Funded Awards

Dr. Ecker's group will use signatures of epigenetics, the switching on-and-off of genes in response to experience, in mouse frontal cortex to help identify different classes of cells and understand their function.

A mechanistic understanding of the neuronal underpinnings of sensory perception, action, emotion, and cognition requires measuring activities of these neuronal circuits at single cell resolution across several millimeters, and at multiple temporal scales. However, methods providing high spatial resolution often lack concurrent high temporal resolution and vice versa, creating technical challenges. Working with Applied Universal Dynamics Corporation, Dr. Kodandaramaiah and team plan to engineer and commercially disseminate digitally generated, functionalized cranial prostheses (“brain windows”) that combine wide‐field optical imaging with concurrent electrical recordings of neuronal activities for widefield activity mapping of the whole cortex during behavior. These developments will inform fundamentally new experimental paradigms in mice and enable new insights into the neuronal computations that underlie sensory perception, action and cognitive processes.

A thorough understanding of the complexities of the brain’s different cell types requires the sharing and integration of myriad genomic information generated from various data sources. Owen White proposes creating a Neuroscience Multi-Omic (NeMO) Archive, a cloud-based data repository for -omic data. White and his team of researchers will establish an archive for multi-omic data and metadata of the BRAIN Initiative. The group will document and archive data processing workflows to ensure standardization, as well as create resources for user engagement and data visualization. The NeMO Archive will provide an accessible community resource for raw -omics data and for other BRAIN Initiative project data, making them available for computation by the general research community.

Studies with freely-moving animals often encounter technical impediments that prevent the recording and perturbation of neural activity at cellular resolution. Working with Intelligent Imaging Innovations Inc (3I), Dr. Karl Kilborn and team will evaluate the feasibility of constructing a compact, stand-alone system that uses a laser source to perform fast, volumetric interrogation of cortical circuits in awake, behaving animals. They will validate the use of a two-photon, fiber-coupled microscope that can transmit light to optogenetically-targeted brain areas, as well as record biochemical signals from the same (or even different) brain areas. The success of this project will greatly increase the types of experiments that can be conducted in freely-moving animals, leading to a better understanding of the links between complex neural activity and behavior.

Identifying individual cell types in the brain is a monumental task that is complicated by the limitations of current molecular technologies. To measure genetic diversity in the whole mouse brain, Huang and Arlotta will lead a team using next-generation droplet-based single-cell transcriptome sequencing along with other highly sensitive single-cell techniques that allow for high-throughput data collection. They plan to map these data onto the spatial locations of forebrain neurons with the help of high-resolution microscopy and genetically driven cell markers. These efforts will provide the scientific community with unprecedented detail about neurons’ molecular and spatial characteristics that can be used to develop additional tools for cell-specific manipulations.

The large number of cells in the brain and the complexity of their molecular and functional characteristics make it difficult to define individual cell types. Zeng and colleagues plan to complement high throughput droplet-based transcriptome survey with deep sequencing technique and multiplexed error-robust fluorescence in situ hybridization (MERFISH) to comprehensively characterize gene expression information from anatomically mapped cells across the entire mouse brain. Additionally, they will use patch clamp method to measure neuronal function in specific brain regions, and combine electrophysiological with transcriptomic and morphological information to provide integrative profiles of individual cell types. These efforts will refine how we define cell types and will produce a census of individual cells in the mouse brain that can then be targeted for further study.

Advances in microscopy and imaging have created new possibilities in many fields of research, but these advances have also generated large amounts of data that can overwhelm traditional data management systems. Along with collaborators at Carnegie Mellon University and the University of Pittsburgh, Alexander Ropelewski plans to establish a BRAIN Imaging Archive that takes advantages of infrastructure and personnel resources at the Pittsburgh Supercomputing Center. The Archive will include a pipeline for data submission, user access and support, and BRAIN Initiative community engagement through an online presence, workshops, and hackathons. This unique resource will provide an accessible and cost-effective way for the research community to analyze, share, and interact with large image datasets of the BRAIN Initiative.

The Human Connectome Project provides one of the largest publicly available datasets of diffusion MRI from a sample of healthy individuals. Dr. Rokem and team will create an end-to-end pipeline for analysis of human white matter connections by using “tractometry” methods to analyze the diffusion MRI dataset from the Human Connectome Project. In tractometry, tissue properties are estimated in the long-range connections between remote brain regions. This project aims to generate a normative distribution of tissue properties in the major white matter connections, develop novel statistical methods to connect the properties of white matter connections to cognitive abilities, and create visualization tools to further explore and communicate the data. These tools may create an easily accessible platform that could be applied to other important neuroscience datasets.

Connectomics describes a field of study that builds maps of the connections within the brain. Dr. Lichtman and colleagues have developed a facility for generating high-resolution, large-volume serial section electron microscopy data that can be used to generate connectomic maps. In this project, access to the facility, techniques, and analytical software will be provided to the broader neuroscience community. This will allow other research groups who may be inexperienced in these techniques to generate data in projects aimed at mapping brain circuitry, a high priority goal in the BRAIN 2025 report. By providing this resource, Dr. Lichtman and colleagues will help researchers classify the cell types within healthy and diseased brains or model systems, which will improve our understanding of brain function and neurological disorders.

The community’s need for an integrated open-source analysis platform is rapidly growing due to the increasing capacity of extracellular electrodes and the limited number of new and validated spike- sorting methods. JRCLUST, a free, open-source, standalone spike sorting software, offers a scalable, automated and well-validated spike sorting workflow for analysis of data generated by large multielectrode arrays. The software can tolerate experimental recording conditions from behaving animals, and it can handle a wide range of datasets using a set of pre-optimized parameters making it practical for wide use in the community. JRCLUST has been adopted in 20+ labs worldwide since its inception less than a year ago. Drs. Kimmel and Nathan seek to expand and maintain JRCLUST, thus empowering researchers to elucidate how functionally defined subpopulations of neurons mediate specific information-processing functions at key moments during behavior.

Composed of epithelial cells and primary non-neuronal cells, the choroid plexus (ChP) produces cerebrospinal fluid (CSF) and forms the blood-CSF barrier. Studies of the ChP have been limited by a lack of tools to target and characterize ChP cells in vivo. Leveraging new single-cell transcriptomic data, Dr. Lethinen and her team aim to engineer genetic driver lines in mice that will allow precision monitoring and control of specific ChP cell types. In collaboration with the Andermann and Moore labs, the team will develop new 3D two-photon imaging methods to observe and control calcium activity, as well as visualize motility, of defined ChP cells, before developing opto- and chemogenetic protocols for ChP regulation. This toolkit aims to improve access and control of cells within the choroid plexus, advancing the knowledge of this deep brain tissue.

Development of targeted gene therapeutics to treat neurological and psychiatric disorders requires improved tools to probe circuit-specific functions. Dr. Stauffer and collaborators plan to combine single-cell RNA-Seq (scRNA-Seq) with high-throughput screening of engineered adeno-associated viruses (AAVs) to create a toolbox to minimally invasively monitor and manipulate of neurons in macaques. The researchers plan to create large libraries of mutated AAV vectors and synthetic regulatory elements, in which each variant is paired with a unique DNA barcode and use scRNA-Seq to capture the transcriptome for each cell, as well as quantify barcode expression. The team will then perform validation studies using the optimized AAVs to explore and inventory cell type-specific circuits for mood, learning, and vision in non-human primates, potentially producing a toolkit that could be applied to other large brains.

