Inserting a Neuropixels probe into awake monkey cortex: two probes, two methods.

BACKGROUND: Neuropixels probes have revolutionized neurophysiological studies in the rodent, but inserting these probes through the much thicker primate dura remains a challenge. NEW METHODS: Here we describe two methods we have developed for the insertion of two types of Neuropixels probes acutely into the awake macaque monkey cortex. For the fine rodent probe (Neuropixels 1.0, IMEC), which is unable to pierce native primate dura, we developed a dural-eyelet method to insert the probe repeatedly without breakage. For the thicker short NHP probe (Neuropixels NP1010), we developed an artificial dura system to insert the probe. RESULTS AND COMPARISON WITH EXISTING METHODS: We have now conducted successful experiments in 3 animals across 7 recording chambers with the procedures described here and have achieved recordings with similar yields over several months in each case. CONCLUSION: We hope that our hardware, surgical preparation, methods for insertion and methods for removal of broken probe parts are of value to primate physiologists everywhere.

Ultra-high density electrodes improve detection, yield, and cell type identification in neuronal recordings.

To understand the neural basis of behavior, it is essential to sensitively and accurately measure neural activity at single neuron and single spike resolution. Extracellular electrophysiology delivers this, but it has biases in the neurons it detects and it imperfectly resolves their action potentials. To minimize these limitations, we developed a silicon probe with much smaller and denser recording sites than previous designs, called Neuropixels Ultra (NP Ultra). This device samples neuronal activity at ultra-high spatial density (~10 times higher than previous probes) with low noise levels, while trading off recording span. NP Ultra is effectively an implantable voltage-sensing camera that captures a planar image of a neuron's electrical field. We use a spike sorting algorithm optimized for these probes to demonstrate that the yield of visually-responsive neurons in recordings from mouse visual cortex improves up to ~3-fold. We show that NP Ultra can record from small neuronal structures including axons and dendrites. Recordings across multiple brain regions and four species revealed a subset of extracellular action potentials with unexpectedly small spatial spread and axon-like features. We share a large-scale dataset of these brain-wide recordings in mice as a resource for studies of neuronal biophysics. Finally, using ground-truth identification of three major inhibitory cortical cell types, we found that these cell types were discriminable with approximately 75% success, a significant improvement over lower-resolution recordings. NP Ultra improves spike sorting performance, detection of subcellular compartments, and cell type classification to enable more powerful dissection of neural circuit activity during behavior.

High-density recording reveals sparse clusters (but not columns) for shape and texture encoding in macaque V4.

Macaque area V4 includes neurons that exhibit exquisite selectivity for visual form and surface texture, but their functional organization across laminae is unknown. We used high-density Neuropixels probes in two awake monkeys to characterize shape and texture tuning of dozens of neurons simultaneously across layers. We found sporadic clusters of neurons that exhibit similar tuning for shape and texture: ~20% exhibited similar tuning with their neighbors. Importantly, these clusters were confined to a few layers, seldom 'columnar' in structure. This was the case even when neurons were strongly driven, and exhibited robust contrast invariance for shape and texture tuning. We conclude that functional organization in area V4 is not columnar for shape and texture stimulus features and in general organization maybe at a coarse scale (e.g. encoding of 2D vs 3D shape) rather than at a fine scale in terms of similarity in tuning for specific features (as in the orientation columns in V1). We speculate that this may be a direct consequence of the great diversity of inputs integrated by V4 neurons to build variegated tuning manifolds in a high-dimensional space.

Inserting a Neuropixels probe into awake monkey cortex: two probes, two methods.

Neuropixels probes have revolutionized neurophysiological studies in the rodent, but inserting these probes through the much thicker primate dura remains a challenge. Here we describe two methods we have developed for the insertion of two types of Neuropixels probes acutely into the awake monkey cortex. For the fine rodent probe, which is unable to pierce native primate dura, we developed a dural-eyelet method to insert the probe repeatedly without breakage. For the thicker NHP probe, we developed an artificial dura system to insert the probe. We have now conducted successful experiments in 3 animals across 7 recording chambers with the procedures described here and have achieved stable recordings over several months in each case. Here we describe our hardware, surgical preparation, methods for insertion and methods for removal of broken probe parts. We hope that our methods are of value to primate physiologists everywhere.

Dissociation in neuronal encoding of object versus surface motion in the primate brain.

A paradox exists in our understanding of motion processing in the primate visual system: neurons in the dorsal motion processing stream often strikingly fail to encode long-range and perceptually salient jumps of a moving stimulus. Psychophysical studies suggest that such long-range motion, which requires integration over more distant parts of the visual field, may be based on higher-order motion processing mechanisms that rely on feature or object tracking. Here, we demonstrate that ventral visual area V4, long recognized as critical for processing static scenes, includes neurons that maintain direction selectivity for long-range motion, even when conflicting local motion is present. These V4 neurons exhibit specific selectivity for the motion of objects, i.e., targets with defined boundaries, rather than the motion of surfaces behind apertures, and are selective for direction of motion over a broad range of spatial displacements and defined by a variety of features. Motion direction at a range of speeds can be accurately decoded on single trials from the activity of just a few V4 neurons. Thus, our results identify a novel motion computation in the ventral stream that is strikingly different from, and complementary to, the well-established system in the dorsal stream, and they support the hypothesis that the ventral stream system interacts with the dorsal stream to achieve the higher level of abstraction critical for tracking dynamic objects.

