{"id":"W4410617217","doi":"10.3389/fpls.2025.1513953","title":"DeepD&Cchl: an AI tool for automated 3D single-cell chloroplast detection, counting, and cell type clustering","year":2025,"lang":"en","type":"article","venue":"Frontiers in Plant Science","topic":"Cell Image Analysis Techniques","field":"Biochemistry, Genetics and Molecular Biology","cited_by":2,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Alberta","funders":"","keywords":"Chloroplast; Cell type; Cell counting; Single-cell analysis; Cell; Plant cell; Microscopy; Biology; Computational biology; Computer science; Biophysics; Biochemistry; Physics; Optics; 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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0009559806,0.001234422,0.0008841619,0.00163406,0.0006321881,0.001937474,0.003862076,0.001644987,0.009606204],"category_scores_gemma":[0.001768486,0.001047877,0.001521273,0.0008903714,0.0006783818,0.001523882,0.002650261,0.002397698,0.003727132],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.001722256,"about_ca_system_score_gemma":0.001811489,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.004824275,"about_ca_topic_score_gemma":0.008980051,"domain_scores_codex":[0.9994687,0.00005561708,0.00003112456,0.0001413991,0.0002362436,0.00006687779],"domain_scores_gemma":[0.999377,0.0002457945,0.00006519661,0.000119996,0.0001278551,0.00006426901],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"design_other","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.0002305042,0.0001617968,0.003304533,0.00112453,0.0002922712,0.0003504172,0.0004113239,0.05953747,0.1040577,0.02327585,0.1104185,0.6968352],"study_design_scores_gemma":[0.0000504438,0.0000442357,0.001124809,0.00006422149,0.00004002874,0.0003002966,0.00006703143,0.859282,0.06655569,0.0175716,0.05479915,0.0001005188],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"empirical","genre_scores_codex":[0.003207424,0.0003156787,0.9510149,0.0001778847,0.00007534109,0.00006804495,0.001512113,0.04175606,0.001872449],"genre_scores_gemma":[0.05069938,0.0004982994,0.93459,0.0007730084,0.00004811398,0.0005104804,0.005296749,0.003944249,0.003639701],"genre_candidate":"empirical","genre_consensus":null,"teacher_disagreement_score":0.009606204,"threshold_uncertainty_score":0.03213596,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.006015708067949469,"score_gpt":0.2438390880014569,"score_spread":0.2378233799335074,"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."}}