{"id":"https://openalex.org/W4362693677","doi":"https://doi.org/10.1117/12.2654542","title":"An end-to-end pipeline for 3D slide-wise multi-stain renal pathology registration","display_name":"An end-to-end pipeline for 3D slide-wise multi-stain renal pathology registration","publication_year":2023,"publication_date":"2023-04-07","ids":{"openalex":"https://openalex.org/W4362693677","doi":"https://doi.org/10.1117/12.2654542","pmid":"https://pubmed.ncbi.nlm.nih.gov/38606194"},"language":"en","primary_location":{"id":"doi:10.1117/12.2654542","is_oa":false,"landing_page_url":"http://dx.doi.org/10.1117/12.2654542","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Medical Imaging 2023: Digital and Computational Pathology","raw_type":"proceedings-article"},"type":"preprint","indexed_in":["arxiv","crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/2305.11968","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5102795939","display_name":"Peize Li","orcid":"https://orcid.org/0000-0002-5321-2176"},"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":"Peize Li","raw_affiliation_strings":["Department of Computer Science, Vanderbilt University, Nashville, TN, 37235 USA","Vanderbilt Univ. (United States)"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Vanderbilt University, Nashville, TN, 37235 USA","institution_ids":["https://openalex.org/I200719446"]},{"raw_affiliation_string":"Vanderbilt Univ. (United States)","institution_ids":["https://openalex.org/I200719446"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037133367","display_name":"Ruining Deng","orcid":"https://orcid.org/0000-0001-6300-8518"},"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":false,"raw_author_name":"Ruining Deng","raw_affiliation_strings":["Department of Computer Science, Vanderbilt University, Nashville, TN, 37235 USA","Vanderbilt Univ. (United States)"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Vanderbilt University, Nashville, TN, 37235 USA","institution_ids":["https://openalex.org/I200719446"]},{"raw_affiliation_string":"Vanderbilt Univ. (United States)","institution_ids":["https://openalex.org/I200719446"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5067191302","display_name":"Yuankai Huo","orcid":"https://orcid.org/0000-0002-2096-8065"},"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":false,"raw_author_name":"Yuankai Huo","raw_affiliation_strings":["Department of Computer Science, Vanderbilt University, Nashville, TN, 37235 USA","Vanderbilt Univ. (United States)"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Vanderbilt University, Nashville, TN, 37235 USA","institution_ids":["https://openalex.org/I200719446"]},{"raw_affiliation_string":"Vanderbilt Univ. (United States)","institution_ids":["https://openalex.org/I200719446"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5102795939"],"corresponding_institution_ids":["https://openalex.org/I200719446"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.32729288,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"12471","issue":null,"first_page":"14","last_page":"14"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10552","display_name":"Colorectal Cancer Screening and Detection","score":0.9952999949455261,"subfield":{"id":"https://openalex.org/subfields/2730","display_name":"Oncology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T10552","display_name":"Colorectal Cancer Screening and Detection","score":0.9952999949455261,"subfield":{"id":"https://openalex.org/subfields/2730","display_name":"Oncology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10052","display_name":"Medical Image Segmentation Techniques","score":0.9941999912261963,"subfield":{"id":"https://openalex.org/subfields/1707","display_name":"Computer Vision and Pattern Recognition"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10862","display_name":"AI in cancer detection","score":0.9860000014305115,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"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/computer-science","display_name":"Computer science","score":0.7773281335830688},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.7474480271339417},{"id":"https://openalex.org/keywords/stain","display_name":"Stain","score":0.6953339576721191},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.5967035293579102},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5073773264884949},{"id":"https://openalex.org/keywords/end-to-end-principle","display_name":"End-to-end