Encoding of Partially Occluded and Occluding Objects in Primate Inferior Temporal Cortex.

Object segmentation-the process of parsing visual scenes-is essential for object recognition and scene understanding. We investigated how responses of neurons in macaque inferior temporal (IT) cortex contribute to object segmentation under partial occlusion. Specifically, we asked whether IT responses to occluding and occluded objects are bound together as in the visual image or linearly separable reflecting their segmentation. We recorded the activity of 121 IT neurons while two male animals performed a shape discrimination task under partial occlusion. We found that for a majority (60%) of neurons, responses were enhanced by partial occlusion, but they were only weakly shape selective for the discriminanda at all levels of occlusion. Enhancement of IT responses in these neurons depended largely on the area of occlusion but only minimally on the color and shape of the occluding dots. In contrast to the above group of neurons, a sizable minority responded best to the unoccluded stimulus and showed strong selectivity for the shape of the discriminanda. In these neurons, response magnitude and shape selectivity declined with increasing levels of occlusion. Simulations revealed that the response characteristics of both classes of neurons were consistent with a model in which the responses to the occluded shape and the occluders are weighted separately and linearly combined. Overall, our results support the hypothesis that information about occluded and occluding stimuli are linearly separable and easily decodable from IT responses and that IT neurons encode a segmented representation of the visual scene.SIGNIFICANCE STATEMENT Recognizing partially occluded objects can be challenging, yet the primate visual system achieves it rapidly and effortlessly. For successful recognition in the face of occlusion, segmentation of the occluded and occluding objects is a critical first step. Using a combination of experimental data and simulations, here we demonstrate that responses of neurons in macaque IT cortex, the highest stage of the form processing pathway, reflect occluded and occluding stimuli as segmented components and are not bound together as they appear in the visual image. These results support the idea that segmentation and perception of occluded and occluding stimuli are directly mirrored in the responses of neurons in the highest form processing stages.

Comparison of the color selectivity of macaque V4 neurons in different color spaces.

Chromatic selectivity has been studied extensively in various visual areas at different stages of visual processing in the macaque brain. In these studies, color stimuli defined in the Derrington-Krauskopf-Lennie (DKL) color space with a limited range of cone contrast were typically used in early stages, whereas those defined in the Commission Internationale de l'Eclairage (CIE) color space, based on human psychophysical measurements across the gamut of the display, were often used in higher visual areas. To understand how the color information is processed along the visual pathway, it is necessary to compare color selectivity obtained in different areas on a common color space. In the present study, we tested whether the neural color selectivity obtained in DKL space can be predicted from responses obtained in CIE space and whether stimuli with limited cone contrast are sufficient to characterize neural color selectivity. We found that for most V4 neurons, there was a strong correlation between responses measured using the two chromatic coordinate systems, and the color selectivities obtained with the two stimulus sets were comparable. However, for some neurons preferring high- or low-saturation colors, stimuli defined in DKL color space did not adequately capture the neural color selectivity. This is mainly due to the use of stimuli within a limited range of cone contrast. We conclude that regardless of the choice of color space, the sampling of colors across the entire gamut is important to characterize neural color selectivity fully or to compare color selectivities in different areas so as to understand color representation in the visual system.

Effects of luminance contrast on the color selectivity of neurons in the macaque area v4 and inferior temporal cortex.

Appearance of a color stimulus is significantly affected by the contrast between its luminance and the luminance of the background. In the present study, we used stimuli evenly distributed on the CIE-xy chromaticity diagram to examine how luminance contrast affects neural representation of color in V4 and the anterior inferior temporal (AITC) and posterior inferior temporal (PITC) color areas (Banno et al., 2011). The activities of single neurons were recorded from monkeys performing a visual fixation task, and the effects of luminance contrast on the color selectivity of individual neurons and their population responses were systematically examined by comparing responses to color stimuli that were brighter or darker than the background. We found that the effects of luminance contrast differed considerably across V4 and the PITC and AITC. In both V4 and the PITC, the effects of luminance contrast on the population responses of color-selective neurons depended on color. In V4, the size of the effect was largest for blue and cyan, whereas in the PITC, the effect gradually increased as the saturation of the color stimulus was reduced, and was especially large with neutral colors (white, gray, black). The pattern observed in the PITC resembles the effect of luminance contrast on color appearance, suggesting PITC neurons are closely involved in the formation of the perceived appearance of color. By contrast, the color selectivities of AITC neurons were little affected by luminance contrast, indicating that hue and saturation of color stimuli are represented independently of luminance contrast in the AITC.