High-resolution three-dimensional microelectrode brain mapping using stereo microfocal X-ray imaging

Design, Fabrication, and Implantation of Invasive Microelectrode Arrays as in vivo Brain Machine Interfaces: A Comprehensive Review

Invasive Microelectrode Arrays (MEAs) have been a significant and useful tool for us to gain a fundamental understanding of how the brain works through high spatiotemporal resolution neuron-level recordings and/or stimulations. Through decades of research, various types of microwire, silicon, and flexible substrate-based MEAs have been developed using the evolving new materials, novel design concepts, and cutting-edge advanced manufacturing capabilities. Surgical implantation of the latest minimal damaging flexible MEAs through the hard-to-penetrate brain membranes introduces new challenges and thus the development of implantation strategies and instruments for the latest MEAs. In this paper, studies on the design considerations and enabling manufacturing processes of various invasive MEAs as in vivo brain-machine interfaces have been reviewed to facilitate the development as well as the state-of-art of such brain-machine interfaces from an engineering perspective. The challenges and solution strategies developed for surgically implanting such interfaces into the brain have also been evaluated and summarized. Finally, the research gaps have been identified in the design, manufacturing, and implantation perspectives, and future research prospects in invasive MEA development have been proposed.

A Fine-Scale and Minimally Invasive Marking Method for Use with Conventional Tungsten Microelectrodes

In neurophysiology, achieving precise correlation between physiological responses and anatomic structures is a significant challenge. Therefore, the accuracy of the electrode marking method is crucial. In this study, we describe a tungsten-deposition method, in which tungsten oxide is generated by applying biphasic current pulses to conventional tungsten electrodes. The electrical current used was 40-50 μA, which is similar to that used in electrical microstimulation experiments. The size of the markings ranged from 10 to 100 μm, corresponding to the size of the electrode tip, which is smaller than that of existing marking methods. Despite the small size of the markings, detection is easy as the marking appears in bright red under dark-field observation after Nissl staining. This marking technique resulted in low tissue damage and was maintained in vivo for at least two years. The feasibility of this method was tested in mouse and macaque brains.

Accurate Localization of Linear Probe Electrode Arrays across Multiple Brains

Recently developed probes for extracellular electrophysiological recordings have large numbers of electrodes on long linear shanks. Linear electrode arrays, such as Neuropixels probes, have hundreds of recording electrodes distributed over linear shanks that span several millimeters. Because of the length of the probes, linear probe recordings in rodents usually cover multiple brain areas. Typical studies collate recordings across several recording sessions and animals. Neurons recorded in different sessions and animals thus have to be aligned to each other and to a standardized brain coordinate system. Here, we evaluate two typical workflows for localization of individual electrodes in standardized coordinates. These workflows rely on imaging brains with fluorescent probe tracks and warping 3D image stacks to standardized brain atlases. One workflow is based on tissue clearing and selective plane illumination microscopy (SPIM), whereas the other workflow is based on serial block-face two-photon (SBF2P) microscopy. In both cases electrophysiological features are then used to anchor particular electrodes along the reconstructed tracks to specific locations in the brain atlas and therefore to specific brain structures. We performed groundtruth experiments, in which motor cortex outputs are labeled with ChR2 and a fluorescence protein. Light-evoked electrical activity and fluorescence can be independently localized. Recordings from brain regions targeted by the motor cortex reveal better than 0.1-mm accuracy for electrode localization, independent of workflow used.

Chronically implantable LED arrays for behavioral optogenetics in primates

Optogenetic methods have been widely used in rodent brains, but remain relatively under-developed for nonhuman primates such as rhesus macaques, an animal model with a large brain expressing sophisticated sensory, motor and cognitive behaviors. To address challenges in behavioral optogenetics in large brains, we developed Opto-Array, a chronically implantable array of light-emitting diodes for high-throughput optogenetic perturbation. We demonstrated that optogenetic silencing in the macaque primary visual cortex with the help of the Opto-Array results in reliable retinotopic visual deficits in a luminance discrimination task. We separately confirmed that Opto-Array illumination results in local neural silencing, and that behavioral effects are not due to tissue heating. These results demonstrate the effectiveness of the Opto-Array for behavioral optogenetic applications in large brains.

