In vivo whole-brain imaging of zebrafish larvae using three-dimensional fluorescence microscopy

As a vertebrate model animal, larval zebrafish are widely used in neuroscience and provide a unique opportunity to monitor whole-brain activity at the cellular resolution. Here, we provide an optimized protocol for performing whole-brain imaging of larval zebrafish using three-dimensional fluorescence microscopy, including sample preparation and immobilization, sample embedding, image acquisition, and visualization after imaging. The current protocol enables in vivo imaging of the structure and neuronal activity of a larval zebrafish brain at a cellular resolution for over 1 h using confocal microscopy and custom-designed fluorescence microscopy. The critical steps in the protocol are also discussed, including sample mounting and positioning, preventing bubble formation and dust in the agarose gel, and avoiding motion in images caused by incomplete solidification of the agarose gel and paralyzation of the fish. The protocol has been validated and confirmed in multiple settings. This protocol can be easily adapted for imaging other organs of a larval zebrafish.

Interference suppression techniques for OPM-based MEG: Opportunities and challenges

One of the primary technical challenges facing magnetoencephalography (MEG) is that the magnitude of neuromagnetic fields is several orders of magnitude lower than interfering signals. Recently, a new type of sensor has been developed - the optically pumped magnetometer (OPM). These sensors can be placed directly on the scalp and move with the head during participant movement, making them wearable. This opens up a range of exciting experimental and clinical opportunities for OPM-based MEG experiments, including paediatric studies, and the incorporation of naturalistic movements into neuroimaging paradigms. However, OPMs face some unique challenges in terms of interference suppression, especially in situations involving mobile participants, and when OPMs are integrated with electrical equipment required for naturalistic paradigms, such as motion capture systems. Here we briefly review various hardware solutions for OPM interference suppression. We then outline several signal processing strategies aimed at increasing the signal from neuromagnetic sources. These include regression-based strategies, temporal filtering and spatial filtering approaches. The focus is on the practical application of these signal processing algorithms to OPM data. In a similar vein, we include two worked-through experiments using OPM data collected from a whole-head sensor array. These tutorial-style examples illustrate how the steps for suppressing external interference can be implemented, including the associated data and code so that researchers can try the pipelines for themselves. With the popularity of OPM-based MEG rising, there will be an increasing need to deal with interference suppression. We hope this practical paper provides a resource for OPM-based MEG researchers to build upon.

Capillary-associated microglia regulate vascular structure and function through PANX1-P2RY12 coupling in mice

Microglia are brain-resident immune cells with a repertoire of functions in the brain. However, the extent of their interactions with the vasculature and potential regulation of vascular physiology has been insufficiently explored. Here, we document interactions between ramified CX3CR1 + myeloid cell somata and brain capillaries. We confirm that these cells are bona fide microglia by molecular, morphological and ultrastructural approaches. Then, we give a detailed spatio-temporal characterization of these capillary-associated microglia (CAMs) comparing them with parenchymal microglia (PCMs) in their morphological activities including during microglial depletion and repopulation. Molecularly, we identify P2RY12 receptors as a regulator of CAM interactions under the control of released purines from pannexin 1 (PANX1) channels. Furthermore, microglial elimination triggered capillary dilation, blood flow increase, and impaired vasodilation that were recapitulated in P2RY12-/- and PANX1-/- mice suggesting purines released through PANX1 channels play important roles in activating microglial P2RY12 receptors to regulate neurovascular structure and function.

PriMa: A low-cost, modular, open hardware, and 3D-printed fMRI manipulandum

Motor actions in fMRI settings require specialized hardware to monitor, record, and control the subjects behavior. Commercially available options for such behavior tracking or control are very restricted and costly. We present a novel grasp manipulandum in a modular design, consisting of MRI-compatible, 3D printable buttons and a chassis for mounting. Button presses are detected by the interruption of an optical fiber path, which is digitized by a photodiode and subsequent signal amplification and thresholding. Two feedback devices (manipulanda) are constructed, one for macaques (Macaca mulatta) and one for human use. Both devices have been tested in their specific experimental setting and possible improvements are reported. Design files are shared under an open hardware license.

Low-cost low-field NMR and MRI: Instrumentation and applications

While NMR and MRI are often thought of as expensive techniques requiring large institutional investment, opportunities for low-cost, low-field NMR and MRI abound. We discuss a number of approaches to performing magnetic resonance experiments with inexpensive, easy to find or build components, aimed at applications in industry, education, and research. Opportunities that aim to make NMR accessible to a broad community are highlighted. We describe and demonstrate some projects from our laboratory, including a new prototype instrument for measurements at frequencies up to ∼200 kHz and demonstrate its application to the study of the rapidly advancing technique known as inhomogeneous magnetization transfer imaging, a promising method for characterizing myelin in vivo.

Use of 2.1 MHz MRI scanner for brain imaging and its preliminary results in stroke

Cerebral stroke greatly contributes to death and disability rates in China and the whole world. Effective non-invasive imaging device for bedside monitoring of stroke is critically needed in clinically. This study developed a lightweight (350 kg) and low-footprint magnetic resonance imaging (MRI) system for brain imaging. Static magnetic field was built using an H-typed permanent magnet, which has 50.9 mT magnetic field strength (corresponding to 2.167 MHz proton Larmor frequency). Biplanar gradient coils were designed using the target field method based on dipole equivalent. Radio-frequency coils were optimized by particle swarm optimization. The 2 MHz MRI system was deployed in the Department of Neurology of hospital to test its performance in stroke imaging detection. Gradient recall echo and fast spin echo sequences were utilized to acquire T1- and T2-weighted MR images, respectively. Brain images of a healthy volunteer, a patient with hemorrhagic stroke, a patient of ischemic stroke, and a patient with ischemic stroke and images from 17-day long-term monitoring of hemorrhagic stroke were obtained with a 1.5 mm * 2.0 mm spatial resolution in plane, and a 10 mm thickness.

