Extended Data Fig. 1: Compartment classification pipeline.

a) Description of the compartment classification pipeline. b–d) Pipeline applied to an example layer 3 pyramidal cell. b) Apical probability per vertex. c) Branch-level apical classification. d) Final organization into four dendritic compartments based on apical classification and distance rules. e) Quantification of quality of apical branch classification based on leave-one-out classification with a training set based on 50 randomly selected cells and 23 cells chosen to improve difficult classifications. Each dot is a branch of a test pyramidal cell, colored red if apical and blue if not apical. X-axis is the net log-odds of the branch being apical (capped at ±200) and the y-axis is the relative apical quality based on a soft-max operation (see Methods for details). Branches in the upper right quadrant were classified as apical. The method was able to correctly classify at least one apical branch for all cells, and “false positives” were often associated with borderline cases. f) Distribution of synaptic inputs onto excitatory neurons with depth by dendritic compartment. Values are based on counting synapses in bins at a given depth, but at any location laterally.