{"id":"https://openalex.org/W2953421783","doi":"https://doi.org/10.1186/s12859-019-2880-8","title":"Cell segmentation methods for label-free contrast microscopy: review and comprehensive comparison","display_name":"Cell segmentation methods for label-free contrast microscopy: review and comprehensive comparison","publication_year":2019,"publication_date":"2019-06-28","ids":{"openalex":"https://openalex.org/W2953421783","doi":"https://doi.org/10.1186/s12859-019-2880-8","mag":"2953421783","pmid":"https://pubmed.ncbi.nlm.nih.gov/31253078"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-019-2880-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-2880-8","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-2880-8.pdf","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"review","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-2880-8.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101801542","display_name":"Tom\u00e1\u0161 Vi\u010dar","orcid":"https://orcid.org/0000-0002-9136-7873"},"institutions":[{"id":"https://openalex.org/I21449261","display_name":"Masaryk University","ror":"https://ror.org/02j46qs45","country_code":"CZ","type":"education","lineage":["https://openalex.org/I21449261"]},{"id":"https://openalex.org/I60587646","display_name":"Brno University of Technology","ror":"https://ror.org/03613d656","country_code":"CZ","type":"education","lineage":["https://openalex.org/I60587646"]}],"countries":["CZ"],"is_corresponding":false,"raw_author_name":"Tomas Vicar","raw_affiliation_strings":["Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Technicka 3058/10, Brno, CZ-61600, Czech Republic","Department of Physiology, Faculty of Medicine, Masaryk University, Kamenice 5, Brno, CZ-62500, Czech Republic"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Technicka 3058/10, Brno, CZ-61600, Czech Republic","institution_ids":["https://openalex.org/I60587646"]},{"raw_affiliation_string":"Department of Physiology, Faculty of Medicine, Masaryk University, Kamenice 5, Brno, CZ-62500, Czech Republic","institution_ids":["https://openalex.org/I21449261"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080848236","display_name":"Jan Balvan","orcid":"https://orcid.org/0000-0001-5463-3338"},"institutions":[{"id":"https://openalex.org/I1310815967","display_name":"Central European Institute of Technology","ror":"https://ror.org/01p7k1986","country_code":"CZ","type":"education","lineage":["https://openalex.org/I1310815967"]},{"id":"https://openalex.org/I21449261","display_name":"Masaryk University","ror":"https://ror.org/02j46qs45","country_code":"CZ","type":"education","lineage":["https://openalex.org/I21449261"]},{"id":"https://openalex.org/I60587646","display_name":"Brno University of Technology","ror":"https://ror.org/03613d656","country_code":"CZ","type":"education","lineage":["https://openalex.org/I60587646"]}],"countries":["CZ"],"is_corresponding":false,"raw_author_name":"Jan Balvan","raw_affiliation_strings":["Central European Institute of Technology, Brno University of Technology, Purkynova 656/123, Brno, CZ-612 00, Czech Republic","Department of Pathological Physiology, Faculty of Medicine, Masaryk University, Kamenice 5, Brno, CZ-62500, Czech Republic"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Central European Institute of Technology, Brno University of Technology, Purkynova 656/123, Brno, CZ-612 00, Czech Republic","institution_ids":["https://openalex.org/I1310815967","https://openalex.org/I60587646"]},{"raw_affiliation_string":"Department of Pathological Physiology, Faculty of Medicine, Masaryk University, Kamenice 5, Brno, CZ-62500, Czech Republic","institution_ids":["https://openalex.org/I21449261"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033840727","display_name":"Josef Jaro\u0161","orcid":"https://orcid.org/0000-0001-7559-2344"},"institutions":[{"id":"https://openalex.org/I21449261","display_name":"Masaryk University","ror":"https://ror.org/02j46qs45","country_code":"CZ","type":"education","lineage":["https://openalex.org/I21449261"]},{"id":"https://openalex.org/I4210136987","display_name":"St. Anne's University Hospital Brno","ror":"https://ror.org/049bjee35","country_code":"CZ","type":"healthcare","lineage":["https://openalex.org/I4210136987"]}],"countries":["CZ"],"is_corresponding":false,"raw_author_name":"Josef