{"id":"https://openalex.org/W4406192924","doi":"https://doi.org/10.48550/arxiv.2501.03880","title":"SELMA3D challenge: Self-supervised learning for 3D light-sheet microscopy image segmentation","display_name":"SELMA3D challenge: Self-supervised learning for 3D light-sheet microscopy image segmentation","publication_year":2025,"publication_date":"2025-01-07","ids":{"openalex":"https://openalex.org/W4406192924","doi":"https://doi.org/10.48550/arxiv.2501.03880"},"language":"en","primary_location":{"id":"pmh:oai:arXiv.org:2501.03880","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2501.03880","pdf_url":"https://arxiv.org/pdf/2501.03880","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},"type":"preprint","indexed_in":["arxiv","datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/2501.03880","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100383143","display_name":"Ying Chen","orcid":"https://orcid.org/0009-0008-8183-6729"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Chen, Ying","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002267486","display_name":"Rami Al-Maskari","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Al-Maskari, Rami","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034341330","display_name":"Izabela Horvath","orcid":"https://orcid.org/0000-0002-1702-2869"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Horvath, Izabela","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037837078","display_name":"Mayar Ali","orcid":"https://orcid.org/0000-0002-0398-5699"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Ali, Mayar","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5092618160","display_name":"Luciano H\u00f6her","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Hoher, Luciano","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011000067","display_name":"Kaiyuan Yang","orcid":"https://orcid.org/0000-0001-5934-1959"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Yang, Kaiyuan","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108780917","display_name":"Zhi Lin","orcid":"https://orcid.org/0009-0005-9240-8242"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Lin, Zengming","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066061437","display_name":"Zhiwei Zhai","orcid":"https://orcid.org/0000-0002-4016-6000"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Zhai, Zhiwei","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014202973","display_name":"Mengzhe Shen","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Shen, Mengzhe","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084288425","display_name":"Dejin Xun","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Xun, Dejin","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024453712","display_name":"Yi Wang","orcid":"https://orcid.org/0000-0002-9248-5732"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Wang, Yi","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044805857","display_name":"Tony Xu","orcid":"https://orcid.org/0000-0002-9825-1005"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Xu, Tony","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056005902","display_name":"Maged Goubran","orcid":"https://orcid.org/0000-0001-5880-0818"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Goubran, Maged","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024861962","display_name":"Yue Wu","orcid":"https://orcid.org/0000-0002-7454-0451"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Wu, Yunheng","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":null,"display_name":"Mori, Kensaku","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Mori, Kensaku","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085027983","display_name":"Johannes C. Paetzold","orcid":"https://orcid.org/0000-0002-4844-6955"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Paetzold, Johannes C.","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":null,"display_name":"Erturk, Ali","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Erturk, Ali","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"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/T13114","display_name":"Image Processing Techniques and Applications","score":0.9657999873161316,"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/T13114","display_name":"Image Processing Techniques and Applications","score":0.9657999873161316,"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.9089999794960022,"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/segmentation","display_name":"Segmentation","score":0.5636258721351624},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5397276878356934},{"id":"https://openalex.org/keywords/microscopy","display_name":"Microscopy","score":0.490013986825943},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4804475009441376},{"id":"https://openalex.org/keywords/light-sheet-fluorescence-microscopy","display_name":"Light sheet fluorescence microscopy","score":0.4790400266647339},{"id":"https://openalex.org/keywords/computer-vision","display_name":"Computer vision","score":0.426196813583374},{"id":"https://openalex.org/keywords/materials-science","display_name":"Materials science","score":0.3417665660381317},{"id":"https://openalex.org/keywords/optics","display_name":"Optics","score":0.16847959160804749},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.11013594269752502},{"id":"https://openalex.org/keywords/scanning-confocal-electron-microscopy","display_name":"Scanning