder","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I157536573","display_name":"Institut Pasteur","ror":"https://ror.org/0495fxg12","country_code":"FR","type":"funder","lineage":["https://openalex.org/I157536573"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Suvadip Mukherjee","raw_affiliation_strings":["Institut Pasteur, BioImage Analysis Unit, CNRS UMR 3691. 25 rue du docteur Roux, Paris, France"],"affiliations":[{"raw_affiliation_string":"Institut Pasteur, BioImage Analysis Unit, CNRS UMR 3691. 25 rue du docteur Roux, Paris, France","institution_ids":["https://openalex.org/I157536573","https://openalex.org/I1294671590"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003562216","display_name":"Jean\u2010Christophe Olivo\u2010Mar\u00edn","orcid":"https://orcid.org/0000-0001-6796-0696"},"institutions":[{"id":"https://openalex.org/I157536573","display_name":"Institut Pasteur","ror":"https://ror.org/0495fxg12","country_code":"FR","type":"funder","lineage":["https://openalex.org/I157536573"]},{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"funder","lineage":["https://openalex.org/I1294671590"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Jean-Christophe Olivo-Marin","raw_affiliation_strings":["Institut Pasteur, BioImage Analysis Unit, CNRS UMR 3691. 25 rue du docteur Roux, Paris, France"],"affiliations":[{"raw_affiliation_string":"Institut Pasteur, BioImage Analysis Unit, CNRS UMR 3691. 25 rue du docteur Roux, Paris, France","institution_ids":["https://openalex.org/I157536573","https://openalex.org/I1294671590"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5028273553","display_name":"Thibault Lagache","orcid":"https://orcid.org/0000-0002-7033-4677"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"funder","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I157536573","display_name":"Institut Pasteur","ror":"https://ror.org/0495fxg12","country_code":"FR","type":"funder","lineage":["https://openalex.org/I157536573"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Thibault Lagache","raw_affiliation_strings":["Institut Pasteur, BioImage Analysis Unit, CNRS UMR 3691. 25 rue du docteur Roux, Paris, France"],"affiliations":[{"raw_affiliation_string":"Institut Pasteur, BioImage Analysis Unit, CNRS UMR 3691. 25 rue du docteur Roux, Paris, France","institution_ids":["https://openalex.org/I157536573","https://openalex.org/I1294671590"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5011334130"],"corresponding_institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I157536573"],"apc_list":null,"apc_paid":null,"fwci":0.2331,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.47530422,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":96},"biblio":{"volume":null,"issue":null,"first_page":"375","last_page":"379"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10581","display_name":"Neural dynamics and brain function","score":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/2805","display_name":"Cognitive Neuroscience"},"field":{"id":"https://openalex.org/fields/28","display_name":"Neuroscience"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10581","display_name":"Neural dynamics and brain function","score":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/2805","display_name":"Cognitive Neuroscience"},"field":{"id":"https://openalex.org/fields/28","display_name":"Neuroscience"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11601","display_name":"Neuroscience and Neural Engineering","score":0.9990000128746033,"subfield":{"id":"https://openalex.org/subfields/2804","display_name":"Cellular and Molecular Neuroscience"},"field":{"id":"https://openalex.org/fields/28","display_name":"Neuroscience"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10423","display_name":"Neurobiology and Insect Physiology Research","score":0.9986000061035156,"subfield":{"id":"https://openalex.org/subfields/2804","display_name":"Cellular and Molecular Neuroscience"},"field":{"id":"https://openalex.org/fields/28","display_name":"Neuroscience"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/robustness","display_name":"Robustness (evolution)","score":0.795768141746521},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7325867414474487},{"id":"https://openalex.org/keywords/spike","display_name":"Spike (software development)","score":0.6832139492034912},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.5765023827552795},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5597925186157227},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.44657060503959656},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.42822128534317017},{"id":"https://openalex.org/keywords/sensitivity","display_name":"Sensitivity (control systems)","score":0.42532968521118164},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.40247949957847595}],"concepts":[{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.795768141746521},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7325867414474487},{"id":"https://openalex.org/C2781390188","wikidata":"https://www.wikidata.org/wiki/Q25203449","display_name":"Spike (software development)","level":2,"score":0.6832139492034912},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.5765023827552795},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5597925186157227},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.44657060503959656},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.42822128534317017},{"id":"https://openalex.org/C21200559","wikidata":"https://www.wikidata.org/wiki/Q7451068","display_name":"Sensitivity (control systems)","level":2,"score":0.42532968521118164},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.40247949957847595},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.0},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C24326235","wikidata":"https://www.wikidata.org/wiki/Q126095","display_name":"Electronic engineering","level":1,"score":0.0},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/isbi48211.2021.9433951","is_oa":false,"landing_page_url":"https://doi.org/10.1109/isbi48211.2021.9433951","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2021 IEEE 18th International Symposium on Biomedical Imaging (ISBI)","raw_type":"proceedings-article"},{"id":"pmh:oai:HAL:pasteur-03699904v1","is_oa":true,"landing_page_url":"https://pasteur.hal.science/pasteur-03699904","pdf_url":"https://pasteur.hal.science/pasteur-03699904/document","source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"2021 IEEE 18th International Symposium on Biomedical Imaging (ISBI), Apr 2021, Nice, France. pp.375-379, &#x27E8;10.1109/ISBI48211.2021.9433951&#x27E9;","raw_type":"Conference papers"}],"best_oa_location":{"id":"pmh:oai:HAL:pasteur-03699904v1","is_oa":true,"landing_page_url":"https://pasteur.hal.science/pasteur-03699904","pdf_url":"https://pasteur.hal.science/pasteur-03699904/document","source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"2021 IEEE 18th International Symposium on Biomedical Imaging (ISBI), Apr 2021, Nice, France. pp.375-379, &#x27E8;10.1109/ISBI48211.2021.9433951&#x27E9;","raw_type":"Conference papers"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/15","display_name":"Life in Land","score":0.4399999976158142}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3164482086.pdf","grobid_xml":"https://content.openalex.org/works/W3164482086.grobid-xml"},"referenced_works_count":18,"referenced_works":["https://openalex.org/W1973108213","https://openalex.org/W2007495909","https://openalex.org/W2037947871","https://openalex.org/W2052923946","https://openalex.org/W2067474937","https://openalex.org/W2091997118","https://openalex.org/W2231009150","https://openalex.org/W2303815889","https://openalex.org/W2502163955","https://openalex.org/W2595012769","https://openalex.org/W2598736099","https://openalex.org/W2603409505","https://openalex.org/W2613025880","https://openalex.org/W2805271873","https://openalex.org/W2885162916","https://openalex.org/W2969635663","https://openalex.org/W3036729077","https://openalex.org/W6779231565"],"related_works":["https://openalex.org/W2378211422","https://openalex.org/W4321353415","https://openalex.org/W2745001401","https://openalex.org/W2130974462","https://openalex.org/W2174331923","https://openalex.org/W2028665553","https://openalex.org/W2086519370","https://openalex.org/W972276598","https://openalex.org/W4246352526","https://openalex.org/W2050175337"],"abstract_inverted_index":{"Calcium":[0],"fluorescence":[1,27,38,81],"imaging":[2,135],"enables":[3],"real-time":[4],"activity":[5],"monitoring":[6],"of":[7,22,33,57,68,87,110,127,133,160,173,178,187],"single":[8],"neurons":[9],"in":[10,18,30,47,167,183,195],"living":[11],"animals.":[12],"A":[13],"critical":[14],"inverse":[15],"problem":[16],"resides":[17],"the":[19,31,48,65,69,100,125,148,154,161,170,185,202],"precise":[20],"inference":[21,104,190],"spike":[23,41,103,189],"locations":[24],"from":[25,83],"noisy":[26],"traces,":[28],"especially":[29],"presence":[32],"burst":[34],"spiking":[35],"and":[36,54,140,152],"non-linear":[37],"intensity.":[39],"Several":[40],"extraction":[42],"algorithms":[43,146],"have":[44],"been":[45],"proposed":[46,149],"recent":[49],"years,":[50],"but":[51,119],"a":[52,74,84,94,107,117,188],"robust":[53],"objective":[55],"evaluation":[56],"their":[58],"performance":[59],"still":[60],"remains":[61],"elusive":[62],"due":[63],"to":[64,78,92,97,123,130,138,169,192,200],"unsupervised":[66],"nature":[67,132],"problem.":[70],"Here":[71],"we":[72],"propose":[73],"biologically-inspired":[75],"mathematical":[76],"framework":[77],"reproduce":[79],"synthetic":[80],"traces":[82],"time-series":[85],"data":[86],"spike-trains.":[88],"The":[89],"idea":[90],"is":[91,181],"create":[93],"versatile":[95],"platform":[96],"objectively":[98],"test":[99],"state-of-the":[101],"art":[102],"methodologies":[105],"over":[106],"large":[108],"range":[109],"experimental":[111,158],"parameters.":[112],"Our":[113],"solution":[114],"appears":[115],"as":[116],"complementary":[118],"more":[120],"exhaustive":[121],"approach":[122],"determine":[124],"robustness":[126,180],"existing":[128],"solutions":[129],"different":[131],"signals,":[134],"artefacts,":[136],"sensitivity":[137],"hyper-parameters":[139],"pre-processing":[141],"steps.":[142],"We":[143,164],"benchmark":[144],"state-of-the-art":[145],"with":[147],"simulation":[150],"platform,":[151],"validate":[153],"results":[155],"on":[156],"an":[157,196],"dataset":[159],"Hydra":[162],"Vulgaris.":[163],"hypothesize":[165],"that,":[166],"contrast":[168],"common":[171],"practice":[172],"qualitative":[174],"evaluation,":[175],"quantitative":[176],"measure":[177],"algorithm":[179,191],"essential":[182],"understanding":[184],"suitability":[186],"be":[193],"used":[194],"automated":[197],"computational":[198],"pipeline":[199],"decipher":[201],"neural":[203],"code.":[204]},"counts_by_year":[{"year":2022,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
