Dimensionality reduction of calcium-imaged neuronal population activity.

Calcium imaging has been widely adopted for its ability to record from large neuronal populations. To summarize the time course of neural activity, dimensionality reduction methods, which have been applied extensively to population spiking activity, may be particularly useful. However, it is unclear if the dimensionality reduction methods applied to spiking activity are appropriate for calcium imaging. We thus carried out a systematic study of design choices based on standard dimensionality reduction methods. We also developed a method to perform deconvolution and dimensionality reduction simultaneously (Calcium Imaging Linear Dynamical System, CILDS). CILDS most accurately recovered the single-trial, low-dimensional time courses from simulated calcium imaging data. CILDS also outperformed the other methods on calcium imaging recordings from larval zebrafish and mice. More broadly, this study represents a foundation for summarizing calcium imaging recordings of large neuronal populations using dimensionality reduction in diverse experimental settings.

Visual experience has opposing influences on the quality of stimulus representation in adult primary visual cortex.

Transient dark exposure, typically 7-10 days in duration, followed by light reintroduction is an emerging treatment for improving the restoration of vision in amblyopic subjects whose occlusion is removed in adulthood. Dark exposure initiates homeostatic mechanisms that together with light-induced changes in cellular signaling pathways result in the re-engagement of juvenile-like plasticity in the adult such that previously deprived inputs can gain cortical territory. It is possible that dark exposure itself degrades visual responses, and this could place constraints on the optimal duration of dark exposure treatment. To determine whether eight days of dark exposure has a lasting negative impact on responses to classic grating stimuli, neural activity was recorded before and after dark exposure in awake head-fixed mice using two-photon calcium imaging. Neural discriminability, assessed using classifiers, was transiently reduced following dark exposure; a decrease in response reliability across a broad range of spatial frequencies likely contributed to the disruption. Both discriminability and reliability recovered. Fixed classifiers were used to demonstrate that stimulus representation rebounded to the original, pre-deprivation state, thus dark exposure did not appear to have a lasting negative impact on visual processing. Unexpectedly, we found that dark exposure significantly stabilized orientation preference and signal correlation. Our results reveal that natural vision exerts a disrupting influence on the stability of stimulus preference for classic grating stimuli and, at the same time, improves neural discriminability for both low and high-spatial frequency stimuli.

Existing function in primary visual cortex is not perturbed by new skill acquisition of a non-matched sensory task.

Acquisition of new skills has the potential to disturb existing network function. To directly assess whether previously acquired cortical function is altered during learning, mice were trained in an abstract task in which selected activity patterns were rewarded using an optical brain-computer interface device coupled to primary visual cortex (V1) neurons. Excitatory neurons were longitudinally recorded using 2-photon calcium imaging. Despite significant changes in local neural activity during task performance, tuning properties and stimulus encoding assessed outside of the trained context were not perturbed. Similarly, stimulus tuning was stable in neurons that remained responsive following a different, visual discrimination training task. However, visual discrimination training increased the rate of representational drift. Our results indicate that while some forms of perceptual learning may modify the contribution of individual neurons to stimulus encoding, new skill learning is not inherently disruptive to the quality of stimulus representation in adult V1.

Development of Natural Scene Representation in Primary Visual Cortex Requires Early Postnatal Experience.

The development of the visual system is known to be shaped by early-life experience. To identify response properties that contribute to enhanced natural scene representation, we performed calcium imaging of excitatory neurons in the primary visual cortex (V1) of awake mice raised in three different conditions (standard-reared, dark-reared, and delayed-visual experience) and compared neuronal responses to natural scene features in relation to simpler grating stimuli that varied in orientation and spatial frequency. We assessed population selectivity in the V1 by using decoding methods and found that natural scene discriminability increased by 75% between the ages of 4 and 6 weeks. Both natural scene and grating discriminability were higher in standard-reared animals than in those raised in the dark. This increase in discriminability was accompanied by a reduction in the number of neurons that responded to low-spatial-frequency gratings. At the same time, there was an increase in neuronal preference for natural scenes. Light exposure restricted to a 2- to 4-week window during adulthood did not induce improvements in natural scene or in grating stimulus discriminability. Our results demonstrate that experience reduces the number of neurons needed to effectively encode grating stimuli and that early visual experience enhances natural scene discriminability by directly increasing responsiveness to natural scene features.