To understand how the activation of individual neurons in the brain leads to particular behaviors, it is necessary to identify synaptic connections to downstream neurons. Although considerable information about neuronal circuits has been generated using rabies virus to trace trans-synaptic connections in the retrograde direction, there is no comparable technique for trans-synaptic tracing in the anterograde direction. In rodent brains, Arnold and colleagues will optimize a non-toxic method for anterograde monosynaptic tracing from single neurons to virtually any postsynaptic receptor. Their method labels only active synapses, ensuring the technique’s physiological relevance.

Despite the success in technology development in neuroscience, there currently lacks a method to directly link activity, connectivity, and molecular identity of individual neurons in a functional circuit at the single cell resolution. Here, Drs. Cai, Cui, and teams aim to use coMAAP, a method that combines Brainbow AAV labeling, calcium imaging, innovative sample preparation, and light-sheet microscopy, to acquire correlative optical mapping of activity, anatomy, and molecular identity of the same neurons in the same animal. After optimizing and validating the coMAAP experimental paradigm, they plan to utilize coMAAP to uncover the heterogenous neuronal populations that are activated in the mouse ventral tegmental area during arousal. Improved understanding of the cellular and circuitry components could accelerate the identification of specific neuronal targets in psychiatric disorders.

Current genetic lineage recorders are limited to a finite number of recording events, making them unsuitable for the study of prolonged development. Here, Dr. Brivanlou’s lab plans to use a new approached called CHRONICLE to enable continuous, dynamic lineage-tracing in non-human primates. CHRONICLE (Cellular Hierarchy Recording in Organisms by Nucleotide Interconversion with Cas9 Linked Editors) combines base-editing with self-targeting guide RNA arrays to generate a large collection of sequence variants that can be used to trace cellular hierarchy lineages. The researchers aim to trace lineages in vitro human and marmoset cortical organoids, as well as in vivo marmoset early embryos, compare developmental lineage trees of the marmoset cortex in projection neurons, interneurons, and glia using single cell RNA analysis. Understanding novel lineage relationships of the primate brain may improve our ability to use developmental principles to restore function in diseased and damaged tissues.

Recent work has revealed the need for a robust system to accurately model the dynamic nature of human microglia in the brain in health and disease. Dr. Gandhi and team aim to validate a novel mouse xenotransplantation platform, XMG, using human induced pluripotent stem cell-derived microglia as a promising model system which they intend to disseminate publicly. The group will compare the transcriptional landscape of XMG to endogenous microglia from mice and humans, as well as use cutting edge multiphoton imaging technique to measure calcium activity and insulin response of XMG following acute insult. Further, the group will query changes in the function of XMG in the context of a pathological state resembling Alzherimer’s disease in the mouse. Developing this novel XMG system may advance the ability to study human microglia in vivo and provide far-reaching insights into microglial biology.

Magnetic resonance imaging (MRI) is an established diagnostic tool. However, while mapping dynamic anatomical and functional connectivity in the human brain is essential, adult MRI systems are not well-suited for clinical use in infants and children. Working with Advanced Imaging Research Inc., Dr. Ravi Srinivasan and team propose to create a compact MRI system that provides MRI systems to infants, children, and adults in any hospital department. The group will develop, test, and refine a compact MRI system with strong connectome gradients, thus alleviating cost and safety burdens that can be posed by large adult whole-body MRIs. The success of the project could stimulate development of mobile mental health and stroke assessment systems, thereby improving accessibility to MRI systems.

Polymer microelectrode arrays are electrical recording devices made of flexible materials. These materials reduce tissue damage and improve the long-term stability of the recording setup. The Meng and Song labs aim to establish a service that will manufacture and test out arrays that are customized to researchers’ needs. The service may help researchers use the latest electrical recording devices for studying a variety of neurological disorders.

Magnetoencephalography (MEG) is a powerful tool for non-invasive imaging of cortical activity with high temporal and spatial resolution. Unfortunately, MEG locations are sparse, largely because of high costs, maintenance, and limited usability due to rigid helmet configuration. To generate a high-density, high-performance, and wearable MEG helmet, Dr. Orang Alem and team will work with FieldLine Inc. on a few key innovations. The group will address technical challenges such as cross-talk between sensors, background field noise, and sensor calibration and localization. The success of this project could move this technology beyond the laboratory to the larger community of neuroscientists and clinicians, providing a turnkey high-density system that will have a significant impact in the field of biomagnetic research and diagnostics.

For a complete understanding of how the brain works, there is a need for a comprehensive parts list (all of the cells in the brain) along with knowledge of how those parts are connected. Current molecular technology has advanced the inventory of cell types in the brain, but detailed information about the circuits they form is limited. Dr. Mueller’s group will develop scalable and affordable cellular imaging and neuro-informatics tools, running preliminary experiments to connect the transcriptome to anatomy, in mice. Tools will be made available to researchers, to help accelerate the creation of detailed maps at cell resolution showing circuitry in whole brains.

Transcranial magnetic stimulation (TMS) is a noninvasive technique used to study brain function and can be used to treat some brain disorders. Researchers use computational simulations of TMS electrical fields to gain a better understanding of how TMS affects the brain. Existing simulations, however, are inherently variable due to factors that impact the accuracy and precision of the technique, such as differences in experimental set-up and coil placement. Dr. Gomez proposes to use a novel computational framework to measure and address the uncertainty and variability of TMS electrical fields. The project will increase the fidelity and reliability of TMS simulations. The results will benefit researchers and clinicians by enabling more precise control of the technique and may help improve medical uses of TMS.

Controlling specific neural circuits across large-scale areas is vital to improve our understanding of the nervous system. Drs. Shapiro, Tsao, and collaborators aim to further develop Acoustically Targeted Chemogenetics (ATAC) to modulate neural circuits non-invasively in non-human primates (NHPs) with spatiotemporal and cell-type specificity, starting in the visual cortex of macaques. The group will develop AAV viruses optimized for chemogenetic receptor delivery using in vivo evolution in mice and NHP, in addition to the development of ultrasound methods to target focused ultrasound-blood brain barrier opening in NHPs. ATAC will then be used to modulate face recognition neurons and sensorimotor circuits in NHPs.  Successful development of ATAC for NHPs will improve the study of neural circuits, and potentially help uncover new therapies for neuropsychiatric disease.

Magnetic resonance imaging (MRI) is a safe, non-invasive diagnostic imaging tool that provides detailed information about major organs of the body, including the brain. But, effective diagnosis depends on the quality of the MR image, and increasing magnet field strength or receiver channels can be burdensome in cost and maintenance. In a collaboration with Advanced Imaging Research Inc., Dr. Srinivasan and team propose to maximize MRI image quality with the intention of alleviating the burden placed on high-cost, high-magnet field-based MRI systems. The group plans to improve the signal-to-noise ratio within MRI systems by increasing the radio-frequency (RF) coil efficiency. The success of the project could significantly reduce scan time and facilitate disease diagnosis.

