{"id":"https://openalex.org/W4313640889","doi":"https://doi.org/10.3390/s23020633","title":"Segment-then-Segment: Context-Preserving Crop-Based Segmentation for Large Biomedical Images","display_name":"Segment-then-Segment: Context-Preserving Crop-Based Segmentation for Large Biomedical Images","publication_year":2023,"publication_date":"2023-01-05","ids":{"openalex":"https://openalex.org/W4313640889","doi":"https://doi.org/10.3390/s23020633","pmid":"https://pubmed.ncbi.nlm.nih.gov/36679429"},"language":"en","primary_location":{"is_oa":true,"landing_page_url":"https://doi.org/10.3390/s23020633","pdf_url":"https://www.mdpi.com/1424-8220/23/2/633/pdf?version=1672995696","source":{"id":"https://openalex.org/S101949793","display_name":"Sensors","issn_l":"1424-8220","issn":["1424-8220"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true},"type":"article","type_crossref":"journal-article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.mdpi.com/1424-8220/23/2/633/pdf?version=1672995696","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5027152185","display_name":"Marin Ben\u010devi\u0107","orcid":"https://orcid.org/0000-0003-4294-0781"},"institutions":[{"id":"https://openalex.org/I51314090","display_name":"University of Osijek","ror":"https://ror.org/05sw4wc49","country_code":"HR","type":"education","lineage":["https://openalex.org/I51314090"]},{"id":"https://openalex.org/I32597200","display_name":"Ghent University","ror":"https://ror.org/00cv9y106","country_code":"BE","type":"education","lineage":["https://openalex.org/I32597200"]}],"countries":["BE","HR"],"is_corresponding":false,"raw_author_name":"Marin Ben\u010devi\u0107","raw_affiliation_strings":["Faculty of Electrical Engineering, Computer Science and Information Technology, J. J. Strossmayer University, 31000 Osijek, Croatia","TELIN-GAIM, Faculty of Engineering and Architecture, Ghent University, 9000 Ghent, Belgium"],"affiliations":[{"raw_affiliation_string":"Faculty of Electrical Engineering, Computer Science and Information Technology, J. J. Strossmayer University, 31000 Osijek, Croatia","institution_ids":["https://openalex.org/I51314090"]},{"raw_affiliation_string":"TELIN-GAIM, Faculty of Engineering and Architecture, Ghent University, 9000 Ghent, Belgium","institution_ids":["https://openalex.org/I32597200"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072665787","display_name":"Yuming Qiu","orcid":"https://orcid.org/0000-0003-0305-3792"},"institutions":[{"id":"https://openalex.org/I4210123021","display_name":"Chongqing Institute of Green and Intelligent Technology","ror":"https://ror.org/031npqv35","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210123021"]},{"id":"https://openalex.org/I32597200","display_name":"Ghent University","ror":"https://ror.org/00cv9y106","country_code":"BE","type":"education","lineage":["https://openalex.org/I32597200"]}],"countries":["BE","CN"],"is_corresponding":false,"raw_author_name":"Yuming Qiu","raw_affiliation_strings":["Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China","TELIN-GAIM, Faculty of Engineering and Architecture, Ghent University, 9000 Ghent, Belgium"],"affiliations":[{"raw_affiliation_string":"Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China","institution_ids":["https://openalex.org/I4210123021"]},{"raw_affiliation_string":"TELIN-GAIM, Faculty of Engineering and Architecture, Ghent University, 9000 Ghent, Belgium","institution_ids":["https://openalex.org/I32597200"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083837803","display_name":"Irena Gali\u0107","orcid":"https://orcid.org/0000-0002-0211-4568"},"institutions":[{"id":"https://openalex.org/I51314090","display_name":"University of Osijek","ror":"https://ror.org/05sw4wc49","country_code":"HR","type":"education","lineage":["https://openalex.org/I51314090"]}],"countries":["HR"],"is_corresponding":true,"raw_author_name":"Irena Gali\u0107","raw_affiliation_strings":["Faculty of Electrical Engineering, Computer Science and Information Technology, J. J. Strossmayer University, 31000 Osijek, Croatia"],"affiliations":[{"raw_affiliation_string":"Faculty of Electrical Engineering, Computer Science and Information Technology, J. J. Strossmayer University, 31000 Osijek, Croatia","institution_ids":["https://openalex.org/I51314090"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5031078128","display_name":"Aleksandra