{"id":"https://openalex.org/W7161894636","doi":"https://doi.org/10.1109/isbi61048.2026.11515940","title":"Self-Supervised Learning for Single Cell Large Scale Neuroimaging","display_name":"Self-Supervised Learning for Single Cell Large Scale Neuroimaging","publication_year":2026,"publication_date":"2026-04-08","ids":{"openalex":"https://openalex.org/W7161894636","doi":"https://doi.org/10.1109/isbi61048.2026.11515940"},"language":null,"primary_location":{"id":"doi:10.1109/isbi61048.2026.11515940","is_oa":false,"landing_page_url":"https://doi.org/10.1109/isbi61048.2026.11515940","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2026 IEEE 23rd 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/A5136546483","display_name":"M. Giraud","orcid":null},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I142476485","display_name":"\u00c9cole Polytechnique","ror":"https://ror.org/05hy3tk52","country_code":"FR","type":"education","lineage":["https://openalex.org/I142476485","https://openalex.org/I4210145102"]},{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"M. Giraud","raw_affiliation_strings":["Institut Polytechnique de Paris,Laboratoire d&#x0027;Optique et Biosciences, CNRS, Inserm, Ecole Polytechnique,Palaiseau,France,91120"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institut Polytechnique de Paris,Laboratoire d&#x0027;Optique et Biosciences, CNRS, Inserm, Ecole Polytechnique,Palaiseau,France,91120","institution_ids":["https://openalex.org/I154526488","https://openalex.org/I142476485","https://openalex.org/I1294671590"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002983222","display_name":"H. Blanc","orcid":null},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I142476485","display_name":"\u00c9cole Polytechnique","ror":"https://ror.org/05hy3tk52","country_code":"FR","type":"education","lineage":["https://openalex.org/I142476485","https://openalex.org/I4210145102"]},{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"H. Blanc","raw_affiliation_strings":["Institut Polytechnique de Paris,Laboratoire d&#x0027;Optique et Biosciences, CNRS, Inserm, Ecole Polytechnique,Palaiseau,France,91120"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institut Polytechnique de Paris,Laboratoire d&#x0027;Optique et Biosciences, CNRS, Inserm, Ecole Polytechnique,Palaiseau,France,91120","institution_ids":["https://openalex.org/I154526488","https://openalex.org/I142476485","https://openalex.org/I1294671590"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5136559164","display_name":"P. Mahou","orcid":null},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I142476485","display_name":"\u00c9cole Polytechnique","ror":"https://ror.org/05hy3tk52","country_code":"FR","type":"education","lineage":["https://openalex.org/I142476485","https://openalex.org/I4210145102"]},{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"P. Mahou","raw_affiliation_strings":["Institut Polytechnique de Paris,Laboratoire d&#x0027;Optique et Biosciences, CNRS, Inserm, Ecole Polytechnique,Palaiseau,France,91120"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institut Polytechnique de Paris,Laboratoire d&#x0027;Optique et Biosciences, CNRS, Inserm, Ecole Polytechnique,Palaiseau,France,91120","institution_ids":["https://openalex.org/I154526488","https://openalex.org/I142476485","https://openalex.org/I1294671590"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5136580334","display_name":"G. Kaddour","orcid":null},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I1340951533","display_name":"Institut de la Vision","ror":"https://ror.org/000zhpw23","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1340951533","https://openalex.org/I39804081"]},{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I39804081","display_name":"Sorbonne Universit\u00e9","ror":"https://ror.org/02en5vm52","country_code":"FR","type":"education","lineage":["https://openalex.org/I39804081"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"G. Kaddour","raw_affiliation_strings":["Institut de la Vision,Sorbonne Universit&#x00E9;, INSERM, CNRS,Paris,France,75012"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institut de la Vision,Sorbonne Universit&#x00E9;, INSERM, CNRS,Paris,France,75012","institution_ids":["https://openalex.org/I154526488","https://openalex.org/I39804081","https://openalex.org/I1340951533","https://openalex.org/I1294671590"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5136583520","display_name":"C. Caporal","orcid":null},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I142476485","display_name":"\u00c9cole