{"id":"https://openalex.org/W4281899891","doi":"https://doi.org/10.1186/s12859-022-04743-6","title":"NODeJ: an ImageJ plugin for 3D segmentation of nuclear objects","display_name":"NODeJ: an ImageJ plugin for 3D segmentation of nuclear objects","publication_year":2022,"publication_date":"2022-06-06","ids":{"openalex":"https://openalex.org/W4281899891","doi":"https://doi.org/10.1186/s12859-022-04743-6","pmid":"https://pubmed.ncbi.nlm.nih.gov/35668354"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-022-04743-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-022-04743-6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-022-04743-6","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":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-022-04743-6","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5048731568","display_name":"Tristan Dubos","orcid":"https://orcid.org/0000-0002-4265-2379"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I169645620","display_name":"Institut Pascal","ror":"https://ror.org/03vgfxd91","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I169645620","https://openalex.org/I198244214","https://openalex.org/I4210095849"]},{"id":"https://openalex.org/I198244214","display_name":"Universit\u00e9 Clermont Auvergne","ror":"https://ror.org/01a8ajp46","country_code":"FR","type":"education","lineage":["https://openalex.org/I198244214"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Tristan Dubos","raw_affiliation_strings":["GReD, CNRS, INSERM, Universit\u00e9 Clermont Auvergne, Clermont-Ferrand, France","Institut Pascal, Universit\u00e9 Clermont Auvergne, Clermont-Ferrand, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"GReD, CNRS, INSERM, Universit\u00e9 Clermont Auvergne, Clermont-Ferrand, France","institution_ids":["https://openalex.org/I198244214","https://openalex.org/I154526488","https://openalex.org/I1294671590"]},{"raw_affiliation_string":"Institut Pascal, Universit\u00e9 Clermont Auvergne, Clermont-Ferrand, France","institution_ids":["https://openalex.org/I169645620","https://openalex.org/I198244214"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045027489","display_name":"Axel Poulet","orcid":"https://orcid.org/0000-0002-3415-8960"},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Axel Poulet","raw_affiliation_strings":["Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, Yale University, New Haven, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, Yale University, New Haven, USA","institution_ids":["https://openalex.org/I32971472"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057239178","display_name":"Geoffrey Thomson","orcid":"https://orcid.org/0000-0003-0848-1550"},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Geoffrey Thomson","raw_affiliation_strings":["Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, Yale University, New Haven, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, Yale University, New Haven, USA","institution_ids":["https://openalex.org/I32971472"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055786485","display_name":"Emilie P\u00e9ry","orcid":"https://orcid.org/0000-0001-6198-9973"},"institutions":[{"id":"https://openalex.org/I169645620","display_name":"Institut Pascal","ror":"https://ror.org/03vgfxd91","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I169645620","https://openalex.org/I198244214","https://openalex.org/I4210095849"]},{"id":"https://openalex.org/I198244214","display_name":"Universit\u00e9 Clermont Auvergne","ror":"https://ror.org/01a8ajp46","country_code":"FR","type":"education","lineage":["https://openalex.org/I198244214"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Emilie P\u00e9ry","raw_affiliation_strings":["Institut Pascal, Universit\u00e9 Clermont Auvergne, Clermont-Ferrand, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institut Pascal, Universit\u00e9 Clermont Auvergne, Clermont-Ferrand, France","institution_ids":["https://openalex.org/I169645620","https://openalex.org/I198244214"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017629534","display_name":"Fr\u00e9d\u00e9ric Chausse","orcid":"https://orcid.org/0000-0001-7794-1587"},"institutions":[{"id":"https://openalex.org/I169645620","display_name":"Institut Pascal","ror":"https://ror.org/03vgfxd91","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I169645620","https://openalex.org/I198244214","https://openalex.org/I4210095849"]},{"id":"https://openalex.org/I198244214","display_name":"Universit\u00e9 Clermont Auvergne","ror":"https://ror.org/01a8ajp46","country_code":"FR","type":"education","lineage":["https://openalex.org/I198244214"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Fr\u00e9d\u00e9ric Chausse","raw_affiliation_strings":["Institut