{"id":"W4401967503","doi":"10.1101/2024.08.27.609868","title":"Whole-embryo Spatial Transcriptomics at Subcellular Resolution from Gastrulation to Organogenesis","year":2024,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Single-cell and spatial transcriptomics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":11,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Toronto","funders":"","keywords":"Gastrulation; Organogenesis; Embryo; Transcriptome; Cell biology; Computer science; Biology; Computational biology; Embryogenesis; Genetics; Gene expression; Gene","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":[0.0003385285,0.0007801245,0.0005715802,0.0002319864,0.0002116672,0.0002352068,0.000615241,0.001148536,0.00005409451],"category_scores_gemma":[0.00008492484,0.0009078398,0.0003614129,0.0003112516,0.00009910676,0.000008783121,0.0006661212,0.0005602826,0.0002315174],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0003588567,"about_ca_system_score_gemma":0.0004757073,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0005271925,"about_ca_topic_score_gemma":0.000156566,"domain_scores_codex":[0.9962805,0.0001556232,0.0007034393,0.001762937,0.0004335532,0.000663932],"domain_scores_gemma":[0.997602,0.00001705403,0.0002115621,0.001426437,0.0003346875,0.0004081909],"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":[0.0002979311,0.0001004563,0.003037472,0.0001959334,0.0001986346,0.00002819965,0.00001998766,0.0007230178,0.9943722,0.00002371335,0.0009937886,0.000008642517],"study_design_scores_gemma":[0.0005700442,0.0001381144,0.02481815,0.0002396956,0.0003034944,4.037523e-8,0.000002193235,0.001548011,0.9537326,0.00000603024,0.01764794,0.0009937122],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9702751,0.002748211,0.02075196,0.0003523926,0.003185847,0.0007836106,0.001672315,0.0002210642,0.000009492957],"genre_scores_gemma":[0.9927555,0.0002522058,0.00419751,0.0003288643,0.001950837,0.0001178949,0.00005083344,0.0002951886,0.00005116302],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.04063965,"threshold_uncertainty_score":0.9993372,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01111778032612496,"score_gpt":0.2009630979926796,"score_spread":0.1898453176665546,"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."}}