Automated identification of benign hematopoietic subsets highlights B-cell maturation stages, which are distinct from leukemic cells. (A) Performance of a DNN cell classifier included in our pipeline, shown as F1 scores for each cell class. (B) Automated classification of events from MRD-negative cases (merged pipeline exports), showing accurately depicted B-cell maturation stages (arrows), and DNN-classes matching clustered events on an unsupervised UMAP projection of all cases. (C) Merged leukemic events from MRD-positive exports (red), compared with MRD-negative exports (black); showing extensive overlap on 2-dimensional plots, high immunophenotypic variability of MRD, and clear MRD segregation from normal events on a UMAP projection. FSC-A, forward scatter amplitude; PDCs, plasmacytoid dendritic cells; SSC-A, side scatter amplitude.