principle","score":0.4730776250362396},{"id":"https://openalex.org/keywords/pathology","display_name":"Pathology","score":0.37318357825279236},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.23815077543258667},{"id":"https://openalex.org/keywords/staining","display_name":"Staining","score":0.16140154004096985},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.09006020426750183},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.08981895446777344}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7773281335830688},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.7474480271339417},{"id":"https://openalex.org/C2781294515","wikidata":"https://www.wikidata.org/wiki/Q2733470","display_name":"Stain","level":3,"score":0.6953339576721191},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.5967035293579102},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5073773264884949},{"id":"https://openalex.org/C74296488","wikidata":"https://www.wikidata.org/wiki/Q2527392","display_name":"End-to-end principle","level":2,"score":0.4730776250362396},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.37318357825279236},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.23815077543258667},{"id":"https://openalex.org/C74864618","wikidata":"https://www.wikidata.org/wiki/Q2332446","display_name":"Staining","level":2,"score":0.16140154004096985},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.09006020426750183},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.08981895446777344},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1117/12.2654542","is_oa":false,"landing_page_url":"http://dx.doi.org/10.1117/12.2654542","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Medical Imaging 2023: Digital and Computational Pathology","raw_type":"proceedings-article"},{"id":"pmid:38606194","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38606194","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":"Proceedings of SPIE--the International Society for Optical Engineering","raw_type":null},{"id":"pmh:oai:arXiv.org:2305.11968","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2305.11968","pdf_url":"https://arxiv.org/pdf/2305.11968","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},{"id":"pmh:oai:pubmedcentral.nih.gov:11008751","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11008751","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11008751/pdf/nihms-1934695.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Proc SPIE Int Soc Opt Eng","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:2305.11968","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2305.11968","pdf_url":"https://arxiv.org/pdf/2305.11968","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/8","score":0.7099999785423279,"display_name":"Decent work and economic growth"}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4362693677.pdf"},"referenced_works_count":9,"referenced_works":["https://openalex.org/W1967433721","https://openalex.org/W1970928383","https://openalex.org/W2072300346","https://openalex.org/W2121075186","https://openalex.org/W2127096431","https://openalex.org/W3034275286","https://openalex.org/W3090112028","https://openalex.org/W3152250781","https://openalex.org/W4226446012"],"related_works":["https://openalex.org/W3179968364","https://openalex.org/W2362517148","https://openalex.org/W2594860026","https://openalex.org/W2382509367","https://openalex.org/W1999612375","https://openalex.org/W2902762162","https://openalex.org/W2077435114","https://openalex.org/W2148148707","https://openalex.org/W2938107654","https://openalex.org/W2136025972"],"abstract_inverted_index":{"Tissue":[0],"examination":[1],"and":[2,17,143],"quantification":[3],"in":[4,86],"a":[5,24,72,87,100],"3D":[6,77],"context":[7],"on":[8,59,81],"serial":[9,44,84],"section":[10],"whole":[11],"slide":[12],"images":[13],"(WSIs)":[14],"were":[15],"labor-intensive":[16],"time-consuming":[18],"tasks.":[19],"Our":[20],"previous":[21],"study":[22,94],"proposed":[23],"novel":[25],"registration-based":[26],"method":[27,55],"(Map3D)":[28],"to":[29,33,135],"automatically":[30],"align":[31],"WSIs":[32,61],"the":[34,39,49,113,128,144],"same":[35],"physical":[36],"space,":[37],"reducing":[38],"human":[40],"efforts":[41],"of":[42,52,92,118],"screening":[43],"sections":[45,85],"from":[46,121],"WSIs.":[47],"However,":[48],"registration":[50,79,120],"performance":[51],"our":[53],"Map3D":[54,114,129],"was":[56],"only":[57],"evaluated":[58],"single-stain":[60],"with":[62],"large-scale":[63],"kidney":[64],"tissue":[65,138],"samples.":[66,139],"In":[67],"this":[68,93],"paper,":[69],"we":[70],"provide":[71],"Docker":[73,102,145],"for":[74,103],"an":[75,104],"end-to-end":[76,105],"slide-wise":[78],"pipeline":[80,115,130],"needle":[82,136],"biopsy":[83,137],"multi-stain":[88,106,122],"paradigm.":[89],"The":[90,140],"contribution":[91],"is":[95,116],"three-fold:":[96],"(1)":[97],"We":[98,110,125],"release":[99],"containerized":[101],"WSI":[107],"registration.":[108],"(2)":[109],"prove":[111],"that":[112,127],"capable":[117],"sectional":[119],"WSI.":[123],"(3)":[124],"verify":[126],"can":[131],"also":[132],"be":[133],"applied":[134],"source":[141],"code":[142],"have":[146],"been":[147],"made":[148],"publicly":[149],"available":[150],"at":[151],"https://github.com/hrlblab/Map3D.":[152]},"counts_by_year":[],"updated_date":"2026-04-15T08:11:43.952461","created_date":"2025-10-10T00:00:00"}