Fully Integrated Time-Gated 3D Fluorescence Imager for Deep Neural Imaging

This paper presents a device for time-gated fluorescence imaging in the deep brain, consisting of two on-chip laser diodes and 512 single-photon avalanche diodes (SPADs). The edge-emitting laser diodes deliver fluorescence excitation above the SPAD array, parallel to the imager. In the time domain, laser diode illumination is pulsed and the SPAD is time-gated, allowing a fluorescence excitation rejection up to O.D. 3 at 1 ns of time-gate delay. Each SPAD pixel is masked with Talbot gratings to enable the mapping of 2D array photon counts into a 3D image. The 3D image achieves a resolution of 40, 35, and 73 μm in the x, y, and z directions, respectively, in a noiseless environment, with a maximum frame rate of 50 kilo-frames-per-second. We present measurement results of the spatial and temporal profiles of the dual-pulsed laser diode illumination and of the photon detection characteristics of the SPAD array. Finally, we show the imager's ability to resolve a glass micropipette filled with red fluorescent microspheres. The system's 420 μm-wide cross section allows it to be inserted at arbitrary depths of the brain while achieving a field of view four times larger than fiber endoscopes of equal diameter.

Fully Integrated Time-Gated 3D Fluorescence Imager for Deep Neural Imaging

This paper presents a device for time-gated fluorescence imaging in the deep brain, consisting of two on-chip laser diodes and 512 single-photon avalanche diodes (SPADs). The edge-emitting laser diodes deliver fluorescence excitation above the SPAD array, parallel to the imager. In the time domain, laser diode illumination is pulsed and the SPAD is time-gated, allowing a fluorescence excitation rejection up to O.D. 3 at 1 ns of time-gate delay. Each SPAD pixel is masked with Talbot gratings to enable the mapping of 2D array photon counts into a 3D image. The 3D image achieves a resolution of 40, 35, and 73 μm in the x, y, and z directions, respectively, in a noiseless environment, with a maximum frame rate of 50 kilo-frames-per-second. We present measurement results of the spatial and temporal profiles of the dual-pulsed laser diode illumination and of the photon detection characteristics of the SPAD array. Finally, we show the imager's ability to resolve a glass micropipette filled with red fluorescent microspheres. The system's 420 μm-wide cross section allows it to be inserted at arbitrary depths of the brain while achieving a field of view four times larger than fiber endoscopes of equal diameter.

Cortical Observation by Synchronous Multifocal Optical Sampling Reveals Widespread Population Encoding of Actions

To advance the measurement of distributed neuronal population representations of targeted motor actions on single trials, we developed an optical method (COSMOS) for tracking neural activity in a largely uncharacterized spatiotemporal regime. COSMOS allowed simultaneous recording of neural dynamics at ∼30 Hz from over a thousand near-cellular resolution neuronal sources spread across the entire dorsal neocortex of awake, behaving mice during a three-option lick-to-target task. We identified spatially distributed neuronal population representations spanning the dorsal cortex that precisely encoded ongoing motor actions on single trials. Neuronal correlations measured at video rate using unaveraged, whole-session data had localized spatial structure, whereas trial-averaged data exhibited widespread correlations. Separable modes of neural activity encoded history-guided motor plans, with similar population dynamics in individual areas throughout cortex. These initial experiments illustrate how COSMOS enables investigation of large-scale cortical dynamics and that information about motor actions is widely shared between areas, potentially underlying distributed computations.

Application of Robot-Assisted Frameless Stereoelectroencephalography Based on Multimodal Image Guidance in Pediatric Refractory Epilepsy: Experience of a Pediatric Center in a Developing Country

OBJECTIVE

To introduce the application of robot-assisted frameless stereoelectroencephalography (SEEG) based on multimodal image fusion technology in pediatric refractory epilepsy in a pediatric center from a developing country.

METHODS

We retrospectively evaluated pediatric patients with drug-resistant epilepsy who underwent SEEG monitoring at the Children's Hospital of Fudan University from July 2014 to August 2017. Application of multimodal image fusion technology in SEEG was described in detail. Seizure outcomes were assessed according to the International League Against Epilepsy classification.

RESULTS

A total of 208 patients were initially eligible and underwent a rigorous phase I evaluation. SEEG explorations were performed in 20 patients who entered phase II assessment (11 male and 9 female patients) with a median age of 7.99 ± 4.07 years. In total, 181 electrodes were implanted (9 per implantation), among which 16 implantations were unilateral (6 left and 10 right) and 4 were bilateral. The mean operating time was 3 hours and no obvious hemorrhage occurred. Electrode displacement and pneumocephalus were observed in 1 and 2 patients, respectively. Thirteen and 7 patients underwent tailored resection and radiofrequency thermocoagulation, respectively. Among resection cases, focal cortical dysplasia was the predominant pathologic type. The overall seizure outcome after a mean follow-up of 2.65 years was International League Against Epilepsy class 1 in 13, class 2 in 2, class 3 in 3, class 4 in 1, and class 5 in 1 patient, respectively.

CONCLUSIONS

The combination of multimodal image fusion and frameless robot-assisted SEEG is demonstrated to be safe and effective on children with refractory epilepsy in developing countries.

Evaluation of neurocognitive function of prefrontal cortex in ornithine transcarbamylase deficiency

Hyperammonia due to ornithine transcarbamylase deficiency (OTCD) can cause a range of deficiencies in domains of executive function and working memory. Only a few fMRI studies have focused on neuroimaging data in a population with OTCD. Yet, there is a need for monitoring the disease progression and neurocognitive function in this population. In this study, we used a non-invasive neuroimaging technique, functional Near Infrared Spectroscopy (fNIRS), to examine the hemodynamics of prefrontal cortex (PFC) based on neural activation in an OTCD population. Using fNIRS, we measured the activation in PFC of the participants while performing the Stroop task. Behavioral assessment such as reaction time and correct response were recorded. We investigated the difference in behavioral measures as well as brain activation in left and right PFC in patients with OTCD and controls. Results revealed a distinction in left PFC activation between controls and patients with OTCD, where control subjects showed higher task related activation increase. Subjects with OTCD also exhibited bilateral increase in PFC activation. There was no significant difference in response time or correct response between the two groups. Our findings suggest the alterations in neurocognitive function of PFC in OTCD compared to the controls despite the behavioral profiles exhibiting no such differences. This is a first study using fNIRS to examine a neurocognitive function in OTCD population and can provide a novel insight into the screening of OTCD progression and examining neurocognitive changes.

