{"id":"https://openalex.org/W2801350946","doi":"https://doi.org/10.1093/bioinformatics/bty210","title":"Comparative analysis of tissue reconstruction algorithms for 3D histology","display_name":"Comparative analysis of tissue reconstruction algorithms for 3D histology","publication_year":2018,"publication_date":"2018-04-18","ids":{"openalex":"https://openalex.org/W2801350946","doi":"https://doi.org/10.1093/bioinformatics/bty210","mag":"2801350946","pmid":"https://pubmed.ncbi.nlm.nih.gov/29684099"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bty210","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty210","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/17/3013/25703075/bty210.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/34/17/3013/25703075/bty210.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5069504905","display_name":"Kimmo Kartasalo","orcid":"https://orcid.org/0000-0002-9470-4783"},"institutions":[{"id":"https://openalex.org/I166825849","display_name":"Tampere University","ror":"https://ror.org/033003e23","country_code":"FI","type":"education","lineage":["https://openalex.org/I166825849"]},{"id":"https://openalex.org/I4210133110","display_name":"Tampere University","ror":null,"country_code":"FI","type":null,"lineage":["https://openalex.org/I4210133110"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Kimmo Kartasalo","raw_affiliation_strings":["BioMediTech Institute, Tampere, Finland","Faculty of Biomedical Sciences and Engineering, Tampere University of Technology, Tampere, Finland","Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland"],"raw_orcid":"https://orcid.org/0000-0002-9470-4783","affiliations":[{"raw_affiliation_string":"BioMediTech Institute, Tampere, Finland","institution_ids":[]},{"raw_affiliation_string":"Faculty of Biomedical Sciences and Engineering, Tampere University of Technology, Tampere, Finland","institution_ids":["https://openalex.org/I4210133110"]},{"raw_affiliation_string":"Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland","institution_ids":["https://openalex.org/I166825849","https://openalex.org/I4210133110"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003926457","display_name":"Leena Latonen","orcid":"https://orcid.org/0000-0003-4502-2193"},"institutions":[{"id":"https://openalex.org/I166825849","display_name":"Tampere University","ror":"https://ror.org/033003e23","country_code":"FI","type":"education","lineage":["https://openalex.org/I166825849"]},{"id":"https://openalex.org/I4210126318","display_name":"Tampere University Hospital","ror":"https://ror.org/02hvt5f17","country_code":"FI","type":"healthcare","lineage":["https://openalex.org/I4210126318"]},{"id":"https://openalex.org/I4210133110","display_name":"Tampere University","ror":null,"country_code":"FI","type":null,"lineage":["https://openalex.org/I4210133110"]},{"id":"https://openalex.org/I4210133601","display_name":"Fimlab (Finland)","ror":"https://ror.org/031y6w871","country_code":"FI","type":"company","lineage":["https://openalex.org/I4210133601"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Leena Latonen","raw_affiliation_strings":["BioMediTech Institute, Tampere, Finland","Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland","Fimlab Laboratories, Tampere University Hospital, Tampere, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BioMediTech Institute, Tampere, Finland","institution_ids":[]},{"raw_affiliation_string":"Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland","institution_ids":["https://openalex.org/I166825849","https://openalex.org/I4210133110"]},{"raw_affiliation_string":"Fimlab Laboratories, Tampere University Hospital, Tampere, Finland","institution_ids":["https://openalex.org/I4210126318","https://openalex.org/I4210133110","https://openalex.org/I4210133601"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005382170","display_name":"Jorma Vihinen","orcid":"https://orcid.org/0000-0001-7396-727X"},"institutions":[{"id":"https://openalex.org/I4210133110","display_name":"Tampere University","ror":null,"country_code":"FI","type":null,"lineage":["https://openalex.org/I4210133110"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Jorma Vihinen","raw_affiliation_strings":["Faculty of Engineering Sciences, Tampere University of Technology, Tampere, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Engineering Sciences, Tampere University of Technology, Tampere, Finland","institution_ids":["https://openalex.org/I4210133110"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085775392","display_name":"Tapio