Seeing the Forest and Its Trees Together: Implementing 3D Light Microscopy Pipelines for Cell Type Mapping in the Mouse Brain

Abstract

The brain is composed of diverse neuronal and non-neuronal cell types with complex regional connectivity patterns that create the anatomical infrastructure underlying cognition. Remarkable advances in neuroscience techniques enable labeling and imaging of these individual cell types and their interactions throughout intact mammalian brains at a cellular resolution allowing neuroscientists to examine microscopic details in macroscopic brain circuits. Nevertheless, implementing these tools is fraught with many technical and analytical challenges with a need for high-level data analysis. Here we review key technical considerations for implementing a brain mapping pipeline using the mouse brain as a primary model system. Specifically, we provide practical details for choosing methods including cell type specific labeling, sample preparation (e.g., tissue clearing), microscopy modalities, image processing, and data analysis (e.g., image registration to standard atlases). We also highlight the need to develop better 3D atlases with standardized anatomical labels and nomenclature across species and developmental time points to extend the mapping to other species including humans and to facilitate data sharing, confederation, and integrative analysis. In summary, this review provides key elements and currently available resources to consider while developing and implementing high-resolution mapping methods.

Advancements in the Quest to Map, Monitor, and Manipulate Neural Circuitry

“…By removing lipids in whole-brain tissue while leaving proteins and nucleic acids intact, tissue effectively becomes transparent, allowing one to image three-dimensional brain architecture or brain-wide neural projections with minimal light scattering. When used in combination with light-sheet microscopy or similar imaging platforms, intricate circuit networks may be visualized in three dimensions, across the entire brain (Newmaster et al, 2021).…”

Building bridges: simultaneous multimodal neuroimaging approaches for exploring the organization of brain networks

“…[45][46][47] A major focus of neuroscience has been the classification of single neurons by their molecular, anatomical, and functional properties, such as tuning of activity to behavior or sensory inputs. [48][49][50] This combined imaging approach now allows us to further characterize cells by their connectivity to both local and large-scale networks.…”

Digital Brain Maps and Virtual Neuroscience: An Emerging Role for Light-Sheet Fluorescence Microscopy in Drug Development

“…Due to its immense complexity, the morphology of the mouse brain is very conserved and the brains from two individual mice are almost identical. For this reason, it is possible to align individual mouse brains to a brain template of a reference atlas ( Renier et al, 2016 ; Murakami et al, 2018 ; Salinas et al, 2018 ; Wang et al, 2020 ; Perens et al, 2021a ; Newmaster et al, 2022 ), and at the same time extract spatial information, volumetric information, number of detected cells and fluorescence intensities using anatomical segmentations. However, one very important feature resulting from the alignment of raw data to a reference atlas is the three-dimensional digital map which encompasses all the spatial information relating to the distribution of the measured fluorescence signal.…”