Photoacoustics can image spreading depolarization deep in gyrencephalic brain

Spreading depolarization (SD) is a self-propagating wave of near-complete neuronal depolarization that is abundant in a wide range of neurological conditions, including stroke. SD was only recently documented in humans and is now considered a therapeutic target for brain injury, but the mechanisms related to SD in complex brains are not well understood. While there are numerous approaches to interventional imaging of SD on the exposed brain surface, measuring SD deep in brain is so far only possible with low spatiotemporal resolution and poor contrast. Here, we show that photoacoustic imaging enables the study of SD and its hemodynamics deep in the gyrencephalic brain with high spatiotemporal resolution. As rapid neuronal depolarization causes tissue hypoxia, we achieve this by continuously estimating blood oxygenation with an intraoperative hybrid photoacoustic and ultrasonic imaging system. Due to its high resolution, promising imaging depth and high contrast, this novel approach to SD imaging can yield new insights into SD and thereby lead to advances in stroke, and brain injury research.

Time course images of cellular injury and recovery in murine brain with high-resolution GRIN lens system

Time course, in vivo imaging of brain cells is crucial to fully understand the progression of secondary cellular damage and recovery in murine models of injury. We have combined high-resolution gradient index lens technology with a model of diffuse axonal injury in rodents to enable repeated visualization of fine features of individual cells in three-dimensional space over several weeks. For example, we recorded changes in morphology in the same axons in the external capsule numerous times over 30 to 60 days, before and after induced traumatic brain injury. We observed the expansion of secondary injury and limited recovery of individual axons in this subcortical white matter tract over time. In another application, changes in microglial activation state were visualized in the penumbra region of mice before and after ischemia induced by middle carotid artery occlusion. The ability to collect a series of high-resolution images of cellular features of the same cells pre- and post-injury enables a unique opportunity to study the progression of damage, spontaneous healing, and effects of therapeutics in mouse models of neurodegenerative disease and brain injury.

Using GPUs to accelerate computational diffusion MRI: From microstructure estimation to tractography and connectomes

The great potential of computational diffusion MRI (dMRI) relies on indirect inference of tissue microstructure and brain connections, since modelling and tractography frameworks map diffusion measurements to neuroanatomical features. This mapping however can be computationally highly expensive, particularly given the trend of increasing dataset sizes and the complexity in biophysical modelling. Limitations on computing resources can restrict data exploration and methodology development. A step forward is to take advantage of the computational power offered by recent parallel computing architectures, especially Graphics Processing Units (GPUs). GPUs are massive parallel processors that offer trillions of floating point operations per second, and have made possible the solution of computationally-intensive scientific problems that were intractable before. However, they are not inherently suited for all problems. Here, we present two different frameworks for accelerating dMRI computations using GPUs that cover the most typical dMRI applications: a framework for performing biophysical modelling and microstructure estimation, and a second framework for performing tractography and long-range connectivity estimation. The former provides a front-end and automatically generates a GPU executable file from a user-specified biophysical model, allowing accelerated non-linear model fitting in both deterministic and stochastic ways (Bayesian inference). The latter performs probabilistic tractography, can generate whole-brain connectomes and supports new functionality for imposing anatomical constraints, such as inherent consideration of surface meshes (GIFTI files) along with volumetric images. We validate the frameworks against well-established CPU-based implementations and we show that despite the very different challenges for parallelising these problems, a single GPU achieves better performance than 200 CPU cores thanks to our parallel designs.

All the light that we can see: a new era in miniaturized microscopy

One major challenge in neuroscience is to uncover how defined neural circuits in the brain encode, store, modify, and retrieve information. Meeting this challenge comprehensively requires tools capable of recording and manipulating the activity of intact neural networks in naturally behaving animals. Head-mounted miniature microscopes are emerging as a key tool to address this challenge. Here we discuss recent work leading to the miniaturization of neural imaging tools, the current state of the art in this field, and the importance and necessity of open-source options. We finish with a discussion on what the future may hold for miniature microscopy.

Assessing bimanual motor skills with optical neuroimaging

Measuring motor skill proficiency is critical for the certification of highly skilled individuals in numerous fields. However, conventional measures use subjective metrics that often cannot distinguish between expertise levels. We present an advanced optical neuroimaging methodology that can objectively and successfully classify subjects with different expertise levels associated with bimanual motor dexterity. The methodology was tested by assessing laparoscopic surgery skills within the framework of the fundamentals of a laparoscopic surgery program, which is a prerequisite for certification in general surgery. We demonstrate that optical-based metrics outperformed current metrics for surgical certification in classifying subjects with varying surgical expertise. Moreover, we report that optical neuroimaging allows for the successful classification of subjects during the acquisition of these skills.

Hybrid PET/MRI Methodology

The hybrid PET/MR scanner represents the first implementation of the effective integration of two modalities allowing truly synchronous/simultaneous acquisition of their imaging signals. This integration, resulting from the innovation and development of specific hardware components has paved the way for new approaches in the study of neurodegenerative diseases. This chapter will describe the hardware development that has led to the availability of different clinical solutions for PET/MR imaging as well as the still-open technological challenges and opportunities related to the processing and exploitation of the simultaneous acquisition in neurological studies.

Assessment of the impact of shared brain imaging data on the scientific literature

Data sharing is increasingly recommended as a means of accelerating science by facilitating collaboration, transparency, and reproducibility. While few oppose data sharing philosophically, a range of barriers deter most researchers from implementing it in practice. To justify the significant effort required for sharing data, funding agencies, institutions, and investigators need clear evidence of benefit. Here, using the International Neuroimaging Data-sharing Initiative, we present a case study that provides direct evidence of the impact of open sharing on brain imaging data use and resulting peer-reviewed publications. We demonstrate that openly shared data can increase the scale of scientific studies conducted by data contributors, and can recruit scientists from a broader range of disciplines. These findings dispel the myth that scientific findings using shared data cannot be published in high-impact journals, suggest the transformative power of data sharing for accelerating science, and underscore the need for implementing data sharing universally.

Pre-Surgical Planning: Multimodality Imaging to Optimize Outcomes in Pediatric Epilepsy Surgery

Neuroimaging is an important component of the pre-surgical planning for pediatric epilepsy. High-resolution structural magnetic resonance images are combined with advanced structural and functional imaging techniques to better define the surgical lesion and decrease morbidity postoperatively. The combination of neuroimaging, electroencephalography (EEG), and neuropsychiatric testing in a multidisciplinary epilepsy conference setting is essential for determining a plan for surgical management.