Pi\u017eurica","orcid":"https://orcid.org/0000-0002-9322-4999"},"institutions":[{"id":"https://openalex.org/I32597200","display_name":"Ghent University","ror":"https://ror.org/00cv9y106","country_code":"BE","type":"education","lineage":["https://openalex.org/I32597200"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"Aleksandra Pi\u017eurica","raw_affiliation_strings":["TELIN-GAIM, Faculty of Engineering and Architecture, Ghent University, 9000 Ghent, Belgium"],"affiliations":[{"raw_affiliation_string":"TELIN-GAIM, Faculty of Engineering and Architecture, Ghent University, 9000 Ghent, Belgium","institution_ids":["https://openalex.org/I32597200"]}]}],"institution_assertions":[],"countries_distinct_count":3,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5083837803"],"corresponding_institution_ids":["https://openalex.org/I51314090"],"apc_list":{"value":2400,"currency":"CHF","value_usd":2598,"provenance":"doaj"},"apc_paid":{"value":2400,"currency":"CHF","value_usd":2598,"provenance":"doaj"},"fwci":1.409,"has_fulltext":true,"fulltext_origin":"pdf","cited_by_count":4,"citation_normalized_percentile":{"value":0.606989,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":88,"max":90},"biblio":{"volume":"23","issue":"2","first_page":"633","last_page":"633"},"is_retracted":false,"is_paratext":false,"primary_topic":{"id":"https://openalex.org/T10862","display_name":"AI in cancer detection","score":0.9985,"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"}},"topics":[{"id":"https://openalex.org/T10862","display_name":"AI in cancer detection","score":0.9985,"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"}},{"id":"https://openalex.org/T10036","display_name":"Advanced Neural Network Applications","score":0.9985,"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/T10052","display_name":"Medical Image Segmentation Techniques","score":0.9984,"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"}}],"keywords":[],"concepts":[{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.7564793},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7373957},{"id":"https://openalex.org/C89600930","wikidata":"https://www.wikidata.org/wiki/Q1423946","display_name":"Segmentation","level":2,"score":0.709669},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.6209294},{"id":"https://openalex.org/C124504099","wikidata":"https://www.wikidata.org/wiki/Q56933","display_name":"Image segmentation","level":3,"score":0.58358693},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.577019},{"id":"https://openalex.org/C160633673","wikidata":"https://www.wikidata.org/wiki/Q355198","display_name":"Pixel","level":2,"score":0.5173568},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.49878144},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.4803806},{"id":"https://openalex.org/C65885262","wikidata":"https://www.wikidata.org/wiki/Q7429708","display_name":"Scale-space segmentation","level":4,"score":0.41188896},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.08613402},{"id":"https://openalex.org/C166957645","wikidata":"https://www.wikidata.org/wiki/Q23498","display_name":"Archaeology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":"","qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":"","qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":"","qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"is_oa":true,"landing_page_url":"https://doi.org/10.3390/s23020633","pdf_url":"https://www.mdpi.com/1424-8220/23/2/633/pdf?version=1672995696","source":{"id":"https://openalex.org/S101949793","display_name":"Sensors","issn_l":"1424-8220","issn":["1424-8220"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true},{"is_oa":true,"landing_page_url":"https://biblio.ugent.be/publication/01GP83BJ3JYN7QZX1DWHRVD43N","pdf_url":"https://biblio.ugent.be/publication/01GP83BJ3JYN7QZX1DWHRVD43N/file/01GSFB5R9S5ZFCW8MJASW4D2P4.pdf","source":{"id":"https://openalex.org/S4306400478","display_name":"Ghent University Academic Bibliography (Ghent University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I32597200","host_organization_name":"Ghent University","host_organization_lineage":["https://openalex.org/I32597200"],"host_organization_lineage_names":["Ghent University"],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true},{"is_oa":true,"landing_page_url":"https://biblio.ugent.be/publication/01GP83BJ3JYN7QZX1DWHRVD43N/file/01GSFB5R9S5ZFCW8MJASW4D2P4","pdf_url":"https://biblio.ugent.be/publication/01GP83BJ3JYN7QZX1DWHRVD43N/file/01GSFB5R9S5ZFCW8MJASW4D2P4","source":{"id":"https://openalex.org/S4306400478","display_name":"Ghent