Brain-wide single neuron reconstruction reveals morphological diversity in molecularly defined striatal, thalamic, cortical and claustral neuron types
Authors: Peng Hanchuan , Xie Peng , Liu Lijuan , Kuang Xiuli , Wang Yimin , Qu Lei , Gong Hui , Jiang Shengdian , Li Anan , Ruan Zongcai , Ding Liya , Chen Chao , Chen Mengya , Daigle Tanya , Ding Zhangcan , Duan Yanjun , Feiner Aaron , He Ping , Hill Chris , Hirokawa Karla , Hong Guodong , Huang Lei , Kebede Sara , Kuo Hsien-Chi , Larsen Rachael , Lesnar Phil , Li Longfei , Li Qi , Li Xiangning , Li Yaoyao , Li Yuanyuan , Liu An , Lu Donghuan , Mok Stephanie , Ng Lydia , Nguyen Thuc , Ouyang Qiang , Pan Jintao , Shen Elise , Song Yuanyuan , Sunkin Susan , Tasic Bosiljka , Veldman Matthew , Wakeman Wayne , Wan Wan , Wang Peng , Wang Quanxin , Wang Tao , Wang Yaping , Xiong Feng , Xiong Wei , Xu Wenjie , Yao Zizhen , Ye Min , Yin Lulu , Yu Yang , Yuan Jia , Yuan Jing , Yun Zhixi , Zeng Shaoqun , Zhang Shichen , Zhao Sujun , Zhao Zijun , Zhou Zhi , Huang Z. Josh , Esposito Luke , Hawrylycz Michael , Sorensen Staci , Yang Xiangdong , Zheng Yefeng , Gu Zhongze , Xie Wei , Koch Christof , Luo Qingming , Harris Julie , Wang Yun , Zeng Hongkui 
Published: October 2020

Abstract
Ever since the seminal findings of Ramon y Cajal, dendritic and axonal morphology has been recognized as a defining feature of neuronal types. Yet our knowledge concerning the diversity of neuronal morphologies, in particular distal axonal projection patterns, is extremely limited. To systematically obtain single neuron full morphology on a brain-wide scale, we established a platform with five major components: sparse labeling, whole-brain imaging, reconstruction, registration, and classification. We achieved sparse, robust and consistent fluorescent labeling of a wide range of neuronal types by combining transgenic or viral Cre delivery with novel transgenic reporter lines. We acquired high-resolution whole-brain fluorescent images from a large set of sparsely labeled brains using fluorescence micro-optical sectioning tomography (fMOST). We developed a set of software tools for efficient large-volume image data processing, registration to the Allen Mouse Brain Common Coordinate Framework (CCF), and computer-assisted morphological reconstruction. We reconstructed and analyzed the complete morphologies of 1,708 neurons from the striatum, thalamus, cortex and claustrum. Finally, we classified these cells into multiple morphological and projection types and identified a set of region-specific organizational rules of long-range axonal projections at the single cell level. Specifically, different neuron types from different regions follow highly distinct rules in convergent or divergent projection, feedforward or feedback axon termination patterns, and between-cell homogeneity or heterogeneity. Major molecularly defined classes or types of neurons have correspondingly distinct morphological and projection patterns, however, we also identify further remarkably extensive morphological and projection diversity at more fine-grained levels within the major types that cannot presently be accounted for by preexisting transcriptomic subtypes. These insights reinforce the importance of full morphological characterization of brain cell types and suggest a plethora of ways different cell types and individual neurons may contribute to the function of their respective circuits.