Jeffrey Markowitz

A carbon-fiber electrode array for long-term neural recording

OBJECTIVE Chronic neural recording in behaving animals is an essential method for studies of neural circuit function. However, stable recordings from small, densely packed neurons remains challenging, particularly over time-scales relevant for learning. APPROACH We describe an assembly method for a 16-channel electrode array consisting of carbon fibers (<5 µm diameter) individually insulated with Parylene-C and fire-sharpened. The diameter of the array is approximately 26 µm along the full extent of the implant. MAIN RESULTS Carbon fiber arrays were tested in HVC (used as a proper name), a song motor nucleus, of singing zebra finches where individual neurons discharge with temporally precise patterns. Previous reports of activity in this population of neurons have required the use of high impedance electrodes on movable microdrives. Here, the carbon fiber electrodes provided stable multi-unit recordings over time-scales of months. Spike-sorting indicated that the multi-unit signals were dominated by one, or a small number of cells. Stable firing patterns during singing confirmed the stability of these clusters over time-scales of months. In addition, from a total of 10 surgeries, 16 projection neurons were found. This cell type is characterized by sparse stereotyped firing patterns, providing unambiguous confirmation of single cell recordings. SIGNIFICANCE Carbon fiber electrode bundles may provide a scalable solution for long-term neural recordings of densely packed neurons.

How does the brain rapidly learn and reorganize view-invariant and position-invariant object representations in the inferotemporal cortex?

All primates depend for their survival on being able to rapidly learn about and recognize objects. Objects may be visually detected at multiple positions, sizes, and viewpoints. How does the brain rapidly learn and recognize objects while scanning a scene with eye movements, without causing a combinatorial explosion in the number of cells that are needed? How does the brain avoid the problem of erroneously classifying parts of different objects together at the same or different positions in a visual scene? In monkeys and humans, a key area for such invariant object category learning and recognition is the inferotemporal cortex (IT). A neural model is proposed to explain how spatial and object attention coordinate the ability of IT to learn invariant category representations of objects that are seen at multiple positions, sizes, and viewpoints. The model clarifies how interactions within a hierarchy of processing stages in the visual brain accomplish this. These stages include the retina, lateral geniculate nucleus, and cortical areas V1, V2, V4, and IT in the brains What cortical stream, as they interact with spatial attention processes within the parietal cortex of the Where cortical stream. The model builds upon the ARTSCAN model, which proposed how view-invariant object representations are generated. The positional ARTSCAN (pARTSCAN) model proposes how the following additional processes in the What cortical processing stream also enable position-invariant object representations to be learned: IT cells with persistent activity, and a combination of normalizing object category competition and a view-to-object learning law which together ensure that unambiguous views have a larger effect on object recognition than ambiguous views. The model explains how such invariant learning can be fooled when monkeys, or other primates, are presented with an object that is swapped with another object during eye movements to foveate the original object. The swapping procedure is predicted to prevent the reset of spatial attention, which would otherwise keep the representations of multiple objects from being combined by learning. Li and DiCarlo (2008) have presented neurophysiological data from monkeys showing how unsupervised natural experience in a target swapping experiment can rapidly alter object representations in IT. The model quantitatively simulates the swapping data by showing how the swapping procedure fools the spatial attention mechanism. More generally, the model provides a unifying framework, and testable predictions in both monkeys and humans, for understanding object learning data using neurophysiological methods in monkeys, and spatial attention, episodic learning, and memory retrieval data using functional imaging methods in humans.

Mesoscopic Patterns of Neural Activity Support Songbird Cortical Sequences

Time-locked sequences of neural activity can be found throughout the vertebrate forebrain in various species and behavioral contexts. From “time cells” in the hippocampus of rodents to cortical activity controlling movement, temporal sequence generation is integral to many forms of learned behavior. However, the mechanisms underlying sequence generation are not well known. Here, we describe a spatial and temporal organization of the songbird premotor cortical microcircuit that supports sparse sequences of neural activity. Multi-channel electrophysiology and calcium imaging reveal that neural activity in premotor cortex is correlated with a length scale of 100 µm. Within this length scale, basal-ganglia–projecting excitatory neurons, on average, fire at a specific phase of a local 30 Hz network rhythm. These results show that premotor cortical activity is inhomogeneous in time and space, and that a mesoscopic dynamical pattern underlies the generation of the neural sequences controlling song.

Long-range Order in Canary Song

Bird songs range in form from the simple notes of a Chipping Sparrow to the rich performance of the nightingale. Non-adjacent correlations can be found in the syntax of some birdsongs, indicating that the choice of what to sing next is determined not only by the current syllable, but also by previous syllables sung. Here we examine the song of the domesticated canary, a complex singer whose song consists of syllables, grouped into phrases that are arranged in flexible sequences. Phrases are defined by a fundamental time-scale that is independent of the underlying syllable duration. We show that the ordering of phrases is governed by long-range rules: the choice of what phrase to sing next in a given context depends on the history of the song, and for some syllables, highly specific rules produce correlations in song over timescales of up to ten seconds. The neural basis of these long-range correlations may provide insight into how complex behaviors are assembled from more elementary, stereotyped modules.

