A Guide to Emerging Technologies for Large-Scale and Whole-Brain Optical Imaging of Neuronal Activity

Abstract

The mammalian brain is a densely interconnected network that consists of millions to billions of neurons. Decoding how information is represented and processed by this neural circuitry requires the ability to capture and manipulate the dynamics of large populations at high speed and high resolution over a large area of the brain. Although the use of optical approaches by the neuroscience community has rapidly increased over the past two decades, most microscopy approaches are unable to record the activity of all neurons comprising a functional network across the mammalian brain at relevant temporal and spatial resolutions. In this review, we survey the recent development in optical technologies for Ca²⁺ imaging in this regard and provide an overview of the strengths and limitations of each modality and its potential for scalability. We provide guidance from the perspective of a biological user driven by the typical biological applications and sample conditions. We also discuss the potential for future advances and synergies that could be obtained through hybrid approaches or other modalities.

Keywords: Ca2+ imaging; functional brain network; high-speed optical neuronal recording; large-scale imaging; neural circuit dynamics; volumetric imaging.

Figure 1

Overview of numerical values for the key anatomical parameters of the nervous systems /brains of traditionally used model organisms in neuroscience. The table illustrates the order of magnitude differences in neuron numbers, synapses, and brain volumes that imaging methods need to cover. Numbers based on (White et al. 1986): C. elegans,(Naumann et al. 2010): zebrafish larvae, (Gouwens & Wilson 2009, Rein et al. 2002): drosophila,(Herculano-Houzel et al. 2006, Howarth et al.2012, Kovacevic 2004, Simpson 2009): mouse, (Braitenberg & Schüz 1998, Buzsaki & Mizuseki 2014, Herculano-Houzel et al. 2006, Martin et al. 2010, Sahin et al.2001): rat, (Buzsaki & Mizuseki 2014, Herculano-Houzelet al. 2007): marmoset.

Figure 2

Illustration of imaging modalities, categorized based on the acquisition mode (fully sequential, 1D parallel, 2D parallel and 3Dparallel) and sampling strategy (unbiased /prior-based sampling). Excitation and detection is in epi-configuration from the top if not indicated otherwise. See legend for an explanation of the used symbols.

Figure 3

Overview of the categories and key imaging properties of the available techniques for functional optical imaging, and their strengths and limitations. The modalities are categorized based on the acquisition mode(fully sequential, 1D parallel, 2D parallel and 3D parallel) and sampling strategy (unbiased/prior-based sampling). The key imaging properties, acquisition speed, scattering compatibility, suitability for awake imaging(including susceptibility to motion artifacts), photodamage, optical access, and scalability of the method, are rated with ++ (best, green), + (green), 0 (yellow), − (red), −− (worst, red). Example references for the techniques are provided.

Figure 4

Overview of excitation modalities and their corresponding PSF of different imaging method: (a) Gaussian focus, (b) under-filled Gaussian focus, (c) Isotropic focus with light sculpting using temporal focusing, (d) Bessel beam generated by an annular pattern in the back aperture, (e) V-shaped PSF.

Figure 5

Selection guide for Ca²⁺ imaging techniques for different sample conditions and biological applications. Methods are categorized regarding their requirement for scattering compatibility and suitability for awake imaging which includes the susceptibility to motion artifacts. Example references for the techniques are provided.