Feature selectivity is stable in primary visual cortex across a range of spatial frequencies.

Reliable perception of environmental signals is a critical first step to generating appropriate responses and actions in awake behaving animals. The extent to which stimulus features are stably represented at the level of individual neurons is not well understood. To address this issue, we investigated the persistence of stimulus response tuning over the course of 1-2 weeks in the primary visual cortex of awake, adult mice. Using 2-photon calcium imaging, we directly compared tuning stability to two stimulus features (orientation and spatial frequency) within the same neurons, specifically in layer 2/3 excitatory neurons. The majority of neurons that were tracked and tuned on consecutive imaging sessions maintained stable orientation and spatial frequency preferences (83% and 76% of the population, respectively) over a 2-week period. Selectivity, measured as orientation and spatial frequency bandwidth, was also stable. Taking into account all 4 parameters, we found that the proportion of stable neurons was less than two thirds (57%). Thus, a substantial fraction of neurons (43%) were unstable in at least one parameter. Furthermore, we found that instability of orientation preference was not predictive of instability of spatial frequency preference within the same neurons. Population analysis revealed that noise correlation values were stable well beyond the estimated decline in monosynaptic connectivity (~250-300 microns). Our results demonstrate that orientation preference is stable across a range of spatial frequencies and that the tuning of distinct stimulus features can be independently maintained within a single neuron.

Binocular deprivation induces both age-dependent and age-independent forms of plasticity in parvalbumin inhibitory neuron visual response properties.

Activity of cortical inhibitory interneurons is rapidly reduced in response to monocular deprivation during the critical period for ocular dominance plasticity and in response to salient events encountered during learning. In the case of primary sensory cortex, a decrease in mean evoked firing rate of parvalbumin-positive (PV) inhibitory neurons is causally linked to a reorganization of excitatory networks following sensory perturbation. Converging evidence indicates that it is deprivation, and not an imbalance between open- and closed-eye inputs, that triggers rapid plasticity in PV neurons. However, this has not been directly tested in vivo. Using two-photon guided cell-attached recording, we examined the impact of closing both eyes for 24 h on PV neuron response properties in mouse primary visual cortex. We found that binocular deprivation induces a 30% reduction in stimulus-evoked mean firing rate and that this reduction is specific to critical period-aged mice. The number of PV neurons showing detectable tuning to orientation increased after 24 h of deprivation, and this effect was also specific to critical period-aged mice. In contrast to evoked mean firing rate and orientation tuning, measurements of trial-to-trial variability revealed that stimulus-driven decreases in variability are significantly dampened by deprivation during both the critical period and the postcritical period. These data establish that open-eye inputs are not required to drive deprivation-induced weakening of PV neuron evoked activity and that other aspects of in vivo PV neuron activity are malleable throughout life. NEW & NOTEWORTHY Parvalbumin-positive (PV) neurons in sensory cortex are generally considered to be mediators of experience-dependent plasticity, and their plasticity is restricted to the critical period. However, in regions outside of sensory cortex, accumulating evidence demonstrates that PV neurons are plastic in adults, raising the possibility that aspects of PV response properties may be plastic throughout life. Here we identify a feature of in vivo PV neuron activity that remains plastic past the critical period.

Introduction to Chronobiology.

A diverse range of species, from cyanobacteria to humans, evolved endogenous biological clocks that allow for the anticipation of daily variations in light and temperature. The ability to anticipate regular environmental rhythms promotes optimal performance and survival. Herein we present a brief historical timeline of how circadian concepts and terminology have emerged since the early observation of daily leaf movement in plants made by an astronomer in the 1700s.

Nonuniform surround suppression of visual responses in mouse V1.

