{"id":"W4411759154","doi":"10.1101/2025.06.25.661424","title":"PatternExtract: A facile, scalable pipeline for point pattern generation from spatial imaging data","year":2025,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"3D Modeling in Geospatial Applications","field":"Engineering","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"BC Cancer Agency","funders":"","keywords":"Scalability; Pipeline (software); Computer science; Point (geometry); Database; Geometry; Operating system; Mathematics","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":[],"consensus_categories":[],"category_scores_codex":[0.0009353978,0.001504006,0.0008964963,0.001704134,0.0005714829,0.002194721,0.001833968,0.0008361724,0.01837717],"category_scores_gemma":[0.003452578,0.00124459,0.001291471,0.001183091,0.0004430987,0.001121798,0.002349362,0.00145484,0.01336187],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000500097,"about_ca_system_score_gemma":0.001309418,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002321304,"about_ca_topic_score_gemma":0.003970193,"domain_scores_codex":[0.999341,0.00005577882,0.00004529737,0.0001769966,0.0003235287,0.00005742114],"domain_scores_gemma":[0.9991313,0.0002774914,0.00007296225,0.000278249,0.0001828647,0.00005714428],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"design_other","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.0005284601,0.0001373374,0.004487655,0.0007430198,0.0002723719,0.0005355391,0.0004058424,0.01475318,0.1730434,0.007240663,0.1471666,0.650686],"study_design_scores_gemma":[0.0002151387,0.0001637945,0.01099833,0.0001069228,0.0001103339,0.001704558,0.0002639503,0.4569559,0.3019417,0.0352879,0.1919981,0.0002532942],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.005374086,0.000156302,0.9073343,0.0001925327,0.0000615739,0.0001426336,0.004664594,0.08062101,0.001452861],"genre_scores_gemma":[0.04952949,0.0003254372,0.9136763,0.0002694612,0.00004867639,0.0006882613,0.01629977,0.01433967,0.004822892],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.01837717,"threshold_uncertainty_score":0.06147772,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02500645118581055,"score_gpt":0.2354019817470156,"score_spread":0.2103955305612051,"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."}}