Pascal, Universit\u00e9 Clermont Auvergne, Clermont-Ferrand, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institut Pascal, Universit\u00e9 Clermont Auvergne, Clermont-Ferrand, France","institution_ids":["https://openalex.org/I169645620","https://openalex.org/I198244214"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042995991","display_name":"Christophe Tatout","orcid":"https://orcid.org/0000-0001-5215-2338"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I198244214","display_name":"Universit\u00e9 Clermont Auvergne","ror":"https://ror.org/01a8ajp46","country_code":"FR","type":"education","lineage":["https://openalex.org/I198244214"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Christophe Tatout","raw_affiliation_strings":["GReD, CNRS, INSERM, Universit\u00e9 Clermont Auvergne, Clermont-Ferrand, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"GReD, CNRS, INSERM, Universit\u00e9 Clermont Auvergne, Clermont-Ferrand, France","institution_ids":["https://openalex.org/I198244214","https://openalex.org/I154526488","https://openalex.org/I1294671590"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073895020","display_name":"Sophie Desset","orcid":"https://orcid.org/0000-0002-4897-4977"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I198244214","display_name":"Universit\u00e9 Clermont Auvergne","ror":"https://ror.org/01a8ajp46","country_code":"FR","type":"education","lineage":["https://openalex.org/I198244214"]},{"id":"https://openalex.org/I4210143836","display_name":"Clermont Universit\u00e9","ror":"https://ror.org/03yf5zr20","country_code":"FR","type":"education","lineage":["https://openalex.org/I4210143836"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Sophie Desset","raw_affiliation_strings":["GReD, CNRS, INSERM, Universit\u00e9 Clermont Auvergne, Clermont-Ferrand, France. sophie.desset@uca.fr","GReD, CNRS, INSERM, Universit\u00e9 Clermont Auvergne, Clermont-Ferrand, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"GReD, CNRS, INSERM, Universit\u00e9 Clermont Auvergne, Clermont-Ferrand, France. sophie.desset@uca.fr","institution_ids":["https://openalex.org/I154526488","https://openalex.org/I4210143836","https://openalex.org/I1294671590"]},{"raw_affiliation_string":"GReD, CNRS, INSERM, Universit\u00e9 Clermont Auvergne, Clermont-Ferrand, France","institution_ids":["https://openalex.org/I198244214","https://openalex.org/I154526488","https://openalex.org/I1294671590"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090580282","display_name":"Josien C. van Wolfswinkel","orcid":"https://orcid.org/0000-0003-4221-3218"},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Josien C. van Wolfswinkel","raw_affiliation_strings":["Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, Yale University, New Haven, USA. josien.van.wolfswinkel@yale.edu","Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, Yale University, New Haven, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, Yale University, New Haven, USA. josien.van.wolfswinkel@yale.edu","institution_ids":["https://openalex.org/I32971472"]},{"raw_affiliation_string":"Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, Yale University, New Haven, USA","institution_ids":["https://openalex.org/I32971472"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5041018507","display_name":"Yannick Jacob","orcid":"https://orcid.org/0000-0003-4741-0755"},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Yannick Jacob","raw_affiliation_strings":["Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, Yale University, New Haven, USA. yannick.jacob@yale.edu","Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, Yale University, New Haven, USA"],"raw_orcid":"https://orcid.org/0000-0003-4741-0755","affiliations":[{"raw_affiliation_string":"Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, Yale University, New Haven, USA. yannick.jacob@yale.edu","institution_ids":["https://openalex.org/I32971472"]},{"raw_affiliation_string":"Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, Yale University, New Haven, USA","institution_ids":["https://openalex.org/I32971472"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5041018507","https://openalex.org/A5073895020","https://openalex.org/A5090580282"],"corresponding_institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I154526488","https://openalex.org/I198244214","https://openalex.org/I32971472","https://openalex.org/I4210143836"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":687,"currency":"EUR","value_usd":740},"fwci":1.2127,"has_fulltext":true,"cited_by_count":14,"citation_normalized_percentile":{"value":0.77797903,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":98},"biblio":{"volume":"23","issue":"1","first_page":"216","last_page":"216"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.7046999931335449,"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"}},"topics":[{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.7046999931335449,"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/T10184","display_name":"Plant