Complex receptive field characteristics, distributed across a population of neurons, are thought to be critical for solving perceptual inference problems that arise during motion and image segmentation. For example, in a class of neurons referred to as "end-stopped," increasing the length of stimuli outside of the bar-responsive region into the surround suppresses responsiveness. It is unknown whether these properties exist for receptive field surrounds in the mouse. We examined surround modulation in layer 2/3 neurons of the primary visual cortex in mice using two-photon calcium imaging. We found that surround suppression was significantly asymmetric in 17% of the visually responsive neurons examined. Furthermore, the magnitude of asymmetry was correlated with orientation selectivity. Our results demonstrate that neurons in mouse primary visual cortex are differentially sensitive to the addition of elements in the surround and that individual neurons can be described as being either uniformly suppressed by the surround, end-stopped, or side-stopped. NEW & NOTEWORTHY Perception of visual scenes requires active integration of both local and global features to successfully segment objects from the background. Although the underlying circuitry and development of perceptual inference is not well understood, converging evidence indicates that asymmetry and diversity in surround modulation are likely fundamental for these computations. We determined that these key features are present in the mouse. Our results support the mouse as a model to explore the neural basis and development of surround modulation as it relates to perceptual inference.

Top-Down-Mediated Facilitation in the Visual Cortex Is Gated by Subcortical Neuromodulation.

Response properties in primary sensory cortices are highly dependent on behavioral state. For example, the nucleus basalis of the forebrain plays a critical role in enhancing response properties of excitatory neurons in primary visual cortex (V1) during active exploration and learning. Given the strong reciprocal connections between hierarchically arranged cortical regions, how are increases in sensory response gain constrained to prevent runaway excitation? To explore this, we used in vivo two-photon guided cell-attached recording in conjunction with spatially restricted optogenetic photo-inhibition of higher-order visual cortex in mice. We found that the principle feedback projection to V1 originating from the lateral medial area (LM) facilitated visual responses in layer 2/3 excitatory neurons by ∼20%. This facilitation was reduced by half during basal forebrain activation due to differential response properties between LM and V1. Our results demonstrate that basal-forebrain-mediated increases in response gain are localized to V1 and are not propagated to LM and establish that subcortical modulation of visual cortex is regionally distinct.

Structural plasticity within the barrel cortex during initial phases of whisker-dependent learning.

We report learning-related structural plasticity in layer 1 branches of pyramidal neurons in the barrel cortex, a known site of sensorimotor integration. In mice learning an active, whisker-dependent object localization task, layer 2/3 neurons showed enhanced spine growth during initial skill acquisition that both preceded and predicted expert performance. Preexisting spines were stabilized and new persistent spines were formed. These findings suggest rapid changes in connectivity between motor centers and sensory cortex guide subsequent sensorimotor learning.

The many layers of specification and plasticity in the neocortex.

In this issue of Neuron, Li et al. (2013) show that transgenically eliminating thalamocortical neurotransmission disrupts the formation of barrel columns in the somatosensory cortex and cortical lamination, providing evidence for the importance of extrinsic activity-dependent factors in cortical development.

A disinhibitory microcircuit initiates critical-period plasticity in the visual cortex.

Early sensory experience instructs the maturation of neural circuitry in the cortex. This has been studied extensively in the primary visual cortex, in which loss of vision to one eye permanently degrades cortical responsiveness to that eye, a phenomenon known as ocular dominance plasticity (ODP). Cortical inhibition mediates this process, but the precise role of specific classes of inhibitory neurons in ODP is controversial. Here we report that evoked firing rates of binocular excitatory neurons in the primary visual cortex immediately drop by half when vision is restricted to one eye, but gradually return to normal over the following twenty-four hours, despite the fact that vision remains restricted to one eye. This restoration of binocular-like excitatory firing rates after monocular deprivation results from a rapid, although transient, reduction in the firing rates of fast-spiking, parvalbumin-positive (PV) interneurons, which in turn can be attributed to a decrease in local excitatory circuit input onto PV interneurons. This reduction in PV-cell-evoked responses after monocular lid suture is restricted to the critical period for ODP and appears to be necessary for subsequent shifts in excitatory ODP. Pharmacologically enhancing inhibition at the time of sight deprivation blocks ODP and, conversely, pharmacogenetic reduction of PV cell firing rates can extend the critical period for ODP. These findings define the microcircuit changes initiating competitive plasticity during critical periods of cortical development. Moreover, they show that the restoration of evoked firing rates of layer 2/3 pyramidal neurons by PV-specific disinhibition is a key step in the progression of ODP.

