Fig. 4: DeepColony in action on three sample clinical plates (P1, P2 and P3).
From: Hierarchical AI enables global interpretation of culture plates in the era of digital microbiology
a Original P1; b P1 segmentation mask (level 0); c P1 enumeration map (level 0); d Good colonies on P1 (level 1); e, g, k level 2 Top-1 ID on P1, P2 and P3 respectively, where different colours are used to mark single good colonies according to the identified species as listed in the plate legends (Streptococcus agalactiae and Pseudomonas aeruginosa for Plate1 in e, Klebsiella oxytoca, Citrobacter freundii, Pseudomonas aeruginosa or Klebsiella pneumoniae for P2 in g, eleven different species for P3 in k).; f, h, l level 3 contextual Top-1 ID on P1, P2 and P3 (Streptococcus agalactiae for Plate1 in f, Klebsiella oxytoca and Pseudomonas aeruginosa for P2 in h, eight species for P3 in l); i 3D representation of the first 3 entries (Top-1 ID, Top-2 ID and Top-3 ID) of the level 2 pIDv for each good colony of P2 (different colours indicate different species) and anticipated indication of following grouping I and II; j the same 3D representation for grouped species operated in level 3; m, n, o Plate-level interpretation generated at level 4 by the combination of species-related information (ID and quantitation) and CML rules (for this case represented in the block diagram of Fig. 5a). Source data for i and j are provided as a Source Data file.
