{"id":"W4404259354","doi":"10.1016/j.xpro.2024.103420","title":"Protocol for Xenium spatial transcriptomics studies using fixed frozen mouse brain sections","year":2024,"lang":"en","type":"article","venue":"STAR Protocols","topic":"Single-cell and spatial transcriptomics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":16,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"National Eye Institute; National Institute of Mental Health; National Institute on Aging; National Institutes of Health; National Heart, Lung, and Blood Institute; University of Arizona; Arizona Biomedical Research Commission; Institut de recherche en santé mentale","keywords":"Protocol (science); Computer science; Computational biology; Biology; Medicine; Pathology","routes":{"ca_aff":false,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":true},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.002169701,0.002664876,0.001406263,0.003845111,0.003518393,0.001460538,0.003933794,0.00174317,0.07236819],"category_scores_gemma":[0.001552114,0.00296422,0.001652234,0.002380301,0.001498886,0.001208408,0.001245601,0.00632983,0.03900744],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.001380319,"about_ca_system_score_gemma":0.003433183,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.003497264,"about_ca_topic_score_gemma":0.01578938,"domain_scores_codex":[0.9987437,0.0002239689,0.0001404185,0.0003031131,0.0004012396,0.0001876828],"domain_scores_gemma":[0.9985088,0.0003221719,0.0001071137,0.0004886206,0.0003921791,0.0001810687],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"not_applicable","study_design_scores_codex":[0.001021881,0.0003048596,0.0006176142,0.002687096,0.000181351,0.0008797831,0.000548942,0.001020937,0.8897494,0.01363032,0.0656802,0.02367761],"study_design_scores_gemma":[0.0005375287,0.0006230778,0.005332734,0.0006610694,0.0002534019,0.003213234,0.0002044573,0.003425484,0.3599215,0.0078996,0.617686,0.0002418869],"study_design_candidate":"not_applicable","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"protocol","genre_scores_codex":[0.02568711,0.006247724,0.8344278,0.001723823,0.002251901,0.0150153,0.05600956,0.01540776,0.04322903],"genre_scores_gemma":[0.02617839,0.006735913,0.7268068,0.001557485,0.00035487,0.07434809,0.0744829,0.004217042,0.08531848],"genre_candidate":"protocol","genre_consensus":null,"teacher_disagreement_score":0.07236819,"threshold_uncertainty_score":0.2420957,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.1262585469445501,"score_gpt":0.4148717911617265,"score_spread":0.2886132442171763,"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."}}