Visakorpi","orcid":"https://orcid.org/0000-0002-5004-0364"},"institutions":[{"id":"https://openalex.org/I166825849","display_name":"Tampere University","ror":"https://ror.org/033003e23","country_code":"FI","type":"education","lineage":["https://openalex.org/I166825849"]},{"id":"https://openalex.org/I4210126318","display_name":"Tampere University Hospital","ror":"https://ror.org/02hvt5f17","country_code":"FI","type":"healthcare","lineage":["https://openalex.org/I4210126318"]},{"id":"https://openalex.org/I4210133110","display_name":"Tampere University","ror":null,"country_code":"FI","type":null,"lineage":["https://openalex.org/I4210133110"]},{"id":"https://openalex.org/I4210133601","display_name":"Fimlab (Finland)","ror":"https://ror.org/031y6w871","country_code":"FI","type":"company","lineage":["https://openalex.org/I4210133601"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Tapio Visakorpi","raw_affiliation_strings":["BioMediTech Institute, Tampere, Finland","Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland","Fimlab Laboratories, Tampere University Hospital, Tampere, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BioMediTech Institute, Tampere, Finland","institution_ids":[]},{"raw_affiliation_string":"Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland","institution_ids":["https://openalex.org/I166825849","https://openalex.org/I4210133110"]},{"raw_affiliation_string":"Fimlab Laboratories, Tampere University Hospital, Tampere, Finland","institution_ids":["https://openalex.org/I4210126318","https://openalex.org/I4210133110","https://openalex.org/I4210133601"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063194021","display_name":"Matti Nykter","orcid":"https://orcid.org/0000-0001-6956-2843"},"institutions":[{"id":"https://openalex.org/I166825849","display_name":"Tampere University","ror":"https://ror.org/033003e23","country_code":"FI","type":"education","lineage":["https://openalex.org/I166825849"]},{"id":"https://openalex.org/I4210133110","display_name":"Tampere University","ror":null,"country_code":"FI","type":null,"lineage":["https://openalex.org/I4210133110"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Matti Nykter","raw_affiliation_strings":["BioMediTech Institute, Tampere, Finland","Faculty of Biomedical Sciences and Engineering, Tampere University of Technology, Tampere, Finland","Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BioMediTech Institute, Tampere, Finland","institution_ids":[]},{"raw_affiliation_string":"Faculty of Biomedical Sciences and Engineering, Tampere University of Technology, Tampere, Finland","institution_ids":["https://openalex.org/I4210133110"]},{"raw_affiliation_string":"Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland","institution_ids":["https://openalex.org/I166825849","https://openalex.org/I4210133110"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5089033830","display_name":"Pekka Ruusuvuori","orcid":"https://orcid.org/0000-0001-9086-9591"},"institutions":[{"id":"https://openalex.org/I166825849","display_name":"Tampere University","ror":"https://ror.org/033003e23","country_code":"FI","type":"education","lineage":["https://openalex.org/I166825849"]},{"id":"https://openalex.org/I4210133110","display_name":"Tampere University","ror":null,"country_code":"FI","type":null,"lineage":["https://openalex.org/I4210133110"]}],"countries":["FI"],"is_corresponding":true,"raw_author_name":"Pekka Ruusuvuori","raw_affiliation_strings":["BioMediTech Institute, Tampere, Finland","Faculty of Computing and Electrical Engineering, Tampere University of Technology, Tampere 33101, Finland","Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland"],"raw_orcid":"https://orcid.org/0000-0001-9086-9591","affiliations":[{"raw_affiliation_string":"BioMediTech Institute, Tampere, Finland","institution_ids":[]},{"raw_affiliation_string":"Faculty of Computing and Electrical Engineering, Tampere University of Technology, Tampere 33101, Finland","institution_ids":["https://openalex.org/I4210133110"]},{"raw_affiliation_string":"Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland","institution_ids":["https://openalex.org/I166825849","https://openalex.org/I4210133110"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5089033830"],"corresponding_institution_ids":["https://openalex.org/I166825849","https://openalex.org/I4210133110"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":2.9509,"has_fulltext":true,"cited_by_count":51,"citation_normalized_percentile":{"value":0.92658231,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":99},"biblio":{"volume":"34","issue":"17","first_page":"3013","last_page":"3021"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10862","display_name":"AI