Abstract

The connectivity among neurons holds the key to understanding brain function. Mapping neural connectivity in brain circuits requires imaging techniques with high spatial resolution to facilitate neuron tracing and high molecular specificity to mark different cellular and molecular populations. Here, we tested a three-dimensional (3D), multicolor super-resolution imaging method, stochastic optical reconstruction microscopy (STORM), for tracing neural connectivity using cultured hippocampal neurons obtained from wild-type neonatal rat embryos as a model system. Using a membrane specific labeling approach that improves labeling density compared to cytoplasmic labeling, we imaged neural processes at 44 nm 2D and 116 nm 3D resolution as determined by considering both the localization precision of the fluorescent probes and the Nyquist criterion based on label density. Comparison with confocal images showed that, with the currently achieved resolution, we could distinguish and trace substantially more neuronal processes in the super-resolution images. The accuracy of tracing was further improved by using multicolor super-resolution imaging. The resolution obtained here was largely limited by the label density and not by the localization precision of the fluorescent probes. Therefore, higher image resolution, and thus higher tracing accuracy, can in principle be achieved by further improving the label density.

Highlights

  • Mapping neural connectivity in the brain is a challenging task [1,2,3]

  • Methods to Improve Label Density To trace neurons with high fidelity, the geometrical arrangement of neural processes must be imaged with high resolution

  • This effect can be quantified by the Nyquist sampling theorem, which states that the obtained resolution is equal to twice the average distance between neighboring labels

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Summary

Introduction

Mapping neural connectivity in the brain is a challenging task [1,2,3]. One problem is size: connectivity mapping requires tracing numerous, densely packed axons and dendrites over relatively long distances, while the finest processes can be as small as ,50 nm. The combination of the high density and the small size of neural processes requires nanometer-scale resolution to disambiguate the closely packed fine processes. Mapping a neural circuit requires an approach that can provide molecular specificity. Electron microscopy (EM) is commonly used for studying synaptic level details of circuits due to its intrinsically high resolution [4,5,6,7]. Imaging molecular content at high density with EM is challenging due to the low labeling efficiency of immunogold [8]. Multicolor coding of different populations of cells, which could help neuron tracing and segmentation, is more difficult with EM

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