Spinal cord MRI at 7T

Magnetic resonance imaging (MRI) of the human spinal cord at 7T has been demonstrated by a handful of research sites worldwide, and the spinal cord remains one of the areas in which higher fields and resolution could have high impact. The small diameter of the cord (∼1 cm) necessitates high spatial resolution to minimize partial volume effects between gray and white matter, and so MRI of the cord can greatly benefit from increased signal-to-noise ratio and contrasts at ultra-high field (UHF). Herein we review the current state of UHF spinal cord imaging. Technical challenges to successful UHF spinal cord MRI include radiofrequency (B1) nonuniformities and a general lack of optimized radiofrequency coils, amplified physiological noise, and an absence of methods for robust B0 shimming along the cord to mitigate image distortions and signal losses. Numerous solutions to address these challenges have been and are continuing to be explored, and include novel approaches for signal excitation and acquisition, dynamic shimming and specialized shim coils, and acquisitions with increased coverage or optimal slice angulations.

Imaging at ultrahigh magnetic fields: History, challenges, and solutions

Following early efforts in applying nuclear magnetic resonance (NMR) spectroscopy to study biological processes in intact systems, and particularly since the introduction of 4 T human scanners circa 1990, rapid progress was made in imaging and spectroscopy studies of humans at 4 T and animal models at 9.4 T, leading to the introduction of 7 T and higher magnetic fields for human investigation at about the turn of the century. Work conducted on these platforms has provided numerous technological solutions to challenges posed at these ultrahigh fields, and demonstrated the existence of significant advantages in signal-to-noise ratio and biological information content. Primary difference from lower fields is the deviation from the near field regime at the radiofrequencies (RF) corresponding to hydrogen resonance conditions. At such ultrahigh fields, the RF is characterized by attenuated traveling waves in the human body, which leads to image non-uniformities for a given sample-coil configuration because of destructive and constructive interferences. These non-uniformities were initially considered detrimental to progress of imaging at high field strengths. However, they are advantageous for parallel imaging in signal reception and transmission, two critical technologies that account, to a large extend, for the success of ultrahigh fields. With these technologies and improvements in instrumentation and imaging methods, today ultrahigh fields have provided unprecedented gains in imaging of brain function and anatomy, and started to make inroads into investigation of the human torso and extremities. As extensive as they are, these gains still constitute a prelude to what is to come given the increasingly larger effort committed to ultrahigh field research and development of ever better instrumentation and techniques.

A Sensitive Dynamic and Active Pixel Vision Sensor for Color or Neural Imaging Applications

Applications requiring detection of small visual contrast require high sensitivity. Event cameras can provide higher dynamic range (DR) and reduce data rate and latency, but most existing event cameras have limited sensitivity. This paper presents the results of a 180-nm Towerjazz CIS process vision sensor called SDAVIS192. It outputs temporal contrast dynamic vision sensor (DVS) events and conventional active pixel sensor frames. The SDAVIS192 improves on previous DAVIS sensors with higher sensitivity for temporal contrast. The temporal contrast thresholds can be set down to 1% for negative changes in logarithmic intensity (OFF events) and down to 3.5% for positive changes (ON events). The achievement is possible through the adoption of an in-pixel preamplification stage. This preamplifier reduces the effective intrascene DR of the sensor (70 dB for OFF and 50 dB for ON), but an automated operating region control allows up to at least 110-dB DR for OFF events. A second contribution of this paper is the development of characterization methodology for measuring DVS event detection thresholds by incorporating a measure of signal-to-noise ratio (SNR). At average SNR of 30 dB, the DVS temporal contrast threshold fixed pattern noise is measured to be 0.3%-0.8% temporal contrast. Results comparing monochrome and RGBW color filter array DVS events are presented. The higher sensitivity of SDAVIS192 make this sensor potentially useful for calcium imaging, as shown in a recording from cultured neurons expressing calcium sensitive green fluorescent protein GCaMP6f.

Minipigs as a Large-Brained Animal Model for Huntington's Disease: From Behavior and Imaging to Gene Therapy

Large animal models offer novel opportunities in exploring safety, biology, and efficacy of novel therapeutic approaches for Huntington's disease (HD). Challenges in the development of, for example, gene therapy, such as delivery, distribution, and persistence of virus vectors or oligo sense nucleotides, can be explored in large brains and organisms approaching human size. We here introduce the transgenic Libechov minipig as a large animal model of HD. Methods developed to assess motor, cognitive, and behavioral features expected to manifest in an HD model are described. We also outline established protocols for magnetic resonance imaging (MRI) including magnetic resonance spectroscopy (MRS) for minipigs. The successful conduct of long-term follow-up studies over several years with repeated behavioral testing and imaging is reported. We discuss the advantages and limitations of using this model with regard to translational reliability, homology to humans and with respect to feasibility, breeding, housing, handling, and finally ethical considerations. It is concluded that minipigs can fulfill an important role in preclinical development to bridge the gap between rodents and nonhuman primate research in the translation to humans.

Quantitative neuroimaging in mucopolysaccharidoses clinical trials

The mucopolysaccharidosis (MPS) disorders are rare lysosomal storage disorders caused by mutations in lysosomal enzymes involved in glycosaminoglycan (GAG) degradation. The resulting intracellular accumulation of GAGs leads to widespread tissue and organ dysfunction. In addition to somatic signs and symptoms, patients with MPS can present with neurological manifestations such as cognitive decline, behavioral problems (e.g. hyperactivity and aggressiveness), sleep disturbances, and/or epilepsy. These are associated with significant abnormalities of the central nervous system (CNS), including white and gray matter lesions, brain atrophy, ventriculomegaly, and spinal cord compression. In order to effectively manage and develop therapies for MPS that target neurological disease, it is important to visualize and quantify these CNS abnormalities. This review describes optimal approaches for conducting magnetic resonance imaging assessments in multi-center clinical studies, and summarizes current knowledge from neuroimaging studies in MPS disorders. The content of the review is based on presentations and discussions on these topics that were held during a meeting of an international group of experts.