Using non-invasive neuroimaging to enhance the care, well-being and experimental outcomes of laboratory non-human primates (monkeys)

Over the past 10-20 years, neuroscience witnessed an explosion in the use of non-invasive imaging methods, particularly magnetic resonance imaging (MRI), to study brain structure and function. Simultaneously, with access to MRI in many research institutions, MRI has become an indispensable tool for researchers and veterinarians to guide improvements in surgical procedures and implants and thus, experimental as well as clinical outcomes, given that access to MRI also allows for improved diagnosis and monitoring for brain disease. As part of the PRIMEatE Data Exchange, we gathered expert scientists, veterinarians, and clinicians who treat humans, to provide an overview of the use of non-invasive imaging tools, primarily MRI, to enhance experimental and welfare outcomes for laboratory non-human primates engaged in neuroscientific experiments. We aimed to provide guidance for other researchers, scientists and veterinarians in the use of this powerful imaging technology as well as to foster a larger conversation and community of scientists and veterinarians with a shared goal of improving the well-being and experimental outcomes for laboratory animals.

Reversible Inactivation of Different Millimeter-Scale Regions of Primate IT Results in Different Patterns of Core Object Recognition Deficits

Extensive research suggests that the inferior temporal (IT) population supports visual object recognition behavior. However, causal evidence for this hypothesis has been equivocal, particularly beyond the specific case of face-selective subregions of IT. Here, we directly tested this hypothesis by pharmacologically inactivating individual, millimeter-scale subregions of IT while monkeys performed several core object recognition subtasks, interleaved trial-by trial. First, we observed that IT inactivation resulted in reliable contralateral-biased subtask-selective behavioral deficits. Moreover, inactivating different IT subregions resulted in different patterns of subtask deficits, predicted by each subregion's neuronal object discriminability. Finally, the similarity between different inactivation effects was tightly related to the anatomical distance between corresponding inactivation sites. Taken together, these results provide direct evidence that the IT cortex causally supports general core object recognition and that the underlying IT coding dimensions are topographically organized.

Neural dynamics at successive stages of the ventral visual stream are consistent with hierarchical error signals

Ventral visual stream neural responses are dynamic, even for static image presentations. However, dynamical neural models of visual cortex are lacking as most progress has been made modeling static, time-averaged responses. Here, we studied population neural dynamics during face detection across three cortical processing stages. Remarkably,~30 milliseconds after the initially evoked response, we found that neurons in intermediate level areas decreased their responses to typical configurations of their preferred face parts relative to their response for atypical configurations even while neurons in higher areas achieved and maintained a preference for typical configurations. These hierarchical neural dynamics were inconsistent with standard feedforward circuits. Rather, recurrent models computing prediction errors between stages captured the observed temporal signatures. This model of neural dynamics, which simply augments the standard feedforward model of online vision, suggests that neural responses to static images may encode top-down prediction errors in addition to bottom-up feature estimates.

A micro-CT-based method for quantitative brain lesion characterization and electrode localization

Lesion verification and quantification is traditionally done via histological examination of sectioned brains, a time-consuming process that relies heavily on manual estimation. Such methods are particularly problematic in posterior cortical regions (e.g. visual cortex), where sectioning leads to significant damage and distortion of tissue. Even more challenging is the post hoc localization of micro-electrodes, which relies on the same techniques, suffers from similar drawbacks and requires even higher precision. Here, we propose a new, simple method for quantitative lesion characterization and electrode localization that is less labor-intensive and yields more detailed results than conventional methods. We leverage staining techniques standard in electron microscopy with the use of commodity micro-CT imaging. We stain whole rat and zebra finch brains in osmium tetroxide, embed these in resin and scan entire brains in a micro-CT machine. The scans result in 3D reconstructions of the brains with section thickness dependent on sample size (12-15 and 5-6 microns for rat and zebra finch respectively) that can be segmented manually or automatically. Because the method captures the entire intact brain volume, comparisons within and across studies are more tractable, and the extent of lesions and electrodes may be studied with higher accuracy than with current methods.

