BRICseq Bridges Brain-wide Interregional Connectivity to Neural Activity and Gene Expression in Single Animals.

Comprehensive analysis of neuronal networks requires brain-wide measurement of connectivity, activity, and gene expression. Although high-throughput methods are available for mapping brain-wide activity and transcriptomes, comparable methods for mapping region-to-region connectivity remain slow and expensive because they require averaging across hundreds of brains. Here we describe BRICseq (brain-wide individual animal connectome sequencing), which leverages DNA barcoding and sequencing to map connectivity from single individuals in a few weeks and at low cost. Applying BRICseq to the mouse neocortex, we find that region-to-region connectivity provides a simple bridge relating transcriptome to activity: the spatial expression patterns of a few genes predict region-to-region connectivity, and connectivity predicts activity correlations. We also exploited BRICseq to map the mutant BTBR mouse brain, which lacks a corpus callosum, and recapitulated its known connectopathies. BRICseq allows individual laboratories to compare how age, sex, environment, genetics, and species affect neuronal wiring and to integrate these with functional activity and gene expression.

Inferring single-trial neural population dynamics using sequential auto-encoders.

Neuroscience is experiencing a revolution in which simultaneous recording of thousands of neurons is revealing population dynamics that are not apparent from single-neuron responses. This structure is typically extracted from data averaged across many trials, but deeper understanding requires studying phenomena detected in single trials, which is challenging due to incomplete sampling of the neural population, trial-to-trial variability, and fluctuations in action potential timing. We introduce latent factor analysis via dynamical systems, a deep learning method to infer latent dynamics from single-trial neural spiking data. When applied to a variety of macaque and human motor cortical datasets, latent factor analysis via dynamical systems accurately predicts observed behavioral variables, extracts precise firing rate estimates of neural dynamics on single trials, infers perturbations to those dynamics that correlate with behavioral choices, and combines data from non-overlapping recording sessions spanning months to improve inference of underlying dynamics.

Posterior Parietal Cortex Guides Visual Decisions in Rats.

Neurons in putative decision-making structures can reflect both sensory and decision signals, making their causal role in decisions unclear. Here, we tested whether rat posterior parietal cortex (PPC) is causal for processing visual sensory signals or instead for accumulating evidence for decision alternatives. We disrupted PPC activity optogenetically during decision making and compared effects on decisions guided by auditory versus visual evidence. Deficits were largely restricted to visual decisions. To further test for visual dominance in PPC, we evaluated electrophysiological responses after individual sensory events and observed much larger response modulation after visual stimuli than auditory stimuli. Finally, we measured trial-to-trial spike count variability during stimulus presentation and decision formation. Variability decreased sharply, suggesting that the network is stabilized by inputs, unlike what would be expected if sensory signals were locally accumulated. Our findings suggest that PPC plays a causal role in processing visual signals that are accumulated elsewhere.SIGNIFICANCE STATEMENT Defining the neural circuits that support decision making bridges a gap between our understanding of simple sensorimotor reflexes and our understanding of truly complex behavior. However, identifying brain areas that play a causal role in decision making has proved challenging. We tested the causal role of a candidate component of decision circuits, the rat posterior parietal cortex (PPC). Our interpretation of the data benefited from our use of animals trained to make decisions guided by either visual or auditory evidence. Our results suggest that PPC plays a causal role specifically in visual decision making and may support sensory aspects of the decision, such as interpreting the visual signals so that evidence for a decision can be accumulated elsewhere.

Neural population dynamics during reaching.

Most theories of motor cortex have assumed that neural activity represents movement parameters. This view derives from what is known about primary visual cortex, where neural activity represents patterns of light. Yet it is unclear how well the analogy between motor and visual cortex holds. Single-neuron responses in motor cortex are complex, and there is marked disagreement regarding which movement parameters are represented. A better analogy might be with other motor systems, where a common principle is rhythmic neural activity. Here we find that motor cortex responses during reaching contain a brief but strong oscillatory component, something quite unexpected for a non-periodic behaviour. Oscillation amplitude and phase followed naturally from the preparatory state, suggesting a mechanistic role for preparatory neural activity. These results demonstrate an unexpected yet surprisingly simple structure in the population response. This underlying structure explains many of the confusing features of individual neural responses.

Perspectives on classical controversies about the motor cortex.