Polytechnique","ror":"https://ror.org/05hy3tk52","country_code":"FR","type":"education","lineage":["https://openalex.org/I142476485","https://openalex.org/I4210145102"]},{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"C. Caporal","raw_affiliation_strings":["Institut Polytechnique de Paris,Laboratoire d&#x0027;Optique et Biosciences, CNRS, Inserm, Ecole Polytechnique,Palaiseau,France,91120"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institut Polytechnique de Paris,Laboratoire d&#x0027;Optique et Biosciences, CNRS, Inserm, Ecole Polytechnique,Palaiseau,France,91120","institution_ids":["https://openalex.org/I154526488","https://openalex.org/I142476485","https://openalex.org/I1294671590"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5136590062","display_name":"G. Le Dr\u00e9au","orcid":null},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I1340951533","display_name":"Institut de la Vision","ror":"https://ror.org/000zhpw23","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1340951533","https://openalex.org/I39804081"]},{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I39804081","display_name":"Sorbonne Universit\u00e9","ror":"https://ror.org/02en5vm52","country_code":"FR","type":"education","lineage":["https://openalex.org/I39804081"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"G. Le Dr\u00e9au","raw_affiliation_strings":["Institut de la Vision,Sorbonne Universit&#x00E9;, INSERM, CNRS,Paris,France,75012"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institut de la Vision,Sorbonne Universit&#x00E9;, INSERM, CNRS,Paris,France,75012","institution_ids":["https://openalex.org/I154526488","https://openalex.org/I39804081","https://openalex.org/I1340951533","https://openalex.org/I1294671590"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5136513536","display_name":"J. Livet","orcid":null},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I1340951533","display_name":"Institut de la Vision","ror":"https://ror.org/000zhpw23","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1340951533","https://openalex.org/I39804081"]},{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I39804081","display_name":"Sorbonne Universit\u00e9","ror":"https://ror.org/02en5vm52","country_code":"FR","type":"education","lineage":["https://openalex.org/I39804081"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"J. Livet","raw_affiliation_strings":["Institut de la Vision,Sorbonne Universit&#x00E9;, INSERM, CNRS,Paris,France,75012"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institut de la Vision,Sorbonne Universit&#x00E9;, INSERM, CNRS,Paris,France,75012","institution_ids":["https://openalex.org/I154526488","https://openalex.org/I39804081","https://openalex.org/I1340951533","https://openalex.org/I1294671590"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082433666","display_name":"E. BEAUREPAIRE","orcid":null},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I142476485","display_name":"\u00c9cole Polytechnique","ror":"https://ror.org/05hy3tk52","country_code":"FR","type":"education","lineage":["https://openalex.org/I142476485","https://openalex.org/I4210145102"]},{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"E. Beaurepaire","raw_affiliation_strings":["Institut Polytechnique de Paris,Laboratoire d&#x0027;Optique et Biosciences, CNRS, Inserm, Ecole Polytechnique,Palaiseau,France,91120"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institut Polytechnique de Paris,Laboratoire d&#x0027;Optique et Biosciences, CNRS, Inserm, Ecole Polytechnique,Palaiseau,France,91120","institution_ids":["https://openalex.org/I154526488","https://openalex.org/I142476485","https://openalex.org/I1294671590"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5136604070","display_name":"A. Chessel","orcid":null},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I142476485","display_name":"\u00c9cole Polytechnique","ror":"https://ror.org/05hy3tk52","country_code":"FR","type":"education","lineage":["https://openalex.org/I142476485","https://openalex.org/I4210145102"]},{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"A. Chessel","raw_affiliation_strings":["Institut Polytechnique de Paris,Laboratoire d&#x0027;Optique et Biosciences, CNRS, Inserm, Ecole Polytechnique,Palaiseau,France,91120"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institut Polytechnique de Paris,Laboratoire d&#x0027;Optique et Biosciences, CNRS, Inserm, Ecole Polytechnique,Palaiseau,France,91120","institution_ids":["https://openalex.org/I154526488","https://openalex.org/I142476485","https://openalex.org/I1294671590"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":9,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.77358223,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.34850001335144043,"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"}},"topics":[{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.34850001335144043,"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":0.19499999284744263,"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/T11307","display_name":"Domain