In vivo calcium imaging from dentate granule cells with wide-field fluorescence microscopy

A combination of genetically-encoded calcium indicators and micro-optics has enabled monitoring of large-scale dynamics of neuronal activity from behaving animals. In these studies, wide-field microscopy is often used to visualize neural activity. However, this method lacks optical sectioning capability, and therefore its axial resolution is generally poor. At present, it is unclear whether wide-field microscopy can visualize activity of densely packed small neurons at cellular resolution. To examine the applicability of wide-field microscopy for small-sized neurons, we recorded calcium activity of dentate granule cells having a small soma diameter of approximately 10 micrometers. Using a combination of high numerical aperture (0.8) objective lens and independent component analysis-based image segmentation technique, activity of putative single granule cell activity was separated from wide-field calcium imaging data. The result encourages wider application of wide-field microscopy in in vivo neurophysiology.

Functional magnetic resonance imaging in clinical practice: State of the art and science

BACKGROUND

Functional magnetic resonance imaging (fMRI) has become a mainstream neuroimaging modality in the assessment of patients being evaluated for brain tumour and epilepsy surgeries. Thus, it is important for doctors in primary care settings to be well acquainted with the present and potential future applications, as well as limitations, of this modality.

OBJECTIVE

The objective of this article is to introduce the theoretical principles and state-of-the-art clinical applications of fMRI in brain tumour and epilepsy surgery, with a focus on the implications for clinical primary care.

DISCUSSION

fMRI enables non-invasive functional mapping of specific cortical tasks (eg motor, language, memory-based, visual), revealing information about functional localisation, anatomical variation in cortical function, and disease effects and adaptations, including the fascinating phenomenon of brain plasticity. fMRI is currently ordered by specialist neurologists and neurosurgeons for the purposes of pre-surgical assessment, and within the context of an experienced multidisciplinary team to prepare, conduct and interpret the scan. With an increasing number of patients undergoing fMRI, general practitioners can expect questions about the current and emerging role of fMRI in clinical care from these patients and their families.

Hybrid multispectral optoacoustic and ultrasound tomography for morphological and physiological brain imaging

Expanding usage of small animal models in biomedical research necessitates development of technologies for structural, functional, or molecular imaging that can be readily integrated in the biological laboratory. Herein, we consider dual multispectral optoacoustic (OA) and ultrasound tomography based on curved ultrasound detector arrays and describe the performance achieved for hybrid morphological and physiological brain imaging of mice in vivo. We showcase coregistered hemodynamic parameters resolved by OA tomography under baseline conditions and during alterations of blood oxygen saturation. As an internal reference, we provide imaging of abdominal organs. We illustrate the performance advantages of hybrid curved detector ultrasound and OA tomography and discuss immediate and long-term implications of our findings in the context of animal and human studies.

Wearable scanning photoacoustic brain imaging in behaving rats

A wearable scanning photoacoustic imaging (wPAI) system is presented for noninvasive brain study in behaving rats. This miniaturized wPAI system consists of four pico linear servos and a single transducer-based PAI probe. It has a dimension of 50 mm × 35 mm × 40 mm, and a weight of 26 g excluding cablings. Phantom evaluation shows that wPAI achieves a lateral resolution of ∼0.5 mm and an axial resolution of ∼0.1 mm at a depth of up to 11 mm. Its imaging ability is also tested in a behaving rat, and the results indicate that wPAI is able to image blood vessels at a depth of up to 5 mm with intact scalp and skull. With its noninvasive, deep penetration, and functional imaging ability in behaving animals, wPAI can be used for behavior, cognition, and preclinical brain disease studies.

Wearable scanning photoacoustic brain imaging in behaving rats

A wearable scanning photoacoustic imaging (wPAI) system is presented for noninvasive brain study in behaving rats. This miniaturized wPAI system consists of four pico linear servos and a single transducer-based PAI probe. It has a dimension of 50 mm × 35 mm × 40 mm, and a weight of 26 g excluding cablings. Phantom evaluation shows that wPAI achieves a lateral resolution of ∼0.5 mm and an axial resolution of ∼0.1 mm at a depth of up to 11 mm. Its imaging ability is also tested in a behaving rat, and the results indicate that wPAI is able to image blood vessels at a depth of up to 5 mm with intact scalp and skull. With its noninvasive, deep penetration, and functional imaging ability in behaving animals, wPAI can be used for behavior, cognition, and preclinical brain disease studies.

Neuroimaging of a minipig model of Huntington's disease: Feasibility of volumetric, diffusion-weighted and spectroscopic assessments

BACKGROUND

As novel treatment approaches for Huntington's disease (HD) evolve, the use of transgenic (tg) large animal models has been considered for preclinical safety and efficacy assessments. It is hoped that large animal models may provide higher reliability in translating preclinical findings to humans, e.g., by using similar endpoints and biomarkers.

NEW METHOD

We here investigated the feasibility to conduct MRI assessments in a recently developed tgHD model in the Libechov minipig. The model is characterized by high genetic homology to humans and a similar body mass and compartments. The minipig brain provides anatomical features that are attractive for imaging studies and could be used as endpoints for disease modifying preclinical studies similar to human HD.

RESULTS

We demonstrate that complex MRI protocols can be successfully acquired with tgHD and wild type (wt) Libechov minipigs. We show that acquisition of anatomical images applicable for volumetric assessments is feasible and outline the development of a segmented MRI brain atlas. Similarly diffusion-weighted imaging (DWI) including fiber tractography is presented. We also demonstrate the feasibility to conduct in vivo metabolic assessments using MR spectroscopy.

COMPARISON WITH EXISTING METHODS

In human HD, these MRI methods are already validated and used as reliable biomarker of disease progression even before the onset of a clinical motor phenotype.

CONCLUSIONS

The results show that the minipig brain is well suited for MRI assessments in preclinical studies. We conclude that further characterization of phenotypical differences between tg and wt animals in sufficiently powered cross-sectional and longitudinal studies is warranted.

Past, present and future of spike sorting techniques

Spike sorting is a crucial step to extract information from extracellular recordings. With new recording opportunities provided by the development of new electrodes that allow monitoring hundreds of neurons simultaneously, the scenario for the new generation of algorithms is both exciting and challenging. However, this will require a new approach to the problem and the development of a common reference framework to quickly assess the performance of new algorithms. In this work, we review the basic concepts of spike sorting, including the requirements for different applications, together with the problems faced by presently available algorithms. We conclude by proposing a roadmap stressing the crucial points to be addressed to support the neuroscientific research of the near future.