Non-invasive brain stimulation methods, like transcranial magnetic stimulation (TMS), transcranial direct current stimulation (tDCS), and transcranial alternating current stimulation (tACS), modulate brain activity in a safe and painless manner. Several BRAIN Initiative projects are combining these non-invasive brain stimulation methods with neuroimaging methods. Dr. Opitz and team will develop a computational tool that integrates empirically validated finite element method (FEM) models with imaging data, by extending and scaling the SimNIBS (Simulation of Non-Invasive Brain Stimulation) software platform. The SimNIBS is the leading open source software platform for generating FEM-based models of the electric field distribution produced by TMS, tDCS, and tACS. The resultant analysis package will allow rapid visualization and analysis of non-invasive brain stimulation (NIBS) BRAIN Initiative data, which could be more broadly used by the general neuroscience community.

Epileptic seizures can be halted or reduced by optogenetic activation of selected inhibitory neurons. By monitoring electroencephalography (EEG) data in real time, seizures can be identified at their onset and correcting pulses of optogenetic stimulation may be applied. Working with Open Source Instruments Inc., Dr. Kevan Hashemi and team propose the development of a fully implantable, wireless EEG monitor that can detect EEG events in real-time and apply correcting pulses of closed-loop optogenetic stimulation. The group will develop the necessary hardware, adapt an algorithm to classify EEG events, and test the device's ability to detect seizures in mice. The success of the project could inform creation of a medical instrument that aborts focal seizures in humans who suffer from epilepsy.

Deep brain stimulation (DBS), a method of modulating brain circuit function, is FDA-approved for certain brain disorders such as Parkinson’s Disease. The NIH BRAIN Initiative aims to launch neurotechnological developments that include new ways of directly affecting brain circuit function. Use of these novel interventions warrants careful consideration about ways in which brain stimulation may affect personal identity, autonomy, authenticity and, more generally, agency. In this project, Dr. Roskies and her team will develop an assessment tool to measure changes in agency due to direct brain interventions, and establish a database to catalogue these changes in agency in various patient populations receiving DBS. These efforts have the potential to facilitate improvements in therapeutic approaches and informed consent and will be used to develop a framework for further neuroethical thought about brain interventions, allowing us to better identify, articulate, and measure effects on agency.

To understand brain function, we need to be able to able to monitor cellular activity in the brain noninvasively over time.  To overcome these limitations Dr. Sayler's group will develop a set of self-exciting, continuously bioluminescent, optical imaging reporters that, unlike existing systems, are pre-engineered to support genetically encoded, autonomous, metabolically-neutral, neuron- or astrocyte-specific fluorescence that can be monitored with common laboratory equipment.

Changes occur to the central nervous system (CNS) throughout life due to activity-dependent plasticity as we learn new behaviors. Adaptive neurotechnologies are systems that can interact with the CNS in ways that produce beneficial neural plasticity. The group led by Schalk and Brunner has created a software platform, BCI2000, that can be used in a variety of adaptive neurotechnology applications. However, the current BCI2000 system requires considerable expertise in programming for successful implementation. This project will produce a configuration of BCI2000 that can be more easily used for adaptive neurotechnology experiments, as well as an introductory course and online training for scientists, engineers, and clinicians using the system. These new resources will allow deployed neurotechnologies to be more quickly used in the study, diagnosis, and treatment of brain disorders.

The proliferation and heterogeneity of magnetic resonance imaging (MRI) experiments, data analysis pipelines, and statistical modeling procedures presents a challenge for effective data sharing and collaboration. Russell Poldrack and colleagues propose expansion of the Brain Imaging Data Structure (BIDS), which standardizes the description and collection of imaging data/metadata for MRI, with development plans for other neuroimaging types as well. Under BIDS, the group will develop standards for pre-processing data pipelines, computational modeling results, and statistical modeling, using quick validation of any implemented standard so that researchers can assess whether their data fit within BIDS guidelines. These standardization goals will facilitate sharing of data, modeling, and results, ensuring their usability and engaging the greater research community in developing highly useable data standards.

Technological advancements in high-resolution imaging of brain volumes permits the accumulation of huge quantities of data that requires solution for storage and archiving. Dr. Brock’s project develops an open, accessible, and cloud-based data archive for electron microscopy and X-ray microtomography data by leveraging the proven architecture of the existing BossDB database. Allowing for petabyte scale data storage, curation, sharing, visualization and analysis, the archive is scalable and allows for a fast in- memory spatial data store, seamless migration of data between low cost and durable object storage (i.e. S3), and rapid access to the enormous datasets. The system enables computing data quality metrics on large datasets and metadata stores through a standardized interface. The archive is developed through an agile process that actively folds in community stakeholders for regular reviews and continuous opportunities for design input.

Dr. Makeig et al. have identified the need for the creation of data archives and standards for specifying, identifying, and annotating the data deposited. Specifically, they aim to create a gateway from the OpenNeuro.org archive for human neuroelectromagnetic data such as EEG and MEG data. This gateway will also provide tools to users for quality evaluation and data visualization. This resource will further allow machine learning methods to be applied to human brain activity data.

AFNI (Analysis of Functional NeuroImages) is an open-source software package for neuroimaging analysis and visualization of both functional and structural MRI as well as other modalities. Drs. Cox and Nielson propose to extend this widely used software package by offering containerization, cloud accessibility and web-accessible visualization. The software extension could support evolving BRAIN Initiative standards for human neuroimaging data organization and experiment specification. The project makes it possible for public integration testing of the software package, thus enabling end-user feedback and wider adoption and dissemination within the neuroimaging community.

Different neurons show widely varying patterns of gene expression and widely varying patterns of electrical spiking. It is not currently possible to predict the electrical spiking properties of a cell from its pattern of gene expression. Cohen’s team seeks to develop tools to record gene expression and spiking patterns in thousands of neurons by combining two novel technologies: all-optical electrophysiology and BRAIN Initiative-funded fluorescent in situ hybridization, MERFISH. They will create correlated brain-wide maps of gene expression and neuronal firing, first in rodent acute brain slices and then in the zebrafish spinal cord in vivo . These maps may ultimately help elucidate the roles of genes in governing neural function in health and disease.

The mammalian brain has unique abilities to process various sensory inputs from the environment, based on efficient and complex brain network structures and dynamics. However, the precise connections between the brain’s intricate wiring and its rich network dynamics are unclear, as is our understanding of how the brain’s connectivity and dynamics relate to underlying neural coding principles. Leveraging the Allen Institute’s Mouse Brain Connectivity Atlas, Dr. Choi will explore these issues, ultimately aiming to help close the gap between brain biophysiology and neural coding principles, with a focus on predictive coding theory using data-driven mathematical models.

Novel neuromodulation, recording, and imaging techniques applied to human and non- human primate brains generate datasets that require tools for organizing, processing and analyzing data that are widely available and easy to use. Drs. Milham and Craddock plan to extend C-PAC (Configurable Pipeline for the Analysis of Connectomes), building a configurable data analysis pipeline that incorporates various statistical analysis, machine learning, and network analytic techniques. In addition to adapting methods used in human imaging for non-human primate data, the project will implement a toolbox for alignment of electrophysiological data with brain imaging data. The resulting software enables high- throughput, semiautomated and end-to-end processing and analysis of structural and functional MRI data that are accessed locally or via the cloud.

