Search

Connectomic reconstruction of neural circuits relies on nanometer resolution microscopy which produces on the order of a petabyte of imagery for each cubic millimeter of brain tissue. The cost of storing such data is a significant barrier to broadening the use of connectomic approaches and scaling to even larger volumes. We present an image compression approach that uses machine learning-based denoising and standard image codecs to compress raw electron microscopy imagery of neuropil up to 17-fold with negligible loss of 3d reconstruction and synaptic detection accuracy.

Reconstruction of neural circuitry at single-synapse resolution is a key target for improving understanding of the nervous system in health and disease. Serial section transmission electron microscopy (ssTEM) is among the most prolific imaging methods employed in pursuit of such reconstructions. We demonstrate how Flood-Filling Networks (FFNs) can be used to computationally segment a forty-teravoxel whole-brain Drosophila ssTEM volume. To compensate for data irregularities and imperfect global alignment, FFNs were combined with procedures that locally re-align serial sections as well as dynamically adjust and synthesize image content. The proposed approach produced a largely merger-free segmentation of the entire ssTEM Drosophila brain, which we make freely available. As compared to manual tracing using an efficient skeletonization strategy, the segmentation enabled circuit reconstruction and analysis workflows that were an order of magnitude faster.

The neural circuits responsible for behavior remain largely unknown. Previous efforts have reconstructed the complete circuits of small animals, with hundreds of neurons, and selected circuits for larger animals. Here we (the FlyEM project at Janelia and collaborators at Google) summarize new methods and present the complete circuitry of a large fraction of the brain of a much more complex animal, the fruit fly Drosophila melanogaster. Improved methods include new procedures to prepare, image, align, segment, find synapses, and proofread such large data sets; new methods that define cell types based on connectivity in addition to morphology; and new methods to simplify access to a large and evolving data set. From the resulting data we derive a better definition of computational compartments and their connections; an exhaustive atlas of cell examples and types, many of them novel; detailed circuits for most of the central brain; and exploration of the statistics and structure of different brain compartments, and the brain as a whole. We make the data public, with a web site and resources specifically designed to make it easy to explore, for all levels of expertise from the expert to the merely curious. The public availability of these data, and the simplified means to access it, dramatically reduces the effort needed to answer typical circuit questions, such as the identity of upstream and downstream neural partners, the circuitry of brain regions, and to link the neurons defined by our analysis with genetic reagents that can be used to study their functions.Note: In the next few weeks, we will release a series of papers with more involved discussions. One paper will detail the hemibrain reconstruction with more extensive analysis and interpretation made possible by this dense connectome. Another paper will explore the central complex, a brain region involved in navigation, motor control, and sleep. A final paper will present insights from the mushroom body, a center of multimodal associative learning in the fly brain.

Reconstruction of neural circuitry at single-synapse resolution is a key target for improving understanding of the nervous system in health and disease. Serial section transmission electron microscopy (ssTEM) is among the most prolific imaging methods employed in pursuit of such reconstructions. We demonstrate how Flood-Filling Networks (FFNs) can be used to computationally segment a forty-teravoxel whole-brain Drosophila ssTEM volume. To compensate for data irregularities and imperfect global alignment, FFNs were combined with procedures that locally re-align serial sections as well as dynamically adjust and synthesize image content. The proposed approach produced a largely merger-free segmentation of the entire ssTEM Drosophila brain, which we make freely available. As compared to manual tracing using an efficient skeletonization strategy, the segmentation enabled circuit reconstruction and analysis workflows that were an order of magnitude faster.