Adaptation and Few-Shot Learning","score":0.06650000065565109,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/scale","display_name":"Scale (ratio)","score":0.5102999806404114},{"id":"https://openalex.org/keywords/neuroimaging","display_name":"Neuroimaging","score":0.475600004196167},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.35580000281333923},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.35350000858306885},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.295199990272522},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.2892000079154968}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5802000164985657},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5665000081062317},{"id":"https://openalex.org/C2778755073","wikidata":"https://www.wikidata.org/wiki/Q10858537","display_name":"Scale (ratio)","level":2,"score":0.5102999806404114},{"id":"https://openalex.org/C58693492","wikidata":"https://www.wikidata.org/wiki/Q551875","display_name":"Neuroimaging","level":2,"score":0.475600004196167},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.35580000281333923},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.35350000858306885},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.295199990272522},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.2892000079154968},{"id":"https://openalex.org/C169760540","wikidata":"https://www.wikidata.org/wiki/Q207011","display_name":"Neuroscience","level":1,"score":0.28859999775886536},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.2784000039100647},{"id":"https://openalex.org/C99498987","wikidata":"https://www.wikidata.org/wiki/Q2210247","display_name":"Noise (video)","level":3,"score":0.26460000872612},{"id":"https://openalex.org/C192209626","wikidata":"https://www.wikidata.org/wiki/Q190909","display_name":"Focus (optics)","level":2,"score":0.25519999861717224},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.25119999051094055}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/isbi61048.2026.11515940","is_oa":false,"landing_page_url":"https://doi.org/10.1109/isbi61048.2026.11515940","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2026 IEEE 23rd International Symposium on Biomedical Imaging (ISBI)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":10,"referenced_works":["https://openalex.org/W1901129140","https://openalex.org/W1936685714","https://openalex.org/W2023365921","https://openalex.org/W2110232607","https://openalex.org/W2937715612","https://openalex.org/W3016836174","https://openalex.org/W3159481202","https://openalex.org/W3171007011","https://openalex.org/W4386113253","https://openalex.org/W4413147663"],"related_works":[],"abstract_inverted_index":{"We":[0],"conduct":[1],"a":[2,120],"systematic":[3],"evaluation":[4],"of":[5],"self-supervised":[6],"learning":[7],"(SSL)":[8],"approaches":[9,76],"to":[10,51],"address":[11],"label":[12],"scarcity":[13],"in":[14,38],"single":[15],"neuron":[16,110],"analysis":[17],"from":[18],"large":[19],"scale":[20],"microscopy":[21],"imaging.":[22],"Our":[23],"comprehensive":[24],"study":[25],"reveals":[26],"that":[27,69],"DINOv2":[28],"significantly":[29],"outperforms":[30],"both":[31],"supervised":[32],"ResNet":[33],"and":[34,87,113],"other":[35],"SSL":[36],"methods":[37],"low-data":[39],"regimes,":[40],"achieving":[41],"82":[42],"%":[43,53],"accuracy":[44],"with":[45,70,90],"only":[46,71],"32":[47],"training":[48,73],"images":[49],"compared":[50],"65":[52],"for":[54,108,124],"ResNet-50.":[55],"Crucially,":[56],"we":[57,67],"identify":[58],"partial":[59],"fine-tuning":[60],"as":[61,106],"the":[62],"optimal":[63],"strategy.":[64],"For":[65],"segmentation,":[66],"demonstrate":[68],"4":[72],"images,":[74],"multiple":[75],"achieve":[77],"competitive":[78],"performance:":[79],"U-Net":[80],"(0.677":[81],"IoU),":[82,86],"pseudo-label":[83],"refinement":[84],"(0.639":[85],"frozen":[88],"backbone":[89],"lightweight":[91],"decoder":[92],"(0.570":[93],"IoU).":[94],"Notably,":[95],"standard":[96],"DINOv3":[97],"features":[98],"provide":[99],"excellent":[100],"out-of-thebox":[101],"performance,":[102],"establishing":[103],"minimal":[104],"supervision":[105],"sufficient":[107],"high-quality":[109],"segmentation.":[111],"Code":[112],"data":[114],"are":[115],"made":[116],"readily":[117],"available,":[118],"providing":[119],"new":[121],"benchmark":[122],"dataset":[123],"those":[125],"methods.":[126]},"counts_by_year":[],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2026-05-21T00:00:00"}
