View in EDS

Standardized metrics for assessment and reproducibility of imaging-based spatial transcriptomics datasets.

Saved in:
Bibliographic Details
Title: Standardized metrics for assessment and reproducibility of imaging-based spatial transcriptomics datasets.
Authors: Plummer JT; Center for Spatial Omics, St. Jude Children's Research Hospital, Memphis, TN, USA. jasmine.plummer@stjude.org.; Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA. jasmine.plummer@stjude.org.; Department of Cellular and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA. jasmine.plummer@stjude.org.; Comprehensive Cancer Center, St. Jude Children's Research Hospital, Memphis, TN, USA. jasmine.plummer@stjude.org., Dezem FS; Center for Spatial Omics, St. Jude Children's Research Hospital, Memphis, TN, USA.; Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA., Cook DP; Lunenfeld-Tanenbaum Research Institute, Toronto, Ontario, Canada.; Cancer Therapeutics Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada.; Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada., Park J; Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA.; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA.; Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.; Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA., Zhang L; Center for Spatial Omics, St. Jude Children's Research Hospital, Memphis, TN, USA.; Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA., Liu Y; Center for Spatial Omics, St. Jude Children's Research Hospital, Memphis, TN, USA.; Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA., Marção M; Center for Spatial Omics, St. Jude Children's Research Hospital, Memphis, TN, USA.; Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA., DuBose H; Center for Spatial Omics, St. Jude Children's Research Hospital, Memphis, TN, USA.; Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA., Wani A; Center for Spatial Omics, St. Jude Children's Research Hospital, Memphis, TN, USA.; Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA., Wise K; Adelaide Centre for Epigenetics, Adelaide, South Australia, Australia.; South Australian immunoGENomics Cancer Institute, Adelaide, South Australia, Australia.; The University of Adelaide, Adelaide, South Australia, Australia., Roach M; Adelaide Centre for Epigenetics, Adelaide, South Australia, Australia.; South Australian immunoGENomics Cancer Institute, Adelaide, South Australia, Australia.; The University of Adelaide, Adelaide, South Australia, Australia., Harvey K; Cancer Ecosystems Program, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia., Wang T; Cancer Ecosystems Program, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia.; School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales Sydney, Sydney, New South Wales, Australia., Jensen KB; Adelaide Centre for Epigenetics, Adelaide, South Australia, Australia.; South Australian immunoGENomics Cancer Institute, Adelaide, South Australia, Australia.; The University of Adelaide, Adelaide, South Australia, Australia.; Australian Genome Research Facility, Adelaide, South Australia, Australia., Morosini N; Center for Spatial Omics, St. Jude Children's Research Hospital, Memphis, TN, USA.; Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA., De Gregorio R; Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA., Alonso A; Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA.; Department of Medicine, Weill Cornell Medicine, New York, NY, USA., Houlihan SL; Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA., Schwartz RE; Department of Medicine, Weill Cornell Medicine, New York, NY, USA., Hissong E; Department of Pathology, Weill Cornell Medicine, New York, NY, USA., Snopkowski C; Single-cell Analytics Innovation Lab, Memorial Sloan Kettering Cancer Center, New York, NY, USA., Wrana JL; Lunenfeld-Tanenbaum Research Institute, Toronto, Ontario, Canada.; Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada., Ryan N; South Australian immunoGENomics Cancer Institute, Adelaide, South Australia, Australia.; Solid Tumour Program, Precision Cancer Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia., Butler LM; South Australian immunoGENomics Cancer Institute, Adelaide, South Australia, Australia., Church G; Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.; Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA., Swarbrick A; Cancer Ecosystems Program, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia.; School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales Sydney, Sydney, New South Wales, Australia., Mason CE; Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA. chm2042@med.cornell.edu.; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA. chm2042@med.cornell.edu., Martelotto LG; Adelaide Centre for Epigenetics, Adelaide, South Australia, Australia. lucianomartelotto@gmail.com.; South Australian immunoGENomics Cancer Institute, Adelaide, South Australia, Australia. lucianomartelotto@gmail.com.; The University of Adelaide, Adelaide, South Australia, Australia. lucianomartelotto@gmail.com.
