{"id":"https://openalex.org/W4401946015","doi":"https://doi.org/10.1371/journal.pcbi.1012344","title":"CNTools: A computational toolbox for cellular neighborhood analysis from multiplexed images","display_name":"CNTools: A computational toolbox for cellular neighborhood analysis from multiplexed images","publication_year":2024,"publication_date":"2024-08-28","ids":{"openalex":"https://openalex.org/W4401946015","doi":"https://doi.org/10.1371/journal.pcbi.1012344","pmid":"https://pubmed.ncbi.nlm.nih.gov/39196899"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1012344","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1012344","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1371/journal.pcbi.1012344","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5045638971","display_name":"Yicheng Tao","orcid":"https://orcid.org/0000-0001-9615-4976"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]},{"id":"https://openalex.org/I4210111179","display_name":"Michigan United","ror":"https://ror.org/0291ys696","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210111179"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Yicheng Tao","raw_affiliation_strings":["Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, Michigan, United States of America"],"raw_orcid":"https://orcid.org/0000-0001-9615-4976","affiliations":[{"raw_affiliation_string":"Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, Michigan, United States of America","institution_ids":["https://openalex.org/I27837315","https://openalex.org/I4210111179"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020296313","display_name":"Fan Feng","orcid":"https://orcid.org/0000-0002-5990-312X"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]},{"id":"https://openalex.org/I4210111179","display_name":"Michigan United","ror":"https://ror.org/0291ys696","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210111179"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Fan Feng","raw_affiliation_strings":["Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America","institution_ids":["https://openalex.org/I27837315","https://openalex.org/I4210111179"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101795155","display_name":"Xin Luo","orcid":"https://orcid.org/0000-0001-5438-7069"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]},{"id":"https://openalex.org/I4210111179","display_name":"Michigan United","ror":"https://ror.org/0291ys696","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210111179"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Xin Luo","raw_affiliation_strings":["Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America","institution_ids":["https://openalex.org/I27837315","https://openalex.org/I4210111179"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024852088","display_name":"Conrad Reihsmann","orcid":"https://orcid.org/0000-0002-1482-5359"},"institutions":[{"id":"https://openalex.org/I901861585","display_name":"Vanderbilt University Medical Center","ror":"https://ror.org/05dq2gs74","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210162197","https://openalex.org/I901861585"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Conrad V. Reihsmann","raw_affiliation_strings":["Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-1482-5359","affiliations":[{"raw_affiliation_string":"Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America","institution_ids":["https://openalex.org/I901861585"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034812020","display_name":"Alexander L. Hopkirk","orcid":"https://orcid.org/0000-0002-1194-4221"},"institutions":[{"id":"https://openalex.org/I901861585","display_name":"Vanderbilt University Medical Center","ror":"https://ror.org/05dq2gs74","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210162197","https://openalex.org/I901861585"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Alexander L. Hopkirk","raw_affiliation_strings":["Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America","institution_ids":["https://openalex.org/I901861585"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032367229","display_name":"Jean\u2010Philippe Cartailler","orcid":"https://orcid.org/0000-0002-0312-2391"},"institutions":[{"id":"https://openalex.org/I200719446","display_name":"Vanderbilt University","ror":"https://ror.org/02vm5rt34","country_code":"US","type":"education","lineage":["https://openalex.org/I200719446"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jean-Philippe Cartailler","raw_affiliation_strings":["Center for Stem Cell Biology, Vanderbilt University, Nashville, Tennessee, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Stem Cell Biology, Vanderbilt University, Nashville, Tennessee, United States of America","institution_ids":["https://openalex.org/I200719446"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051320789","display_name":"Marcela Bri\u0161\u0161ov\u00e1","orcid":"https://orcid.org/0000-0002-4999-3280"},"institutions":[{"id":"https://openalex.org/I901861585","display_name":"Vanderbilt University Medical Center","ror":"https://ror.org/05dq2gs74","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210162197","https://openalex.org/I901861585"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Marcela Brissova","raw_affiliation_strings":["Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America","institution_ids":["https://openalex.org/I901861585"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054883884","display_name":"Stephen