{"id":"W4410617217","doi":"10.3389/fpls.2025.1513953","title":"DeepD&amp;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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0004272768,0.000124475,0.0001366561,0.0002197312,0.0001707607,0.0001163722,0.0002661723,0.00009423216,0.000001313446],"category_scores_gemma":[0.0001103404,0.0001286174,0.00002491916,0.0003964789,0.000198472,0.00002775039,0.0001295654,0.00007114647,6.520369e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00004949052,"about_ca_system_score_gemma":0.00009591262,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00003001116,"about_ca_topic_score_gemma":0.0002487337,"domain_scores_codex":[0.9989269,0.0000195328,0.0001888277,0.0004771459,0.0001119466,0.0002756398],"domain_scores_gemma":[0.9994845,0.000009419246,0.00006969462,0.0002759817,0.0001162316,0.00004410838],"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":[0.00005977263,0.00004858688,0.006688773,0.00003130829,0.000005068315,0.000001213437,0.00003741785,0.0001653946,0.9853135,0.000001119444,0.006006637,0.001641179],"study_design_scores_gemma":[0.0002925418,0.000137556,0.0006780755,0.00002069557,0.00002031348,0.000006259359,0.00005708378,0.0647152,0.9076898,0.00002463066,0.02617233,0.0001855195],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.7053828,0.0002648907,0.2931692,0.00001588996,0.00025759,0.0002231492,0.000009953937,0.00008214841,0.0005943926],"genre_scores_gemma":[0.9542401,0.00008793519,0.04462808,0.0002859554,0.00003237078,0.00001769496,0.00005803533,0.00001107261,0.0006387149],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.2488574,"threshold_uncertainty_score":0.5244863,"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."}}