Source: Nature biotechnology [Nat Biotechnol] 2026 Jul; Vol. 44 (7), pp. 1213-1225. Date of Electronic Publication: 2025 Dec 03.
Publication Type: Journal Article
Journal Info: Publisher: Nature America Publishing Country of Publication: United States NLM ID: 9604648 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1546-1696 (Electronic) Linking ISSN: 10870156 NLM ISO Abbreviation: Nat Biotechnol Subsets: MEDLINE
Database: MEDLINE Ultimate
FullText Text:
  Availability: 0
Header DbId: mdl
DbLabel: MEDLINE Ultimate
An: 41339526
AccessLevel: 2
PubType: Academic Journal
PubTypeId: academicJournal
PreciseRelevancyScore: 0
IllustrationInfo
Items – Name: Title
  Label: Title
  Group: Ti
  Data: Standardized metrics for assessment and reproducibility of imaging-based spatial transcriptomics datasets.
– Name: Author
  Label: Authors
  Group: Au
  Data: <searchLink fieldCode="AU" term="%22Plummer+JT%22">Plummer JT</searchLink>; Center for Spatial Omics, St. Jude Children's Research Hospital, Memphis, TN, USA. jasmine.plummer@stjude.org.; Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA. jasmine.plummer@stjude.org.; Department of Cellular and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA. jasmine.plummer@stjude.org.; Comprehensive Cancer Center, St. Jude Children's Research Hospital, Memphis, TN, USA. jasmine.plummer@stjude.org.<br /><searchLink fieldCode="AU" term="%22Dezem+FS%22">Dezem FS</searchLink>; Center for Spatial Omics, St. Jude Children's Research Hospital, Memphis, TN, USA.; Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA.<br /><searchLink fieldCode="AU" term="%22Cook+DP%22">Cook DP</searchLink>; Lunenfeld-Tanenbaum Research Institute, Toronto, Ontario, Canada.; Cancer Therapeutics Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada.; Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada.<br /><searchLink fieldCode="AU" term="%22Park+J%22">Park J</searchLink>; Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA.; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA.; Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.; Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA.<br /><searchLink fieldCode="AU" term="%22Zhang+L%22">Zhang L</searchLink>; Center for Spatial Omics, St. Jude Children's Research Hospital, Memphis, TN, USA.; Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA.<br /><searchLink fieldCode="AU" term="%22Liu+Y%22">Liu Y</searchLink>; Center for Spatial Omics, St. Jude Children's Research Hospital, Memphis, TN, USA.; Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA.<br /><searchLink fieldCode="AU" term="%22Marção+M%22">Marção M</searchLink>; Center for Spatial Omics, St. Jude Children's Research Hospital, Memphis, TN, USA.; Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA.<br /><searchLink fieldCode="AU" term="%22DuBose+H%22">DuBose H</searchLink>; Center for Spatial Omics, St. Jude Children's Research Hospital, Memphis, TN, USA.; Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA.<br /><searchLink fieldCode="AU" term="%22Wani+A%22">Wani A</searchLink>; Center for Spatial Omics, St. Jude Children's Research Hospital, Memphis, TN, USA.; Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA.<br /><searchLink fieldCode="AU" term="%22Wise+K%22">Wise K</searchLink>; Adelaide Centre for Epigenetics, Adelaide, South Australia, Australia.; South Australian immunoGENomics Cancer Institute, Adelaide, South Australia, Australia.; The University of Adelaide, Adelaide, South Australia, Australia.<br /><searchLink fieldCode="AU" term="%22Roach+M%22">Roach M</searchLink>; Adelaide Centre for Epigenetics, Adelaide, South Australia, Australia.; South Australian immunoGENomics Cancer Institute, Adelaide, South Australia, Australia.; The University of Adelaide, Adelaide, South Australia, Australia.