Systematic studies on the brain-spinal cord connectome are lacking despite great efforts to characterize neuronal cell types in the brain. Zhang’s multi- laboratories project aims to systematically characterize neuronal types in the mouse spinal cord based on their anatomy, connectivity, neuronal morphologies, molecular identities, and electrophysiological properties. Via multiple newly-developed techniques, including an anterograde/retrograde trans-synaptic tagging method to label neurons, gene expression bard coding, and a fast 3D light sheet microscopy method, the team will establish a complete cell-type based brain-spinal cord connectome database, which will be made accessible to the neuroscience community.

To gain a complete understanding of how certain cell types work, researchers must be able to access those specific cells. Despite advances in single-cell transcriptomics, commonly used genetic tools and methodologies have variable expression, can lack specificity, and often take a long time to create. Dr. Tasic’s group aims to develop a set of adeno-associated viruses containing enhancers to target specific cell types following administration via an injection behind the eye to access the whole brain, in mice. The enhancers will be defined via RNA and epigenetic sequencing, before being screened for their specificity. Once made publicly available, this toolkit could offer a more efficient method to access specific cell classes, facilitating investigations into their roles in circuit function.

Monitoring endogenous synaptic proteins in neuronal subtypes of behaving animals is needed to better understand neural circuits underlying behavior, but current visualization methods can produce altered protein function and off-target effects. Here, Dr. Zhong, Mao, and labs aim to develop a novel genetic strategy called endogenous labeling via exon duplication (ENABLED) to label endogenous synaptic proteins for in vivo imaging. Expanding on their success of labeling PSD-95 in neurons, the team will optimize the ENABLED method to label several additional synaptic proteins in mice, with the goal of generating ENABLED mice in which synaptic proteins are labeled with different colors for simultaneous imaging. This work could provide new tools for researchers to advance our understanding of synaptic connectivity and plasticity under physiological conditions in behaving animals.

To better understand human-specific glial diversity, Dr. Tsankova’s lab has endeavored to improve isolation methods of glial cells from human brain tissue, via cell-specific immunotagging techniques to isolate nuclear RNA and chromatin from frozen brain. Building off this work, the team aims to profile the epigenetic and molecular features of developing and adult human astrocyte and oligodenroglial lineages. They will use high throughput technologies like Tn5-HiC, ChIP-, RNA-, and ATAC-seq to characterize the chromatin structure, transcriptional factor binding activity, and differentiation kinetics across different developmental stages of human astrocytes and oligodenroglial progenitors. These epigenetic and functional datasets should enable the creation of an integrated map of glial plasticity, providing a reference tool for comparative studies of human health and disease.

Typically, we experience the world as a continuous sequence of events; but when recalling memories, we remember segmented episodes. The hippocampus and prefrontal cortex (PFC) play a role in segmenting, linking, and retrieving memories of associated events, but the neural circuit mechanism of this process is not well understood. Dr. Jafarpour aims to use intracranial encephalography (iEEG) to identify the neural dynamics in the hippocampal-PFC circuit that support the encoding of sequences of words. By combining iEEG with advanced analytical techniques, natural language processing models, and research with patients with hippocampal lesions, this project will offer insights into the neural basis of speech encoding and memory formation. The work may inform the development of neural prosthetics for use by patients with memory impairments.

Many traumatic brain injury (TBI) patients often experience chronic cognitive impairments that disrupt functioning and can interfere with societal reentry – current efforts aim to rapidly restore cognitive function to TBI patients. In doing so, a thorough understanding of the opportunities and challenges posed by rapid cognitive restoration is critical. To address this need, Dr. Joseph Fins and his team will interview patients and family members before implantation of thalamic deep brain stimulation (DBS) devices. These interviews will collect perspectives on risks and benefits, expectations and fears, as well as factors that are weighed during decision making. After implantation, interviews will collect perspectives on the impact of cognitive impairment and restoration. The project aims to develop legal theory that supports social reentry for TBI subjects who have achieved cognitive restoration, paving the way for maximizing patient-centered benefits of any therapeutic advance.

Recent tissue-clearing techniques and advances in microscopy have made it possible to produce 3D images of intact brains. to help ensure consistency in data collection and analysis, Dr. Hamilton and her team will develop a set of standards for3D imaging of whole brains for the neuroscience research community.. Dr. Hamilton’s group will convene a Working Group of experts who will work through a consensus process to establish standards that will be distributed to the research community. These standards should help improve the efficiency of imaging research and allow comparisons across studies.

Working memory is crucial to many human functions, and a better understanding of its underlying mechanisms could improve our understanding of memory abnormalities in advanced age. Current hypotheses suggest that working memory is maintained by a hierarchy of interconnected cortical areas, but more work is needed to understand the unique role of each area. Dr. Resulaj aims to study visual working memory at the systems and cellular level in the mouse. Utilizing novel behavior assays, a laser scanning galvo system, and optogenetics, this work ultimately will develop a computational model of visual working memory in the mouse cortex.

Activity in the striatum is known to be linked to perceptual decision-making processes orchestrated by the cortex. Dr. Sun proposes to use genetically-encoded calcium indicators to examine cortex-wide activity patterns in mice performing perceptual decision tasks. This will be combined with wide-field calcium imaging in order to correlate behavior with changes in neural activity. The research will enhance our understanding of how activity in the cortico-striatal pathway supports decision-making.

Dr. Ghosh and colleagues propose to develop a new computer infrastructure for scientists to share, collaborate, and process neurophysiological data. The data will be open to both scientists and also be used to engage high school and college students. The team will also develop tools to facilitate data submission and access and to encourage adoption of the Neurodata Without Borders data standard.

Neuropharmaceuticals provide relief to millions suffering from an array of neurological and neuropsychiatric disorders. However, a barrier to identifying novel therapeutic targets can be attributed to a poor understanding of how the behavioral effects of drugs are mediated by specific neural cell types in the brain. Tadross’ team recently developed DART (Drugs Acutely Restricted by Tethering), the first and only method to date that can map the behavioral effects of clinical drugs by cell type. These tools would reveal circuit origins of desired vs harmful drug effects, explain why some drugs have higher efficacy than others, and potentially empower future rational efficacy advances. This project aims to expand the catalog of available DARTs, increase their subcellular specificity, and improve ease of use – particularly in combination with recording devices across larger brain areas. If successful, these tools will maximize utility to the neuroscience community, enabling previously intractable questions to be addressed.

This project develops DABI (Data Archive for the Brain Initiative) to aid the dissemination of human neurophysiological data generated through the BRAIN Initiative. Incorporating infrastructure from a pre- existing hub for delivering effective informatics and analytics solutions for major projects in the study of neurological diseases, Drs. Toga, Duncan, and Pouratian will aggregate data related to human electrophysiology, making the data broadly available and accessible to the research community. The group plans to incorporate analysis tools with user interfaces, implement tools for data management and use, and link metadata across different data modalities. The overarching goal of this project is to secure, link, and disseminate BRAIN Initiative data with all pertinent recording and imaging parameters coming from participating sites

Many labs develop unique software to manage and interpret their findings, but those programs are often specific for certain types of datasets, making them difficult to share among researchers. Dr. Van Hooser’s team plans to create an interface standard that establishes a common set of processes for accessing neurophysiological and imaging data. The standard will be tested, and revised accordingly, based on feedback from graduate students and postdoctoral researchers during data access events, or “hack-a-thons.” The interface standard will help increase the speed of research and make data widely available, allowing individuals outside of the neuroscience and research communities to make discoveries.