Real-Time Neuroimaging and Cognitive Monitoring Using Wearable Dry EEG

GOAL

We present and evaluate a wearable high-density dry-electrode EEG system and an open-source software framework for online neuroimaging and state classification.

METHODS

The system integrates a 64-channel dry EEG form factor with wireless data streaming for online analysis. A real-time software framework is applied, including adaptive artifact rejection, cortical source localization, multivariate effective connectivity inference, data visualization, and cognitive state classification from connectivity features using a constrained logistic regression approach (ProxConn). We evaluate the system identification methods on simulated 64-channel EEG data. Then, we evaluate system performance, using ProxConn and a benchmark ERP method, in classifying response errors in nine subjects using the dry EEG system.

RESULTS

Simulations yielded high accuracy (AUC = 0.97 ± 0.021) for real-time cortical connectivity estimation. Response error classification using cortical effective connectivity [short-time direct-directed transfer function (sdDTF)] was significantly above chance with similar performance (AUC) for cLORETA (0.74 ±0.09) and LCMV (0.72 ±0.08) source localization. Cortical ERP-based classification was equivalent to ProxConn for cLORETA (0.74 ±0.16) but significantly better for LCMV (0.82 ±0.12) .

CONCLUSION

We demonstrated the feasibility for real-time cortical connectivity analysis and cognitive state classification from high-density wearable dry EEG.

SIGNIFICANCE

This paper is the first validated application of these methods to 64-channel dry EEG. This study addresses a need for robust real-time measurement and interpretation of complex brain activity in the dynamic environment of the wearable setting. Such advances can have broad impact in research, medicine, and brain-computer interfaces. The pipelines are made freely available in the open-source SIFT and BCILAB toolboxes.

Implantable image sensor based on intra-brain image transmission

We developed and fabricated a micro-imager based on wireless intra-brain communication using conductive property of living tissues. An pixel array, analog-to-digital converter and transmitter are integrated on a single chip. The dimensions of the chip are 1 mm × 1mm × 0.15 mm. We demonstrate wireless image transmission through phosphate buffer saline as a brain phantom.

Wearable near-infrared spectroscopy neuroimaging and its applications

Wearable near-infrared spectroscopy (NIRS) systems are expected to be applied in various fields such as health care (medical use), education (teaching), and biofeedback. An investigation on hyperscanning by using NIRS is discussed first, where multiple brains were simultaneously measured for investigating and evaluating important social interactions, such as communication. The relationship between interacting brain activities and performance in cooperation has been demonstrated. An investigation on mood-state measurements in a return-to-work program is next discussed. It has been reported that a specified index calculated using NIRS signals obtained during performance of a working memory task correlated with a mood score. Using this index, the mood states of volunteers who participated in a return-to-work program after psychiatric clinical treatment were monitored. It has been suggested that the relationship between brain activities and subjective assessment of depression mood will be useful for evaluating the recovery stage for return-to-work programs. These techniques open new applications of wearable NIRS systems in mental health care.

The Travelling-Wave Primate System: A New Solution for Magnetic Resonance Imaging of Macaque Monkeys at 7 Tesla Ultra-High Field

Introduction

Neuroimaging of macaques at ultra-high field (UHF) is usually conducted by combining a volume coil for transmit (Tx) and a phased array coil for receive (Rx) tightly enclosing the monkey’s head. Good results have been achieved using vertical or horizontal magnets with implanted or near-surface coils. An alternative and less costly approach, the travelling-wave (TW) excitation concept, may offer more flexible experimental setups on human whole-body UHF magnetic resonance imaging (MRI) systems, which are now more widely available. Goal of the study was developing and validating the TW concept for in vivo primate MRI.

Methods

The TW Primate System (TWPS) uses the radio frequency shield of the gradient system of a human whole-body 7 T MRI system as a waveguide to propagate a circularly polarized B1 field represented by the TE11 mode. This mode is excited by a specifically designed 2-port patch antenna. For receive, a customized neuroimaging monkey head receive-only coil was designed. Field simulation was used for development and evaluation. Signal-to-noise ratio (SNR) was compared with data acquired with a conventional monkey volume head coil consisting of a homogeneous transmit coil and a 12-element receive coil.

Results

The TWPS offered good image homogeneity in the volume-of-interest Turbo spin echo images exhibited a high contrast, allowing a clear depiction of the cerebral anatomy. As a prerequisite for functional MRI, whole brain ultrafast echo planar images were successfully acquired.

Conclusion

The TWPS presents a promising new approach to fMRI of macaques for research groups with access to a horizontal UHF MRI system.

In vivo deep brain imaging of rats using oral-cavity illuminated photoacoustic computed tomography

Using internal illumination with an optical fiber in the oral cavity, we demonstrate, for the first time, photoacoustic computed tomography (PACT) of the deep brain of rats in vivo. The experiment was performed on a full-ring-array PACT system, with the capability of providing high-speed cross-sectional imaging of the brain. Compared with external illumination through the cranial skull, internal illumination delivers more light to the base of the brain. Consequently, in vivo photoacoustic images clearly reveal deep brain structures such as the hypothalamus, brain stem, and cerebral medulla.

Hyperscanning neuroimaging technique to reveal the "two-in-one" system in social interactions

Using a technique for measuring brain activity simultaneously from two people, known as hyperscanning, we can calculate inter-brain neural effects that appear only in interactions between individuals. Hyperscanning studies using fMRI are advantageous in that they can precisely determine the region(s) involved in inter-brain effects. However, it is almost impossible to record inter-brain effects in daily life. By contrast, hyperscanning EEG studies have high temporal resolution and could be used to capture moment-to-moment interactions. In addition, EEG instrumentation is portable and easy to wear, offering the opportunity to record inter-brain effects during daily-life interactions. However, the disadvantage of this approach is that it is difficult to localize the epicenter of the inter-brain effect. fNIRS has better temporal resolution and portability than fMRI, but has limited spatial resolution and a limited ability to record deep brain structures. Future studies should employ hyperscanning EEG-fMRI, because this approach combines the high temporal resolution of EEG with the high spatial resolution of fMRI. Hyperscanning EEG-fMRI allows us to use inter-brain effects as neuromarkers of the properties of social interactions in daily life. We also wish to emphasize the need to develop a mathematical model explaining how two brains can exhibit synchronized activity.

