{"id":"https://openalex.org/W3204072589","doi":"https://doi.org/10.1109/tip.2021.3116792","title":"Graph-Theoretic Post-Processing of Segmentation With Application to Dense Biofilms","display_name":"Graph-Theoretic Post-Processing of Segmentation With Application to Dense Biofilms","publication_year":2021,"publication_date":"2021-01-01","ids":{"openalex":"https://openalex.org/W3204072589","doi":"https://doi.org/10.1109/tip.2021.3116792","mag":"3204072589","pmid":"https://pubmed.ncbi.nlm.nih.gov/34613914"},"language":"en","primary_location":{"id":"doi:10.1109/tip.2021.3116792","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tip.2021.3116792","pdf_url":null,"source":{"id":"https://openalex.org/S4210173141","display_name":"IEEE Transactions on Image Processing","issn_l":"1057-7149","issn":["1057-7149","1941-0042"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Image Processing","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9159353","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100440133","display_name":"Jie Wang","orcid":"https://orcid.org/0000-0002-8662-9488"},"institutions":[{"id":"https://openalex.org/I51556381","display_name":"University of Virginia","ror":"https://ror.org/0153tk833","country_code":"US","type":"education","lineage":["https://openalex.org/I51556381"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jie Wang","raw_affiliation_strings":["C.L. Brown Department of Electrical and Computer Engineering, University of Virginia, Charlottesville, VA, 22904 USA"],"raw_orcid":"https://orcid.org/0000-0002-8662-9488","affiliations":[{"raw_affiliation_string":"C.L. Brown Department of Electrical and Computer Engineering, University of Virginia, Charlottesville, VA, 22904 USA","institution_ids":["https://openalex.org/I51556381"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100621293","display_name":"Mingxing Zhang","orcid":"https://orcid.org/0000-0002-1534-0273"},"institutions":[{"id":"https://openalex.org/I51556381","display_name":"University of Virginia","ror":"https://ror.org/0153tk833","country_code":"US","type":"education","lineage":["https://openalex.org/I51556381"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mingxing Zhang","raw_affiliation_strings":["Department of Chemistry, University of Virginia, Charlottesville, VA, 22904 USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, University of Virginia, Charlottesville, VA, 22904 USA","institution_ids":["https://openalex.org/I51556381"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100760106","display_name":"Ji Zhang","orcid":"https://orcid.org/0000-0002-0535-4452"},"institutions":[{"id":"https://openalex.org/I51556381","display_name":"University of Virginia","ror":"https://ror.org/0153tk833","country_code":"US","type":"education","lineage":["https://openalex.org/I51556381"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ji Zhang","raw_affiliation_strings":["Department of Chemistry, University of Virginia, Charlottesville, VA, 22904 USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, University of Virginia, Charlottesville, VA, 22904 USA","institution_ids":["https://openalex.org/I51556381"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100354980","display_name":"Yibo Wang","orcid":"https://orcid.org/0000-0003-1262-4497"},"institutions":[{"id":"https://openalex.org/I51556381","display_name":"University of Virginia","ror":"https://ror.org/0153tk833","country_code":"US","type":"education","lineage":["https://openalex.org/I51556381"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yibo Wang","raw_affiliation_strings":["Department of Chemistry, University of Virginia, Charlottesville, VA, 22904 USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, University of Virginia, Charlottesville, VA, 22904 USA","institution_ids":["https://openalex.org/I51556381"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012742735","display_name":"Andreas Gahlmann","orcid":"https://orcid.org/0000-0001-7521-6787"},"institutions":[{"id":"https://openalex.org/I51556381","display_name":"University of Virginia","ror":"https://ror.org/0153tk833","country_code":"US","type":"education","lineage":["https://openalex.org/I51556381"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Andreas Gahlmann","raw_affiliation_strings":["Department of Chemistry, University of Virginia, Charlottesville, VA, 22904 USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, University of Virginia, Charlottesville, VA, 22904 USA","institution_ids":["https://openalex.org/I51556381"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5034452294","display_name":"Scott T. Acton","orcid":"https://orcid.org/0000-0003-3288-1255"},"institutions":[{"id":"https://openalex.org/I51556381","display_name":"University of Virginia","ror":"https://ror.org/0153tk833","country_code":"US","type":"education","lineage":["https://openalex.org/I51556381"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Scott T. Acton","raw_affiliation_strings":["C.L. Brown Department of Electrical and Computer Engineering, University of Virginia, Charlottesville, VA, 22904 USA. (e-mail: acton@virginia.edu)"],"raw_orcid":"https://orcid.org/0000-0003-3288-1255","affiliations":[{"raw_affiliation_string":"C.L. Brown Department of Electrical and Computer Engineering, University of Virginia, Charlottesville, VA, 22904 USA. (e-mail: acton@virginia.edu)","institution_ids":["https://openalex.org/I51556381"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5100440133"],"corresponding_institution_ids":["https://openalex.org/I51556381"],"apc_list":null,"apc_paid":null,"fwci":2.0052,"has_fulltext":false,"cited_by_count":10,"citation_normalized_percentile":{"value":0.88365268,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"30","issue":null,"first_page":"8580","last_page":"8594"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.9998000264167786,"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"}},"topics":[{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.9998000264167786,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9817000031471252,"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/T10593","display_name":"Bacterial biofilms and quorum sensing","score":0.9799000024795532,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/segmentation","display_name":"Segmentation","score":0.7682414650917053},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6549214124679565},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.6464214324951172},{"id":"https://openalex.org/keywords/collinearity","display_name":"Collinearity","score":0.5790789723396301},{"id":"https://openalex.org/keywords/scale-space-segmentation","display_name":"Scale-space segmentation","score":0.5603659152984619},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.5250855684280396},{"id":"https://openalex.org/keywords/segmentation-based-object-categorization","display_name":"Segmentation-based object categorization","score":0.5095877647399902},{"id":"https://openalex.org/keywords/image-segmentation","display_name":"Image segmentation","score":0.5024762153625488},{"id":"https://openalex.org/keywords/outlier","display_name":"Outlier","score":0.5024030208587646},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.4975424110889435},{"id":"https://openalex.org/keywords/ground-truth","display_name":"Ground truth","score":0.4879416823387146},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.20113873481750488}],"concepts":[{"id":"https://openalex.org/C89600930","wikidata":"https://www.wikidata.org/wiki/Q1423946","display_name":"Segmentation","level":2,"score":0.7682414650917053},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6549214124679565},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6464214324951172},{"id":"https://openalex.org/C106192678","wikidata":"https://www.wikidata.org/wiki/Q1419761","display_name":"Collinearity","level":2,"score":0.5790789723396301},{"id":"https://openalex.org/C65885262","wikidata":"https://www.wikidata.org/wiki/Q7429708","display_name":"Scale-space segmentation","level":4,"score":0.5603659152984619},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.5250855684280396},{"id":"https://openalex.org/C25694479","wikidata":"https://www.wikidata.org/wiki/Q7446278","display_name":"Segmentation-based object categorization","level":5,"score":0.5095877647399902},{"id":"https://openalex.org/C124504099","wikidata":"https://www.wikidata.org/wiki/Q56933","display_name":"Image segmentation","level":3,"score":0.5024762153625488},{"id":"https://openalex.org/C79337645","wikidata":"https://www.wikidata.org/wiki/Q779824","display_name":"Outlier","level":2,"score":0.5024030208587646},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.4975424110889435},{"id":"https://openalex.org/C146849305","wikidata":"https://www.wikidata.org/wiki/Q370766","display_name":"Ground truth","level":2,"score":0.4879416823387146},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.20113873481750488},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018441","descriptor_name":"Biofilms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018441","descriptor_name":"Biofilms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018441","descriptor_name":"Biofilms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1109/tip.2021.3116792","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tip.2021.3116792","pdf_url":null,"source":{"id":"https://openalex.org/S4210173141","display_name":"IEEE Transactions on Image Processing","issn_l":"1057-7149","issn":["1057-7149","1941-0042"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Image Processing","raw_type":"journal-article"},{"id":"pmid:34613914","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34613914","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":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE transactions on image processing : a publication of the IEEE Signal Processing Society","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:9159353","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9159353","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":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"IEEE Trans Image