University Academic Bibliography (Ghent University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I32597200","host_organization_name":"Ghent University","host_organization_lineage":["https://openalex.org/I32597200"],"host_organization_lineage_names":["Ghent University"],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true},{"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9866819","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":["National Institutes of Health"],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true},{"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36679429","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":["National Institutes of Health"],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false}],"best_oa_location":{"is_oa":true,"landing_page_url":"https://doi.org/10.3390/s23020633","pdf_url":"https://www.mdpi.com/1424-8220/23/2/633/pdf?version=1672995696","source":{"id":"https://openalex.org/S101949793","display_name":"Sensors","issn_l":"1424-8220","issn":["1424-8220"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true},"sustainable_development_goals":[],"grants":[],"datasets":[],"versions":[],"referenced_works_count":21,"referenced_works":["https://openalex.org/W2102605133","https://openalex.org/W2134304618","https://openalex.org/W2302302587","https://openalex.org/W245430726","https://openalex.org/W2618237340","https://openalex.org/W2766934651","https://openalex.org/W2810559801","https://openalex.org/W2884436604","https://openalex.org/W2886667086","https://openalex.org/W2963150697","https://openalex.org/W2964309882","https://openalex.org/W2980998394","https://openalex.org/W2981669902","https://openalex.org/W2997286550","https://openalex.org/W2999580839","https://openalex.org/W3002669799","https://openalex.org/W3120171445","https://openalex.org/W3138516171","https://openalex.org/W3203782569","https://openalex.org/W4206532578","https://openalex.org/W4297337463"],"related_works":["https://openalex.org/W4313052709","https://openalex.org/W4298131179","https://openalex.org/W3199300986","https://openalex.org/W3144569342","https://openalex.org/W3011384228","https://openalex.org/W2945274617","https://openalex.org/W2375430703","https://openalex.org/W2185902295","https://openalex.org/W2103507220","https://openalex.org/W1522196789"],"abstract_inverted_index":{"Medical":[0],"images":[1,23],"are":[2,24,115],"often":[3],"of":[4,13,36,66,90,112,162],"huge":[5],"size,":[6,60],"which":[7],"presents":[8],"a":[9,34,40,76,103],"challenge":[10],"in":[11,160],"terms":[12,161],"memory":[14],"requirements":[15],"when":[16,150],"training":[17,44],"machine":[18],"learning":[19],"models.":[20],"Commonly,":[21],"the":[22,58,72,86,91,95,119],"downsampled":[25],"to":[26,33,84,117,152],"overcome":[27],"this":[28,31,139],"challenge,":[29],"but":[30],"leads":[32],"loss":[35],"information.":[37],"We":[38,123],"present":[39],"general":[41],"approach":[42,126,140],"for":[43],"semantic":[45],"segmentation":[46,74,80,110,143],"neural":[47,69,107],"networks":[48],"on":[49,75,127,156],"much":[50],"smaller":[51],"input":[52,59,148],"sizes":[53,149],"called":[54],"Segment-then-Segment.":[55],"To":[56],"reduce":[57],"we":[61],"use":[62],"image":[63,93,130],"crops":[64,89],"instead":[65],"downscaling.":[67],"One":[68],"network":[70,147],"performs":[71],"initial":[73],"downscaled":[77,157],"image.":[78,122],"This":[79],"is":[81,100],"then":[82],"used":[83],"take":[85],"most":[87],"salient":[88],"full-resolution":[92],"with":[94,145],"surrounding":[96],"context.":[97],"Each":[98],"crop":[99,114],"segmented":[101],"using":[102],"second":[104],"specially":[105],"trained":[106,155],"network.":[108],"The":[109],"masks":[111],"each":[113],"joined":[116],"form":[118],"final":[120],"output":[121],"evaluate":[124],"our":[125],"multiple":[128],"medical":[129],"modalities":[131],"(microscopy,":[132],"colonoscopy,":[133],"and":[134,136],"CT)":[135],"show":[137],"that":[138],"greatly":[141],"improves":[142],"performance":[144],"small":[146],"compared":[151],"baseline":[153],"models":[154],"images,":[158],"especially":[159],"pixel-wise":[163],"recall.":[164]},"cited_by_api_url":"https://api.openalex.org/works?filter=cites:W4313640889","counts_by_year":[{"year":2024,"cited_by_count":4}],"updated_date":"2025-01-04T14:15:50.160189","created_date":"2023-01-07"}