Neurophysiological Organization of the Middle Face Patch in Macaque Inferior Temporal Cortex

While early cortical visual areas contain fine scale spatial organization of neuronal properties, such as orientation preference, the spatial organization of higher-level visual areas is less well understood. The fMRI demonstration of face-preferring regions in human ventral cortex and monkey inferior temporal cortex ("face patches") raises the question of how neural selectivity for faces is organized. Here, we targeted hundreds of spatially registered neural recordings to the largest fMRI-identified face-preferring region in monkeys, the middle face patch (MFP), and show that the MFP contains a graded enrichment of face-preferring neurons. At its center, as much as 93% of the sites we sampled responded twice as strongly to faces than to nonface objects. We estimate the maximum neurophysiological size of the MFP to be ∼6 mm in diameter, consistent with its previously reported size under fMRI. Importantly, face selectivity in the MFP varied strongly even between neighboring sites. Additionally, extremely face-selective sites were ∼40 times more likely to be present inside the MFP than outside. These results provide the first direct quantification of the size and neural composition of the MFP by showing that the cortical tissue localized to the fMRI defined region consists of a very high fraction of face-preferring sites near its center, and a monotonic decrease in that fraction along any radial spatial axis.

SIGNIFICANCE STATEMENT

The underlying organization of neurons that give rise to the large spatial regions of activity observed with fMRI is not well understood. Neurophysiological studies that have targeted the fMRI identified face patches in monkeys have provided evidence for both large-scale clustering and a heterogeneous spatial organization. Here we used a novel x-ray imaging system to spatially map the responses of hundreds of sites in and around the middle face patch. We observed that face-selective signal localized to the middle face patch was characterized by a gradual spatial enrichment. Furthermore, strongly face-selective sites were ∼40 times more likely to be found inside the patch than outside of the patch.

Large-scale, high-resolution neurophysiological maps underlying FMRI of macaque temporal lobe

Maps obtained by functional magnetic resonance imaging (fMRI) are thought to reflect the underlying spatial layout of neural activity. However, previous studies have not been able to directly compare fMRI maps to high-resolution neurophysiological maps, particularly in higher level visual areas. Here, we used a novel stereo microfocal x-ray system to localize thousands of neural recordings across monkey inferior temporal cortex (IT), construct large-scale maps of neuronal object selectivity at subvoxel resolution, and compare those neurophysiology maps with fMRI maps from the same subjects. While neurophysiology maps contained reliable structure at the sub-millimeter scale, fMRI maps of object selectivity contained information at larger scales (>2.5 mm) and were only partly correlated with raw neurophysiology maps collected in the same subjects. However, spatial smoothing of neurophysiology maps more than doubled that correlation, while a variety of alternative transforms led to no significant improvement. Furthermore, raw spiking signals, once spatially smoothed, were as predictive of fMRI maps as local field potential signals. Thus, fMRI of the inferior temporal lobe reflects a spatially low-passed version of neurophysiology signals. These findings strongly validate the widespread use of fMRI for detecting large (>2.5 mm) neuronal domains of object selectivity but show that a complete understanding of even the most pure domains (e.g., faces vs nonface objects) requires investigation at fine scales that can currently only be obtained with invasive neurophysiological methods.

Shape similarity, better than semantic membership, accounts for the structure of visual object representations in a population of monkey inferotemporal neurons

The anterior inferotemporal cortex (IT) is the highest stage along the hierarchy of visual areas that, in primates, processes visual objects. Although several lines of evidence suggest that IT primarily represents visual shape information, some recent studies have argued that neuronal ensembles in IT code the semantic membership of visual objects (i.e., represent conceptual classes such as animate and inanimate objects). In this study, we investigated to what extent semantic, rather than purely visual information, is represented in IT by performing a multivariate analysis of IT responses to a set of visual objects. By relying on a variety of machine-learning approaches (including a cutting-edge clustering algorithm that has been recently developed in the domain of statistical physics), we found that, in most instances, IT representation of visual objects is accounted for by their similarity at the level of shape or, more surprisingly, low-level visual properties. Only in a few cases we observed IT representations of semantic classes that were not explainable by the visual similarity of their members. Overall, these findings reassert the primary function of IT as a conveyor of explicit visual shape information, and reveal that low-level visual properties are represented in IT to a greater extent than previously appreciated. In addition, our work demonstrates how combining a variety of state-of-the-art multivariate approaches, and carefully estimating the contribution of shape similarity to the representation of object categories, can substantially advance our understanding of neuronal coding of visual objects in cortex.

