Anan Li, Elise Shen, Lijuan Liu, Wan Wan, Hui Gong, Yanjun Duan, Rachel A. Dalley, Sujun Zhao, Luke Esposito, Zhixi Yun, Shaoqun Zeng, An Liu, Susan M. Sunkin, Zhi Zhou, Tanya L. Daigle, Jintao Pan, Liya Ding, Yaoyao Li, Chris Hill, Yimin Wang, Yefeng Zheng, Qingming Luo, Phil Lesnar, Karla E. Hirokawa, Zijun Zhao, Christof Koch, Qi Li, Ping He, Donghuan Lu, Staci A. Sorensen, Longfei Li, Zhongze Gu, Xiangning Li, Zhangcan Ding, Lei Qu, Jia Yuan, Hsien-Chi Kuo, Aaron Feiner, Stephanie Mok, Julie A. Harris, Jing Yuan, Yang Yu, Qiang Ouyang, Z. Josh Huang, X. William Yang, Guodong Hong, Thuc Nghi Nguyen, Rachael Larsen, Michael Hawrylycz, Wenjie Xu, Peng Wang, Chao Chen, Wei Xiong, Hongkui Zeng, Mengya Chen, Zongcai Ruan, Feng Xiong, Shichen Zhang, Lydia Ng, Min Ye, Wayne Wakeman, Peng Xie, Yaping Wang, Quanxin Wang, Yun Wang, Sara Kebede, Bosiljka Tasic, Lulu Yin, Yuanyuan Song, Tao Wang, Lei Huang, Wei Xie, Zizhen Yao, Matthew B. Veldman, Yuanyuan Li, Xiuli Kuang, Shengdian Jiang, and Hanchuan Peng
Dendritic and axonal morphology reflects the input and output of neurons and is a defining feature of neuronal types1,2, yet our knowledge of its diversity remains limited. Here, to systematically examine complete single-neuron morphologies on a brain-wide scale, we established a pipeline encompassing sparse labelling, whole-brain imaging, reconstruction, registration and analysis. We fully reconstructed 1,741 neurons from cortex, claustrum, thalamus, striatum and other brain regions in mice. We identified 11 major projection neuron types with distinct morphological features and corresponding transcriptomic identities. Extensive projectional diversity was found within each of these major types, on the basis of which some types were clustered into more refined subtypes. This diversity follows a set of generalizable principles that govern long-range axonal projections at different levels, including molecular correspondence, divergent or convergent projection, axon termination pattern, regional specificity, topography, and individual cell variability. Although clear concordance with transcriptomic profiles is evident at the level of major projection type, fine-grained morphological diversity often does not readily correlate with transcriptomic subtypes derived from unsupervised clustering, highlighting the need for single-cell cross-modality studies. Overall, our study demonstrates the crucial need for quantitative description of complete single-cell anatomy in cell-type classification, as single-cell morphological diversity reveals a plethora of ways in which different cell types and their individual members may contribute to the configuration and function of their respective circuits., Sparse labelling and whole-brain imaging are used to reconstruct and classify brain-wide complete morphologies of 1,741 individual neurons in the mouse brain, revealing a dependence on both brain region and transcriptomic profile.