Nanoscale-resolution reconstructions of the complete architectures of neurons offer the potential to revolutionize the study of neuronal circuitry in normal and diseased brains but this promise is far from realized because the larger neuroscience community cannot access the technologies that provide nanoscale reconstructions over large volumes and the computational infrastructure required to analyze them. As a result, neuroanatomy at the nanoscale is restricted to one-off studies of smaller volumes, rarely extending past small volume reconstructions in single animals (n<=1), and accessible only to labs that can afford the extraordinary time commitment, labor, and expense required to reconstruct even simple neuronal circuits. Here we propose a novel approach: rather than developing more and more sophisticated hardware for nanoscale reconstructions of the brain, we propose to develop a toolbox of accessible molecular, chemical, and computational approaches for accurate nanoscale reconstructions of large volumes of the brain targeting fluorescence microscopy and the conventional confocal microscope ? two of the most widely accessed tools in the neuroscience arsenal. By providing an accessible pipeline to reconstructing the natural shape and space between brain cells found in the living brain over wide range of experimental conditions, we will help deliver access to comprehensive nanoscale neuroanatomy to the broader neuroscience community.

Public Health Relevance

Here we propose to radically transform access to complete nanoscale reconstructions of brain architecture over large volumes. By dramatically increasing the ease with which nanoscale reconstructions can be accomplished, we will enable a new generation of large scale nanometer resolution studies of brains that will finally detail the anatomical patterns in normal and diseased brains, potentially identifying therapies for many neurological disorders.

National Institute of Health (NIH)
National Institute of Mental Health (NIMH)
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Molecular Neurogenetics Study Section (MNG)
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Freund, Michelle
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University of Michigan Ann Arbor
Anatomy/Cell Biology
Schools of Medicine
Ann Arbor
United States
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Asano, Shoh M; Gao, Ruixuan; Wassie, Asmamaw T et al. (2018) Expansion Microscopy: Protocols for Imaging Proteins and RNA in Cells and Tissues. Curr Protoc Cell Biol 80:e56
Hill, Mackenna; Rios, Estefania; Sudhakar, Shyam Kumar et al. (2018) Quantitative simulation of extracellular single unit recording from the surface of cortex. J Neural Eng 15:056007
Karagiannis, Emmanouil D; Boyden, Edward S (2018) Expansion microscopy: development and neuroscience applications. Curr Opin Neurobiol 50:56-63
Yoon, Young-Gyu; Dai, Peilun; Wohlwend, Jeremy et al. (2017) Feasibility of 3D Reconstruction of Neural Morphology Using Expansion Microscopy and Barcode-Guided Agglomeration. Front Comput Neurosci 11:97
Freifeld, Limor; Odstrcil, Iris; Förster, Dominique et al. (2017) Expansion microscopy of zebrafish for neuroscience and developmental biology studies. Proc Natl Acad Sci U S A 114:E10799-E10808
Zhao, Yongxin; Bucur, Octavian; Irshad, Humayun et al. (2017) Nanoscale imaging of clinical specimens using pathology-optimized expansion microscopy. Nat Biotechnol 35:757-764
Chang, Jae-Byum; Chen, Fei; Yoon, Young-Gyu et al. (2017) Iterative expansion microscopy. Nat Methods 14:593-599