Jaros","raw_affiliation_strings":["Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Kamenice 5, Brno, CZ-62500, Czech Republic","International Clinical Research Center, St. Anne's University Hospital, Pekarska 664/53, Brno, CZ-65691, Czech Republic"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Kamenice 5, Brno, CZ-62500, Czech Republic","institution_ids":["https://openalex.org/I21449261"]},{"raw_affiliation_string":"International Clinical Research Center, St. Anne's University Hospital, Pekarska 664/53, Brno, CZ-65691, Czech Republic","institution_ids":["https://openalex.org/I4210136987"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045834690","display_name":"Florian Jug","orcid":"https://orcid.org/0000-0002-8499-5812"},"institutions":[{"id":"https://openalex.org/I4210159854","display_name":"Max Planck Institute of Molecular Cell Biology and Genetics","ror":"https://ror.org/05b8d3w18","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210159854"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Florian Jug","raw_affiliation_strings":["Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, Dresden, DE-01307, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, Dresden, DE-01307, Germany","institution_ids":["https://openalex.org/I4210159854"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083548103","display_name":"Radim Kol\u00e1\u0159","orcid":"https://orcid.org/0000-0002-0469-6397"},"institutions":[{"id":"https://openalex.org/I60587646","display_name":"Brno University of Technology","ror":"https://ror.org/03613d656","country_code":"CZ","type":"education","lineage":["https://openalex.org/I60587646"]}],"countries":["CZ"],"is_corresponding":false,"raw_author_name":"Radim Kolar","raw_affiliation_strings":["Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Technicka 3058/10, Brno, CZ-61600, Czech Republic"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Technicka 3058/10, Brno, CZ-61600, Czech Republic","institution_ids":["https://openalex.org/I60587646"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029424206","display_name":"Michal Masa\u0159\u00edk","orcid":"https://orcid.org/0000-0003-1172-7195"},"institutions":[{"id":"https://openalex.org/I1310815967","display_name":"Central European Institute of Technology","ror":"https://ror.org/01p7k1986","country_code":"CZ","type":"education","lineage":["https://openalex.org/I1310815967"]},{"id":"https://openalex.org/I21449261","display_name":"Masaryk University","ror":"https://ror.org/02j46qs45","country_code":"CZ","type":"education","lineage":["https://openalex.org/I21449261"]},{"id":"https://openalex.org/I60587646","display_name":"Brno University of Technology","ror":"https://ror.org/03613d656","country_code":"CZ","type":"education","lineage":["https://openalex.org/I60587646"]}],"countries":["CZ"],"is_corresponding":false,"raw_author_name":"Michal Masarik","raw_affiliation_strings":["Central European Institute of Technology, Brno University of Technology, Purkynova 656/123, Brno, CZ-612 00, Czech Republic","Department of Pathological Physiology, Faculty of Medicine, Masaryk University, Kamenice 5, Brno, CZ-62500, Czech Republic"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Central European Institute of Technology, Brno University of Technology, Purkynova 656/123, Brno, CZ-612 00, Czech Republic","institution_ids":["https://openalex.org/I1310815967","https://openalex.org/I60587646"]},{"raw_affiliation_string":"Department of Pathological Physiology, Faculty of Medicine, Masaryk University, Kamenice 5, Brno, CZ-62500, Czech Republic","institution_ids":["https://openalex.org/I21449261"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5020780800","display_name":"Jarom\u00edr Gumulec","orcid":"https://orcid.org/0000-0002-9658-3444"},"institutions":[{"id":"https://openalex.org/I1310815967","display_name":"Central European Institute of Technology","ror":"https://ror.org/01p7k1986","country_code":"CZ","type":"education","lineage":["https://openalex.org/I1310815967"]},{"id":"https://openalex.org/I21449261","display_name":"Masaryk University","ror":"https://ror.org/02j46qs45","country_code":"CZ","type":"education","lineage":["https://openalex.org/I21449261"]},{"id":"https://openalex.org/I4210117288","display_name":"Central European Institute of