OBJECTIVEThe activation of the sensorimotor cortex as measured by electrocorticographic (ECoG) signals has been correlated with contralateral hand movements in humans, as precisely as the level of individual digits. However, the relationship between individual and multiple synergistic finger movements and the neural signal as detected by ECoG has not been fully explored. The authors used intraoperative high-resolution micro-ECoG (µECoG) on the sensorimotor cortex to link neural signals to finger movements across several context-specific motor tasks.METHODSThree neurosurgical patients with cortical lesions over eloquent regions participated. During awake craniotomy, a sensorimotor cortex area of hand movement was localized by high-frequency responses measured by an 8 × 8 µECoG grid of 3-mm interelectrode spacing. Patients performed a flexion movement of the thumb or index finger, or a pinch movement of both, based on a visual cue. High-gamma (HG; 70–230 Hz) filtered µECoG was used to identify dominant electrodes associated with thumb and index movement. Hand movements were recorded by a dataglove simultaneously with µECoG recording.RESULTSIn all 3 patients, the electrodes controlling thumb and index finger movements were identifiable approximately 3–6-mm apart by the HG-filtered µECoG signal. For HG power of cortical activation measured with µECoG, the thumb and index signals in the pinch movement were similar to those observed during thumb-only and index-only movement, respectively (all p > 0.05). Index finger movements, measured by the dataglove joint angles, were similar in both the index-only and pinch movements (p > 0.05). However, despite similar activation across the conditions, markedly decreased thumb movement was observed in pinch relative to independent thumb-only movement (all p < 0.05).CONCLUSIONSHG-filtered µECoG signals effectively identify dominant regions associated with thumb and index finger movement. For pinch, the µECoG signal comprises a combination of the signals from individual thumb and index movements. However, while the relationship between the index finger joint angle and HG-filtered signal remains consistent between conditions, there is not a fixed relationship for thumb movement. Although the HG-filtered µECoG signal is similar in both thumb-only and pinch conditions, the actual thumb movement is markedly smaller in the pinch condition than in the thumb-only condition. This implies a nonlinear relationship between the cortical signal and the motor output for some, but importantly not all, movement types. This analysis provides insight into the tuning of the motor cortex toward specific types of motor behaviors.

Reconstruction of neural circuits from volume electron microscopy data requires the tracing of cells in their entirety, including all their neurites. Automated approaches have been developed for tracing, but their error rates are too high to generate reliable circuit diagrams without extensive human proofreading. We present flood-filling networks, a method for automated segmentation that, similar to most previous efforts, uses convolutional neural networks, but contains in addition a recurrent pathway that allows the iterative optimization and extension of individual neuronal processes. We used flood-filling networks to trace neurons in a dataset obtained by serial block-face electron microscopy of a zebra finch brain. Using our method, we achieved a mean error-free neurite path length of 1.1 mm, and we observed only four mergers in a test set with a path length of 97 mm. The performance of flood-filling networks was an order of magnitude better than that of previous approaches applied to this dataset, although with substantially increased computational costs.

Electrocorticography (ECoG) signals can provide high spatio-temporal resolution and high signal to noise ratio recordings of local neural activity from the surface of the brain. Previous studies have shown that broad-band, spatially focal, high-frequency increases in ECoG signals are highly correlated with movement and other cognitive tasks and can be volitionally modulated. However, significant additional information may be present in inter-electrode interactions, but adding additional higher order inter-electrode interactions can be impractical from a computational aspect, if not impossible.In this paper we present a new method of calculating high frequency interactions between electrodes called Short-Time Windowed Covariance (STWC) that builds on mathematical techniques currently used in neural signal analysis, along with an implementation that accelerates the algorithm by orders of magnitude by leveraging commodity, off-the-shelf graphics processing unit (GPU) hardware.Using the hardware-accelerated implementation of STWC, we identify many types of event-related inter-electrode interactions from human ECoG recordings on global and local scales that have not been identified by previous methods. Unique temporal patterns are observed for digit flexion in both low- (10mm spacing) and high-resolution (3mm spacing) electrode arrays.Covariance is a commonly used metric for identifying correlated signals, but the standard covariance calculations do not allow for temporally varying covariance. In contrast STWC allows and identifies event-driven changes in covariance without identifying spurious noise correlations.STWC can be used to identify event-related neural interactions whose high computational load is well suited to GPU capabilities.

