{"id":"W3194988201","doi":"10.1093/bioinformatics/btab589","title":"PyJAMAS: open-source, multimodal segmentation and analysis of microscopy images","year":2021,"lang":"en","type":"article","venue":"Bioinformatics","topic":"Cell Image Analysis Techniques","field":"Biochemistry, Genetics and Molecular Biology","cited_by":26,"is_retracted":false,"has_abstract":true,"ca_institutions":"Ted Rogers Centre for Heart Research; Hospital for Sick Children; University of Toronto","funders":"Natural Sciences and Engineering Research Council of Canada; Canada Foundation for Innovation; Canadian Institutes of Health Research; Government of Ontario","keywords":"Python (programming language); Scripting language; Computer science; Graphical user interface; Open source; Segmentation; Software; Extensibility; Mac OS; Image segmentation; Open source software; Interface (matter); Image processing; Computer graphics (images); User interface; Artificial intelligence; Data mining; Programming language; Operating system; Image (mathematics)","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":[0.002354533,0.001906245,0.001721184,0.00244721,0.001231344,0.002997582,0.005241091,0.001249211,0.05885307],"category_scores_gemma":[0.00698467,0.001521247,0.001726578,0.001440496,0.000923911,0.003482875,0.003563733,0.003148956,0.0375746],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0007654903,"about_ca_system_score_gemma":0.002260641,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002359713,"about_ca_topic_score_gemma":0.002875018,"domain_scores_codex":[0.9986034,0.0001394757,0.00009747461,0.0004190874,0.0005760683,0.0001645307],"domain_scores_gemma":[0.9982473,0.0005041267,0.0001911923,0.000385075,0.000388644,0.0002836612],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"not_applicable","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.001527088,0.000213367,0.002414299,0.00274423,0.00051077,0.0005380402,0.0006250463,0.006746214,0.08638001,0.009485158,0.6998262,0.1889896],"study_design_scores_gemma":[0.0004456317,0.0001855888,0.008300924,0.0004950078,0.0001681756,0.001374265,0.0001548535,0.170719,0.1780741,0.03514766,0.6043747,0.0005601705],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"software","genre_gemma":"software","genre_scores_codex":[0.00488565,0.0004598456,0.327174,0.000387694,0.0003536275,0.0002880717,0.02454111,0.637195,0.004715022],"genre_scores_gemma":[0.05711214,0.0008680553,0.6524603,0.0008092261,0.000253216,0.002489141,0.07118923,0.2020558,0.012763],"genre_candidate":"software","genre_consensus":"software","teacher_disagreement_score":0.05885307,"threshold_uncertainty_score":0.1968831,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.00716577433905271,"score_gpt":0.2882043148524268,"score_spread":0.2810385405133741,"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."}}