{"id":"W4317242699","doi":"10.1101/2023.01.15.524135","title":"AnnoSpat annotates cell types and quantifies cellular arrangements from spatial proteomics","year":2023,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Single-cell and spatial transcriptomics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"Princess Margaret Cancer Centre; University Health Network","funders":"Canada Research Chairs; Human Islet Research Network","keywords":"Cell type; Mass cytometry; Cell; Computational biology; Proteomics; Biology; Computer science; Cell biology; Biochemistry; Gene; Phenotype","routes":{"ca_aff":true,"ca_fund":true,"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":[],"consensus_categories":[],"category_scores_codex":[0.0007496661,0.0009427813,0.0008280527,0.002304494,0.0006587047,0.001471898,0.0007380599,0.0007328423,0.003309795],"category_scores_gemma":[0.001229372,0.000469886,0.000755149,0.001556907,0.0005027922,0.0009308073,0.001211395,0.0008150247,0.001892259],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0005013102,"about_ca_system_score_gemma":0.0006186828,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002059207,"about_ca_topic_score_gemma":0.004041786,"domain_scores_codex":[0.9994018,0.0000496894,0.00004063316,0.0002465651,0.0002068649,0.00005446752],"domain_scores_gemma":[0.9990942,0.0002792718,0.0001149151,0.0002398113,0.0002150101,0.00005681103],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.0007962033,0.00008744436,0.02494037,0.0007689261,0.0001416274,0.0002451526,0.0002634562,0.009550618,0.9032865,0.002151947,0.008254025,0.04951388],"study_design_scores_gemma":[0.00006037962,0.0001795453,0.07939928,0.00006409729,0.0001088637,0.0008756948,0.0003106943,0.1690591,0.6993014,0.006260932,0.0442425,0.0001375546],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"methods","genre_scores_codex":[0.5662475,0.0009022261,0.3111999,0.0002623009,0.0001667439,0.0001912585,0.07965703,0.03552964,0.005843471],"genre_scores_gemma":[0.5306027,0.0006489743,0.34682,0.0002123186,0.00005233996,0.0005344432,0.1088629,0.004594081,0.007672396],"genre_candidate":"methods","genre_consensus":null,"teacher_disagreement_score":0.003309795,"threshold_uncertainty_score":0.01107234,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01720325405328663,"score_gpt":0.2061793160946192,"score_spread":0.1889760620413326,"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."}}