C.J. Parker","orcid":"https://orcid.org/0000-0001-8122-0117"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]},{"id":"https://openalex.org/I4210111179","display_name":"Michigan United","ror":"https://ror.org/0291ys696","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210111179"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Stephen C. J. Parker","raw_affiliation_strings":["Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America","institution_ids":["https://openalex.org/I27837315","https://openalex.org/I4210111179"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064768454","display_name":"Diane C. Saunders","orcid":"https://orcid.org/0000-0002-8849-6746"},"institutions":[{"id":"https://openalex.org/I901861585","display_name":"Vanderbilt University Medical Center","ror":"https://ror.org/05dq2gs74","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210162197","https://openalex.org/I901861585"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Diane C. Saunders","raw_affiliation_strings":["Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America","institution_ids":["https://openalex.org/I901861585"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100454161","display_name":"Jie Liu","orcid":"https://orcid.org/0000-0002-9504-0587"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]},{"id":"https://openalex.org/I4210111179","display_name":"Michigan United","ror":"https://ror.org/0291ys696","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210111179"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jie Liu","raw_affiliation_strings":["Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America","Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, Michigan, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-9504-0587","affiliations":[{"raw_affiliation_string":"Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America","institution_ids":["https://openalex.org/I27837315","https://openalex.org/I4210111179"]},{"raw_affiliation_string":"Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, Michigan, United States of America","institution_ids":["https://openalex.org/I27837315","https://openalex.org/I4210111179"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":10,"corresponding_author_ids":["https://openalex.org/A5020296313","https://openalex.org/A5024852088","https://openalex.org/A5032367229","https://openalex.org/A5034812020","https://openalex.org/A5045638971","https://openalex.org/A5051320789","https://openalex.org/A5054883884","https://openalex.org/A5064768454","https://openalex.org/A5100454161","https://openalex.org/A5101795155"],"corresponding_institution_ids":["https://openalex.org/I200719446","https://openalex.org/I27837315","https://openalex.org/I4210111179","https://openalex.org/I901861585"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":4.342,"has_fulltext":true,"cited_by_count":7,"citation_normalized_percentile":{"value":0.93704269,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"20","issue":"8","first_page":"e1012344","last_page":"e1012344"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.9998999834060669,"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":0.9998999834060669,"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":0.9997000098228455,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9948999881744385,"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/smoothing","display_name":"Smoothing","score":0.8718984127044678},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.7408974170684814},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7102470993995667},{"id":"https://openalex.org/keywords/toolbox","display_name":"Toolbox","score":0.6023224592208862},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5010511875152588},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4205610156059265},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.40539079904556274},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.3942109942436218},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3427640199661255},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.17006385326385498},{"id":"https://openalex.org/keywords/computer-vision","display_name":"Computer vision","score":0.12608200311660767}],"concepts":[{"id":"https://openalex.org/C3770464","wikidata":"https://www.wikidata.org/wiki/Q775963","display_name":"Smoothing","level":2,"score":0.8718984127044678},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.7408974170684814},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7102470993995667},{"id":"https://openalex.org/C2777655017","wikidata":"https://www.wikidata.org/wiki/Q1501161","display_name":"Toolbox","level":2,"score":0.6023224592208862},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5010511875152588},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4205610156059265},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.40539079904556274},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3942109942436218},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3427640199661255},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.17006385326385498},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.12608200311660767},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"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":"D000465","descriptor_name":"Algorithms","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":"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":"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":"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":"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1371/journal.pcbi.1012344","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1012344","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:39196899","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39196899","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:11355562","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11355562","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11355562/pdf/pcbi.1012344.pdf","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":"PLoS