Primary motor cortex has been studied for more than a century, yet a consensus on its functional contribution to movement control is still out of reach. In particular, there remains controversy as to the level of control produced by motor cortex ("low-level" movement dynamics vs. "high-level" movement kinematics) and the role of sensory feedback. In this review, we present different perspectives on the two following questions: What does activity in motor cortex reflect? and How do planned motor commands interact with incoming sensory feedback during movement? The four authors each present their independent views on how they think the primary motor cortex (M1) controls movement. At the end, we present a dialogue in which the authors synthesize their views and suggest possibilities for moving the field forward. While there is not yet a consensus on the role of M1 or sensory feedback in the control of upper limb movements, such dialogues are essential to take us closer to one.

Tensor Analysis Reveals Distinct Population Structure that Parallels the Different Computational Roles of Areas M1 and V1.

Cortical firing rates frequently display elaborate and heterogeneous temporal structure. One often wishes to compute quantitative summaries of such structure-a basic example is the frequency spectrum-and compare with model-based predictions. The advent of large-scale population recordings affords the opportunity to do so in new ways, with the hope of distinguishing between potential explanations for why responses vary with time. We introduce a method that assesses a basic but previously unexplored form of population-level structure: when data contain responses across multiple neurons, conditions, and times, they are naturally expressed as a third-order tensor. We examined tensor structure for multiple datasets from primary visual cortex (V1) and primary motor cortex (M1). All V1 datasets were 'simplest' (there were relatively few degrees of freedom) along the neuron mode, while all M1 datasets were simplest along the condition mode. These differences could not be inferred from surface-level response features. Formal considerations suggest why tensor structure might differ across modes. For idealized linear models, structure is simplest across the neuron mode when responses reflect external variables, and simplest across the condition mode when responses reflect population dynamics. This same pattern was present for existing models that seek to explain motor cortex responses. Critically, only dynamical models displayed tensor structure that agreed with the empirical M1 data. These results illustrate that tensor structure is a basic feature of the data. For M1 the tensor structure was compatible with only a subset of existing models.

The roles of monkey M1 neuron classes in movement preparation and execution.

The motor cortices exhibit substantial activity while preparing movements, yet the arm remains still during preparation. We investigated whether a subpopulation of presumed inhibitory neurons in primary motor cortex (M1) might be involved in "gating" motor output during preparation, while permitting output during movement. This hypothesis predicts a release of inhibition just before movement onset. In data from M1 of two monkeys, we did not find evidence for this hypothesis: few neurons exhibited a clear pause during movement, and these were at the tail end of a broad distribution. We then identified a subpopulation likely to be enriched for inhibitory interneurons, using their waveform shapes. We found that the firing rates of this subpopulation tended to increase during movement instead of decreasing as predicted by the M1 gating model. No clear subset that might implement an inhibitory gate was observed. Together with previous evidence against upstream inhibitory mechanisms in premotor cortex, this provides evidence against an inhibitory "gate" for motor output in cortex. Instead, it appears that some other mechanism must likely exist.

Microstimulation of human somatosensory cortex evokes task-dependent, spatially patterned responses in motor cortex.

The primary motor (M1) and somatosensory (S1) cortices play critical roles in motor control but the signaling between these structures is poorly understood. To fill this gap, we recorded - in three participants in an ongoing human clinical trial (NCT01894802) for people with paralyzed hands - the responses evoked in the hand and arm representations of M1 during intracortical microstimulation (ICMS) in the hand representation of S1. We found that ICMS of S1 activated some M1 neurons at short, fixed latencies consistent with monosynaptic activation. Additionally, most of the ICMS-evoked responses in M1 were more variable in time, suggesting indirect effects of stimulation. The spatial pattern of M1 activation varied systematically: S1 electrodes that elicited percepts in a finger preferentially activated M1 neurons excited during that finger's movement. Moreover, the indirect effects of S1 ICMS on M1 were context dependent, such that the magnitude and even sign relative to baseline varied across tasks. We tested the implications of these effects for brain-control of a virtual hand, in which ICMS conveyed tactile feedback. While ICMS-evoked activation of M1 disrupted decoder performance, this disruption was minimized using biomimetic stimulation, which emphasizes contact transients at the onset and offset of grasp, and reduces sustained stimulation.

The implications of categorical and category-free mixed selectivity on representational geometries.