Technology","ror":"https://ror.org/01nvdnb36","country_code":"AT","type":"education","lineage":["https://openalex.org/I4210117288"]},{"id":"https://openalex.org/I60587646","display_name":"Brno University of Technology","ror":"https://ror.org/03613d656","country_code":"CZ","type":"education","lineage":["https://openalex.org/I60587646"]}],"countries":["AT","CZ"],"is_corresponding":false,"raw_author_name":"Jaromir Gumulec","raw_affiliation_strings":["Central European Institute of Technology, Brno University of Technology, Purkynova 656/123, Brno, CZ-612 00, Czech Republic. j.gumulec@med.muni.cz","Department of Pathological Physiology, Faculty of Medicine, Masaryk University, Kamenice 5, Brno, CZ-62500, Czech Republic. j.gumulec@med.muni.cz","Department of Physiology, Faculty of Medicine, Masaryk University, Kamenice 5, Brno, CZ-62500, Czech Republic. j.gumulec@med.muni.cz","Department of Physiology, Faculty of Medicine, Masaryk University, Kamenice 5, Brno, CZ-62500, Czech Republic","Central European Institute of Technology, Brno University of Technology, Purkynova 656/123, Brno, CZ-612 00, Czech Republic","Department of Pathological Physiology, Faculty of Medicine, Masaryk University, Kamenice 5, Brno, CZ-62500, Czech Republic"],"raw_orcid":"https://orcid.org/0000-0002-9658-3444","affiliations":[{"raw_affiliation_string":"Central European Institute of Technology, Brno University of Technology, Purkynova 656/123, Brno, CZ-612 00, Czech Republic. j.gumulec@med.muni.cz","institution_ids":["https://openalex.org/I1310815967","https://openalex.org/I4210117288"]},{"raw_affiliation_string":"Department of Pathological Physiology, Faculty of Medicine, Masaryk University, Kamenice 5, Brno, CZ-62500, Czech Republic. j.gumulec@med.muni.cz","institution_ids":["https://openalex.org/I21449261"]},{"raw_affiliation_string":"Department of Physiology, Faculty of Medicine, Masaryk University, Kamenice 5, Brno, CZ-62500, Czech Republic. j.gumulec@med.muni.cz","institution_ids":["https://openalex.org/I21449261"]},{"raw_affiliation_string":"Department of Physiology, Faculty of Medicine, Masaryk University, Kamenice 5, Brno, CZ-62500, Czech Republic","institution_ids":["https://openalex.org/I21449261"]},{"raw_affiliation_string":"Central European Institute of Technology, Brno University of Technology, Purkynova 656/123, Brno, CZ-612 00, Czech Republic","institution_ids":["https://openalex.org/I1310815967","https://openalex.org/I60587646"]},{"raw_affiliation_string":"Department of Pathological Physiology, Faculty of Medicine, Masaryk University, Kamenice 5, Brno, CZ-62500, Czech Republic","institution_ids":["https://openalex.org/I21449261"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":6,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":15.8541,"has_fulltext":true,"cited_by_count":237,"citation_normalized_percentile":{"value":0.99424634,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"20","issue":"1","first_page":"360","last_page":"360"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11897","display_name":"Digital Holography and Microscopy","score":0.9549000263214111,"subfield":{"id":"https://openalex.org/subfields/3107","display_name":"Atomic and Molecular Physics, and Optics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11897","display_name":"Digital Holography and Microscopy","score":0.9549000263214111,"subfield":{"id":"https://openalex.org/subfields/3107","display_name":"Atomic and Molecular Physics, and Optics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11183","display_name":"Advanced X-ray Imaging Techniques","score":0.015200000256299973,"subfield":{"id":"https://openalex.org/subfields/3108","display_name":"Radiation"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10638","display_name":"Optical measurement and interference techniques","score":0.008999999612569809,"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/segmentation","display_name":"Segmentation","score":0.8338656425476074},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6927635669708252},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.6913203001022339},{"id":"https://openalex.org/keywords/phase-contrast-microscopy","display_name":"Phase contrast microscopy","score":0.6680170297622681},{"id":"https://openalex.org/keywords/contrast","display_name":"Contrast (vision)","score":0.6082128286361694},{"id":"https://openalex.org/keywords/shadow","display_name":"Shadow (psychology)","score":0.5576138496398926},{"id":"https://openalex.org/keywords/image-segmentation","display_name":"Image segmentation","score":0.5480343699455261},{"id":"https://openalex.org/keywords/region-growing","display_name":"Region growing","score":0.544399082660675},{"id":"https://openalex.org/keywords/computer-vision","display_name":"Computer vision","score":0.5421584248542786},{"id":"https://openalex.org/keywords/scale-space-segmentation","display_name":"Scale-space segmentation","score":0.4947144687175751},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.4435620605945587},{"id":"https://openalex.org/keywords/segmentation-based-object-categorization","display_name":"Segmentation-based object categorization","score":0.4224432110786438}],"concepts":[{"id":"https://openalex.org/C89600930","wikidata":"https://www.wikidata.org/wiki/Q1423946","display_name":"Segmentation","level":2,"score":0.8338656425476074},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6927635669708252},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6913203001022339},{"id":"https://openalex.org/C151193507","wikidata":"https://www.wikidata.org/wiki/Q898815","display_name":"Phase contrast microscopy","level":2,"score":0.6680170297622681},{"id":"https://openalex.org/C2776502983","wikidata":"https://www.wikidata.org/wiki/Q690182","display_name":"Contrast (vision)","level":2,"score":0.6082128286361694},{"id":"https://openalex.org/C117797892","wikidata":"https://www.wikidata.org/wiki/Q286363","display_name":"Shadow (psychology)","level":2,"score":0.5576138496398926},{"id":"https://openalex.org/C124504099","wikidata":"https://www.wikidata.org/wiki/Q56933","display_name":"Image segmentation","level":3,"score":0.5480343699455261},{"id":"https://openalex.org/C206824153","wikidata":"https://www.wikidata.org/wiki/Q1169834","display_name":"Region growing","level":5,"score":0.544399082660675},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.5421584248542786},{"id":"https://openalex.org/C65885262","wikidata":"https://www.wikidata.org/wiki/Q7429708","display_name":"Scale-space segmentation","level":4,"score":0.4947144687175751},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.4435620605945587},{"id":"https://openalex.org/C25694479","wikidata":"https://www.wikidata.org/wiki/Q7446278","display_name":"Segmentation-based object categorization","level":5,"score":0.4224432110786438},{"id":"https://openalex.org/C15744967","wikidata":"https://www.wikidata.org/wiki/Q9418","display_name":"Psychology","level":0,"score":0.0},{"id":"https://openalex.org/C542102704","wikidata":"https://www.wikidata.org/wiki/Q183257","display_name":"Psychotherapist","level":1,"score":0.0},{"id":"https://openalex.org/C120665830","wikidata":"https://www.wikidata.org/wiki/Q14620","display_name":"Optics","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002458","descriptor_name":"Cell Fractionation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002458","descriptor_name":"Cell Fractionation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002458","descriptor_name":"Cell Fractionation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002458","descriptor_name":"Cell Fractionation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","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":"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":"D008853","descriptor_name":"Microscopy","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D008853","descriptor_name":"Microscopy","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D008853","descriptor_name":"Microscopy","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D008853","descriptor_name":"Microscopy","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1186/s12859-019-2880-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-2880-8","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-2880-8.pdf","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:31253078","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31253078","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:6599268","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6599268","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:https://dspace.vut.cz:11012/195836","is_oa":true,"landing_page_url":"http://hdl.handle.net/11012/195836","pdf_url":"http://hdl.handle.net/11012/195836","source":{"id":"https://openalex.org/S4306400317","display_name":"Brno