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

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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
Description
ISSN:1546-1696
DOI:10.1038/s41587-025-02811-9