in cancer detection","score":0.8001999855041504,"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"}},"topics":[{"id":"https://openalex.org/T10862","display_name":"AI in cancer detection","score":0.8001999855041504,"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"}},{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.05640000104904175,"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/T10052","display_name":"Medical Image Segmentation Techniques","score":0.028699999675154686,"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/computer-science","display_name":"Computer science","score":0.8094034194946289},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.6054120063781738},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.5810319185256958},{"id":"https://openalex.org/keywords/benchmarking","display_name":"Benchmarking","score":0.5193689465522766},{"id":"https://openalex.org/keywords/digital-pathology","display_name":"Digital pathology","score":0.5102090835571289},{"id":"https://openalex.org/keywords/3d-reconstruction","display_name":"3D reconstruction","score":0.4581313729286194},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4542333781719208},{"id":"https://openalex.org/keywords/high-resolution","display_name":"High resolution","score":0.4309238791465759},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4285995662212372},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.42058682441711426},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.39616650342941284},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3853321969509125},{"id":"https://openalex.org/keywords/computer-vision","display_name":"Computer vision","score":0.3831687569618225},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.09422814846038818}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8094034194946289},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.6054120063781738},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.5810319185256958},{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.5193689465522766},{"id":"https://openalex.org/C2777522853","wikidata":"https://www.wikidata.org/wiki/Q5276128","display_name":"Digital pathology","level":2,"score":0.5102090835571289},{"id":"https://openalex.org/C109950114","wikidata":"https://www.wikidata.org/wiki/Q4464732","display_name":"3D reconstruction","level":2,"score":0.4581313729286194},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4542333781719208},{"id":"https://openalex.org/C3020199158","wikidata":"https://www.wikidata.org/wiki/Q210521","display_name":"High resolution","level":2,"score":0.4309238791465759},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4285995662212372},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.42058682441711426},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.39616650342941284},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3853321969509125},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.3831687569618225},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.09422814846038818},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C144133560","wikidata":"https://www.wikidata.org/wiki/Q4830453","display_name":"Business","level":0,"score":0.0},{"id":"https://openalex.org/C162853370","wikidata":"https://www.wikidata.org/wiki/Q39809","display_name":"Marketing","level":1,"score":0.0},{"id":"https://openalex.org/C127313418","wikidata":"https://www.wikidata.org/wiki/Q1069","display_name":"Geology","level":0,"score":0.0},{"id":"https://openalex.org/C62649853","wikidata":"https://www.wikidata.org/wiki/Q199687","display_name":"Remote sensing","level":1,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006652","descriptor_name":"Histological Techniques","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006652","descriptor_name":"Histological Techniques","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006652","descriptor_name":"Histological Techniques","qualifier_ui":null,"qualifier_name":null,"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":7,"locations":[{"id":"doi:10.1093/bioinformatics/bty210","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty210","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/17/3013/25703075/bty210.