{"id":"https://openalex.org/W4409783571","doi":"https://doi.org/10.1093/bioinformatics/btaf246","title":"TissueViewer: a web-based multiplexed image viewer","display_name":"TissueViewer: a web-based multiplexed image viewer","publication_year":2025,"publication_date":"2025-04-24","ids":{"openalex":"https://openalex.org/W4409783571","doi":"https://doi.org/10.1093/bioinformatics/btaf246","pmid":"https://pubmed.ncbi.nlm.nih.gov/40279289"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf246","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf246","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf246/63011552/btaf246.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"gold","oa_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf246/63011552/btaf246.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5088442164","display_name":"David G.P. van IJzendoorn","orcid":"https://orcid.org/0000-0002-2249-5919"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"David Gerardus Pieter van IJzendoorn","raw_affiliation_strings":["Department of Pathology, Stanford University , Stanford, CA 94305,","Stanford University , Department of Pathology, Stanford, CA 94305"],"raw_orcid":"https://orcid.org/0000-0002-2249-5919","affiliations":[{"raw_affiliation_string":"Department of Pathology, Stanford University , Stanford, CA 94305,","institution_ids":["https://openalex.org/I97018004"]},{"raw_affiliation_string":"Stanford University , Department of Pathology, Stanford, CA 94305","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009009669","display_name":"Magdalena Matusiak","orcid":"https://orcid.org/0000-0002-8201-1621"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Magdalena Matusiak","raw_affiliation_strings":["Department of Pathology, Stanford University , Stanford, CA 94305,","Stanford University , Department of Pathology, Stanford, CA 94305"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pathology, Stanford University , Stanford, CA 94305,","institution_ids":["https://openalex.org/I97018004"]},{"raw_affiliation_string":"Stanford University , Department of Pathology, Stanford, CA 94305","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044981994","display_name":"Robert B. West","orcid":"https://orcid.org/0000-0002-8330-8283"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rob West","raw_affiliation_strings":["Department of Pathology, Stanford University , Stanford, CA 94305,","Stanford University , Department of Pathology, Stanford, CA 94305"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pathology, Stanford University , Stanford, CA 94305,","institution_ids":["https://openalex.org/I97018004"]},{"raw_affiliation_string":"Stanford University , Department of Pathology, Stanford, CA 94305","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5023048831","display_name":"Matt van de Rijn","orcid":"https://orcid.org/0000-0002-1909-9739"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Matt van de Rijn","raw_affiliation_strings":["Department of Pathology, Stanford University , Stanford, CA 94305,","Stanford University , Department of Pathology, Stanford, CA 94305"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pathology, Stanford University , Stanford, CA 94305,","institution_ids":["https://openalex.org/I97018004"]},{"raw_affiliation_string":"Stanford University , Department of Pathology, Stanford, CA 94305","institution_ids":["https://openalex.org/I97018004"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I97018004"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.06832882,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"41","issue":"5","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.7271000146865845,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.7271000146865845,"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.23430000245571136,"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/T10862","display_name":"AI in cancer detection","score":0.01850000023841858,"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":0.8521761894226074},{"id":"https://openalex.org/keywords/upload","display_name":"Upload","score":0.8306012153625488},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.5842248201370239},{"id":"https://openalex.org/keywords/profiling","display_name":"Profiling (computer programming)","score":0.5504131317138672},{"id":"https://openalex.org/keywords/web-application","display_name":"Web application","score":0.49722984433174133},{"id":"https://openalex.org/keywords/multiplex","display_name":"Multiplex","score":0.46869778633117676},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.4401698410511017},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.41846179962158203},{"id":"https://openalex.org/keywords/file-format","display_name":"File format","score":0.4118974804878235},{"id":"https://openalex.org/keywords/multimedia","display_name":"Multimedia","score":0.38334009051322937},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3580194115638733},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.1716163456439972},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.16479143500328064},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.12419119477272034}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8521761894226074},{"id":"https://openalex.org/C71901391","wikidata":"https://www.wikidata.org/wiki/Q7126699","display_name":"Upload","level":2,"score":0.8306012153625488},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.5842248201370239},{"id":"https://openalex.org/C187191949","wikidata":"https://www.wikidata.org/wiki/Q1138496","display_name":"Profiling (computer programming)","level":2,"score":0.5504131317138672},{"id":"https://openalex.org/C118643609","wikidata":"https://www.wikidata.org/wiki/Q189210","display_name":"Web application","level":2,"score":0.49722984433174133},{"id":"https://openalex.org/C2781188995","wikidata":"https://www.wikidata.org/wiki/Q6934982","display_name":"Multiplex","level":2,"score":0.46869778633117676},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.4401698410511017},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.41846179962158203},{"id":"https://openalex.org/C97250363","wikidata":"https://www.wikidata.org/wiki/Q235557","display_name":"File format","level":2,"score":0.4118974804878235},{"id":"https://openalex.org/C49774154","wikidata":"https://www.wikidata.org/wiki/Q131765","display_name":"Multimedia","level":1,"score":0.38334009051322937},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3580194115638733},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.1716163456439972},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.16479143500328064},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.12419119477272034},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0}],"mesh":[{"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"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":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaf246","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf246","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf246/63011552/btaf246.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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:40279289","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40279289","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:pubmedcentral.nih.gov:12119129","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12119129","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"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaf246","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf246","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf246/63011552/btaf246.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":[{"id":"https://metadata.un.org/sdg/9","score":0.4300000071525574,"display_name":"Industry, innovation and infrastructure"}],"awards":[{"id":"https://openalex.org/G1152033112","display_name":null,"funder_award_id":"R01 CA229529","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"}],"funders":[{"id":"https://openalex.org/F4320309014","display_name":"Virginia and D.K. Ludwig Fund for Cancer Research","ror":"https://ror.org/05qdwtz81"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4409783571.pdf"},"referenced_works_count":4,"referenced_works":["https://openalex.org/W2168166653","https://openalex.org/W3214014138","https://openalex.org/W4280610419","https://openalex.org/W4391532779"],"related_works":["https://openalex.org/W2944823289","https://openalex.org/W3037018281","https://openalex.org/W2003209439","https://openalex.org/W4321854979","https://openalex.org/W2358319515","https://openalex.org/W2972592048","https://openalex.org/W4312214821","https://openalex.org/W2497626292","https://openalex.org/W2390344072","https://openalex.org/W3089066832"],"abstract_inverted_index":{"MOTIVATION:":[0],"Datasets":[1],"generated":[2],"by":[3],"spatial":[4,13],"biology":[5],"techniques":[6],"such":[7],"as":[8],"multiplex":[9],"immunofluorescence":[10],"staining":[11],"or":[12],"transcriptomics":[14],"profiling":[15],"of":[16,23,51,125],"histologic":[17],"sections":[18],"carry":[19],"a":[20,123],"tremendous":[21],"wealth":[22],"information.":[24],"Several":[25],"commercial":[26],"platforms":[27],"exist":[28],"that":[29],"can":[30,108,117],"simultaneously":[31],"acquire":[32],"1-1000":[33],"distinct":[34],"marker":[35],"signals":[36],"(e.g.":[37],"MIBI,":[38],"CODEX,":[39],"Orion,":[40],"Nanostring":[41],"CosMX":[42],"SMI,":[43],"Vizgen).":[44],"However,":[45],"due":[46],"to":[47,76,83,128],"the":[48,88,112],"large":[49],"size":[50],"these":[52,69],"datasets,":[53],"their":[54,119],"viewing":[55],"and":[56,61,78,94,107],"sharing":[57],"are":[58],"slow,":[59],"laborious,":[60],"require":[62],"extensive":[63],"computational":[64],"resources.":[65],"RESULTS:":[66],"To":[67],"overcome":[68],"challenges,":[70],"we":[71],"developed":[72],"TissueViewer,":[73],"an":[74],"easy":[75],"setup":[77],"use":[79],"web-based":[80],"viewer":[81],"designed":[82],"deliver":[84],"high-resolution":[85],"images":[86],"over":[87],"internet":[89],"with":[90,122,130],"low":[91],"bandwidth":[92],"requirements":[93],"at":[95],"high":[96],"speed.":[97],"AVAILABILITY":[98],"AND":[99],"IMPLEMENTATION:":[100],"TissueViewer":[101],"is":[102],"available":[103],"on":[104,111],"GitHub":[105],"(https://github.com/davidvi/tissueviewer)":[106],"be":[109],"used":[110],"TissueViewer.org":[113],"platform,":[114],"where":[115],"readers":[116],"upload":[118],"own":[120],"data":[121],"limit":[124],"50":[126],"GB":[127],"share":[129],"colleagues.":[131]},"counts_by_year":[],"updated_date":"2026-06-26T08:34:08.712188","created_date":"2025-10-10T00:00:00"}
