Computational processing of neural recordings from calcium imaging data

A Single Silicon Nanowire-Based Ratiometric Biosensor for Ca2+ at Various Locations in a Neuron

Ionic calcium (Ca²⁺) is an important second messenger in cells, particularly in the neuron. A deficiency or excess of Ca²⁺ would lead to neuronal apoptosis and further injury to the brain. For accurate analysis of intracellular Ca²⁺, a single silicon nanowire (SiNW)-based ratiometric biosensor was constructed by simultaneously anchoring Ru(bpy)₂(mcbpy-O-Su-ester)(PF₆)₂, as a reference molecule, and Fluo-3, as a response molecule, onto the surface of a single SiNW. The SiNW-based biosensor exhibits high sensitivity and favorable selectivity for detecting Ca²⁺. With the assistance of a micromanipulator and laser scanning confocal microscope, two single SiNW sensors were placed in the body and the neurites of an individual neuron to detect Ca²⁺. The difference between the concentrations of Ca²⁺ in the body and neurites was identified. The results from the present study provide new insights into Ca²⁺ in neurons at a high spatial resolution, and the strategy used in this study provides a new opportunity to investigate cellular metabolism by combining the advantages of a single-cell detection technique and physiology.

Investigating learning-related neural circuitry with chronic in vivo optical imaging

Fundamental aspects of brain function, including development, plasticity, learning, and memory, can take place over time scales of days to years. Chronic in vivo imaging of neural activity with cellular resolution is a powerful method for tracking the long-term activity of neural circuits. We review recent advances in our understanding of neural circuit function from diverse brain regions that have been enabled by chronic in vivo cellular imaging. Insight into the neural basis of learning and decision-making, in particular, benefit from the ability to acquire longitudinal data from genetically identified neuronal populations, deep brain areas, and subcellular structures. We propose that combining chronic imaging with further experimental and computational innovations will advance our understanding of the neural circuit mechanisms of brain function.

Interpreting in vivo calcium signals from neuronal cell bodies, axons, and dendrites: a review

Calcium imaging is emerging as a popular technique in neuroscience. A major reason is that intracellular calcium transients are reflections of electrical events in neurons. For example, calcium influx in the soma and axonal boutons accompanies spiking activity, whereas elevations in dendrites and dendritic spines are associated with synaptic inputs and local regenerative events. However, calcium transients have complex spatiotemporal dynamics, and since most optical methods visualize only one of the somatic, axonal, and dendritic compartments, a straightforward inference of the underlying electrical event is typically challenging. We highlight experiments that have directly calibrated in vivo calcium signals recorded using fluorescent indicators against electrophysiological events. We address commonly asked questions such as: Can calcium imaging be used to characterize neurons with high firing rates? Can the fluorescent signal report a decrease in spiking activity? What is the evidence that calcium transients in subcellular compartments correspond to distinct presynaptic axonal and postsynaptic dendritic events? By reviewing the empirical evidence and limitations, we suggest that, despite some caveats, calcium imaging is a versatile method to characterize a variety of neuronal events in vivo.

A roadmap to integrate astrocytes into Systems Neuroscience

Systems neuroscience is still mainly a neuronal field, despite the plethora of evidence supporting the fact that astrocytes modulate local neural circuits, networks, and complex behaviors. In this article, we sought to identify which types of studies are necessary to establish whether astrocytes, beyond their well-documented homeostatic and metabolic functions, perform computations implementing mathematical algorithms that sub-serve coding and higher-brain functions. First, we reviewed Systems-like studies that include astrocytes in order to identify computational operations that these cells may perform, using Ca2+ transients as their encoding language. The analysis suggests that astrocytes may carry out canonical computations in a time scale of subseconds to seconds in sensory processing, neuromodulation, brain state, memory formation, fear, and complex homeostatic reflexes. Next, we propose a list of actions to gain insight into the outstanding question of which variables are encoded by such computations. The application of statistical analyses based on machine learning, such as dimensionality reduction and decoding in the context of complex behaviors, combined with connectomics of astrocyte-neuronal circuits, is, in our view, fundamental undertakings. We also discuss technical and analytical approaches to study neuronal and astrocytic populations simultaneously, and the inclusion of astrocytes in advanced modeling of neural circuits, as well as in theories currently under exploration such as predictive coding and energy-efficient coding. Clarifying the relationship between astrocytic Ca2+ and brain coding may represent a leap forward toward novel approaches in the study of astrocytes in health and disease.

Fluorescent Biosensors for Neurotransmission and Neuromodulation: Engineering and Applications

Understanding how neuronal activity patterns in the brain correlate with complex behavior is one of the primary goals of modern neuroscience. Chemical transmission is the major way of communication between neurons, however, traditional methods of detection of neurotransmitter and neuromodulator transients in mammalian brain lack spatiotemporal precision. Modern fluorescent biosensors for neurotransmitters and neuromodulators allow monitoring chemical transmission in vivo with millisecond precision and single cell resolution. Changes in the fluorescent biosensor brightness occur upon neurotransmitter binding and can be detected using fiber photometry, stationary microscopy and miniaturized head-mounted microscopes. Biosensors can be expressed in the animal brain using adeno-associated viral vectors, and their cell-specific expression can be achieved with Cre-recombinase expressing animals. Although initially fluorescent biosensors for chemical transmission were represented by glutamate biosensors, nowadays biosensors for GABA, acetylcholine, glycine, norepinephrine, and dopamine are available as well. In this review, we overview functioning principles of existing intensiometric and ratiometric biosensors and provide brief insight into the variety of neurotransmitter-binding proteins from bacteria, plants, and eukaryotes including G-protein coupled receptors, which may serve as neurotransmitter-binding scaffolds. We next describe a workflow for development of neurotransmitter and neuromodulator biosensors. We then discuss advanced setups for functional imaging of neurotransmitter transients in the brain of awake freely moving animals. We conclude by providing application examples of biosensors for the studies of complex behavior with the single-neuron precision.

Imaging spinal cord activity in behaving animals

The spinal cord is the primary neurological link between the brain and peripheral organs. How important it is in everyday life is apparent in patients with spinal cord injury or motoneuron disease, who have dramatically reduced musculoskeletal control or capacity to sense their environment. Despite its crucial role in sensory and motor processing little is known about the cellular and molecular signaling events that underlie spinal cord function under naturalistic conditions. While genetic, electrophysiological, pharmacological, and circuit tracing studies have revealed important roles for different molecularly defined neurons, these approaches insufficiently describe the moment-to-moment neuronal and non-neuronal activity patterns that underlie sensory-guided motor behaviors in health and disease. The recent development of imaging methods for real-time interrogation of cellular activity in the spinal cord of behaving mice has removed longstanding technical obstacles to spinal cord research and allowed new insight into how different cell types encode sensory information from mechanoreceptors and nociceptors in the skin. Here, we review the current state-of-the-art in interrogating cellular and microcircuit function in the spinal cord of behaving mammals and discuss current opportunities and technological challenges.