{"id":"https://openalex.org/W4406138281","doi":"https://doi.org/10.1109/bibe63649.2024.10820469","title":"Semantic Image Segmentation of Cell Volumes Using 3D U-Net Convolutional Neural Network","display_name":"Semantic Image Segmentation of Cell Volumes Using 3D U-Net Convolutional Neural Network","publication_year":2024,"publication_date":"2024-11-27","ids":{"openalex":"https://openalex.org/W4406138281","doi":"https://doi.org/10.1109/bibe63649.2024.10820469"},"language":"en","primary_location":{"id":"doi:10.1109/bibe63649.2024.10820469","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibe63649.2024.10820469","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2024 IEEE 24th International Conference on Bioinformatics and Bioengineering (BIBE)","raw_type":"proceedings-article"},"type":"conference-paper","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/A5022942714","display_name":"Lazar Da\u0161i\u0107","orcid":"https://orcid.org/0000-0002-8055-100X"},"institutions":[{"id":"https://openalex.org/I14245010","display_name":"University of Kragujevac","ror":"https://ror.org/04f7vj627","country_code":"RS","type":"education","lineage":["https://openalex.org/I14245010"]}],"countries":["RS"],"is_corresponding":false,"raw_author_name":"Lazar Da\u0161i\u0107","raw_affiliation_strings":["Institute for Information Technologies, University of Kragujevac,Kragujevac,Serbia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Information Technologies, University of Kragujevac,Kragujevac,Serbia","institution_ids":["https://openalex.org/I14245010"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047875012","display_name":"Jorge Barrasa\u2010Fano","orcid":"https://orcid.org/0000-0002-8650-0457"},"institutions":[{"id":"https://openalex.org/I99464096","display_name":"KU Leuven","ror":"https://ror.org/05f950310","country_code":"BE","type":"education","lineage":["https://openalex.org/I99464096"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"Jorge Barrasa-Fano","raw_affiliation_strings":["KU Leuven,Department of Mechanical Engineering,Leuven,Belgium"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"KU Leuven,Department of Mechanical Engineering,Leuven,Belgium","institution_ids":["https://openalex.org/I99464096"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5092556821","display_name":"Ognjen Pavi\u0107","orcid":"https://orcid.org/0000-0003-2533-1079"},"institutions":[{"id":"https://openalex.org/I14245010","display_name":"University of Kragujevac","ror":"https://ror.org/04f7vj627","country_code":"RS","type":"education","lineage":["https://openalex.org/I14245010"]}],"countries":["RS"],"is_corresponding":false,"raw_author_name":"Ognjen Pavi\u0107","raw_affiliation_strings":["Institute for Information Technologies, University of Kragujevac,Kragujevac,Serbia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Information Technologies, University of Kragujevac,Kragujevac,Serbia","institution_ids":["https://openalex.org/I14245010"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008564157","display_name":"Tijana Geroski","orcid":"https://orcid.org/0000-0003-1417-0521"},"institutions":[{"id":"https://openalex.org/I14245010","display_name":"University of Kragujevac","ror":"https://ror.org/04f7vj627","country_code":"RS","type":"education","lineage":["https://openalex.org/I14245010"]}],"countries":["RS"],"is_corresponding":false,"raw_author_name":"Tijana Geroski","raw_affiliation_strings":["University of Kragujevac,Faculty of Engineering,Kragujevac,Serbia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Kragujevac,Faculty of Engineering,Kragujevac,Serbia","institution_ids":["https://openalex.org/I14245010"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015337454","display_name":"Apeksha Shapeti","orcid":"https://orcid.org/0000-0002-9177-3986"},"institutions":[{"id":"https://openalex.org/I99464096","display_name":"KU Leuven","ror":"https://ror.org/05f950310","country_code":"BE","type":"education","lineage":["https://openalex.org/I99464096"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"Apeksha Shapeti","raw_affiliation_strings":["KU Leuven,Department of Mechanical Engineering,Leuven,Belgium"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"KU Leuven,Department of Mechanical Engineering,Leuven,Belgium","institution_ids":["https://openalex.org/I99464096"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043262409","display_name":"Hans Van Oosterwyck","orcid":"https://orcid.org/0000-0002-2142-9717"},"institutions":[{"id":"https://openalex.org/I99464096","display_name":"KU Leuven","ror":"https://ror.org/05f950310","country_code":"BE","type":"education","lineage":["https://openalex.org/I99464096"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"Hans