The precise number of neuronal cell types of about one hundred million highly-interconnected neurons in the mouse brain is unknown. Ultimately, the classification of neuronal cell types in the mammalian brain will require integrating molecular, morphological, and connectomic properties. Yang and colleagues propose to classify neuronal cell types via brain-wide comprehensive profiling of the dendritic morphology of neurons with subsequent digital reconstruction. Their transgenic mouse lines, MORF, enable sparse labeling of genetically-defined neurons in mice, which allow for the resolution and reconstruction of individual cells’ dendritic morphologies within densely populated neuronal networks. This project will help contribute to the BICCN effort to generate a reference mouse brain cell atlas, and data will be shared publicly through the BRAIN Cell Data Center.

To advance our understanding of the function of dynamical neural circuits, there is a need for technologies that can record the activity of hundreds to thousands of neurons simultaneously within and across brain regions in intact brains. Through Neural Dynamics Technologies, LLC, Drs. van Welie, Scholvin, and Boyden propose one way to resolve this issue by developing customizable high-density neural probes for use in acute or chronic recordings of neural population activity with a spatial and temporal resolution that is required for studying neural circuit activity.

Olfaction is an extremely important sensory modality across species, and it is one of the first to be disrupted in many neurodegenerative diseases. Dr. Doyle will conduct a full census of all cell types in the mouse olfactory bulb, to better understand information integration and processing in the olfactory system. This approach will utilize transcriptomic (single cell RNA-sequencing) and epigenomic (single nucleus methylome- and single nucleus ATAC-sequencing) data generated by members of the BRAIN Initiative Cell Census Network (BICCN). Overall, this will allow for a fuller understanding of the roles of cell diversity, regulatory elements, and transcription factors in the mouse olfactory system.

While it is known that proprioception plays an important role in movement, how the brain translates proprioceptive information into information for movement in the somatosensory cortex (S1) is poorly understood. Dr. Blum aims to study how active and passive movements of limbs elicit different responses from muscle spindles and Golgi tendon organs, especially as reflected in area 3a of S1. Using electrophysiological data, arm kinematic measurements, and EMGs in monkeys trained to perform an arm-reaching task, this research aims to model afferent proprioceptive signals and motor outputs in a neural network model. These results will improve our understand of the neural control of movement.

Dr. Hobert and colleagues will create a highly selective technology for experimentally manipulating genes in neurons, by tapping into the regulatory machinery of individual cell types.

Due to their chemically inert nature and delayed signaling pathways, neuropeptides have been difficult to study by conventional electrophysiology or with oxidizable probes. To overcome this, Dr. Pang’s group aims to develop genetically encoded optical sensors for neuropeptides, named Chimeric Detectors for Neuropeptide Release (CDNRs), using unique structural features of neuropeptide-recognizing receptors. To validate the new probes, the researchers will express CDNRs in defined glucagon-like peptide-1 (GLP-1) and corticotropin-releasing hormone/factor (CRF) circuitry using viral transduction in mice and perform high-resolution optical recording to detect the release of endogenous GLP-1 and CRF, ex vivo and in vivo. This work may lay a foundation for the development of other neuropeptides detectors to advance our understanding of neuropeptide functional connectivity in the brain.

Optogenetics and chemo-optogenetics are emerging tools for neuroscience research, providing ways to modulate cell function with light. However, current limitations for these tools include limited ability to target cells deep in the brain, the relatively small effects they elicit, and safety concerns over long-term use. Dr. Lam proposes to develop new chemo-optogenetic tools to address these issues, based on the TRPA1 and TRPV1 receptor channels. Further, she will develop this technology for in vivo use, testing its utility in behavioral assays of zebrafish. The work will improve our ability to understand brain circuit function, and will create a platform for the discovery of other novel chemo-optogenetic approaches that mimic natural cell activity.

The ability to genetically target specific neuron populations in non-human primates (NHPs) and humans is needed to understand neural circuits in epilepsy and psychiatric disorders. Here, Drs. Fishell, Dimidschstein, and Deverman and collaborators aim to develop a Cre-based, high-throughput screening platform to identify AAV-enhancer vectors that could target specific disease-relevant neuronal populations. The team plans to evaluate the performance of promising AAV vectors across model systems (mice, NHPs, and human cell-derived organoids), before mapping the functional connectivity of inhibitory and disinhibitory interneurons in prefrontal cortex of NHPs. This work may provide a validated toolkit of AAV vectors to investigate the brain activity of specific neuronal cell populations to further our understanding of disease-relevant circuits.

Low-cost, portable Magnetic Resonance Imaging (MRI) systems require use of small-bore magnets that are unable to capture the detail necessary to image the human brain. In this project, Drs. Wang and Wagner propose to further develop an imaging method previously funded by The BRAIN Initiative, by designing, building, and testing a portable 1.5T MRI system to image human brain activity. The novel imaging technology works with a small, lightweight (250 lb.), portable, low-cost, head-only magnet. The compactness and efficiency of this non-invasive imaging system makes the study of the human brain possible in more clinics and in subjects who previously were unable to receive an MRI scan due to constraints of standard systems.

Dr. Zhao's project aims to build a highly innovative and low-cost imaging tool that addresses a technological gap in neuroscience research for non-invasive recording of large neuron populations with high spatial and temporal resolution. The team plan to build and validate a fluorescent imaging system that enables parallel recording of multiple neuron populations with sub-cellular and sub-millisecond resolution. The system will include optimization of a benchtop microscope with two detection channels, and subsequent development of a head-mounted device for imaging in rodents. Successful development and commercialization of this technology could significantly advance neuroscience research, and thus improve our understanding of brain function.

Various improvements are being considered to create next generation biophysical models of blood oxygenation and fMRI measurements in brain. Dr. Sencan plans to quantify spatial and temporal diversity in cortical metabolism in order to inform these scientific advancements. By measuring processes of cortical oxygenation, metabolic rate, and blood flow responses at microvascular scales, she aims to understand how these processes contribute to brain function and vary across age, region, and depth in the awake, mouse brain. To achieve these goals, she will use novel experimental techniques, related to faster, deeper, and more realistic imaging of oxygen concentration. This work may support better interpretation of clinical results derived through imaging technologies like fMRI.

Noninvasive neuromodulation technologies use a variety of electrical, magnetic, optical, and sonic techniques to stimulate the brain. The ensuing modulation of brain network dynamics can be used as a tool to study healthy brain processes, as well as for treatment of brain disorders. He’s team will develop an acousto-modulated electrophysiological source imaging (ESI) technique with improved spatial precision, and use it to monitor and image transcranial focused ultrasound (tFUS)-induced brain activity in real-time. The group will validate this integrated ESI-guided tFUS system in rats, using simultaneous intracranial recordings of neural spikes and local field potentials, and ultimately test it in human subjects. This non-invasive neuromodulation, with high spatiotemporal precision, promises stimulation which is individualized and responsive to dynamic neural activity.

Dr. Adey’s team will use advanced single cell analysis techniques to explore the epigenetic properties of non-neuronal brain cells. Techniques will include performing chromatin access assays and genome-wide profiling of DNA methylation, along with studying how a cell’s chromatin folds. Some of their methods will be used to profile and compare glial and vascular cells across brain regions in both rodents and humans. To help further understand the role of non-neuronal cells in the brain, the group plans to make these tools and data available to the research community for additional analyses.