Fast-spiking interneurons have an initial orientation bias that is lost with vision.

We found that in mice, following eye opening, fast-spiking, parvalbumin-positive GABAergic interneurons had well-defined orientation tuning preferences and that subsequent visual experience broadened this tuning. Broad inhibitory tuning was not required for the developmental sharpening of excitatory tuning but did precede binocular matching of excitatory orientation tuning. We propose that experience-dependent broadening of inhibition is a candidate for initiating the critical period of excitatory binocular plasticity in developing visual cortex.

Response features of parvalbumin-expressing interneurons suggest precise roles for subtypes of inhibition in visual cortex.

Inhibitory interneurons in the cerebral cortex include a vast array of subtypes, varying in their molecular signatures, electrophysiological properties, and connectivity patterns. This diversity suggests that individual inhibitory classes have unique roles in cortical circuits; however, their characterization to date has been limited to broad classifications including many subtypes. We used the Cre/LoxP system, specifically labeling parvalbumin(PV)-expressing interneurons in visual cortex of PV-Cre mice with red fluorescent protein (RFP), followed by targeted loose-patch recordings and two-photon imaging of calcium responses in vivo to characterize the visual receptive field properties of these cells. Despite their relative molecular and morphological homogeneity, we find that PV+ neurons have a diversity of feature-specific visual responses that include sharp orientation and direction-selectivity, small receptive fields, and band-pass spatial frequency tuning. These results suggest that subsets of parvalbumin interneurons are components of specific cortical networks and that perisomatic inhibition contributes to the generation of precise response properties.

Maturation of GABAergic inhibition promotes strengthening of temporally coherent inputs among convergent pathways.

Spike-timing-dependent plasticity (STDP), a form of Hebbian plasticity, is inherently stabilizing. Whether and how GABAergic inhibition influences STDP is not well understood. Using a model neuron driven by converging inputs modifiable by STDP, we determined that a sufficient level of inhibition was critical to ensure that temporal coherence (correlation among presynaptic spike times) of synaptic inputs, rather than initial strength or number of inputs within a pathway, controlled postsynaptic spike timing. Inhibition exerted this effect by preferentially reducing synaptic efficacy, the ability of inputs to evoke postsynaptic action potentials, of the less coherent inputs. In visual cortical slices, inhibition potently reduced synaptic efficacy at ages during but not before the critical period of ocular dominance (OD) plasticity. Whole-cell recordings revealed that the amplitude of unitary IPSCs from parvalbumin positive (Pv+) interneurons to pyramidal neurons increased during the critical period, while the synaptic decay time-constant decreased. In addition, intrinsic properties of Pv+ interneurons matured, resulting in an increase in instantaneous firing rate. Our results suggest that maturation of inhibition in visual cortex ensures that the temporally coherent inputs (e.g. those from the open eye during monocular deprivation) control postsynaptic spike times of binocular neurons, a prerequisite for Hebbian mechanisms to induce OD plasticity.

High-resolution labeling and functional manipulation of specific neuron types in mouse brain by Cre-activated viral gene expression.

We describe a method that combines Cre-recombinase knockin mice and viral-mediated gene transfer to genetically label and functionally manipulate specific neuron types in the mouse brain. We engineered adeno-associated viruses (AAVs) that express GFP, dsRedExpress, or channelrhodopsin (ChR2) upon Cre/loxP recombination-mediated removal of a transcription-translation STOP cassette. Fluorescent labeling was sufficient to visualize neuronal structures with synaptic resolution in vivo, and ChR2 expression allowed light activation of neuronal spiking. The structural dynamics of a specific class of neocortical neuron, the parvalbumin-containing (Pv) fast-spiking GABAergic interneuron, was monitored over the course of a week. We found that although the majority of Pv axonal boutons were stable in young adults, bouton additions and subtractions on axonal shafts were readily observed at a rate of 10.10% and 9.47%, respectively, over 7 days. Our results indicate that Pv inhibitory circuits maintain the potential for structural re-wiring in post-adolescent cortex. With the generation of an increasing number of Cre knockin mice and because viral transfection can be delivered to defined brain regions at defined developmental stages, this strategy represents a general method to systematically visualize the structure and manipulate the function of different cell types in the mouse brain.