Van Oosterwyck","raw_affiliation_strings":["KU Leuven,Department of Mechanical Engineering,Leuven,Belgium"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"KU Leuven,Department of Mechanical Engineering,Leuven,Belgium","institution_ids":["https://openalex.org/I99464096"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032820264","display_name":"Vesna Rankovi\u0107","orcid":"https://orcid.org/0000-0002-5445-9971"},"institutions":[{"id":"https://openalex.org/I14245010","display_name":"University of Kragujevac","ror":"https://ror.org/04f7vj627","country_code":"RS","type":"education","lineage":["https://openalex.org/I14245010"]}],"countries":["RS"],"is_corresponding":false,"raw_author_name":"Vesna Rankovi\u0107","raw_affiliation_strings":["University of Kragujevac,Faculty of Engineering,Kragujevac,Serbia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Kragujevac,Faculty of Engineering,Kragujevac,Serbia","institution_ids":["https://openalex.org/I14245010"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5006131395","display_name":"Nenad Filipovi\u0107","orcid":"https://orcid.org/0000-0001-9964-5615"},"institutions":[{"id":"https://openalex.org/I14245010","display_name":"University of Kragujevac","ror":"https://ror.org/04f7vj627","country_code":"RS","type":"education","lineage":["https://openalex.org/I14245010"]}],"countries":["RS"],"is_corresponding":false,"raw_author_name":"Nenad Filipovi\u0107","raw_affiliation_strings":["University of Kragujevac,Faculty of Engineering,Kragujevac,Serbia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Kragujevac,Faculty of Engineering,Kragujevac,Serbia","institution_ids":["https://openalex.org/I14245010"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":1.5353,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.8500618,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":96},"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"6"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12111","display_name":"Industrial Vision Systems and Defect Detection","score":0.7188000082969666,"subfield":{"id":"https://openalex.org/subfields/2209","display_name":"Industrial and Manufacturing 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/T12111","display_name":"Industrial Vision Systems and Defect Detection","score":0.7188000082969666,"subfield":{"id":"https://openalex.org/subfields/2209","display_name":"Industrial and Manufacturing Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/convolutional-neural-network","display_name":"Convolutional neural network","score":0.796850323677063},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7485580444335938},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.6919872164726257},{"id":"https://openalex.org/keywords/image","display_name":"Image (mathematics)","score":0.5350524187088013},{"id":"https://openalex.org/keywords/image-segmentation","display_name":"Image segmentation","score":0.5330219268798828},{"id":"https://openalex.org/keywords/segmentation","display_name":"Segmentation","score":0.48055699467658997},{"id":"https://openalex.org/keywords/net","display_name":"Net (polyhedron)","score":0.47785207629203796},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.4325827658176422},{"id":"https://openalex.org/keywords/computer-vision","display_name":"Computer vision","score":0.4130553603172302},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.08802330493927002}],"concepts":[{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.796850323677063},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7485580444335938},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6919872164726257},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.5350524187088013},{"id":"https://openalex.org/C124504099","wikidata":"https://www.wikidata.org/wiki/Q56933","display_name":"Image segmentation","level":3,"score":0.5330219268798828},{"id":"https://openalex.org/C89600930","wikidata":"https://www.wikidata.org/wiki/Q1423946","display_name":"Segmentation","level":2,"score":0.48055699467658997},{"id":"https://openalex.org/C14166107","wikidata":"https://www.wikidata.org/wiki/Q253829","display_name":"Net (polyhedron)","level":2,"score":0.47785207629203796},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.4325827658176422},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.4130553603172302},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.08802330493927002},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibe63649.2024.10820469","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibe63649.2024.10820469","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2024 