Endoscopic and keyhole endoscope-assisted neurosurgical approaches: a qualitative survey on technical challenges and technological solutions

INTRODUCTION

The literature reflects a resurgence of interest in endoscopic and keyhole endoscope-assisted neurosurgical approaches as alternatives to conventional microsurgical approaches in carefully selected cases. The aim of this study was to assess the technical challenges of neuroendoscopy, and the scope for technological innovations to overcome these barriers.

MATERIALS AND METHODS

All full members of the Society of British Neurosurgeons (SBNS) were electronically invited to participate in an online survey. The open-ended structured survey asked three questions; firstly, whether the surgeon presently utilises or has experience with endoscopic or endoscope-assisted approaches; secondly, what they consider to be the major technical barriers to adopting such approaches; and thirdly, what technological advances they foresee improving safety and efficacy in the field. Responses were subjected to a qualitative research method of multi-rater emergent theme analysis.

RESULTS

Three clear themes emerged: 1) surgical approach and better integration with image-guidance systems (20%), 2) intra-operative visualisation and improvements in neuroendoscopy (49%), and 3) surgical manipulation and improvements in instruments (74%).

DISCUSSION

The analysis of responses to our open-ended survey revealed that although opinion was varied three major themes could be identified. Emerging technological advances such as augmented reality, high-definition stereo-endoscopy, and robotic joint-wristed instruments may help overcome the technical difficulties associated with neuroendoscopic approaches.

CONCLUSIONS

Results of this qualitative survey provide consensus amongst the technology end-user community such that unambiguous goals and priorities may be defined. Systems integrating these advances could improve the safety and efficacy of endoscopic and endoscope-assisted neurosurgical approaches.

Development of new optical imaging systems of oxygen metabolism and simultaneous measurement in hemodynamic changes using awake mice

BACKGROUND

PET allows the measurement of CBF, CBV and CMRO2 in human and plays an important role in the diagnosis of pathologic conditions and clinical research. On the other hand, in animal studies, there is no optical imaging system for evaluating changes in CBF and CBV, and oxygen metabolism, from the same brain area under awake condition.

NEW METHOD

In the present study, we developed a simultaneous measurement system of LSI and IOSI, which was verified by LDF. Moreover, to evaluate oxygen metabolism, FAI was performed from the same brain area as LSI and IOSI measurements.

RESULTS

The change in CBF according to LSI was correlated with that by LDF. Similarly, the change in CBV obtained by IOSI was also correlated with RBC concentration change measured by LDF. The change in oxygen metabolism by FAI was associated with that in CBF obtained by LSI, although the change in CBF was greater than that in oxygen metabolism.

COMPARISON WITH EXISTING METHOD(S)

We revealed that the relationship between oxygen metabolism and CBF as measured by our system was in good agreement with the relationship between CMRO2 and CBF in human PET studies.

CONCLUSIONS

Our measurement system of CBF, CBV and oxygen metabolism is not only useful for studying neurovascular coupling, but also easily corroborates human PET studies.

A DAQ-device-based continuous wave near-infrared spectroscopy system for measuring human functional brain activity

In the last two decades, functional near-infrared spectroscopy (fNIRS) is getting more and more popular as a neuroimaging technique. The fNIRS instrument can be used to measure local hemodynamic response, which indirectly reflects the functional neural activities in human brain. In this study, an easily implemented way to establish DAQ-device-based fNIRS system was proposed. Basic instrumentation components (light sources driving, signal conditioning, sensors, and optical fiber) of the fNIRS system were described. The digital in-phase and quadrature demodulation method was applied in LabVIEW software to distinguish light sources from different emitters. The effectiveness of the custom-made system was verified by simultaneous measurement with a commercial instrument ETG-4000 during Valsalva maneuver experiment. The light intensity data acquired from two systems were highly correlated for lower wavelength (Pearson's correlation coefficient r = 0.92, P < 0.01) and higher wavelength (r = 0.84, P < 0.01). Further, another mental arithmetic experiment was implemented to detect neural activation in the prefrontal cortex. For 9 participants, significant cerebral activation was detected in 6 subjects (P < 0.05) for oxyhemoglobin and in 8 subjects (P < 0.01) for deoxyhemoglobin.

Measurement of T1 of the ultrashort T2* components in white matter of the brain at 3T

Recent research demonstrates that white matter of the brain contains not only long T2 components, but a minority of ultrashort T2* components. Adiabatic inversion recovery prepared dual echo ultrashort echo time (IR-dUTE) sequences can be used to selectively image the ultrashort T2* components in white matter of the brain using a clinical whole body scanner. The T2*s of the ultrashort T2* components can be quantified using mono-exponential decay fitting of the IR-dUTE signal at a series of different TEs. However, accurate T1 measurement of the ultrashort T2* components is technically challenging. Efficient suppression of the signal from the majority of long T2 components is essential for robust T1 measurement. In this paper we describe a novel approach to this problem based on the use of IR-dUTE data acquisitions with different TR and TI combinations to selectively detect the signal recovery of the ultrashort T2* components. Exponential recovery curve fitting provides efficient T1 estimation, with minimized contamination from the majority of long T2 components. A rubber phantom and a piece of bovine cortical bone were used for validation of this approach. Six healthy volunteers were studied. An averaged T2* of 0.32±0.09 ms, and a short mean T1 of 226±46 ms were demonstrated for the healthy volunteers at 3T.

Inter-vendor reproducibility of pseudo-continuous arterial spin labeling at 3 Tesla

PURPOSE

Prior to the implementation of arterial spin labeling (ASL) in clinical multi-center studies, it is important to establish its status quo inter-vendor reproducibility. This study evaluates and compares the intra- and inter-vendor reproducibility of pseudo-continuous ASL (pCASL) as clinically implemented by GE and Philips.

MATERIAL AND METHODS

22 healthy volunteers were scanned twice on both a 3T GE and a 3T Philips scanner. The main difference in implementation between the vendors was the readout module: spiral 3D fast spin echo vs. 2D gradient-echo echo-planar imaging respectively. Mean and variation of cerebral blood flow (CBF) were compared for the total gray matter (GM) and white matter (WM), and on a voxel-level.

RESULTS

Whereas the mean GM CBF of both vendors was almost equal (p = 1.0), the mean WM CBF was significantly different (p<0.01). The inter-vendor GM variation did not differ from the intra-vendor GM variation (p = 0.3 and p = 0.5 for GE and Philips respectively). Spatial inter-vendor CBF and variation differences were observed in several GM regions and in the WM.