Object The gold-standard method for determining cortical functional organization in the context of neurosurgical intervention is electrical cortical stimulation (ECS), which disrupts normal cortical function to evoke movement. This technique is imprecise, however, as motor responses are not limited to the precentral gyrus. Electrical cortical stimulation also can trigger seizures, is not always tolerated, and is often unsuccessful, especially in children. Alternatively, endogenous motor and sensory signals can be mapped by somatosensory evoked potentials (SSEPs), functional MRI (fMRI), and electrocorticography of high gamma (70–150 Hz) signal power, which reflect normal cortical function. The authors evaluated whether these 4 modalities of mapping sensorimotor function in children produce concurrent results. Methods The authors retrospectively examined the charts of all patients who underwent epilepsy surgery at Seattle Children's Hospital between July 20, 1999, and July 1, 2011, and they included all patients in whom the primary motor or somatosensory cortex was localized via 2 or more of the following tests: ECS, SSEP, fMRI, or high gamma electrocorticography (hgECoG). Results Inclusion criteria were met by 50 patients, whose mean age at operation was 10.6 years. The youngest patient who underwent hgECoG mapping was 2 years and 10 months old, which is younger than any patient reported on in the literature. The authors localized the putative sensorimotor cortex most often with hgECoG, followed by SSEP and fMRI; ECS was most likely to fail to localize the sensorimotor cortex. Conclusions Electrical cortical stimulation, SSEP, fMRI, and hgECoG generally produced concordant localization of motor and sensory function in children. When attempting to localize the sensorimotor cortex in children, hgECoG was more likely to produce results, was faster, safer, and did not require cooperation. The hgECoG maps in pediatric patients are similar to those in adult patients published in the literature. The sensorimotor cortex can be mapped by hgECoG and fMRI in children younger than 3 years old to localize cortical function.

Brain-computer interfaces (BCIs)—systems that can record neural activity and translate them into commands for computer systems—are sufficiently advanced to allow users to volitionally guide them through simple tasks. Contemporary BCI research focuses on squeezing additional functionality out of standardized paradigms, be it achieving more bits per second, increased degrees of freedom, or increasing accuracy. While these studies have shown marginal advancements in recent years, our lack of understanding concerning the underlying neurophysiology continues to be the limiting factor in BCI development. In this chapter, we propose turning the way research is done on BCI systems on its head; instead of using our understanding of neural signals to incrementally advance the state of brain-machine interfaces, we apply a BCI system as a form of experimental control to study changes in neural activity. By using current BCI systems as a tool for neuroscientific study, we can probe the underlying neuroanatomy in novel, behaviorally controlled ways.

In this paper we present our low-level software framework that allows human neuromuscular properties and behaviors to be programmed modularly onto biologically inspired prosthetic devices. Specifically this software framework is used at the lowest level of the Anatomically Correct Testbed (ACT) Hand. It abstracts away from the robotic details and allows users including biologists to program individual muscle physiology, multiple muscle synergistic activities, neural commands, etc. independently. Our system has been designed to be fault-tolerant with the idea of safe and continued operation of prostheses if a new prototype behavior were to perform incorrectly or outright fail. Example coding of Hills model is shown.

We present results of cortical activity during phoneme pronunciation, recorded using miniaturized electrocorticography grids with high spatial resolution. A patient implanted with the miniature grid was instructed to audibly pronounce one of four phonemes. For each phoneme, we observed distinct spatial correlation patterns at the 3mm electrode spacing. We applied a support vector machine classification scheme and, for the first time, were able to distinguish discrete phonemes with high accuracy. In addition, we found that sub-regions of our miniature array were specific for distinct pairs of phonemes, showing that cortical phoneme processing occurs at a higher resolution than previously though.

All previous multiple-day brain-computer interface (BCI) experiments have dynamically adjusted the parameterization between the signals measured from the brain and the features used to control the interface. The authors present the results of a multiple-day electrocorticographic (ECoG) BCI experiment. A patient with a subdural electrode array implanted for seizure localization performed tongue motor tasks. After an initial screening and feature selection on the 1st day, 5 consecutive days of cursor-based feedback were performed with a fixed parameterization. Control of the interface was robust throughout all days, with performance increasing to a stable state in which high-frequency ECoG signal could immediately be translated into cursor control. These findings demonstrate that ECoG-based BCIs can be implemented for multiple-day control without the necessity for sophisticated retraining and adaptation.