Miniature microscopes for manipulating and recording in vivo brain activity

Abstract

Here we describe the development and application of miniature integrated microscopes (miniscopes) paired with microendoscopes that allow for the visualization and manipulation of neural circuits in superficial and subcortical brain regions in freely behaving animals. Over the past decade the miniscope platform has expanded to include simultaneous optogenetic capabilities, electrically-tunable lenses that enable multi-plane imaging, color-corrected optics, and an integrated data acquisition platform that streamlines multimodal experiments. Miniscopes have given researchers an unprecedented ability to monitor hundreds to thousands of genetically-defined neurons from weeks to months in both healthy and diseased animal brains. Sophisticated algorithms that take advantage of constrained matrix factorization allow for background estimation and reliable cell identification, greatly improving the reliability and scalability of source extraction for large imaging datasets. Data generated from miniscopes have empowered researchers to investigate the neural circuit underpinnings of a wide array of behaviors that cannot be studied under head-fixed conditions, such as sleep, reward seeking, learning and memory, social behaviors, and feeding. Importantly, the miniscope has broadened our understanding of how neural circuits can go awry in animal models of progressive neurological disorders, such as Parkinson’s disease. Continued miniscope development, including the ability to record from multiple populations of cells simultaneously, along with continued multimodal integration of techniques such as electrophysiology, will allow for deeper understanding into the neural circuits that underlie complex and naturalistic behavior.

In vivo imaging of the GnRH pulse generator reveals a temporal order of neuronal activation and synchronization during each pulse

“…Currently, there are two main segmentation programs used for microendoscope data: PCA-ICA and constrained nonnegative matrix factorization for microendoscope imaging (CNMFe). Although CNMFe reduces the contribution of fluorescent signal from cells above and below the imaging plane when compared to PCA-ICA, it also has lower precision and identifies false positive cells ( 55 ). In our hands, we found CNMFe had poor recognition for the somatic compartment of cells and therefore opted to use PCA-ICA data for analysis of calcium traces.…”

Early Changes in Striatal Activity and Motor Kinematics in a Huntington's Disease Mouse Model

“…Costa and colleagues showed that the number of newly recruited neurons decreased over 3 days of rotarod training, whereas the number of neurons no longer activated during the task increased. 14 Future studies using techniques to visualize individual neurons, such as activity-dependent protein expression (see, eg, Cao and colleagues 16 ) or miniscope imaging, 35 could help determine whether specific neuronal ensembles in the striatum are consolidated during rotarod learning.…”

Cranial and Spinal Window Preparation for in vivo Optical Neuroimaging in Rodents and Related Experimental Techniques

“…Optical in vivo imaging using cranial and spinal windows can be compared to imaging with miniaturized microscopes (miniscopes). In general, using the cranial and spinal window provides more expandability to combine with other techniques and a larger optical FOV [ 128 , 129 ]. Furthermore, multimodal imaging is easier for simultaneous acquisition of various data (neuronal activity, cerebral hemodynamics, structural imaging).…”