confocal electron microscopy","score":0.10062268376350403}],"concepts":[{"id":"https://openalex.org/C89600930","wikidata":"https://www.wikidata.org/wiki/Q1423946","display_name":"Segmentation","level":2,"score":0.5636258721351624},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5397276878356934},{"id":"https://openalex.org/C147080431","wikidata":"https://www.wikidata.org/wiki/Q1074953","display_name":"Microscopy","level":2,"score":0.490013986825943},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4804475009441376},{"id":"https://openalex.org/C113976765","wikidata":"https://www.wikidata.org/wiki/Q1823502","display_name":"Light sheet fluorescence microscopy","level":4,"score":0.4790400266647339},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.426196813583374},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.3417665660381317},{"id":"https://openalex.org/C120665830","wikidata":"https://www.wikidata.org/wiki/Q14620","display_name":"Optics","level":1,"score":0.16847959160804749},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.11013594269752502},{"id":"https://openalex.org/C187921700","wikidata":"https://www.wikidata.org/wiki/Q7430074","display_name":"Scanning confocal electron microscopy","level":3,"score":0.10062268376350403}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:arXiv.org:2501.03880","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2501.03880","pdf_url":"https://arxiv.org/pdf/2501.03880","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},{"id":"doi:10.48550/arxiv.2501.03880","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2501.03880","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"Preprint"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:2501.03880","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2501.03880","pdf_url":"https://arxiv.org/pdf/2501.03880","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4406192924.pdf"},"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2094643072","https://openalex.org/W2772917594","https://openalex.org/W2036807459","https://openalex.org/W2586711169","https://openalex.org/W2058170566","https://openalex.org/W2755342338","https://openalex.org/W2166024367","https://openalex.org/W3116076068","https://openalex.org/W2229312674","https://openalex.org/W2951359407"],"abstract_inverted_index":{"Recent":[0],"innovations":[1,37],"in":[2,9,28,57,86,109,171,183],"light":[3],"sheet":[4],"microscopy,":[5],"paired":[6],"with":[7,21,25,69,142],"developments":[8],"tissue":[10],"clearing":[11],"techniques,":[12],"enable":[13],"the":[14,26,43,58,103,115,119,175],"3D":[15,140,225],"imaging":[16],"of":[17,48,106,128,174],"large":[18,139,199],"mammalian":[19],"tissues":[20],"cellular":[22],"resolution.":[23],"Combined":[24],"progress":[27],"large-scale":[29],"data":[30,91],"analysis,":[31],"driven":[32],"by":[33,102],"deep":[34,66],"learning,":[35],"these":[36,73],"empower":[38],"researchers":[39],"to":[40,78,82,90,210],"rapidly":[41],"investigate":[42],"morphological":[44],"and":[45,100,134,154,165,177,187,205,212],"functional":[46],"properties":[47],"diverse":[49,160],"biological":[50,161],"samples.":[51],"Segmentation,":[52],"a":[53,83,125],"crucial":[54],"preliminary":[55,152],"step":[56],"analysis":[59],"process,":[60],"can":[61],"be":[62],"automated":[63],"using":[64],"domain-specific":[65],"learning":[67,108,197,223],"models":[68,74],"expert-level":[70],"performance.":[71],"However,":[72],"exhibit":[75],"high":[76],"sensitivity":[77],"domain":[79],"shifts,":[80],"leading":[81],"significant":[84],"drop":[85],"accuracy":[87],"when":[88],"applied":[89],"outside":[92],"their":[93,178],"training":[94,110],"distribution.":[95],"To":[96],"address":[97],"this":[98,184],"limitation,":[99],"inspired":[101],"recent":[104],"success":[105],"self-supervised":[107,196,222],"generalizable":[111],"models,":[112],"we":[113],"organized":[114],"SELMA3D":[116,123,214],"Challenge":[117],"during":[118],"MICCAI":[120,218],"2024":[121],"conference.":[122],"provides":[124],"vast":[126],"collection":[127],"light-sheet":[129],"images":[130],"from":[131,190],"cleared":[132],"mice":[133],"human":[135],"brains,":[136],"comprising":[137],"35":[138],"images-each":[141],"over":[143],"1000^3":[144],"voxels-and":[145],"315":[146],"annotated":[147],"small":[148],"patches":[149],"for":[150,224],"finetuning,":[151],"testing":[153],"final":[155],"testing.":[156],"The":[157],"dataset":[158],"encompasses":[159],"structures,":[162],"including":[163],"vessel-like":[164],"spot-like":[166],"structures.":[167],"Five":[168],"teams":[169,193],"participated":[170],"all":[172],"phases":[173],"challenge,":[176],"proposed":[179],"methods":[180],"are":[181],"reviewed":[182],"paper.":[185],"Quantitative":[186],"qualitative":[188],"results":[189],"most":[191],"participating":[192],"demonstrate":[194],"that":[195],"on":[198,221],"datasets":[200],"improves":[201],"segmentation":[202],"model":[203],"performance":[204],"generalization.":[206],"We":[207],"will":[208],"continue":[209],"support":[211],"extend":[213],"as":[215],"an":[216],"inaugural":[217],"challenge":[219],"focused":[220],"microscopy":[226],"image":[227],"segmentation.":[228]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-08-11T07:18:39.950985","created_date":"2025-10-10T00:00:00"}
