Large-scale unsupervised discovery of excitatory morphological cell types in mouse visual cortex

Neurons in the neocortex exhibit astonishing morphological diversity which is critical for properly wiring neural circuits and giving neurons their functional properties. The extent to which the morphological diversity of excitatory neurons forms a continuum or is built from distinct clusters of cell types remains an open question. Here we took a data-driven approach using graph-based machine learning methods to obtain a low-dimensional morphological “bar code” describing more than 30,000 excitatory neurons in mouse visual areas V1, AL and RL that were reconstructed from a millimeter scale serial-section electron microscopy volume. We found a set of principles that captured the morphological diversity of the dendrites of excitatory neurons. First, their morphologies varied with respect to three major axes: soma depth, total apical and basal skeletal length. Second, neurons in layer 2/3 showed a strong trend of a decreasing width of their dendritic arbor and a smaller tuft with increasing cortical depth. Third, in layer 4, atufted neurons were primarily located in the primary visual cortex, while tufted neurons were more abundant in higher visual areas. Fourth, we discovered layer 4 neurons in V1 on the border to layer 5 which showed a tendency towards avoiding deeper layers with their dendrites. In summary, excitatory neurons exhibited a substantial degree of dendritic morphological variation, both within and across cortical layers, but this variation mostly formed a continuum, with only a few notable exceptions in deeper layers.