<br /><searchLink fieldCode="AU" term="%22Harvey+K%22">Harvey K</searchLink>; Cancer Ecosystems Program, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia.<br /><searchLink fieldCode="AU" term="%22Wang+T%22">Wang T</searchLink>; Cancer Ecosystems Program, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia.; School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales Sydney, Sydney, New South Wales, Australia.<br /><searchLink fieldCode="AU" term="%22Jensen+KB%22">Jensen KB</searchLink>; Adelaide Centre for Epigenetics, Adelaide, South Australia, Australia.; South Australian immunoGENomics Cancer Institute, Adelaide, South Australia, Australia.; The University of Adelaide, Adelaide, South Australia, Australia.; Australian Genome Research Facility, Adelaide, South Australia, Australia.<br /><searchLink fieldCode="AU" term="%22Morosini+N%22">Morosini N</searchLink>; Center for Spatial Omics, St. Jude Children's Research Hospital, Memphis, TN, USA.; Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA.<br /><searchLink fieldCode="AU" term="%22De+Gregorio+R%22">De Gregorio R</searchLink>; Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA.<br /><searchLink fieldCode="AU" term="%22Alonso+A%22">Alonso A</searchLink>; Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA.; Department of Medicine, Weill Cornell Medicine, New York, NY, USA.<br /><searchLink fieldCode="AU" term="%22Houlihan+SL%22">Houlihan SL</searchLink>; Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA.<br /><searchLink fieldCode="AU" term="%22Schwartz+RE%22">Schwartz RE</searchLink>; Department of Medicine, Weill Cornell Medicine, New York, NY, USA.<br /><searchLink fieldCode="AU" term="%22Hissong+E%22">Hissong E</searchLink>; Department of Pathology, Weill Cornell Medicine, New York, NY, USA.<br /><searchLink fieldCode="AU" term="%22Snopkowski+C%22">Snopkowski C</searchLink>; Single-cell Analytics Innovation Lab, Memorial Sloan Kettering Cancer Center, New York, NY, USA.<br /><searchLink fieldCode="AU" term="%22Wrana+JL%22">Wrana JL</searchLink>; Lunenfeld-Tanenbaum Research Institute, Toronto, Ontario, Canada.; Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.<br /><searchLink fieldCode="AU" term="%22Ryan+N%22">Ryan N</searchLink>; South Australian immunoGENomics Cancer Institute, Adelaide, South Australia, Australia.; Solid Tumour Program, Precision Cancer Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia.<br /><searchLink fieldCode="AU" term="%22Butler+LM%22">Butler LM</searchLink>; South Australian immunoGENomics Cancer Institute, Adelaide, South Australia, Australia.<br /><searchLink fieldCode="AU" term="%22Church+G%22">Church G</searchLink>; Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.; Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA.<br /><searchLink fieldCode="AU" term="%22Swarbrick+A%22">Swarbrick A</searchLink>; Cancer Ecosystems Program, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia.; School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales Sydney, Sydney, New South Wales, Australia.<br /><searchLink fieldCode="AU" term="%22Mason+CE%22">Mason CE</searchLink>; Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA. chm2042@med.cornell.edu.; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA. chm2042@med.cornell.edu.<br /><searchLink fieldCode="AU" term="%22Martelotto+LG%22">Martelotto LG</searchLink>; Adelaide Centre for Epigenetics, Adelaide, South Australia, Australia. lucianomartelotto@gmail.com.; South Australian immunoGENomics Cancer Institute, Adelaide, South Australia, Australia. lucianomartelotto@gmail.com.; The University of Adelaide, Adelaide, South Australia, Australia. lucianomartelotto@gmail.com.