IEEE 24th International Conference on Bioinformatics and Bioengineering (BIBE)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1819872193","display_name":"Data-driven 3D Traction Force Microscopy to unravel microvascular disease mechanisms.","funder_award_id":"1259223N","funder_id":"https://openalex.org/F4320321730","funder_display_name":"Fonds Wetenschappelijk Onderzoek"}],"funders":[{"id":"https://openalex.org/F4320321730","display_name":"Fonds Wetenschappelijk Onderzoek","ror":"https://ror.org/03qtxy027"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":29,"referenced_works":["https://openalex.org/W1901129140","https://openalex.org/W1972544340","https://openalex.org/W1985356640","https://openalex.org/W2017536526","https://openalex.org/W2260168908","https://openalex.org/W2402517981","https://openalex.org/W2464708700","https://openalex.org/W2675059502","https://openalex.org/W2888011474","https://openalex.org/W2914493539","https://openalex.org/W2914540786","https://openalex.org/W2963454900","https://openalex.org/W2970108562","https://openalex.org/W2970800669","https://openalex.org/W2979447087","https://openalex.org/W2991915699","https://openalex.org/W3021592636","https://openalex.org/W3039368862","https://openalex.org/W3093569261","https://openalex.org/W3107214201","https://openalex.org/W3132455321","https://openalex.org/W3139211629","https://openalex.org/W3172157145","https://openalex.org/W3174323841","https://openalex.org/W3193430061","https://openalex.org/W4206353330","https://openalex.org/W4293546472","https://openalex.org/W6638667902","https://openalex.org/W6768003366"],"related_works":["https://openalex.org/W2912321008","https://openalex.org/W4391621807","https://openalex.org/W1998607122","https://openalex.org/W2324368075","https://openalex.org/W2972124131","https://openalex.org/W338149487","https://openalex.org/W4403012196","https://openalex.org/W2972032537","https://openalex.org/W150363521","https://openalex.org/W1522196789"],"abstract_inverted_index":{"Image":[0],"segmentation":[1,27,50,88,168,191,218,233],"is":[2,45,67,74],"the":[3,19,37,63,145,161,186,196,222],"process":[4],"of":[5,40,62,71,89,93,140,147,160,176,182,204,214,232],"assigning":[6],"a":[7,46,68],"label":[8,21],"to":[9,36,185,195],"every":[10],"pixel":[11],"in":[12,58,95,97,144],"an":[13,96],"image":[14,26,217],"such":[15],"that":[16,52],"pixels":[17],"with":[18],"same":[20],"share":[22],"certain":[23],"characteristics.":[24],"Traditionally":[25],"was":[28],"used":[29,157],"on":[30,83],"2D":[31],"imaging":[32],"data,":[33],"but":[34],"due":[35],"increased":[38],"usage":[39],"3D":[41,49,72,84,113,122,136,216],"volumetric":[42],"data":[43,73,142,226],"there":[44,66],"need":[47],"for":[48,87,158,225],"techniques":[51],"could":[53,219],"utilize":[54],"spatial":[55],"information":[56],"contained":[57],"these":[59],"volumes.":[60],"One":[61],"fields":[64],"where":[65,107],"great":[69,167],"amount":[70],"microscopy.":[75],"This":[76,212],"paper":[77],"introduces":[78],"convolutional":[79,114,137],"neural":[80],"network":[81],"based":[82],"U-net":[85],"architecture":[86],"confocal":[90],"microscopy":[91],"images":[92],"cells":[94],"vitro":[98],"sprouting":[99],"angiogenesis":[100],"model.":[101,163],"Developed":[102],"model":[103,165,199],"contains":[104,111,130],"4":[105],"layers":[106],"each":[108,127],"encoder":[109],"block":[110,129],"two":[112,135],"layers,":[115],"Batch":[116],"Normalization,":[117],"ReLU":[118],"activation":[119],"function":[120],"and":[121,134,178,208],"max":[123],"pooling":[124],"layer,":[125],"while":[126,228],"decoder":[128],"upconvolution,":[131],"skip":[132],"connections":[133],"layers.":[138],"Preprocessing":[139],"this":[141],"resulted":[143],"volumes":[146],"shape":[148],"256":[149,151,153],"\u00d7":[150,152],"voxels":[154],"which":[155],"were":[156],"training":[159],"developed":[162],"The":[164],"achieves":[166,201],"results":[169,192,203],"as":[170],"showed":[171],"by":[172],"Jaccard":[173,206],"index":[174,207],"value":[175,181],"94.52%":[177],"Dice":[179,210],"coefficient":[180],"99.31%":[183],"compared":[184,194],"preprocessed":[187],"dataset.":[188],"Even":[189],"when":[190],"are":[193],"original":[197],"dataset,":[198],"still":[200],"respectable":[202],"84.22%":[205],"88.18%":[209],"coefficient.":[211],"introduction":[213],"automatic":[215],"greatly":[220],"reduce":[221],"time":[223],"required":[224],"preparation,":[227],"achieving":[229],"high":[230],"degree":[231],"accuracy.":[234]},"counts_by_year":[{"year":2025,"cited_by_count":2}],"updated_date":"2026-07-29T14:22:42.915294","created_date":"2025-10-10T00:00:00"}
