Brain-wide single neuron reconstruction reveals morphological diversity in molecularly defined striatal, thalamic, cortical and claustral neuron types

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.

Regional, Layer, and Cell-Type-Specific Connectivity of the Mouse Default Mode Network

“…This is perhaps not surprising, given that the ACAd has been reported to be a key integrative hub region for the mouse DMN ( Coletta et al., 2020 ), but further suggests that network features like hubs may emerge at cell type and regional levels. Whether individual neurons within the ACAd project to most of ACAd’s targets or whether the specific set of targets tested here are shared among many projection types may be better addressed by ongoing efforts to reconstruct the complete morphology of single labeled neurons ( Peng et al., 2020 ; Winnubst et al., 2019 ).…”

Genetic dissection of glutamatergic neuron subpopulations and developmental trajectories in the cerebral cortex

“…Inducibility also allows investigators to control the density of labeling and manipulating PyN subpopulations, from dense coverage to single cell analysis. Single cell analysis provides the ultimate resolution to examine the variability and/or reliability of individual neurons within driver and anatomy defined PyN subpopulations 71 , and can be better achieved by inducible driver lines 72, 73 . Furthermore, temporal control allows gene manipulations (e.g.…”

Cross-Modality Coherent Registration of Whole Mouse Brains

“…The topography of thalamic neurons was characterized previously at the neuron population level 49 . Here, we used mBrainAligner to map neurons reconstructed via our BICCN consortium effort 32 to Allen CCFv3. We identified 1268 cortical axon arbor clusters that projected to the major cortical areas (e.g., SSp-bfd/m/n for VPM neurons) and studied their correlation with soma locations (Fig.…”