– Name: TitleSource
  Label: Source
  Group: Src
  Data: <searchLink fieldCode="JN" term="%229604648%22">Nature biotechnology</searchLink> [Nat Biotechnol] 2026 Jul; Vol. 44 (7), pp. 1213-1225. <i>Date of Electronic Publication: </i>2025 Dec 03.
– Name: TypePub
  Label: Publication Type
  Group: TypPub
  Data: Journal Article
– Name: TitleSource
  Label: Journal Info
  Group: Src
  Data: <i>Publisher: </i><searchLink fieldCode="PB" term="%22Nature+America+Publishing%22">Nature America Publishing </searchLink><i>Country of Publication: </i>United States <i>NLM ID: </i>9604648 <i>Publication Model: </i>Print-Electronic <i>Cited Medium: </i>Internet <i>ISSN: </i>1546-1696 (Electronic) <i>Linking ISSN: </i><searchLink fieldCode="IS" term="%2210870156%22">10870156 </searchLink><i>NLM ISO Abbreviation: </i>Nat Biotechnol <i>Subsets: </i>MEDLINE
PLink https://search.ebscohost.com/login.aspx?direct=true&site=eds-live&db=mdl&AN=41339526
RecordInfo BibRecord:
  BibEntity:
    Identifiers:
      – Type: doi
        Value: 10.1038/s41587-025-02811-9
    Languages:
      – Code: eng
        Text: English
    PhysicalDescription:
      Pagination:
        StartPage: 1213
    Titles:
      – TitleFull: Standardized metrics for assessment and reproducibility of imaging-based spatial transcriptomics datasets.
        Type: main
  BibRelationships:
    HasContributorRelationships:
      – PersonEntity:
          Name:
            NameFull: Plummer JT
      – PersonEntity:
          Name:
            NameFull: Dezem FS
      – PersonEntity:
          Name:
            NameFull: Cook DP
      – PersonEntity:
          Name:
            NameFull: Park J
      – PersonEntity:
          Name:
            NameFull: Zhang L
      – PersonEntity:
          Name:
            NameFull: Liu Y
      – PersonEntity:
          Name:
            NameFull: Marção M
      – PersonEntity:
          Name:
            NameFull: DuBose H
      – PersonEntity:
          Name:
            NameFull: Wani A
      – PersonEntity:
          Name:
            NameFull: Wise K
      – PersonEntity:
          Name:
            NameFull: Roach M
      – PersonEntity:
          Name:
            NameFull: Harvey K
      – PersonEntity:
          Name:
            NameFull: Wang T
      – PersonEntity:
          Name:
            NameFull: Jensen KB
      – PersonEntity:
          Name:
            NameFull: Morosini N
      – PersonEntity:
          Name:
            NameFull: De Gregorio R
      – PersonEntity:
          Name:
            NameFull: Alonso A
      – PersonEntity:
          Name:
            NameFull: Houlihan SL
      – PersonEntity:
          Name:
            NameFull: Schwartz RE
      – PersonEntity:
          Name:
            NameFull: Hissong E
      – PersonEntity:
          Name:
            NameFull: Snopkowski C
      – PersonEntity:
          Name:
            NameFull: Wrana JL
      – PersonEntity:
          Name:
            NameFull: Ryan N
      – PersonEntity:
          Name:
            NameFull: Butler LM
      – PersonEntity:
          Name:
            NameFull: Church G
      – PersonEntity:
          Name:
            NameFull: Swarbrick A
      – PersonEntity:
          Name:
            NameFull: Mason CE
      – PersonEntity:
          Name:
            NameFull: Martelotto LG
    IsPartOfRelationships:
      – BibEntity:
          Dates:
            – D: 01
              M: 07
              Text: 2026 Jul
              Type: published
              Y: 2026
          Identifiers:
            – Type: issn-electronic
              Value: 1546-1696
          Numbering:
            – Type: volume
              Value: 44
            – Type: issue
              Value: 7
          Titles:
            – TitleFull: Nature biotechnology
              Type: main
ResultId 1