{"id":"https://openalex.org/W2970800669","doi":"https://doi.org/10.1109/icip.2019.8803095","title":"Accurate 3D Cell Segmentation Using Deep Features and CRF Refinement","display_name":"Accurate 3D Cell Segmentation Using Deep Features and CRF Refinement","publication_year":2019,"publication_date":"2019-08-26","ids":{"openalex":"https://openalex.org/W2970800669","doi":"https://doi.org/10.1109/icip.2019.8803095","mag":"2970800669"},"language":"en","primary_location":{"id":"doi:10.1109/icip.2019.8803095","is_oa":false,"landing_page_url":"https://doi.org/10.1109/icip.2019.8803095","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2019 IEEE International Conference on Image Processing (ICIP)","raw_type":"proceedings-article"},"type":"article","indexed_in":["arxiv","crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/1902.04729","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5027799796","display_name":"Jiaxiang Jiang","orcid":null},"institutions":[{"id":"https://openalex.org/I154570441","display_name":"University of California, Santa Barbara","ror":"https://ror.org/02t274463","country_code":"US","type":"education","lineage":["https://openalex.org/I154570441"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jiaxiang Jiang","raw_affiliation_strings":["University of California, Santa Barbara, Santa Barbara, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of California, Santa Barbara, Santa Barbara, CA, USA","institution_ids":["https://openalex.org/I154570441"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013063709","display_name":"Po-Yu Kao","orcid":"https://orcid.org/0000-0002-9439-8819"},"institutions":[{"id":"https://openalex.org/I154570441","display_name":"University of California, Santa Barbara","ror":"https://ror.org/02t274463","country_code":"US","type":"education","lineage":["https://openalex.org/I154570441"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Po-Yu Kao","raw_affiliation_strings":["University of California, Santa Barbara, Santa Barbara, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of California, Santa Barbara, Santa Barbara, CA, USA","institution_ids":["https://openalex.org/I154570441"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055566430","display_name":"Samuel A. Belteton","orcid":"https://orcid.org/0000-0003-3733-4824"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Samuel A. Belteton","raw_affiliation_strings":["Department of Botany and Plant Pathology, Purdue University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Botany and Plant Pathology, Purdue University","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040302699","display_name":"Daniel B. Szymanski","orcid":"https://orcid.org/0000-0001-8255-424X"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Daniel B. Szymanski","raw_affiliation_strings":["Department of Botany and Plant Pathology, Purdue University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Botany and Plant Pathology, Purdue University","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5071938464","display_name":"B.S. Manjunath","orcid":"https://orcid.org/0000-0003-2804-3611"},"institutions":[{"id":"https://openalex.org/I154570441","display_name":"University of California, Santa Barbara","ror":"https://ror.org/02t274463","country_code":"US","type":"education","lineage":["https://openalex.org/I154570441"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"B.S. Manjunath","raw_affiliation_strings":["University of California, Santa Barbara, Santa Barbara, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of California, Santa Barbara, Santa Barbara, CA, USA","institution_ids":["https://openalex.org/I154570441"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":2.433,"has_fulltext":false,"cited_by_count":16,"citation_normalized_percentile":{"value":0.89776939,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":null,"issue":null,"first_page":"1555","last_page":"1559"},"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/T12874","display_name":"Digital Imaging for Blood Diseases","score":0.9980999827384949,"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":0.9976000189781189,"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":[{"id":"https://openalex.org/keywords/conditional-random-field","display_name":"Conditional random field","score":0.8438748717308044},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7470593452453613},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.7234705686569214},{"id":"https://openalex.org/keywords/segmentation","display_name":"Segmentation","score":0.705028772354126},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.5505481362342834},{"id":"https://openalex.org/keywords/image-segmentation","display_name":"Image segmentation","score":0.5475429892539978},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.5323866605758667},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.48344168066978455},{"id":"https://openalex.org/keywords/computer-vision","display_name":"Computer vision","score":0.4708249866962433},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.45712465047836304},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.430787056684494},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.42040809988975525},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.08891022205352783}],"concepts":[{"id":"https://openalex.org/C152565575","wikidata":"https://www.wikidata.org/wiki/Q1124538","display_name":"Conditional