University of Technology Digital Library (Brno University of Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I60587646","host_organization_name":"Brno University of Technology","host_organization_lineage":["https://openalex.org/I60587646"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"},{"id":"pmh:oai:doaj.org/article:bce2c3002c4a47e2a3008136bc467e8a","is_oa":true,"landing_page_url":"https://doaj.org/article/bce2c3002c4a47e2a3008136bc467e8a","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 20, Iss 1, Pp 1-25 (2019)","raw_type":"article"},{"id":"pmh:oai:pure.mpg.de:item_3235974","is_oa":false,"landing_page_url":"http://hdl.handle.net/21.11116/0000-0006-7D52-2","pdf_url":null,"source":{"id":"https://openalex.org/S4306400654","display_name":"MPG.PuRe (Max Planck Society)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I149899117","host_organization_name":"Max Planck Society","host_organization_lineage":["https://openalex.org/I149899117"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC bioinformatics","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1186/s12859-019-2880-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-2880-8","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-2880-8.pdf","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2548689587","display_name":null,"funder_award_id":"GACR 18-24089S","funder_id":"https://openalex.org/F4320321006","funder_display_name":"Grantov\u00e1 Agentura \u010cesk\u00e9 Republiky"},{"id":"https://openalex.org/G4697717539","display_name":null,"funder_award_id":"18-24089S","funder_id":"https://openalex.org/F4320321006","funder_display_name":"Grantov\u00e1 Agentura \u010cesk\u00e9 Republiky"},{"id":"https://openalex.org/G6303082954","display_name":null,"funder_award_id":"18-24089S","funder_id":"https://openalex.org/F4320326548","funder_display_name":"Masarykova Univerzita"},{"id":"https://openalex.org/G7312032132","display_name":null,"funder_award_id":"MUNI/A/1298/2017","funder_id":"https://openalex.org/F4320326548","funder_display_name":"Masarykova Univerzita"}],"funders":[{"id":"https://openalex.org/F4320309480","display_name":"Nvidia","ror":"https://ror.org/03jdj4y14"},{"id":"https://openalex.org/F4320321006","display_name":"Grantov\u00e1 Agentura \u010cesk\u00e9 Republiky","ror":"https://ror.org/01pv73b02"},{"id":"https://openalex.org/F4320322748","display_name":"Vysok\u00e9 U\u010den\u00ed Technick\u00e9 v Brn\u011b","ror":"https://ror.org/03613d656"},{"id":"https://openalex.org/F4320326548","display_name":"Masarykova Univerzita","ror":"https://ror.org/02j46qs45"},{"id":"https://openalex.org/F4320327186","display_name":"L\u00e9ka\u0159sk\u00e1 fakulta, Masarykova univerzita","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2953421783.pdf","grobid_xml":"https://content.openalex.org/works/W2953421783.grobid-xml"},"referenced_works_count":64,"referenced_works":["https://openalex.org/W57946318","https://openalex.org/W1592027922","https://openalex.org/W1731215281","https://openalex.org/W1751426552","https://openalex.org/W1901129140","https://openalex.org/W1945243521","https://openalex.org/W1975150215","https://openalex.org/W1983656531","https://openalex.org/W1995030392","https://openalex.org/W2003345727","https://openalex.org/W2011604289","https://openalex.org/W2012231760","https://openalex.org/W2026448092","https://openalex.org/W2044221450","https://openalex.org/W2060872376","https://openalex.org/W2063694676","https://openalex.org/W2064088471","https://openalex.org/W2074738290","https://openalex.org/W2084885502","https://openalex.org/W2090133300","https://openalex.org/W2098947870","https://openalex.org/W2106818787","https://openalex.org/W2107554012","https://openalex.org/W2109200236","https://openalex.org/W2109722393","https://openalex.org/W2113137767","https://openalex.org/W2116040950","https://openalex.org/W2117539524","https://openalex.org/W2119126373","https://openalex.org/W2121979828","https://openalex.org/W2124404372","https://openalex.org/W2129003022","https://openalex.org/W2131229808","https://openalex.org/W2133059825","https://openalex.org/W2141122227","https://openalex.org/W2141273399","https://openalex.org/W2142054519","https://openalex.org/W2142332605","https://openalex.org/W2148743296","https://openalex.org/W2149482407","https://openalex.org