Although major categories of cell types have been identified in the human brain, less is known about the different subtypes or their locations. Drs. Ecker and Behrens’ groups will create an epigenetic atlas of the human brain focusing on DNA methylation, open chromatic patterns, and transcriptomic signatures at the single-cell level. In addition to defining new cell types and their markers, this analysis may uncover new information on genetic variants associated with psychiatric and neurological disorders.

Determining how brain cells communicate with each other bolsters understanding of the causes of disorders. The new Neuropixels probe allows for highly detailed recordings of neurons communicating; however, sophisticated software is required to use this tool and to understand the data it generates, which include nearly 1000 recording sites from a single probe. For other labs to use this system, a support network is needed to address user requests, maintain the software code, and improve documentation. Through this project, Dr. Siegle and colleagues will support other labs that wish to use Neuropixel probes to better understand the underpinnings of neurological and mental disorders.

The brain’s inferior colliculus is described to have a patch- or matrix-like “modular” anatomical organization, with various nuclei and distinct chemical boundaries. However, the functional implications of this organization are unknown. Dr. Lesicko’s experiments aim to determine whether this modularity underlies distinct streams of information processing in the inferior colliculus. Using a combination of two-photon calcium imaging, clustering analysis, optogenetics, and behavioral assays in mice performing a behavioral task, the work will examine distinctions in neural activity and mechanisms for auditory and somatosensory signaling in the inferior colliculus.

Different laboratories use different behavioral systems, hardware, and software, which makes it difficult to standardize, communicate, and replicate experiments. Dr. Kepecs et al. have led the creation of a laboratory consortium to address this problem by developing requirements for behavioral data formats and an open source software suite for editing, executing, and visualizing behavioral tasks. They will also engage the scientific community to promote the adoption of these standards and tools.

Due to the relatively poor performance of current anterograde viral tracers, Drs. Xu, Horwitz, Luo, Sandri-Goldin and teams aim to engineer improved anterograde monosynaptic tracers with increased labeling efficacy and reduced toxicity for the analysis of neural circuits. Using a bacterial artificial chromosome-based engineering system, the team will generate recombinant Herpes simplex virus type 1 strain 129 (H129) vectors for targeted expression in multiple neural circuits. The researchers will then validate their anterograde tracers in the visual system, hippocampus, and stress-relevant hypothalamus circuits of rodents and non-human primates. The tools developed here will be disseminated through a service platform with the goal of improving the ability to study neuronal projection networks.

The ability to record the activity patterns of genetically-defined neuronal populations in freely behaving animals is transforming neural circuits research. To advance our understanding of higher-cognitive function, complex behavior and mental health, a critical need remains to translate such capabilities to research using non-human primates. Working with Inscopix Inc., Dr. Jonathan Nassi and team will build on the success of nVista for rodents, Inscopix's flagship product, to develop and commercialize a next-generation platform for integrated calcium imaging and electrophysiology in behaving macaques. The group will prototype and validate a system that enables cellular-resolution, large-scale recordings deep and distributed throughout the macaque brain. Success of the project could produce a commercial-ready, next-generation platform for neural circuit research in behaving macaques.

Brain-computer interfaces (BCI) show promising potential in treating symptoms of various brain diseases. A collaborative group at the University of California, San Diego, has developed a high-density array of microgrid electrodes that are thin, non-destructive, and sit lightly on the surface of the brain, for improved decoding and resolution of neural activity. This study will implement this technology to study cortical physiology and organization in the rat somatosensory cortex. Dr. Cleary aims to test the capabilities of these surface microgrids for discriminating cortical columns in the rat “barrel cortex,” representing innervation of the whiskers. He also will study how surface stimulation of the cortex affects neural activity in different layers of the cortex, initially in rats and subsequently in human neurosurgical patients. This work may improve BCI technology, providing additional treatment strategies for various brain diseases.

Recent tools have led to advances in 3-D imaging of whole brains, opening the door for proteomic imaging that can increase our understanding of how the structure and activity in cells lead to brain functions. Unfortunately, proteomic imaging is limited by antibodies currently available for this type of research. Dr. Chung’s team aims to develop a comprehensive, open-source toolbox of antibodies generated against 300 proteins that are critical for understanding how the brain works. These antibodies should be more cost-effective, targeted, and compatible with a variety of tissue processing techniques.

Agency, our ability to act and experience a sense of responsibility for our actions, is central to individual identity and societal conceptions of moral responsibility. Neural devices are currently used to treat some brain disorders, such as Parkinson’s disease, and are being developed to treat others such as depression and obsessive-compulsive disorder, yet their use raises important ethical concerns about potential effects on agency. Dr. Goering, Dr. Klein and their team will investigate agency in individuals receiving brain computer interface devices for sensory, motor, communication, and psychiatric indications. They aim to build a user-centered neural agency framework, and, ultimately, to enhance the informed consent process by developing a communication tool that patient participants might use to better understand and discuss potential changes in agency associated with use of neural devices.

Molecular and cellular neuroscientists often lack the training in computer programming to fully explore “-omics” data common in the BRAIN Initiative. Drs. Hertzano and White will implement analytic software for visualization and interactive genome browsing of gene expression and RNA-seq data, including simple and complex cross-dataset analysis. These tools will be made available in the BRAIN Initiative funded Neuroscience Multi-Omic Data Archive (NeMO) which hosts multi-omic data. The software will provide an easy-to-use web-based work environment for visualization and analysis of multi-modality and multi- omic data, interrogation of relationships between epigenomic signatures and gene expression, and integration of analytical techniques for multivariate analysis, gene co- expression and other analyses.

Three-dimensional human brain atlases are increasingly important for integrating complex datasets into useful community resources. Fischl’s team proposes to create a multi-scale atlas—akin to Google Earth™ for the human brain—to map hemisphere-wide networks and also zoom in to see individual, labeled cells at micron resolution. This advance will be made possible through multiple imaging technologies, including light-sheet microscopy, tissue clearing, immunohistochemistry, magnetic resonance imaging, and newly-developed techniques in Optical Coherence Tomography. The ability to probe the cellular properties and multi-scale networks of specific areas in the human brain could evolve to an automated system for visualizing across the entire human brain in health and disease.

Neurotransmitter (NT) sensors that are versatile, selective, sensitive and reliable can facilitate investigation of the neurobiological mechanisms of behavior and disease symptoms. However, existing monitoring methods suffer from the inability to measure NT dynamics continuously, in real time. Working with Alcorix, Dr. Moldovan and team will develop a novel implantable probe for real-time detection of excitatory and inhibitory NTs. The group plans to create the next generation of their biosensor microelectrode array probe, capable of higher sensitivity, selectivity, and reliability, with no need for external reagents. The multiplexing and in vivo capabilities of the probe will facilitate a fundamental understanding of NT homeostasis that can inform more effective animal models and therapeutics for brain diseases and disorders.

Understanding the dynamics of neural activity requires new tools to record and manipulate neural signals in real-time. However, current cortical electrophysiological recording and stimulation implant systems puncture the skin, present a constant danger of infection and irritation, and require extensive attention from investigators to clean and maintain. Working with Ripple LLC, Dr. Andrew Wilder and a team of investigators will develop the Grapevine IRIS (Implantable Recording with Integrated Stimulation) system. IRIS will be a fully implantable system capable of both recording and stimulation on a large number of channels, enabling closed-loop experiments while mitigating the need for skin puncture. The success of IRIS will provide a research platform to enable longer, safer, and better chronic animal studies.