random field","level":2,"score":0.8438748717308044},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7470593452453613},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.7234705686569214},{"id":"https://openalex.org/C89600930","wikidata":"https://www.wikidata.org/wiki/Q1423946","display_name":"Segmentation","level":2,"score":0.705028772354126},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.5505481362342834},{"id":"https://openalex.org/C124504099","wikidata":"https://www.wikidata.org/wiki/Q56933","display_name":"Image segmentation","level":3,"score":0.5475429892539978},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.5323866605758667},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.48344168066978455},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.4708249866962433},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.45712465047836304},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.430787056684494},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.42040809988975525},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.08891022205352783},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1109/icip.2019.8803095","is_oa":false,"landing_page_url":"https://doi.org/10.1109/icip.2019.8803095","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2019 IEEE International Conference on Image Processing (ICIP)","raw_type":"proceedings-article"},{"id":"pmh:oai:arXiv.org:1902.04729","is_oa":true,"landing_page_url":"http://arxiv.org/abs/1902.04729","pdf_url":"https://arxiv.org/pdf/1902.04729","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":null,"raw_type":"text"},{"id":"pmh:oai:escholarship.org/ark:/13030/qt9dk368f2","is_oa":false,"landing_page_url":"https://escholarship.org/uc/item/9dk368f2","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"article"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:1902.04729","is_oa":true,"landing_page_url":"http://arxiv.org/abs/1902.04729","pdf_url":"https://arxiv.org/pdf/1902.04729","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":null,"raw_type":"text"},"sustainable_development_goals":[{"score":0.5799999833106995,"id":"https://metadata.un.org/sdg/15","display_name":"Life in Land"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":24,"referenced_works":["https://openalex.org/W1507965490","https://openalex.org/W1561442812","https://openalex.org/W1901129140","https://openalex.org/W2071122929","https://openalex.org/W2130623599","https://openalex.org/W2150151285","https://openalex.org/W2161236525","https://openalex.org/W2161537907","https://openalex.org/W2260455672","https://openalex.org/W2285518352","https://openalex.org/W2464708700","https://openalex.org/W2599336189","https://openalex.org/W2772956779","https://openalex.org/W2784138245","https://openalex.org/W2952793010","https://openalex.org/W2963276418","https://openalex.org/W2964234715","https://openalex.org/W3098080070","https://openalex.org/W4250482878","https://openalex.org/W4322615161","https://openalex.org/W6639824700","https://openalex.org/W6735865073","https://openalex.org/W6748542448","https://openalex.org/W6785540970"],"related_works":["https://openalex.org/W2356597680","https://openalex.org/W2093471820","https://openalex.org/W50079190","https://openalex.org/W2114846443","https://openalex.org/W3102147106","https://openalex.org/W2347460059","https://openalex.org/W2111726165","https://openalex.org/W1984858032","https://openalex.org/W4301042974","https://openalex.org/W1522196789"],"abstract_inverted_index":{"We":[0],"consider":[1],"the":[2,88,97,107,111,122],"problem":[3],"of":[4,21,29,43,66,90],"accurately":[5],"identifying":[6],"cell":[7,25,30,44,51,67],"boundaries":[8],"and":[9,34,75,121],"labeling":[10],"individual":[11],"cells":[12,22],"in":[13],"confocal":[14],"microscopy":[15],"images,":[16],"specifically,":[17],"3D":[18,72],"image":[19],"stacks":[20],"with":[23],"tagged":[24],"membranes.":[26],"Precise":[27],"identification":[28],"boundaries,":[31,68],"their":[32],"shapes,":[33],"quantifying":[35],"inter-cellular":[36],"space":[37],"leads":[38],"to":[39,61,86,93,103,109],"a":[40,50,56,63,71,76,80],"better":[41],"understanding":[42],"morphogenesis.":[45],"Towards":[46],"this,":[47],"we":[48],"outline":[49],"segmentation":[52,91],"method":[53],"that":[54],"uses":[55],"deep":[57],"neural":[58],"network":[59,112],"architecture":[60],"extract":[62],"confidence":[64],"map":[65],"followed":[69],"by":[70],"watershed":[73],"algorithm":[74],"final":[77],"refinement":[78],"using":[79],"conditional":[81],"random":[82],"field.":[83],"In":[84],"addition":[85],"improving":[87],"accuracy":[89],"compared":[92],"other":[94],"state-of-the-art":[95],"methods,":[96],"proposed":[98],"approach":[99],"also":[100],"generalizes":[101],"well":[102],"different":[104],"datasets":[105],"without":[106],"need":[108],"retrain":[110],"for":[113],"each":[114],"dataset.":[115],"Detailed":[116],"experimental":[117],"results":[118],"are":[119],"provided,":[120],"source":[123],"code":[124],"is":[125],"available":[126],"on":[127],"GitHub":[128],"<sup":[129],"xmlns:mml=\"http://www.w3.org/1998/Math/MathML\"":[130],"xmlns:xlink=\"http://www.w3.org/1999/xlink\">1</sup>":[131],".":[132]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":3}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2019-09-05T00:00:00"}