/W2160041854","https://openalex.org/W2167435976","https://openalex.org/W2245479309","https://openalex.org/W2276106123","https://openalex.org/W2312947295","https://openalex.org/W2344654247","https://openalex.org/W2488118557","https://openalex.org/W2495449163","https://openalex.org/W2507783863","https://openalex.org/W2521021694","https://openalex.org/W2529631604","https://openalex.org/W2548342201","https://openalex.org/W2575458506","https://openalex.org/W2586671327","https://openalex.org/W2592920807","https://openalex.org/W2601810315","https://openalex.org/W2758694956","https://openalex.org/W2769141948","https://openalex.org/W2782757030","https://openalex.org/W2806530968","https://openalex.org/W2911964244","https://openalex.org/W2982783913","https://openalex.org/W3100296314","https://openalex.org/W3211330693"],"related_works":["https://openalex.org/W2394279717","https://openalex.org/W2364730859","https://openalex.org/W1978085585","https://openalex.org/W3144569342","https://openalex.org/W2386644571","https://openalex.org/W2551987074","https://openalex.org/W2372421320","https://openalex.org/W2185902295","https://openalex.org/W2531745538","https://openalex.org/W2353364291"],"abstract_inverted_index":{"BACKGROUND:":[0],"Because":[1],"of":[2,35,44,47,65,79,85,114,137,161,186,206,221],"its":[3],"non-destructive":[4],"nature,":[5],"label-free":[6,120,144,213],"imaging":[7],"is":[8,126],"an":[9],"important":[10],"strategy":[11],"for":[12,119,188,212],"studying":[13],"biological":[14],"processes.":[15],"However,":[16],"routine":[17],"microscopic":[18,72],"techniques":[19],"like":[20],"phase":[21,96,106],"contrast":[22,71,103],"or":[23],"DIC":[24],"suffer":[25],"from":[26,69],"shadow-cast":[27],"artifacts":[28],"making":[29],"automatic":[30],"segmentation":[31,42,48,84,116,138,150,180,207],"challenging.":[32],"The":[33],"aim":[34],"this":[36],"study":[37],"was":[38],"to":[39,128,217],"compare":[40],"the":[41,66,91,130,135,204,218],"efficacy":[43],"published":[45,193],"steps":[46],"work-flow":[49],"(image":[50],"reconstruction,":[51],"foreground":[52,149],"segmentation,":[53],"cell":[54,59,179],"detection":[55],"(seed-point":[56],"extraction)":[57],"and":[58,104,108,165,175,177,192,224,228],"(instance)":[60],"segmentation)":[61],"on":[62,90,143],"a":[63,77,111],"dataset":[64],"same":[67],"cells":[68,88],"multiple":[70],"modalities.":[73],"RESULTS:":[74],"We":[75,122,182,197],"built":[76],"collection":[78],"routines":[80],"aimed":[81],"at":[82],"image":[83,131,200],"viable":[86],"adherent":[87],"grown":[89],"culture":[92],"dish":[93],"acquired":[94],"by":[95],"contrast,":[97,100],"differential":[98],"interference":[99],"Hoffman":[101],"modulation":[102],"quantitative":[105],"imaging,":[107],"we":[109,147],"performed":[110],"comprehensive":[112,219],"comparison":[113,220],"available":[115],"methods":[117,139,151,159,187,208],"applicable":[118,142],"data.":[121],"demonstrated":[123],"that":[124,199],"it":[125],"crucial":[127],"perform":[129],"reconstruction":[132,201],"step,":[133],"enabling":[134],"use":[136,205],"originally":[140,210],"not":[141,209],"images.":[145],"Further":[146],"compared":[148],"(thresholding,":[152],"feature-extraction,":[153],"level-set,":[154],"graph-cut,":[155],"learning-based),":[156],"seed-point":[157],"extraction":[158],"(Laplacian":[160],"Gaussians,":[162],"radial":[163,169],"symmetry":[164],"distance":[166],"transform,":[167],"iterative":[168],"voting,":[170],"maximally":[171],"stable":[172],"extremal":[173],"region":[174],"learning-based)":[176],"single":[178],"methods.":[181],"validated":[183],"suitable":[184],"set":[185],"each":[189],"microscopy":[190],"modality":[191],"them":[194],"online.":[195],"CONCLUSIONS:":[196],"demonstrate":[198],"step":[202],"allows":[203],"intended":[211],"imaging.":[214],"In":[215],"addition":[216],"methods,":[222],"raw":[223],"reconstructed":[225],"annotated":[226],"data":[227],"Matlab":[229],"codes":[230],"are":[231],"provided.":[232]},"counts_by_year":[{"year":2026,"cited_by_count":9},{"year":2025,"cited_by_count":37},{"year":2024,"cited_by_count":38},{"year":2023,"cited_by_count":39},{"year":2022,"cited_by_count":54},{"year":2021,"cited_by_count":43},{"year":2020,"cited_by_count":14},{"year":2019,"cited_by_count":1},{"year":2017,"cited_by_count":2}],"updated_date":"2026-07-02T09:51:11.867554","created_date":"2025-10-10T00:00:00"}
