Large-scale unsupervised discovery of excitatory morphological cell types in mouse visual cortex
Author:
Weis Marissa A., Papadopoulos SteliosORCID, Hansel LauraORCID, Lüddecke TimoORCID, Celii Brendan, Fahey Paul G.ORCID, Bae J. AlexanderORCID, Bodor Agnes L.ORCID, Brittain DerrickORCID, Buchanan JoAnnORCID, Bumbarger Daniel J.ORCID, Castro Manuel A., Collman ForrestORCID, da Costa Nuno MaçaricoORCID, Dorkenwald SvenORCID, Elabbady LeilaORCID, Halageri AkhileshORCID, Jia Zhen, Jordan Chris, Kapner Dan, Kemnitz NicoORCID, Kinn SamORCID, Lee KisukORCID, Li Kai, Lu RanORCID, Macrina ThomasORCID, Mahalingam GayathriORCID, Mitchell EricORCID, Mondal Shanka SubhraORCID, Mu ShangORCID, Nehoran BarakORCID, Popovych SergiyORCID, Reid R. ClayORCID, Schneider-Mizell Casey M.ORCID, Seung H. SebastianORCID, Silversmith WilliamORCID, Takeno MarcORCID, Torres RusselORCID, Turner Nicholas L.ORCID, Wong William, Wu JingpengORCID, Yin Wenjing, Yu Szi-chiehORCID, Reimer JacobORCID, Tolias Andreas S.ORCID, Ecker Alexander S.ORCID
Abstract
AbstractNeurons 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.
Publisher
Cold Spring Harbor Laboratory
Cited by
2 articles.
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