Activity-dependent PSA expression regulates inhibitory maturation and onset of critical period plasticity.

Functional maturation of GABAergic innervation in the developing visual cortex is regulated by neural activity and sensory inputs and in turn influences the critical period of ocular dominance plasticity. Here we show that polysialic acid (PSA), presented by the neural cell adhesion molecule, has a role in the maturation of GABAergic innervation and ocular dominance plasticity. Concentrations of PSA significantly decline shortly after eye opening in the adolescent mouse visual cortex; this decline is hindered by visual deprivation. The developmental and activity-dependent regulation of PSA expression is inversely correlated with the maturation of GABAergic innervation. Premature removal of PSA in visual cortex results in precocious maturation of perisomatic innervation by basket interneurons, enhanced inhibitory synaptic transmission, and earlier onset of ocular dominance plasticity. The developmental and activity-dependent decline of PSA expression therefore regulates the timing of the maturation of GABAergic inhibition and the onset of ocular dominance plasticity.

Encoding the ins and outs of circadian pacemaking.

The SCN of the mammalian hypothalamus comprises a self-sustained, biological clock that generates endogenous ca. 24-h (circadian) rhythms. Circadian rhythmicity in the SCN originates from the interaction of a defined set of "clock genes" that participate in transcription/translation feedback loops. In order for the SCN to serve as an internal clock that times an internal day corresponding to the external solar day, the intracellular molecular oscillations must be output as physiological signals and be reset by appropriate environmental inputs. Here, the authors consider the mechanisms by which the SCN circadian pacemaker encodes rhythmic output and light input. In particular, they focus on the ionic mechanisms by which SCN neurons encode clock gene output as circa-dian rhythms in spike frequency, as well as cellular and molecular mechanisms by which SCN neurons encode circadian light input through phase heterogeneity in the SCN network. The authors propose that there are 2 distinct classes of ionic mechanisms supporting spike frequency rhythms output--modulation of basal membrane potential and conductance versus modulation of spike production--whereas light input is transformed by cellular communication within the SCN network and encoded by the relative phase relationships among SCN neurons.

Experience and activity-dependent maturation of perisomatic GABAergic innervation in primary visual cortex during a postnatal critical period.

The neocortical GABAergic network consists of diverse interneuron cell types that display distinct physiological properties and target their innervations to subcellular compartments of principal neurons. Inhibition directed toward the soma and proximal dendrites is crucial in regulating the output of pyramidal neurons, but the development of perisomatic innervation is poorly understood because of the lack of specific synaptic markers. In the primary visual cortex, for example, it is unknown whether, and to what extent, the formation and maturation of perisomatic synapses are intrinsic to cortical circuits or are regulated by sensory experience. Using bacterial artificial chromosome transgenic mice that label a defined class of perisomatic synapses with green fluorescent protein, here we show that perisomatic innervation developed during a protracted postnatal period after eye opening. Maturation of perisomatic innervation was significantly retarded by visual deprivation during the third, but not the fifth, postnatal week, implicating an important role for sensory input. To examine the role of cortical intrinsic mechanisms, we developed a method to visualize perisomatic synapses from single basket interneurons in cortical organotypic cultures. Characteristic perisomatic synapses formed through a stereotyped process, involving the extension of distinct terminal branches and proliferation of perisomatic boutons. Neuronal spiking in organotypic cultures was necessary for the proliferation of boutons and the extension, but not the maintenance, of terminal branches. Together, our results suggest that although the formation of perisomatic synapses is intrinsic to the cortex, visual experience can influence the maturation and pattern of perisomatic innervation during a postnatal critical period by modulating the level of neural activity within cortical circuits.