More than 500,000 children in the US and Canada suffer from epilepsy and 30% of these children continue to experience seizures despite being treated with anti-seizure medication. Unmanaged, epilepsy can result in cognitive decline, social isolation, and poor quality of life, and has substantial economic impact on families and society. Novel approaches for treating epilepsy such as vagal nerve stimulation and responsive neurostimulation are being developed, but this work has been conducted predominately in adults and the outcomes of these trials are often not clearly generalizable to children. In this project, Drs. Illes and McDonald will explore ethical issues confronting families and clinicians when considering new treatment options for drug-resistant epilepsy in children. They aim to develop, evaluate, and deliver patient-directed resources in the form of infographics and informational materials and videos, and clinician resources for family decision-making, clinician counseling, and care.

In an effort to improve our understanding of how synaptic plasticity contributes to social memory, Dr. Phillips aim to create a tool to modulate synaptic plasticity in specific circuits during behavior. Using advanced imaging techniques and various innovative biochemical assays, she plans to create a photo-activatable inhibitor of presynaptic plasticity and will use this tool to understand the circuitry of social memory. The researcher will develop constructs of a photo-activatable PKA inhibitor and screen the constructs using 2-photon fluorescence lifetime imaging in HeLa cells. The optimized inhibitor constructs will then be expressed in the dCA2-vCA1, vCA1-PL, and PL-dPAG projections in mice and used to block presynaptic plasticity during social learning in either aggressive or neutral contexts.  Successful development of these tools will enable investigation of neural circuitry to better our understanding of behavior and neuropsychiatric diseases.

Neurodevelopmental disorders can arise from impairments in sensory-dependent refinement or strengthening of synapses during postnatal brain development. However, treatment strategies focused on addressing such impairments lack an advanced understanding of the cellular and molecular mechanisms of this process. Building on prior results showing that expression of the gene Fn14 is driven by visual experience and encodes a receptor required for synaptic refinement, Dr. Cheadle aims to use slice electrophysiology and bioinformatics to study how microglia-to-neuron signaling is involved in refinement via examining the role of TWEAK, an Fn14 receptor ligand, in healthy and neurodevelopmentally-impaired mice. The results may offer insights into the development of treatments for neurodevelopmental disorders.

Hippocampal microcircuits include excitatory pyramidal cells, which integrate information and signal to downstream brain regions, and inhibitory interneurons, which function locally to regulate pyramidal cell activity. Circuit dysfunction in the ventral hippocampus (vHipp) has been associated with various brain disorders. Dr. Donegan will use techniques including mammalian GFP reconstitution across synaptic partners (mGRASP), fiber photometry, in vivo electrophysiology, and optogenetics, to test the hypothesis that different types of interneurons in the vHipp differentially regulate the function of ventral hippocampus pyramidal cells depending on their projection target. She will also test whether vHipp microcircuit anatomy and function are altered by chronic stress, shedding light on the potential link between circuit dysfunction in the hippocampus and brain disorders.

Brain-computer interfaces and neuroprosthetics have provided a significant benefit to patients with cervical spinal cord injuries. However, current technology is limited in its abilities to allow the user to control how much force is exerted by the prosthesis and to provide sensory feedback from the prosthetic hand. In a public-private collaboration with Blackrock Microsystems, Dr. Boninger and colleagues are looking to improve the dexterity of neuroprostheses by incorporating microstimulation of the somatosensory cortex. This stimulation could provide tactile feedback to the user and hopefully allow the user to better control the force applied. Ultimately, this approach will improve the dexterity and control of prosthetic limbs used by patients with spinal cord injuries.

The NIH BRAIN Initiative aims to catalyze novel tools and technologies to modulate brain circuit function, paving the way for new treatment options for brain disorders. However, such interventions also have the potential to cause unintended changes in aspects of cognition, behavior, and emotion. These changes, in turn, raise concerns regarding autonomy, personal identity, and capacity for informed consent. In this study, Dr. Cabrera Trujillo and her team will study ethical concerns, beliefs, and attitudes about the use of novel bioelectric approaches among clinicians, patients, and the broader public. The work will provide stakeholder perspectives that will be valuable for informing the responsible development and use of these novel neurotechnologies.

Individuals with severe, disabling, chronic mental illness, such as treatment-refractory schizophrenia/schizoaffective disorder (TRS), have often been excluded from research, leading to challenges in developing treatment for their illnesses as well as access to that treatment. Here, Dr. Judith Gault will examine the ethical issues that will lay a foundation for conducting clinical research in TRS patients who have traditionally been excluded in studies. These ethical principles will include transparency, accessibility and safety of clinical trials testing neurosurgical intervention in TRS patients who are in urgent need of effective novel interventions. The team will explore the ethical implications of excluding individuals based on their capacity to consent, surgical risks, and severity of symptoms for a planned clinical trial to treat TRS. Successful completion of the project could revolutionize our understanding of how to overcome research disparities among severely disabled individuals by improving transparency, accessibility, and safety of clinical trials.

A camera that could image neuronal current distributions with a large array of pixels and a spatial resolution better than 1 ms resolution could dramatically enhance our understanding of neuronal circuitry. In this Phase I STTR, Fieldline, Inc. will develop a novel type of magnetographic camera, capable of providing single-shot images of electrical currents in neuronal circuits in vitro and in vivo with a millisecond time resolution. The team will first build a bench-top camera before combining it with electrode arrays, testing the ability to image neuronal connections across the circuit in vitro with turtle cerebellem. This will potentially lead to a completely portable, economical multi-pixel camera that can be produced for neuroscience research. 

Small, tightly-packed granule cells (GrCs) in the cerebellum have been associated with sensory and motor events, but their specific roles remain unclear due to their close packing.  Dr. Broussard aims to precisely record from and perturb GrCs and measure the resulting effects on neural firing patterns and activity in mice. The researcher will develop a spike-counting method for genetically encoded indicators by optimizing the kinetics of the calcium sensor GCaMP. After developing a cleared skull preparation to access the full posterior cerebellum in mice, the new indicator will be used to map the neocortical drivers of GrC activity across the cerebellum, and rodent behavioral tasks will be used to disambiguate sensory, motor and internal-state contributions to granule cell activity patterns. Better knowledge of GrCs activity will further our understanding of neural circuits that guide sensory processing and plays roles in neurological disorders.

A variety of cell types across the cerebral cortex develop from a small number of radial glia neural stem cells, though current tools lack the ability to connect this lineage to genetic mutations underlying developmental perturbations in a scalable manner. Dr. Nowakowski’s team will combine developmental lineage tracing and spatial transcriptomic technologies into molecular barcodes that trace the origin of cortical cells in mice. In addition to potentially increasing understanding of brain development, these studies may introduce a scalable framework to integrate lineage tracing technologies with spatial tissue mapping.

To process information about the world, the nervous system must distinguish external stimuli from internally generated sensory stimuli, but the mechanisms underlying the cellular basis of internally generated sensation and movement are not well understood. Here, Dr. Suver plans to develop a small circuit model of this process using the antennae of the fruit fly as a model system. Using electrophysiological recordings, optogenetics, and immunohistochemistry, she will develop the neural circuits controlling and sensing antennal movement as a cellular model for studying principles of active sensing. The insights gained from a tractable genetic circuit model may improve understanding of active sensation, as well as how these mechanisms might fail in disease.