The firing rates of individual neurons displaying mixed selectivity are modulated by multiple task variables. When mixed selectivity is nonlinear, it confers an advantage by generating a high-dimensional neural representation that can be flexibly decoded by linear classifiers. Although the advantages of this coding scheme are well accepted, the means of designing an experiment and analyzing the data to test for and characterize mixed selectivity remain unclear. With the growing number of large datasets collected during complex tasks, the mixed selectivity is increasingly observed and is challenging to interpret correctly. We review recent approaches for analyzing and interpreting neural datasets and clarify the theoretical implications of mixed selectivity in the variety of forms that have been reported in the literature. We also aim to provide a practical guide for determining whether a neural population has linear or nonlinear mixed selectivity and whether this mixing leads to a categorical or category-free representation.

A deep learning framework for inference of single-trial neural population dynamics from calcium imaging with subframe temporal resolution.

In many areas of the brain, neural populations act as a coordinated network whose state is tied to behavior on a millisecond timescale. Two-photon (2p) calcium imaging is a powerful tool to probe such network-scale phenomena. However, estimating the network state and dynamics from 2p measurements has proven challenging because of noise, inherent nonlinearities and limitations on temporal resolution. Here we describe Recurrent Autoencoder for Discovering Imaged Calcium Latents (RADICaL), a deep learning method to overcome these limitations at the population level. RADICaL extends methods that exploit dynamics in spiking activity for application to deconvolved calcium signals, whose statistics and temporal dynamics are quite distinct from electrophysiologically recorded spikes. It incorporates a new network training strategy that capitalizes on the timing of 2p sampling to recover network dynamics with high temporal precision. In synthetic tests, RADICaL infers the network state more accurately than previous methods, particularly for high-frequency components. In 2p recordings from sensorimotor areas in mice performing a forelimb reach task, RADICaL infers network state with close correspondence to single-trial variations in behavior and maintains high-quality inference even when neuronal populations are substantially reduced.

Roles of monkey premotor neuron classes in movement preparation and execution.

Dorsal premotor cortex (PMd) is known to be involved in the planning and execution of reaching movements. However, it is not understood how PMd plan activity-often present in the very same neurons that respond during movement-is prevented from itself producing movement. We investigated whether inhibitory interneurons might "gate" output from PMd, by maintaining high levels of inhibition during planning and reducing inhibition during execution. Recently developed methods permit distinguishing interneurons from pyramidal neurons using extracellular recordings. We extend these methods here for use with chronically implanted multi-electrode arrays. We then applied these methods to single- and multi-electrode recordings in PMd of two monkeys performing delayed-reach tasks. Responses of putative interneurons were not generally in agreement with the hypothesis that they act to gate output from the area: in particular it was not the case that interneurons tended to reduce their firing rates around the time of movement. In fact, interneurons increased their rates more than putative pyramidal neurons during both the planning and movement epochs. The two classes of neurons also differed in a number of other ways, including greater modulation across conditions for interneurons, and interneurons more frequently exhibiting increases in firing rate during movement planning and execution. These findings provide novel information about the greater responsiveness of putative PMd interneurons in motor planning and execution and suggest that we may need to consider new possibilities for how planning activity is structured such that it does not itself produce movement.

Single-trial neural dynamics are dominated by richly varied movements.

When experts are immersed in a task, do their brains prioritize task-related activity? Most efforts to understand neural activity during well-learned tasks focus on cognitive computations and task-related movements. We wondered whether task-performing animals explore a broader movement landscape and how this impacts neural activity. We characterized movements using video and other sensors and measured neural activity using widefield and two-photon imaging. Cortex-wide activity was dominated by movements, especially uninstructed movements not required for the task. Some uninstructed movements were aligned to trial events. Accounting for them revealed that neurons with similar trial-averaged activity often reflected utterly different combinations of cognitive and movement variables. Other movements occurred idiosyncratically, accounting for trial-by-trial fluctuations that are often considered 'noise'. This held true throughout task-learning and for extracellular Neuropixels recordings that included subcortical areas. Our observations argue that animals execute expert decisions while performing richly varied, uninstructed movements that profoundly shape neural activity.

Accurate Estimation of Neural Population Dynamics without Spike Sorting.

