{"id":"https://openalex.org/W4392222455","doi":"https://doi.org/10.48550/arxiv.2402.16368","title":"SPINEPS -- Automatic Whole Spine Segmentation of T2-weighted MR images using a Two-Phase Approach to Multi-class Semantic and Instance Segmentation","display_name":"SPINEPS -- Automatic Whole Spine Segmentation of T2-weighted MR images using a Two-Phase Approach to Multi-class Semantic and Instance Segmentation","publication_year":2024,"publication_date":"2024-02-26","ids":{"openalex":"https://openalex.org/W4392222455","doi":"https://doi.org/10.48550/arxiv.2402.16368"},"language":"en","primary_location":{"id":"pmh:oai:arXiv.org:2402.16368","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2402.16368","pdf_url":"https://arxiv.org/pdf/2402.16368","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"text"},"type":"preprint","indexed_in":["arxiv","datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/2402.16368","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5076037370","display_name":"Hendrik M\u00f6ller","orcid":"https://orcid.org/0009-0001-1978-5894"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"M\u00f6ller, Hendrik","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047280055","display_name":"Robert Graf","orcid":"https://orcid.org/0000-0003-2302-0760"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Graf, Robert","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034336913","display_name":"Joachim Schmitt","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Schmitt, Joachim","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5018057828","display_name":"Benjamin Keinert","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Keinert, Benjamin","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006898887","display_name":"Matan Atad","orcid":"https://orcid.org/0000-0001-6952-517X"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Atad, Matan","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087664142","display_name":"Anjany Sekuboyina","orcid":"https://orcid.org/0000-0002-5601-284X"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Sekuboyina, Anjany","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046653529","display_name":"Felix Streckenbach","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Streckenbach, Felix","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108314703","display_name":"H. Sch\u00f6n","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Sch\u00f6n, Hanna","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023181480","display_name":"Florian Kofler","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Kofler, Florian","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108096392","display_name":"Thomas Kroencke","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Kroencke, Thomas","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008365108","display_name":"Stefanie Bette","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Bette, Stefanie","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5105351693","display_name":"Stefan N. Willich","orcid":"https://orcid.org/0009-0006-1270-2597"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Willich, Stefan","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5109584411","display_name":"Thomas Keil","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Keil, Thomas","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080735824","display_name":"Thoralf Niendorf","orcid":"https://orcid.org/0000-0001-7584-6527"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Niendorf, Thoralf","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060584500","display_name":"Tobias Pischon","orcid":"https://orcid.org/0000-0003-1568-767X"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Pischon, Tobias","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033434014","display_name":"Beate Endemann","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Endemann, Beate","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002068604","display_name":"Bjoern Menze","orcid":"https://orcid.org/0000-0003-4136-5690"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Menze, Bjoern","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006461848","display_name":"Daniel Rueckert","orcid":"https://orcid.org/0000-0002-5683-5889"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Rueckert, Daniel","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5003938965","display_name":"Jan S. Kirschke","orcid":"https://orcid.org/0000-0002-7557-0003"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Kirschke, Jan S.","raw_affiliation_strings":[],"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":19,"corresponding_author_ids":["https://openalex.org/A5076037370"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":0,"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/T14510","display_name":"Medical Imaging and Analysis","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"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/T14510","display_name":"Medical Imaging and Analysis","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"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/T10052","display_name":"Medical Image Segmentation Techniques","score":0.989300012588501,"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/T12422","display_name":"Radiomics and Machine Learning in Medical Imaging","score":0.9876999855041504,"subfield":{"id":"https://openalex.org/subfields/2741","display_name":"Radiology, Nuclear Medicine and Imaging"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/segmentation","display_name":"Segmentation","score":0.809280276298523},{"id":"https://openalex.org/keywords/class","display_name":"Class (philosophy)","score":0.6820017099380493},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.6574016213417053},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5966156125068665},{"id":"https://openalex.org/keywords/phase","display_name":"Phase (matter)","score":0.4924510419368744},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.45759376883506775},{"id":"https://openalex.org/keywords/computer-vision","display_name":"Computer vision","score":0.42897751927375793},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.12819382548332214}],"concepts":[{"id":"https://openalex.org/C89600930","wikidata":"https://www.wikidata.org/wiki/Q1423946","display_name":"Segmentation","level":2,"score":0.809280276298523},{"id":"https://openalex.org/C2777212361","wikidata":"https://www.wikidata.org/wiki/Q5127848","display_name":"Class (philosophy)","level":2,"score":0.6820017099380493},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6574016213417053},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5966156125068665},{"id":"https://openalex.org/C44280652","wikidata":"https://www.wikidata.org/wiki/Q104837","display_name":"Phase (matter)","level":2,"score":0.4924510419368744},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.45759376883506775},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.42897751927375793},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.12819382548332214},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:arXiv.org:2402.16368","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2402.16368","pdf_url":"https://arxiv.org/pdf/2402.16368","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"text"},{"id":"doi:10.48550/arxiv.2402.16368","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2402.16368","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"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":"article-journal"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:2402.16368","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2402.16368","pdf_url":"https://arxiv.org/pdf/2402.16368","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"text"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4392222455.pdf"},"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W4379231730","https://openalex.org/W4389858081","https://openalex.org/W4324315429","https://openalex.org/W2501551404","https://openalex.org/W4385583601","https://openalex.org/W4298131179","https://openalex.org/W2113201962","https://openalex.org/W2799953226","https://openalex.org/W4366343436","https://openalex.org/W3204400600"],"abstract_inverted_index":{"Purpose.":[0],"To":[1],"present":[2],"SPINEPS,":[3],"an":[4],"open-source":[5],"deep":[6],"learning":[7],"approach":[8,134,196,221],"for":[9,65,166,169,174,243],"semantic":[10,225],"and":[11,27,50,67,72,89,106,150,172,218,226],"instance":[12,227],"segmentation":[13,104,195,199,246],"of":[14,53,164,200],"14":[15,80,201],"spinal":[16,23,25,81,176,202,210,212],"structures":[17,82,203],"(ten":[18],"vertebra":[19,139],"substructures,":[20],"intervertebral":[21,170,214],"discs,":[22,171,215],"cord,":[24,211],"canal,":[26,213],"sacrum)":[28],"in":[29,83,204,247],"whole":[30,244],"body":[31],"T2w":[32,73,84,205,249],"MRI.":[33],"Methods.":[34],"During":[35],"this":[36],"HIPPA-compliant,":[37],"retrospective":[38],"study,":[39],"we":[40],"utilized":[41],"the":[42,54,114,130,136,158,175,179,209,238],"public":[43,131],"SPIDER":[44,180],"dataset":[45,120,181],"(218":[46],"subjects,":[47,59],"63%":[48],"female)":[49,64],"a":[51,224],"subset":[52],"German":[55],"National":[56],"Cohort":[57],"(1423":[58],"mean":[60],"age":[61],"53,":[62],"49%":[63],"training":[66,183],"evaluation.":[68],"We":[69],"combined":[70],"CT":[71],"segmentations":[74],"to":[75,123,187,234],"train":[76],"models":[77],"that":[78],"segment":[79],"sagittal":[85,206,248],"scans":[86],"both":[87,223],"semantically":[88],"instance-wise.":[90],"Performance":[91],"evaluation":[92],"metrics":[93],"included":[94],"Dice":[95],"similarity":[96],"coefficient,":[97],"average":[98],"symmetrical":[99],"surface":[100],"distance,":[101],"panoptic":[102],"quality,":[103,105],"recognition":[107],"quality.":[108],"Statistical":[109],"significance":[110],"was":[111,121],"assessed":[112],"using":[113],"Wilcoxon":[115],"signed-rank":[116],"test.":[117],"An":[118],"in-house":[119],"used":[122],"qualitatively":[124],"evaluate":[125],"out-of-distribution":[126],"samples.":[127],"Results.":[128],"On":[129],"dataset,":[132],"our":[133],"outperformed":[135],"baseline":[137],"(instance-wise":[138],"dice":[140,162],"score":[141],"0.929":[142],"vs.":[143],"0.907,":[144],"p-value&lt;0.001).":[145],"Training":[146],"on":[147,152],"auto-generated":[148],"annotations":[149],"evaluating":[151],"manually":[153],"corrected":[154],"test":[155],"data":[156],"from":[157],"GNC":[159],"yielded":[160],"global":[161],"scores":[163,186],"0.900":[165],"vertebrae,":[167],"0.960":[168],"0.947":[173],"canal.":[177],"Incorporating":[178],"during":[182],"increased":[184],"these":[185],"0.920,":[188],"0.967,":[189],"0.958,":[190],"respectively.":[191],"Conclusions.":[192],"The":[193,220],"proposed":[194],"offers":[197],"robust":[198],"images,":[207],"including":[208],"endplate,":[216],"sacrum,":[217],"vertebrae.":[219],"yields":[222],"mask":[228],"as":[229],"output,":[230],"thus":[231],"being":[232],"easy":[233],"utilize.":[235],"This":[236],"marks":[237],"first":[239],"publicly":[240],"available":[241],"algorithm":[242],"spine":[245],"MR":[250],"imaging.":[251]},"counts_by_year":[],"updated_date":"2026-03-14T08:43:22.919905","created_date":"2025-10-10T00:00:00"}