Molecular Biology Research","score":0.21250000596046448,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11841","display_name":"Nuclear Structure and Function","score":0.020099999383091927,"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/plug-in","display_name":"Plug-in","score":0.7951972484588623},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5687875151634216},{"id":"https://openalex.org/keywords/segmentation","display_name":"Segmentation","score":0.4955674409866333},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.43747588992118835},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.43203532695770264},{"id":"https://openalex.org/keywords/computer-vision","display_name":"Computer vision","score":0.3972661793231964},{"id":"https://openalex.org/keywords/computer-graphics","display_name":"Computer graphics (images)","score":0.3350660800933838},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.27273768186569214},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.1279962658882141}],"concepts":[{"id":"https://openalex.org/C4924752","wikidata":"https://www.wikidata.org/wiki/Q184148","display_name":"Plug-in","level":2,"score":0.7951972484588623},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5687875151634216},{"id":"https://openalex.org/C89600930","wikidata":"https://www.wikidata.org/wiki/Q1423946","display_name":"Segmentation","level":2,"score":0.4955674409866333},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.43747588992118835},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.43203532695770264},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.3972661793231964},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","level":1,"score":0.3350660800933838},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.27273768186569214},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.1279962658882141}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002467","descriptor_name":"Cell Nucleus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002467","descriptor_name":"Cell Nucleus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002467","descriptor_name":"Cell Nucleus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017360","descriptor_name":"Arabidopsis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D017360","descriptor_name":"Arabidopsis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D017360","descriptor_name":"Arabidopsis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D021621","descriptor_name":"Imaging, Three-Dimensional","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D021621","descriptor_name":"Imaging, Three-Dimensional","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D021621","descriptor_name":"Imaging, Three-Dimensional","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1186/s12859-022-04743-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-022-04743-6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-022-04743-6","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:35668354","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35668354","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:HAL:inserm-03692276v1","is_oa":true,"landing_page_url":"https://inserm.hal.science/inserm-03692276","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, 2022, 23 (1), pp.216. &#x27E8;10.1186/s12859-022-04743-6&#x27E9;","raw_type":"Journal articles"},{"id":"pmh:oai:doaj.org/article:5b8249155f3d449fbb5660f4903a251d","is_oa":true,"landing_page_url":"https://doaj.org/article/5b8249155f3d449fbb5660f4903a251d","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 23, Iss 1, Pp 1-11 (2022)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:9169307","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9169307","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-022-04743-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-022-04743-6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-022-04743-6","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/G3723541920","display_name":null,"funder_award_id":"R35GM128661","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4157942577","display_name":null,"funder_award_id":"R35GM128661","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G433109575","display_name":null,"funder_award_id":"R35GM128619","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G4950536974","display_name":null,"funder_award_id":"-0001","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6287694742","display_name":null,"funder_award_id":"ANR-16-IDEX-0001","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G8114022736","display_name":null,"funder_award_id":"R35GM128619","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320320883","display_name":"Agence