{"id":"W3212706811","doi":"10.7554/elife.72129","title":"Standardizing workflows in imaging transcriptomics with the abagen toolbox","year":2021,"lang":"en","type":"article","venue":"eLife","topic":"Single-cell and spatial transcriptomics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":504,"is_retracted":false,"has_abstract":true,"ca_institutions":"McGill University; Montreal Neurological Institute and Hospital","funders":"National Institute of Biomedical Imaging and Bioengineering; National Institute of Mental Health; National Health and Medical Research Council; Natural Sciences and Engineering Research Council of Canada; National Institutes of Health","keywords":"Toolbox; Workflow; Pipeline (software); Standardization; Normalization (sociology); Software; Transcriptome; Expression (computer science)","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":[0.01364591,0.00216693,0.001475206,0.002992492,0.00182861,0.004589276,0.002973497,0.001672256,0.02082075],"category_scores_gemma":[0.03276128,0.001725256,0.002800561,0.002356782,0.001703485,0.00268369,0.003336406,0.004816808,0.01512376],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.001480851,"about_ca_system_score_gemma":0.004644967,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.003157839,"about_ca_topic_score_gemma":0.006489772,"domain_scores_codex":[0.9953749,0.001160106,0.0005546726,0.001364024,0.001240414,0.0003059071],"domain_scores_gemma":[0.9877911,0.006817616,0.0008639151,0.002798291,0.001413671,0.0003154212],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"design_other","study_design_gemma":"not_applicable","study_design_scores_codex":[0.0029921,0.0004338502,0.02305539,0.004585528,0.001970724,0.001110454,0.00344096,0.03935212,0.2677993,0.04649761,0.2255124,0.3832497],"study_design_scores_gemma":[0.0006217348,0.0004385846,0.02658629,0.0009638835,0.0005569886,0.001246099,0.0008135794,0.2085538,0.3432335,0.1174341,0.2986329,0.0009186029],"study_design_candidate":"not_applicable","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"software","genre_scores_codex":[0.007377143,0.0003861465,0.8421577,0.0004199338,0.000372857,0.0003458324,0.01301027,0.1327352,0.003195022],"genre_scores_gemma":[0.04038556,0.0005948453,0.8889807,0.0009542659,0.0001122273,0.003778056,0.01774885,0.04474105,0.002704418],"genre_candidate":"software","genre_consensus":null,"teacher_disagreement_score":0.02082075,"threshold_uncertainty_score":0.0721674,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.006088086840882922,"score_gpt":0.2055707983867058,"score_spread":0.1994827115458229,"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."}}