PT  - JOURNAL ARTICLE
AU  - Marissa A. Weis
AU  - Stelios Papadopoulos
AU  - Laura Hansel
AU  - Timo Lüddecke
AU  - Brendan Celii
AU  - Paul G. Fahey
AU  - J. Alexander Bae
AU  - Agnes L. Bodor
AU  - Derrick Brittain
AU  - JoAnn Buchanan
AU  - Daniel J. Bumbarger
AU  - Manuel A. Castro
AU  - Erick Cobos
AU  - Forrest Collman
AU  - Nuno Maçarico da Costa
AU  - Sven Dorkenwald
AU  - Leila Elabbady
AU  - Emmanouil Froudarakis
AU  - Akhilesh Halageri
AU  - Zhen Jia
AU  - Chris Jordan
AU  - Dan Kapner
AU  - Nico Kemnitz
AU  - Sam Kinn
AU  - Kisuk Lee
AU  - Kai Li
AU  - Ran Lu
AU  - Thomas Macrina
AU  - Gayathri Mahalingam
AU  - Eric Mitchell
AU  - Shanka Subhra Mondal
AU  - Shang Mu
AU  - Barak Nehoran
AU  - Saumil Patel
AU  - Xaq Pitkow
AU  - Sergiy Popovych
AU  - R. Clay Reid
AU  - Casey M. Schneider-Mizell
AU  - H. Sebastian Seung
AU  - William Silversmith
AU  - Fabian H. Sinz
AU  - Marc Takeno
AU  - Russel Torres
AU  - Nicholas L. Turner
AU  - William Wong
AU  - Jingpeng Wu
AU  - Wenjing Yin
AU  - Szi-chieh Yu
AU  - Jacob Reimer
AU  - Andreas S. Tolias
AU  - Alexander S. Ecker
TI  - Large-scale unsupervised discovery of excitatory morphological cell types in mouse visual cortex
AID  - 10.1101/2022.12.22.521541
DP  - 2022 Jan 01
TA  - bioRxiv
PG  - 2022.12.22.521541
4099  - http://biorxiv.org/content/early/2022/12/22/2022.12.22.521541.short
4100  - http://biorxiv.org/content/early/2022/12/22/2022.12.22.521541.full
AB  - 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.Competing Interest StatementThe authors have declared no competing interest.