{"id":"W4387998733","doi":"10.1101/2023.10.25.562925","title":"A spatial human thymus cell atlas mapped to a continuous tissue axis","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":19,"is_retracted":false,"has_abstract":true,"ca_institutions":"Institute of Infection and Immunity","funders":"Wellcome Trust","keywords":"Biology; Thymocyte; Fate mapping; CD8; Anatomy; Computational biology; Cell biology; Progenitor cell; Immunology; Stem cell; Immune system","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":"codex-gemma-dda1882f352a","candidate_categories":["metaepi_narrow"],"consensus_categories":[],"category_scores_codex":[0.0003900545,0.0007733526,0.0007064817,0.0002297342,0.0002269313,0.0002351666,0.0009303686,0.001006772,0.00003446702],"category_scores_gemma":[0.0001223153,0.0008830823,0.0002707916,0.0002960407,0.0001135918,0.000005907494,0.0008047554,0.0006127367,0.0002855289],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001000851,"about_ca_system_score_gemma":0.0003984888,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0007483026,"about_ca_topic_score_gemma":0.0001533293,"domain_scores_codex":[0.9963934,0.0001383677,0.0006562823,0.00160812,0.0003750661,0.0008287133],"domain_scores_gemma":[0.9971943,0.00001988961,0.0002885762,0.001646267,0.0003912075,0.0004597569],"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":[0.00008677362,0.000192575,0.002648985,0.0002503048,0.0001318259,0.00007234707,0.00001786467,0.00006311815,0.9943413,0.00001543612,0.002170435,0.000009035352],"study_design_scores_gemma":[0.0007893634,0.0004083025,0.01072378,0.0001508805,0.0001015539,2.582619e-8,0.000003953567,0.00003517176,0.9336621,0.000001810618,0.05306061,0.001062415],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9874021,0.0006284328,0.00740052,0.0002012249,0.002275943,0.001201116,0.0005135442,0.0003313199,0.00004582899],"genre_scores_gemma":[0.9944229,0.0001662032,0.002157944,0.0003234823,0.002079834,0.0002740627,0.0000100615,0.0003050975,0.0002603917],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.06067917,"threshold_uncertainty_score":0.999362,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01575637776571727,"score_gpt":0.2293307415716011,"score_spread":0.2135743638058839,"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."}}