Process","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:9159353","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9159353","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":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"IEEE Trans Image Process","raw_type":"Text"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/9","score":0.41999998688697815,"display_name":"Industry, innovation and infrastructure"}],"awards":[{"id":"https://openalex.org/G7668896460","display_name":null,"funder_award_id":"1R01GM139002","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":51,"referenced_works":["https://openalex.org/W79749824","https://openalex.org/W1561442812","https://openalex.org/W1673310716","https://openalex.org/W1901129140","https://openalex.org/W1938292773","https://openalex.org/W1975639159","https://openalex.org/W1984095925","https://openalex.org/W2016133308","https://openalex.org/W2027181118","https://openalex.org/W2053270078","https://openalex.org/W2091695913","https://openalex.org/W2119774436","https://openalex.org/W2120601853","https://openalex.org/W2121947440","https://openalex.org/W2123269393","https://openalex.org/W2127218421","https://openalex.org/W2165168736","https://openalex.org/W2165835468","https://openalex.org/W2254714379","https://openalex.org/W2305684009","https://openalex.org/W2464708700","https://openalex.org/W2478394825","https://openalex.org/W2480077488","https://openalex.org/W2507231691","https://openalex.org/W2515544675","https://openalex.org/W2548342201","https://openalex.org/W2548555170","https://openalex.org/W2582983410","https://openalex.org/W2683421136","https://openalex.org/W2740924709","https://openalex.org/W2756000255","https://openalex.org/W2783536156","https://openalex.org/W2793372796","https://openalex.org/W2811106513","https://openalex.org/W2900643491","https://openalex.org/W2911368677","https://openalex.org/W2948265816","https://openalex.org/W2948730236","https://openalex.org/W2970304678","https://openalex.org/W2975634117","https://openalex.org/W2991915699","https://openalex.org/W3038287229","https://openalex.org/W3039368862","https://openalex.org/W3105054740","https://openalex.org/W3109005319","https://openalex.org/W3111521801","https://openalex.org/W6603244412","https://openalex.org/W6637131181","https://openalex.org/W6639824700","https://openalex.org/W6678914141","https://openalex.org/W6697758640"],"related_works":["https://openalex.org/W3144569342","https://openalex.org/W2185902295","https://openalex.org/W2945274617","https://openalex.org/W2372421320","https://openalex.org/W2057775483","https://openalex.org/W2041871225","https://openalex.org/W2386644571","https://openalex.org/W2387793296","https://openalex.org/W1558398159","https://openalex.org/W2118381968"],"abstract_inverted_index":{"Recent":[0],"deep":[1,30],"learning":[2,31],"methods":[3,32],"have":[4],"provided":[5],"successful":[6],"initial":[7],"segmentation":[8,13,153],"results":[9],"for":[10,17,27,52,66,71,177],"generalized":[11],"cell":[12,50,133],"in":[14,76,101,115,132,148],"microscopy.":[15],"However,":[16],"dense":[18],"arrangements":[19],"of":[20,49,61,107,125,138,146,150,165,168,185],"small":[21],"cells":[22,75,100,139,169],"with":[23,135,182],"limited":[24],"ground":[25],"truth":[26],"training,":[28],"the":[29,43,46,59,112,116,130,166,174,183,194],"produce":[33],"both":[34],"over-segmentation":[35],"and":[36,55,95],"under-segmentation":[37],"errors.":[38],"Post-processing":[39],"attempts":[40],"to":[41,58,89,97,110,121,170],"balance":[42],"trade-off":[44],"between":[45],"global":[47],"goal":[48],"counting":[51,134],"instance":[53],"segmentation,":[54],"local":[56],"fidelity":[57],"morphology":[60],"identified":[62],"cells.":[63],"The":[64,123],"need":[65,162],"post-processing":[67],"is":[68,87,127,155],"especially":[69],"evident":[70],"segmenting":[72],"3D":[73,102],"bacterial":[74,103],"densely-packed":[77],"communities":[78],"called":[79],"biofilms.":[80],"A":[81],"graph-based":[82],"recursive":[83],"clustering":[84],"approach,":[85],"m-LCuts,":[86],"proposed":[88,158],"automatically":[90],"detect":[91],"collinearly":[92],"structured":[93],"clusters":[94],"applied":[96],"post-process":[98],"unsolved":[99],"biofilm":[104],"segmentation.":[105],"Construction":[106],"outlier-removed":[108],"graphs":[109],"extract":[111],"collinearity":[113],"feature":[114],"data":[117,186],"adds":[118],"additional":[119],"novelty":[120],"m-LCuts.":[122],"superiority":[124],"m-LCuts":[126,190],"observed":[128],"by":[129],"evaluation":[131],"over":[136],"90%":[137],"correctly":[140],"identified,":[141],"while":[142],"a":[143],"lower":[144],"bound":[145],"0.8":[147],"terms":[149],"average":[151],"single-cell":[152],"accuracy":[154],"maintained.":[156],"This":[157],"method":[159],"does":[160],"not":[161],"manual":[163],"specification":[164],"number":[167],"be":[171],"segmented.":[172],"Furthermore,":[173],"broad":[175],"adaptation":[176],"working":[178],"on":[179],"various":[180],"applications,":[181],"presence":[184],"collinearity,":[187],"also":[188],"makes":[189],"stand":[191],"out":[192],"from":[193],"other":[195],"approaches.":[196]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