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:29684099","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29684099","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:tampub.uta.fi:10024/104249","is_oa":true,"landing_page_url":"http://tampub.uta.fi/handle/10024/104249","pdf_url":null,"source":{"id":"https://openalex.org/S4306401860","display_name":"Tampere University Institutional Repository (Tampere University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I150589677","host_organization_name":"Tampere University of Applied Sciences","host_organization_lineage":["https://openalex.org/I150589677"],"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":"","raw_type":"publishedVersion"},{"id":"pmh:oai:europepmc.org:5083555","is_oa":true,"landing_page_url":"http://europepmc.org/pmc/articles/PMC6129300","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:6129300","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6129300","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":"Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:trepo.tuni.fi:10024/104249","is_oa":true,"landing_page_url":"https://trepo.tuni.fi/handle/10024/104249","pdf_url":null,"source":{"id":"https://openalex.org/S4306401860","display_name":"Tampere University Institutional Repository (Tampere University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I150589677","host_organization_name":"Tampere University of Applied Sciences","host_organization_lineage":["https://openalex.org/I150589677"],"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":"","raw_type":"publishedVersion"},{"id":"pmh:oai:trepo.tuni.fi:10024/212751","is_oa":true,"landing_page_url":"https://trepo.tuni.fi/handle/10024/212751","pdf_url":null,"source":{"id":"https://openalex.org/S4306401860","display_name":"Tampere University Institutional Repository (Tampere University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I150589677","host_organization_name":"Tampere University of Applied Sciences","host_organization_lineage":["https://openalex.org/I150589677"],"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":"publishedVersion"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bty210","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty210","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/17/3013/25703075/bty210.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.4000000059604645,"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure"}],"awards":[{"id":"https://openalex.org/G5128652953","display_name":null,"funder_award_id":"269474","funder_id":"https://openalex.org/F4320321108","funder_display_name":"Academy of Finland"},{"id":"https://openalex.org/G8828289544","display_name":"Terveytt\u00e4 biteist\u00e4 \u2014 Tampereen Yliopisto (269/31/2015)","funder_award_id":"269/31/2015","funder_id":"https://openalex.org/F4320321855","funder_display_name":"Tekes"}],"funders":[{"id":"https://openalex.org/F4320311269","display_name":"KAUTE-S\u00e4\u00e4ti\u00f6","ror":"https://ror.org/00zwv5854"},{"id":"https://openalex.org/F4320321108","display_name":"Academy of Finland","ror":"https://ror.org/05k73zm37"},{"id":"https://openalex.org/F4320321855","display_name":"Tekes","ror":"https://ror.org/02ag8cq23"},{"id":"https://openalex.org/F4320322861","display_name":"Emil Aaltosen S\u00e4\u00e4ti\u00f6","ror":"https://ror.org/005rt3g54"},{"id":"https://openalex.org/F4320323337","display_name":"Tekniikan Edist\u00e4miss\u00e4\u00e4ti\u00f6","ror":"https://ror.org/03f420b93"},{"id":"https://openalex.org/F4320323824","display_name":"Sy\u00f6p\u00e4j\u00e4rjest\u00f6t","ror":"https://ror.org/05pgg4z49"},{"id":"https://openalex.org/F4320324148","display_name":"Orionin Tutkimuss\u00e4\u00e4ti\u00f6","ror":"https://ror.org/0296s4x19"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2801350946.pdf","grobid_xml":"https://content.openalex.org/works/W2801350946.grobid-xml"},"referenced_works_count":61,"referenced_works":["https://openalex.org/W363173866","https://openalex.org/W1480656389","https://openalex.org/W1808798321","https://openalex.org/W1963620954","https://openalex.org/W1972603165","https://openalex.org/W1977838454","https://openalex.org/W1979105493","https://openalex.org/W1980971505","https://openalex.org/W1996883058","https://openalex.org/W2000601094","https://openalex.org/W2016277672","https://openalex.org/W2026140461","https://openalex.org/W2026527241","https://openalex.org/W2035945901","https://openalex.org/W2037192432","https://openalex.org/W2044465660","https://openalex.org/W2054870083","https://openalex.org/W2054902886","https://openalex.org/W2058110575","https://openalex.org/W2062389118","https://openalex.org/W2068067564","https://openalex.org/W2072120417","https://openalex.org/W2084665040","https://openalex.org/W2085261163","https://openalex.org/W2099540110","https://openalex.org/W2100229771","https://openalex.org/W2105456967","https://openalex.org/W2111574404","https://openalex.org/W2114451602","https://openalex.org/W2115167851","https://openalex.org/W2117561707","https://openalex.org/W2121075186","https://openalex.org/W2122313934","https://openalex.org/W2123491442","https://openalex.org/W2131241448","https://openalex.org/W2131938193","https://openalex.org/W2132763945","https://openalex.org/W2147762902","https://openalex.org/W2151103935","https://openalex.org/W2151238122","https://openalex.org/W2157631276","https://openalex.org/W2167279371","https://openalex.org/W2169435361","https://openalex.org/W2192203593","https://openalex.org/W2313043924","https://openalex.org/W2418982272","https://openalex.org/W2471536144","https://openalex.org/W2518570910","https://openalex.org/W2541869304","https://openalex.org/W2559756885","https://openalex.org/W2564463480","https://openalex.org/W2570599740","https://openalex.org/W2588781808","https://openalex.org/W2589034008","https://openalex.org/W2603648722","https://openalex.org/W2964172739","https://openalex.org/W4210984231","https://openalex.org/W6603710349","https://openalex.org/W6677764299","https://openalex.org/W6678911119","https://openalex.org/W6698896426"],"related_works":["https://openalex.org/W4238897586","https://openalex.org/W435179959","https://openalex.org/W2619091065","https://openalex.org/W2059640416","https://openalex.org/W1490753184","https://openalex.org/W2284465472","https://openalex.org/W2291782699","https://openalex.org/W1993948687","https://openalex.org/W2000169967","https://openalex.org/W2112883198"],"abstract_inverted_index":{"Motivation:":[0],"Digital":[1],"pathology":[2],"enables":[3,55],"new":[4],"approaches":[5],"that":[6,136],"expand":[7],"beyond":[8],"storage,":[9],"visualization":[10],"or":[11],"analysis":[12],"of":[13,29,58,71,90,105,130,139],"histological":[14],"samples":[15],"in":[16,45,66],"digital":[17],"format.":[18],"One":[19],"novel":[20],"opportunity":[21],"is":[22,32,93],"3D":[23,53,69,110,131],"histology,":[24],"where":[25],"a":[26,87,98,122],"three-dimensional":[27],"reconstruction":[28,84,111],"the":[30,67,72,83,103],"sample":[31],"formed":[33],"computationally":[34],"based":[35],"on":[36],"serial":[37],"tissue":[38,43,73,143],"sections.":[39],"This":[40],"allows":[41],"examining":[42],"architecture":[44],"3D,":[46],"for":[47,49,82,125,141],"example,":[48],"diagnostic":[50],"purposes.":[51],"Importantly,":[52],"histology":[54,132],"joint":[56],"mapping":[57],"cellular":[59],"morphology":[60],"with":[61],"spatially":[62],"resolved":[63],"omics":[64],"data":[65,166],"true":[68],"context":[70],"at":[74,169],"microscopic":[75],"resolution.":[76],"Several":[77],"algorithms":[78,133],"have":[79],"been":[80],"proposed":[81],"task,":[85],"but":[86],"quantitative":[88],"comparison":[89],"their":[91],"accuracy":[92,104],"lacking.":[94],"Results:":[95],"We":[96],"developed":[97],"benchmarking":[99],"framework":[100],"to":[101,147],"evaluate":[102],"several":[106],"free":[107],"and":[108,128,134,151],"commercial":[109],"methods":[112,137],"using":[113],"two":[114],"whole":[115],"slide":[116,156],"image":[117,157],"datasets.":[118],"The":[119],"results":[120],"provide":[121],"solid":[123],"basis":[124],"further":[126],"development":[127],"application":[129],"indicate":[135],"capable":[138],"compensating":[140],"local":[142],"deformation":[144],"are":[145,167],"superior":[146],"simpler":[148],"approaches.":[149],"Availability":[150],"implementation:":[152],"Code:":[153],"https://github.com/BioimageInformaticsTampere/RegBenchmark.":[154],"Whole":[155],"datasets:":[158],"http://urn.fi/urn:":[159],"nbn:":[160],"fi:":[161],"csc-kata20170705131652639702.":[162],"Supplementary":[163,165],"information:":[164],"available":[168],"Bioinformatics":[170],"online.":[171]},"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":6},{"year":2023,"cited_by_count":14},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":6},{"year":2020,"cited_by_count":5},{"year":2019,"cited_by_count":5}],"updated_date":"2026-07-28T07:46:37.118299","created_date":"2025-10-10T00:00:00"}