Nationale de la Recherche","ror":"https://ror.org/00rbzpz17"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4281899891.pdf","grobid_xml":"https://content.openalex.org/works/W4281899891.grobid-xml"},"referenced_works_count":20,"referenced_works":["https://openalex.org/W1547714734","https://openalex.org/W1972956034","https://openalex.org/W1978291928","https://openalex.org/W1979042611","https://openalex.org/W2030948026","https://openalex.org/W2099540110","https://openalex.org/W2116529502","https://openalex.org/W2120847972","https://openalex.org/W2124260943","https://openalex.org/W2147728748","https://openalex.org/W2156447791","https://openalex.org/W2167723066","https://openalex.org/W2467628122","https://openalex.org/W2512365985","https://openalex.org/W2564434207","https://openalex.org/W2773343583","https://openalex.org/W3096074721","https://openalex.org/W3119693300","https://openalex.org/W3160158271","https://openalex.org/W4254687493"],"related_works":["https://openalex.org/W47352601","https://openalex.org/W2981957539","https://openalex.org/W4287378204","https://openalex.org/W2461489085","https://openalex.org/W2545422590","https://openalex.org/W4240705470","https://openalex.org/W2945311252","https://openalex.org/W631546281","https://openalex.org/W4206501676","https://openalex.org/W88292646"],"abstract_inverted_index":{"BACKGROUND:":[0],"The":[1,225],"three-dimensional":[2],"nuclear":[3],"arrangement":[4],"of":[5,57,98,105,131,157,160,171],"chromatin":[6,60],"impacts":[7],"many":[8],"cellular":[9],"processes":[10],"operating":[11],"at":[12,222,234],"the":[13,58,96,103,155,176],"DNA":[14,150],"level":[15],"in":[16,85,147,180,190,228],"animal":[17],"and":[18,33,80,108,116,184,192,218,236],"plant":[19],"systems.":[20],"Chromatin":[21],"organization":[22],"is":[23,120,141,188],"a":[24,47,92,99,128,199],"dynamic":[25,43],"process":[26],"that":[27,118],"can":[28,209],"be":[29,210],"affected":[30],"by":[31,174],"biotic":[32],"abiotic":[34],"stresses.":[35],"Three-dimensional":[36],"imaging":[37],"technology":[38],"allows":[39,166],"to":[40,101,122,144,203],"follow":[41],"these":[42],"changes,":[44],"but":[45],"only":[46],"few":[48],"semi-automated":[49,177],"processing":[50,182],"methods":[51],"currently":[52],"exist":[53],"for":[54,154,167],"quantitative":[55],"analysis":[56,156,170],"3D":[59,88],"organization.":[61],"RESULTS:":[62],"We":[63,112],"present":[64],"an":[65,74,195],"automated":[66,169],"method,":[67],"Nuclear":[68],"Object":[69],"DetectionJ":[70],"(NODeJ),":[71],"developed":[72],"as":[73,194],"imageJ":[75],"plugin.":[76],"This":[77],"program":[78],"segments":[79],"analyzes":[81],"high":[82],"intensity":[83],"domains":[84,126],"nuclei":[86,134,148],"from":[87,127,149,212],"images.":[89],"NODeJ":[90,119,140,165,187,208],"performs":[91],"Laplacian":[93],"convolution":[94],"on":[95],"mask":[97],"nucleus":[100],"enhance":[102],"contrast":[104],"intra-nuclear":[106],"objects":[107],"allow":[109],"their":[110],"detection.":[111],"reanalyzed":[113],"public":[114],"datasets":[115],"determined":[117],"able":[121,143],"accurately":[123],"identify":[124],"heterochromatin":[125],"diverse":[129],"set":[130],"Arabidopsis":[132],"thaliana":[133],"stained":[135],"with":[136,198,214],"DAPI":[137],"or":[138],"Hoechst.":[139],"also":[142],"detect":[145],"signals":[146],"FISH":[151],"experiments,":[152],"allowing":[153],"specific":[158],"targets":[159],"interest.":[161],"CONCLUSION":[162],"AND":[163],"AVAILABILITY:":[164],"efficient":[168],"subnuclear":[172],"structures":[173],"avoiding":[175],"steps,":[178],"resulting":[179],"reduced":[181],"time":[183],"analytical":[185],"bias.":[186],"written":[189],"Java":[191],"provided":[193],"ImageJ":[196],"plugin":[197],"command":[200],"line":[201],"option":[202],"perform":[204],"more":[205],"high-throughput":[206],"analyses.":[207],"downloaded":[211],"https://gitlab.com/axpoulet/image2danalysis/-/releases":[213],"source":[215],"code,":[216],"documentation":[217],"further":[219],"information":[220],"avaliable":[221],"https://gitlab.com/axpoulet/image2danalysis":[223],".":[224,238],"images":[226],"used":[227],"this":[229],"study":[230],"are":[231],"publicly":[232],"available":[233],"https://www.brookes.ac.uk/indepth/images/":[235],"https://doi.org/10.15454/1HSOIE":[237]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":2}],"updated_date":"2026-06-20T22:02:38.213706","created_date":"2025-10-10T00:00:00"}