CONCLUSION

These results show that total GM CBF-values can be exchanged between vendors. For the inter-vendor comparison of GM regions or WM, these results encourage further standardization of ASL implementation among vendors.

The Network Modification (NeMo) Tool: elucidating the effect of white matter integrity changes on cortical and subcortical structural connectivity

Accurate prediction of brain dysfunction caused by disease or injury requires the quantification of resultant neural connectivity changes compared with the normal state. There are many methods with which to assess anatomical changes in structural or diffusion magnetic resonance imaging, but most overlook the topology of white matter (WM) connections that make up the healthy brain network. Here, a new neuroimaging software pipeline called the Network Modification (NeMo) Tool is presented that associates alterations in WM integrity with expected changes in neural connectivity between gray matter regions. The NeMo Tool uses a large reference set of healthy tractograms to assess implied network changes arising from a particular pattern of WM alteration on a region- and network-wise level. In this way, WM integrity changes can be extrapolated to the cortices and deep brain nuclei, enabling assessment of functional and cognitive alterations. Unlike current techniques that assess network dysfunction, the NeMo tool does not require tractography in pathological brains for which the algorithms may be unreliable or diffusion data are unavailable. The versatility of the NeMo Tool is demonstrated by applying it to data from patients with Alzheimer's disease, fronto-temporal dementia, normal pressure hydrocephalus, and mild traumatic brain injury. This tool fills a gap in the quantitative neuroimaging field by enabling an investigation of morphological and functional implications of changes in structural WM integrity.

Reduced cortical and subcortical volumes in female adolescents with borderline personality disorder

Volumetric alterations in limbic structures have been detected in adults, but not in adolescents with borderline personality disorder (BPD). We examined adolescents in the early stages of BPD to provide a unique opportunity to investigate which parts of the brain are initially affected by the disorder before confounding factors such as long-term medication or chronicity can mask them. A group of 60 right-handed female adolescents between 14 and 18 years of age (20 patients with BPD, 20 clinical controls, and 20 healthy controls) underwent magnetic resonance imaging (MRI). Focus was on the examination of hippocampal and amygdalar volume differences. Furthermore, a cortical thickness analysis was conducted. FreeSurfer software detected significant group differences in the right and left hippocampus and in the right amygdala. Additionally, significant volume reductions in frontal (right middle frontal gyrus, orbital part of the inferior frontal gyrus bilaterally), and parietal regions (superior parietal gyrus bilaterally) were found in adolescents with BPD compared with controls. No group differences in cortical thickness were revealed.

Localized diffusion magnetic resonance micro-imaging of the live mouse brain

High-resolution diffusion MRI (dMRI) is useful for resolving complex microstructures in the mouse brain, but technically challenging for in vivo studies due to the long scan time. In this study, selective excitation and a three-dimensional fast imaging sequence were used to achieve in vivo high-resolution dMRI of the mouse brain at 11.7Tesla. By reducing the field of view using spatially selective radio frequency pulses, we were able to focus on targeted brain structures and acquire high angular resolution diffusion imaging (HARDI) data at an isotropic resolution of 0.1mm and 30 diffusion encoding directions in approximately 1h. We investigated the complex tissue microstructures of the mouse hippocampus, cerebellum, and several cortical areas using this localized dMRI approach, and compared the results with histological sections stained with several axonal and dendritic markers. In the mouse visual cortex, the results showed predominately radially arranged structures in an outer layer and tangentially arranged structures in an inner layer, similar to observations from postmortem human brain specimens.

Diffuse correlation spectroscopy for non-invasive, micro-vascular cerebral blood flow measurement

Diffuse correlation spectroscopy (DCS) uses the temporal fluctuations of near-infrared (NIR) light to measure cerebral blood flow (CBF) non-invasively. Here, we provide a brief history of DCS applications in the brain with an emphasis on the underlying physical ideas, common instrumentation and validation. Then we describe recent clinical research that employs DCS-measured CBF as a biomarker of patient well-being, and as an indicator of hemodynamic and metabolic responses to functional stimuli.

Imaging natural cognition in action

The primary function of the human brain is arguably to optimize the results of our motor actions in an ever-changing environment. Our cognitive processes and supporting brain dynamics are inherently coupled both to our environment and to our physical structure and actions. To investigate human cognition in its most natural forms demands imaging of brain activity while participants perform naturally motivated actions and interactions within a full three-dimensional environment. Transient, distributed brain activity patterns supporting spontaneous motor actions, performed in pursuit of naturally motivated goals, may involve any or all parts of cortex and must be precisely timed at a speed faster than the speed of thought and action. Hemodynamic imaging methods give information about brain dynamics on a much slower scale, and established techniques for imaging brain dynamics in all modalities forbid participants from making natural extensive movements so as to avoid intractable movement-related artifacts. To overcome these limitations, we are developing mobile brain/body imaging (MoBI) approaches to study natural human cognition. By synchronizing lightweight, high-density electroencephalographic (EEG) recording with recordings of participant sensory experience, body and eye movements, and other physiological measures, we can apply advanced data analysis techniques to the recorded signal ensemble. This MoBI approach enables the study of human brain dynamics accompanying active human cognition in its most natural forms. Results from our studies have provided new insights into the brain dynamics supporting natural cognition and can extend theories of human cognition and its evolutionary function - to optimize the results of our behavior to meet ever-changing goals, challenges, and opportunities.

Chronic cellular imaging of entire cortical columns in awake mice using microprisms

Two-photon imaging of cortical neurons in vivo has provided unique insights into the structure, function, and plasticity of cortical networks, but this method does not currently allow simultaneous imaging of neurons in the superficial and deepest cortical layers. Here, we describe a simple modification that enables simultaneous, long-term imaging of all cortical layers. Using a chronically implanted glass microprism in barrel cortex, we could image the same fluorescently labeled deep-layer pyramidal neurons across their entire somatodendritic axis for several months. We could also image visually evoked and endogenous calcium activity in hundreds of cell bodies or long-range axon terminals, across all six layers in visual cortex of awake mice. Electrophysiology and calcium imaging of evoked and endogenous activity near the prism face were consistent across days and comparable with previous observations. These experiments extend the reach of in vivo two-photon imaging to chronic, simultaneous monitoring of entire cortical columns.