Comput Biol","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:fa5d8a4580c940c98d6914fa30f9c20e","is_oa":true,"landing_page_url":"https://doaj.org/article/fa5d8a4580c940c98d6914fa30f9c20e","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":"PLoS Computational Biology, Vol 20, Iss 8, p e1012344 (2024)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1012344","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1012344","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.7200000286102295,"id":"https://metadata.un.org/sdg/11","display_name":"Sustainable cities and communities"}],"awards":[{"id":"https://openalex.org/G5716684874","display_name":null,"funder_award_id":"G-2207-05399","funder_id":"https://openalex.org/F4320309446","funder_display_name":"Leona M. and Harry B. Helmsley Charitable Trust"}],"funders":[{"id":"https://openalex.org/F4320309446","display_name":"Leona M. and Harry B. Helmsley Charitable Trust","ror":"https://ror.org/011x6n313"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":38,"referenced_works":["https://openalex.org/W101836494","https://openalex.org/W1978394996","https://openalex.org/W1987971958","https://openalex.org/W2071949631","https://openalex.org/W2100235303","https://openalex.org/W2117852776","https://openalex.org/W2121947440","https://openalex.org/W2130146349","https://openalex.org/W2131681506","https://openalex.org/W2151936673","https://openalex.org/W2187089797","https://openalex.org/W2624431344","https://openalex.org/W2768707988","https://openalex.org/W2899235059","https://openalex.org/W2946991347","https://openalex.org/W2949238013","https://openalex.org/W3011036412","https://openalex.org/W3014494607","https://openalex.org/W3016553397","https://openalex.org/W3017023874","https://openalex.org/W3047081808","https://openalex.org/W3099768174","https://openalex.org/W3178174162","https://openalex.org/W3193419934","https://openalex.org/W3205432617","https://openalex.org/W3217102738","https://openalex.org/W4231510805","https://openalex.org/W4286462293","https://openalex.org/W4294558607","https://openalex.org/W4307497973","https://openalex.org/W4307715791","https://openalex.org/W4308770506","https://openalex.org/W4376643112","https://openalex.org/W4381328668","https://openalex.org/W4389304734","https://openalex.org/W4396781858","https://openalex.org/W6639619044","https://openalex.org/W6763491233"],"related_works":["https://openalex.org/W4205140848","https://openalex.org/W2068663075","https://openalex.org/W2978678743","https://openalex.org/W2797837731","https://openalex.org/W4393677513","https://openalex.org/W4390832911","https://openalex.org/W829257147","https://openalex.org/W4385302116","https://openalex.org/W2209007751","https://openalex.org/W2620387633"],"abstract_inverted_index":{"Recent":[0],"studies":[1],"show":[2],"that":[3,118],"cellular":[4,28,52,69],"neighborhoods":[5,29],"play":[6],"an":[7],"important":[8],"role":[9],"in":[10],"evolving":[11],"biological":[12,131],"events":[13],"such":[14],"as":[15,90,92],"cancer":[16],"and":[17,25,63,73,86,106,114,127,144],"diabetes.":[18],"Therefore,":[19],"it":[20],"is":[21],"critical":[22],"to":[23,139,148],"accurately":[24],"efficiently":[26],"identify":[27],"from":[30],"spatially-resolved":[31],"single-cell":[32,36],"transcriptomic":[33],"data":[34],"or":[35],"resolution":[37],"tissue":[38],"imaging":[39],"data.":[40,150],"In":[41],"this":[42],"work,":[43],"we":[44],"develop":[45],"CNTools,":[46],"a":[47],"computational":[48],"toolbox":[49],"for":[50],"end-to-end":[51],"neighborhood":[53,70],"analysis":[54,64,96],"on":[55,101,137],"annotated":[56],"cell":[57],"images,":[58],"comprising":[59],"both":[60],"the":[61],"identification":[62,71,108,142],"steps.":[65],"It":[66,116],"includes":[67],"state-of-the-art":[68],"methods":[72,109,126,143],"post-identification":[74],"smoothing":[75,111,145],"techniques,":[76],"with":[77,110,120],"our":[78],"newly":[79],"proposed":[80],"Cellular":[81],"Neighbor":[82],"Embedding":[83],"(CNE)":[84],"method":[85],"Naive":[87,121],"Smoothing":[88,122],"technique,":[89],"well":[91],"several":[93],"established":[94],"downstream":[95],"approaches.":[97],"We":[98,133],"applied":[99],"CNTools":[100],"three":[102],"real-world":[103],"CODEX":[104],"datasets":[105],"evaluated":[107],"techniques":[112,146],"quantitatively":[113],"qualitatively.":[115],"shows":[117],"CNE":[119],"overall":[123],"outperformed":[124],"other":[125],"revealed":[128],"more":[129],"convincing":[130],"insights.":[132],"also":[134],"provided":[135],"suggestions":[136],"how":[138],"choose":[140],"proper":[141],"according":[147],"input":[149]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":2}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}