Precedence of the eye region in neural processing of faces

Functional magnetic resonance imaging (fMRI) has revealed multiple subregions in monkey inferior temporal cortex (IT) that are selective for images of faces over other objects. The earliest of these subregions, the posterior lateral face patch (PL), has not been studied previously at the neurophysiological level. Perhaps not surprisingly, we found that PL contains a high concentration of "face-selective" cells when tested with standard image sets comparable to those used previously to define the region at the level of fMRI. However, we here report that several different image sets and analytical approaches converge to show that nearly all face-selective PL cells are driven by the presence of a single eye in the context of a face outline. Most strikingly, images containing only an eye, even when incorrectly positioned in an outline, drove neurons nearly as well as full-face images, and face images lacking only this feature led to longer latency responses. Thus, bottom-up face processing is relatively local and linearly integrates features-consistent with parts-based models-grounding investigation of how the presence of a face is first inferred in the IT face processing hierarchy.

pyElectrode: an open-source tool using structural MRI for electrode positioning and neuron mapping

Neurophysiologists want to place the tip of an electrode in a specific area of the brain. The coordinates of this area can be obtained from standard stereotaxic atlases. However, individual brains may not align with the atlas exactly. Additionally, for chronic recordings, electrodes are placed through a chamber attached to the animal's skull. Thus, the user wants to know where the area of interest is in chamber coordinates, not stereotaxic coordinates. After the chamber has been attached an MRI is often made. This assists in electrode placement, as the location of a target relative to the chamber can be determined based on the atlas. However, doing this in practice requires rough estimation or cumbersome calculations. pyElectrode provides a graphical display and performs calculations necessary to convert between stereotaxic and chamber coordinates, thus facilitating MR-based targeting from an implanted chamber. It also allows the experimenter to visualize recording or stimulation sites during experiments. Finally, it can display and output those sites on an MRI slice background in a format suitable for publication.

In vivo visualization of single-unit recording sites using MRI-detectable elgiloy deposit marking

Precise localization of single-neuron activity has elucidated functional architectures of the primate cerebral cortex, related to vertically stacked layers and horizontally aligned columns. The traditional "gold standard" method for localizing recorded neuron is histological examination of electrolytic lesion marks at recording sites. Although this method can localize recorded neurons with fine neuroanatomy, the necessity for postmortem analysis prohibits its use in long-term chronic experiments. To localize recorded single-neuron positions in vivo, we introduced MRI-detectable elgiloy deposit marks, which can be created by electrolysis of an elgiloy microelectrode tip and visualized on highly contrasted magnetic resonance (MR) images. Histological analysis validated that the deposit mark centers could be localized relative to neuroanatomy in vivo with single-voxel accuracy, at an in-plane resolution of 200 μm. To demonstrate practical applications of the technique, we recorded single-neuron activity from a monkey performing a cognitive task and localized it in vivo using deposit marks (deposition: 2 μA for 3 min; scanning: fast-spin-echo sequence with 0.15 × 0.15 × 0.8 mm(3) resolution, 120/4,500 ms of echo-time/repetition-time and 8 echo-train-length), as is usually performed with conventional postmortem methods using electrolytic lesion marks. Two localization procedures were demonstrated: 1) deposit marks within a microelectrode track were used to reconstruct a dozen recorded neuron positions along the track directly on MR images; 2) combination with X-ray imaging allowed estimation of hundreds of neuron positions on MR images. This new in vivo method is feasible for chronic experiments with nonhuman primates, enabling analysis of the functional architecture of the cerebral cortex underlying cognitive processes.

Intention and attention: different functional roles for LIPd and LIPv

Establishing the circuitry underlying attentional and oculomotor control is a long-standing goal of systems neuroscience. The macaque lateral intraparietal area (LIP) has been implicated in both processes, but numerous studies have produced contradictory findings. Anatomically, LIP consists of a dorsal and ventral subdivision, but the functional importance of this division remains unclear. We injected muscimol, a GABA(A) agonist, and manganese, a magnetic resonance imaging lucent paramagnetic ion, into different portions of LIP, examined the effects of the resulting reversible inactivation on saccade planning and attention, and visualized each injection using anatomical magnetic resonance imaging. We found that dorsal LIP (LIPd) is primarily involved in oculomotor planning, whereas ventral LIP (LIPv) contributes to both attentional and oculomotor processes. Additional testing revealed that the two functions were dissociable, even in LIPv. Using our technique, we found a clear structure-function relationship that distinguishes LIPv from LIPd and found dissociable circuits for attention and eye movements in the posterior parietal cortex.