A central goal of systems neuroscience is to relate an organism's neural activity to behavior. Neural population analyses often reduce the data dimensionality to focus on relevant activity patterns. A major hurdle to data analysis is spike sorting, and this problem is growing as the number of recorded neurons increases. Here, we investigate whether spike sorting is necessary to estimate neural population dynamics. The theory of random projections suggests that we can accurately estimate the geometry of low-dimensional manifolds from a small number of linear projections of the data. We recorded data using Neuropixels probes in motor cortex of nonhuman primates and reanalyzed data from three previous studies and found that neural dynamics and scientific conclusions are quite similar using multiunit threshold crossings rather than sorted neurons. This finding unlocks existing data for new analyses and informs the design and use of new electrode arrays for laboratory and clinical use.

Publisher Correction: Development of an optogenetic toolkit for neural circuit dissection in squirrel monkeys.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Adapting Fine with a Little Help from the Null Space.

During motor adaptation, the brain must learn to produce new muscle outputs without disrupting the intricate coordination between numerous motor areas. A new paper (Perich et al., 2018) shows how adaptation can occur in a subset of neural dimensions and avoid muddling inter-area communication.

Development of an optogenetic toolkit for neural circuit dissection in squirrel monkeys.

Optogenetic tools have opened a rich experimental landscape for understanding neural function and disease. Here, we present the first validation of eight optogenetic constructs driven by recombinant adeno-associated virus (AAV) vectors and a WGA-Cre based dual injection strategy for projection targeting in a widely-used New World primate model, the common squirrel monkey Saimiri sciureus. We observed opsin expression around the local injection site and in axonal projections to downstream regions, as well as transduction to thalamic neurons, resembling expression patterns observed in macaques. Optical stimulation drove strong, reliable excitatory responses in local neural populations for two depolarizing opsins in anesthetized monkeys. Finally, we observed continued, healthy opsin expression for at least one year. These data suggest that optogenetic tools can be readily applied in squirrel monkeys, an important first step in enabling precise, targeted manipulation of neural circuits in these highly trainable, cognitively sophisticated animals. In conjunction with similar approaches in macaques and marmosets, optogenetic manipulation of neural circuits in squirrel monkeys will provide functional, comparative insights into neural circuits which subserve dextrous motor control as well as other adaptive behaviors across the primate lineage. Additionally, development of these tools in squirrel monkeys, a well-established model system for several human neurological diseases, can aid in identifying novel treatment strategies.

The Largest Response Component in the Motor Cortex Reflects Movement Timing but Not Movement Type.

Neural activity in monkey motor cortex (M1) and dorsal premotor cortex (PMd) can reflect a chosen movement well before that movement begins. The pattern of neural activity then changes profoundly just before movement onset. We considered the prediction, derived from formal considerations, that the transition from preparation to movement might be accompanied by a large overall change in the neural state that reflects when movement is made rather than which movement is made. Specifically, we examined "components" of the population response: time-varying patterns of activity from which each neuron's response is approximately composed. Amid the response complexity of individual M1 and PMd neurons, we identified robust response components that were "condition-invariant": their magnitude and time course were nearly identical regardless of reach direction or path. These condition-invariant response components occupied dimensions orthogonal to those occupied by the "tuned" response components. The largest condition-invariant component was much larger than any of the tuned components; i.e., it explained more of the structure in individual-neuron responses. This condition-invariant response component underwent a rapid change before movement onset. The timing of that change predicted most of the trial-by-trial variance in reaction time. Thus, although individual M1 and PMd neurons essentially always reflected which movement was made, the largest component of the population response reflected movement timing rather than movement type.

Reorganization between preparatory and movement population responses in motor cortex.

Neural populations can change the computation they perform on very short timescales. Although such flexibility is common, the underlying computational strategies at the population level remain unknown. To address this gap, we examined population responses in motor cortex during reach preparation and movement. We found that there exist exclusive and orthogonal population-level subspaces dedicated to preparatory and movement computations. This orthogonality yielded a reorganization in response correlations: the set of neurons with shared response properties changed completely between preparation and movement. Thus, the same neural population acts, at different times, as two separate circuits with very different properties. This finding is not predicted by existing motor cortical models, which predict overlapping preparation-related and movement-related subspaces. Despite orthogonality, responses in the preparatory subspace were lawfully related to subsequent responses in the movement subspace. These results reveal a population-level strategy for performing separate but linked computations.