{"id":"W4416943551","doi":"10.1038/s41587-025-02811-9","title":"Standardized metrics for assessment and reproducibility of imaging-based spatial transcriptomics datasets","year":2025,"lang":"en","type":"article","venue":"Nature Biotechnology","topic":"Single-cell and spatial transcriptomics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":17,"is_retracted":false,"has_abstract":false,"ca_institutions":"University of Toronto; Ottawa Hospital; Lunenfeld-Tanenbaum Research Institute; University of Ottawa","funders":"","keywords":"Spatial analysis; Annotation; Imputation (statistics); Data collection; Reproducibility; Data type","routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":["metaresearch"],"consensus_categories":[],"category_scores_codex":[0.04533274,0.002298556,0.002098761,0.009134342,0.001980317,0.005904536,0.003837389,0.002861848,0.002191236],"category_scores_gemma":[0.1547489,0.001043158,0.001821123,0.01019081,0.002690689,0.003462133,0.004472571,0.002319187,0.000852079],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.003327858,"about_ca_system_score_gemma":0.003556818,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00353648,"about_ca_topic_score_gemma":0.005933479,"domain_scores_codex":[0.9510826,0.0122008,0.009077829,0.008215201,0.01827743,0.001146087],"domain_scores_gemma":[0.8417419,0.07071833,0.01890307,0.03050471,0.036852,0.001279911],"domain_codex":null,"domain_gemma":"reproducibility","domain_candidate":"reproducibility","domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"theoretical_or_conceptual","study_design_scores_codex":[0.002874547,0.0009863192,0.09031634,0.006799848,0.003362099,0.0006445984,0.002969543,0.0922649,0.3776802,0.04424063,0.01733268,0.3605283],"study_design_scores_gemma":[0.0003398625,0.001222575,0.1311963,0.0008904056,0.001403616,0.001904221,0.00113427,0.3521512,0.4371996,0.03658512,0.03516371,0.0008091459],"study_design_candidate":"theoretical_or_conceptual","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.08412661,0.001563401,0.894292,0.0002018235,0.0002801302,0.001187281,0.007572152,0.007758325,0.003018341],"genre_scores_gemma":[0.2818256,0.0005833829,0.6912405,0.0002316714,0.00009883881,0.004774828,0.01734952,0.003003791,0.000891918],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.9546673,"threshold_uncertainty_score":0.2397453,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01020075081528942,"score_gpt":0.3020751388142645,"score_spread":0.2918743879989751,"validation_status":"score_only:v0-immature-baseline","note":"Baseline scores from an immature model (maturity gate not passed). Scores rank; they never assert a category."}}