Unstable neurons underlie a stable learned behavior

Motor skills can be maintained for decades, but the biological basis of this memory persistence remains largely unknown. The zebra finch, for example, sings a highly stereotyped song that is stable for years, but it is not known whether the precise neural patterns underlying song are stable or shift from day to day. Here we demonstrate that the population of projection neurons coding for song in the premotor nucleus, HVC, change from day to day. The most dramatic shifts occur over intervals of sleep. In contrast to the transient participation of excitatory neurons, ensemble measurements dominated by inhibition persist unchanged even after damage to downstream motor nerves. These observations offer a principle of motor stability: spatiotemporal patterns of inhibition can maintain a stable scaffold for motor dynamics while the population of principal neurons that directly drive behavior shift from one day to the next.

On the road to invariant recognition: Explaining tradeoff and morph properties of cells in inferotemporal cortex using multiple-scale task-sensitive attentive learning

Visual object recognition is an essential accomplishment of advanced brains. Object recognition needs to be tolerant, or invariant, with respect to changes in object position, size, and view. In monkeys and humans, a key area for recognition is the anterior inferotemporal cortex (ITa). Recent neurophysiological data show that ITa cells with high object selectivity often have low position tolerance. We propose a neural model whose cells learn to simulate this tradeoff, as well as ITa responses to image morphs, while explaining how invariant recognition properties may arise in stages due to processes across multiple cortical areas. These processes include the cortical magnification factor, multiple receptive field sizes, and top-down attentive matching and learning properties that may be tuned by task requirements to attend to either concrete or abstract visual features with different levels of vigilance. The model predicts that data from the tradeoff and image morph tasks emerge from different levels of vigilance in the animals performing them. This result illustrates how different vigilance requirements of a task may change the course of category learning, notably the critical features that are attended and incorporated into learned category prototypes. The model outlines a path for developing an animal model of how defective vigilance control can lead to symptoms of various mental disorders, such as autism and amnesia.

Dynamic illumination of spatially restricted or large brain volumes via a single tapered optical fiber

Optogenetics promises precise spatiotemporal control of neural processes using light. However, the spatial extent of illumination within the brain is difficult to control and cannot be adjusted using standard fiber optics. We demonstrate that optical fibers with tapered tips can be used to illuminate either spatially restricted or large brain volumes. Remotely adjusting the light input angle to the fiber varies the light-emitting portion of the taper over several millimeters without movement of the implant. We use this mode to activate dorsal versus ventral striatum of individual mice and reveal different effects of each manipulation on motor behavior. Conversely, injecting light over the full numerical aperture of the fiber results in light emission from the entire taper surface, achieving broader and more efficient optogenetic activation of neurons, compared to standard flat-faced fiber stimulation. Thus, tapered fibers permit focal or broad illumination that can be precisely and dynamically matched to experimental needs.

The Song Must Go On: Resilience of the Songbird Vocal Motor Pathway

Stereotyped sequences of neural activity underlie learned vocal behavior in songbirds; principle neurons in the cortical motor nucleus HVC fire in stereotyped sequences with millisecond precision across multiple renditions of a song. The geometry of neural connections underlying these sequences is not known in detail though feed-forward chains are commonly assumed in theoretical models of sequential neural activity. In songbirds, a well-defined cortical-thalamic motor circuit exists but little is known the fine-grain structure of connections within each song nucleus. To examine whether the structure of song is critically dependent on long-range connections within HVC, we bilaterally transected the nucleus along the anterior-posterior axis in normal-hearing and deafened birds. The disruption leads to a slowing of song as well as an increase in acoustic variability. These effects are reversed on a time-scale of days even in deafened birds or in birds that are prevented from singing post-transection. The stereotyped song of zebra finches includes acoustic details that span from milliseconds to seconds–one of the most precise learned behaviors in the animal kingdom. This detailed motor pattern is resilient to disruption of connections at the cortical level, and the details of song variability and duration are maintained by offline homeostasis of the song circuit.

The Striatum Organizes 3D Behavior via Moment-to-Moment Action Selection

Many naturalistic behaviors are built from modular components that are expressed sequentially. Although striatal circuits have been implicated in action selection and implementation, the neural mechanisms that compose behavior in unrestrained animals are not well understood. Here, we record bulk and cellular neural activity in the direct and indirect pathways of dorsolateral striatum (DLS) as mice spontaneously express action sequences. These experiments reveal that DLS neurons systematically encode information about the identity and ordering of sub-second 3D behavioral motifs; this encoding is facilitated by fast-timescale decorrelations between the direct and indirect pathways. Furthermore, lesioning the DLS prevents appropriate sequence assembly during exploratory or odor-evoked behaviors. By characterizing naturalistic behavior at neural timescales, these experiments identify a code for elemental 3D pose dynamics built from complementary pathway dynamics, support a role for DLS in constructing meaningful behavioral sequences, and suggest models for how actions are sculpted over time.

From retinal waves to activity-dependent retinogeniculate map development.

A neural model is described of how spontaneous retinal waves are formed in infant mammals, and how these waves organize activity-dependent development of a topographic map in the lateral geniculate nucleus, with connections from each eye segregated into separate anatomical layers. The model simulates the spontaneous behavior of starburst amacrine cells and retinal ganglion cells during the production of retinal waves during the first few weeks of mammalian postnatal development. It proposes how excitatory and inhibitory mechanisms within individual cells, such as Ca2+-activated K+ channels, and cAMP currents and signaling cascades, can modulate the spatiotemporal dynamics of waves, notably by controlling the after-hyperpolarization currents of starburst amacrine cells. Given the critical role of the geniculate map in the development of visual cortex, these results provide a foundation for analyzing the temporal dynamics whereby the visual cortex itself develops.