Evidence suggests that both spontaneous and learned behaviors engage activity in various regions of the cortex. However, for perceptual decision-making, more complex and demanding tasks involve decorrelated cortical activity as a more distributed, widespread process throughout the cortex. Dr. Pinto aims to understand this phenomenon, using cutting-edge technology to study how distributed cortical acitivity mediates complex decision-making and the mechanisms of task-induced changes in large-scale cortical dynamics. The research will utilize two-photon calcium imaging, virtual reality behavioral tasks, pharmacogenetics, optogenetics, and modelling, increasing our understanding of the neural basis of decision-making.

Despite the ability of scientists to record from and modulate the activity of individual neurons and neuronal circuits, it has been difficult to translate those observations into a readout of behavior. Dr. Datta and colleagues have developed a technology called Motion Sequencing (MoSeq) that captures, in three dimensions, the behavior of a freely moving mouse and then, using machine learning, turns that data into standard “syllables” of behavior. While MoSeq could have broad applications for several research projects, the complex math makes it difficult for non-expert users to implement. This project will adapt the MoSeq system to make it more accessible for researchers and will provide a training course on how to set up and use MoSeq. This will enable a wider range of research projects to use the technology, which could improve our ability to study the effects of drugs or genetic and neuronal changes on behavior.

Given the increasing use of magnetic resonance imaging (MRI) in brain research, understanding of what MRI signals really represent has become a fundamental yet fully elusive research topic. Recent neuroscience/neuroimaging research has also emphasized the importance of using multi-modal approaches, in which the data are acquired by multiple techniques to combine higher temporal resolution with spatial resolution of brain activity.  Drs. Shih and Franklin aim to bridge two of the most powerful and widely used research/clinical tools used in neuroscience – MRI and electrophysiology – by creating a novel MR-compatible 16-channel microelectrode array. This microelectrode array addresses two major applications: high resolution electrophysiology and deep brain stimulation. Both of which, in combination with simultaneous MRI, comprise a highly innovative platform which is intended to improve our understanding of brain function and neural circuit connectivity.

Given the increasing use of magnetic resonance imaging (MRI) in brain research, understanding of what MRI signals really represent has become a fundamental yet fully elusive research topic. Recent neuroscience/neuroimaging research has also emphasized the importance of using multi-modal approaches, in which the data are acquired by multiple techniques to combine higher temporal resolution with spatial resolution of brain activity.  Drs. Shih and Franklin aim to bridge two of the most powerful and widely used research/clinical tools used in neuroscience – MRI and electrophysiology – by creating a novel MR-compatible 16-channel microelectrode array. This microelectrode array addresses two major applications: high resolution electrophysiology and deep brain stimulation. Both of which, in combination with simultaneous MRI, comprise a highly innovative platform which is intended to improve our understanding of brain function and neural circuit connectivity.

A thorough understanding of brain function requires the integration of neuroscience data across species and scales. While current software can verify data quality within one or a handful of data sources, reproducibility across multiple data sources is limited. Xenophon Papademetris and colleagues are developing software tools with cross-scale, cross-species reproducibility analysis in mind. By leveraging data created by two other BRAIN Initiative projects at Yale University, Papademetris will extend current software algorithms to incorporate data from multiple sources, design the software to be cross-platform compatible, validate the software through rigorous testing, and finally, distribute it to the community. The potential for a set of software tools to reliably and reproducibly analyze multiple heterogeneous neuroscience data types will help to break down data barriers for the greater neuroscience community.

To monitor brain states under various conditions, multielectrode arrays can sense neurotransmitters across distributed parts of the brain. However, the brain's complexity and heterogeneity - coupled with technological limitations of these arrays - have created challenges for this approach. Working with Microprobes for Life Science, Dr. Alexander Zestos and a team of investigators will develop and commercialize multielectrode arrays for neurotransmitter detection with fast scan cyclic voltammetry. Multielectrode arrays will be either constructed with carbon fibers or carbon-modified metal microelectrodes and coupled with multichannel hardware to measure neurotransmitter changes in multiple brain regions simultaneously. The success of this project will meet a crucial and currently unmet need in the greater neuroscience community by providing multielectrode arrays with neurotransmitter sensing capabilities.

Three separate research groups are collaborating to understand in detail how three distinct areas of the brain function and work together to enable learning and decision-making behaviors. Drs. Kreitzer, Komiyama, and Lim are leveraging an impressive set of technologies to monitor and perturb different cell types in each brain region while the mice perform learning and decision-making tasks. By applying multiple recording methods across these brain regions at both the level of a single neuron and entire subpopulations of neurons, while the animals perform the same set of tasks, researchers hope to develop a single model of how vertebrate animals make choices about what to do next.

Penetrating electrode arrays have an expanding application in neuroscience research as they can provide direct access to neural signals across the central and peripheral nervous system with high spatial resolution. Chronic electrode implants could revolutionize treatment for a range of medical conditions, including prosthetic motor control and proprioception for amputees, and brain-machine interfacing for paraplegics. Unfortunately, device implantation applies forces to the neural tissue resulting in significant brain compression (dimpling) at the implant site, which increases risk of implantation trauma, bleeding and inflammation. Actuated Medical, Inc. will develop a neural implant inserter, the Ultrasonic Precision Insertion of Neural Devices (UPIND) system, that will reduce the insertion force by applying ultrasonic energy to electrode arrays during insertion. This system aims to enable greater placement control of floating microware arrays, while reducing tissue trauma.

The ability to learn, think, and make decisions in complex environments is extremely important to critical life functions across species, but the neural correlates of external and internal representative states are largely unstudied. Recent studies suggest activity in the amygdala and orbitofrontal cortex correlate to state representation, but their exact roles are unknown. Dr. Barack aims to investigate how monkeys learn these state representations, using a complex, sequential decision-making task. During this novel behavioral task, similar to the boardgame “Battleship,” the team with elucidate learning in a complex environment, measuring associated neural mechanisms of circuits in the amygdala and orbitofrontal cortex activated in learning and decision-making. These results could promote the creation of computational models that may provide insights about animal and human interactions with the world.

With the goal of understanding the interplay between astrocyte, neuronal activities, and regional neurovascular response, Dr. Pan and his team aim to develop an optical platform to image synchronized activity, via genetically encoded calcium indicators, alongside local cerebral blood flow dynamics. The team plans to develop multimodality fluorescence – swept-source optical Doppler microscopy (fl-ssODM) to image large-scale astrocyte/neuronal calcium fluorescence and cerebral blood flow velocities in the cortex of mice. fl-ssODM will provide real-time spatiotemporal dynamics of astrocyte/neural calcium activity and vascular responses at rest and during activation of the cortex. The researchers will employ inhibition of astrocyte signaling using designer receptor exclusively activated by designer drugs to further validate fl-ssODM as a useful tool to investigate the interactions of astrocytic and neuronal activities and local cerebral blood flow in the brain.

Despite physical therapy, about 50% of stroke survivors must live with impaired hand function, impacting daily activities for the remainder of their life. However, recent studies in rats have suggested that low-frequency cortical stimulation may help alleviate such symptoms. In order to translate this work to humans, Dr. Khanna aims to use a multiscale model of electrophysiological recording to monitor motor and somatosensory activity during dexterous control, comparing affected and unaffected hemispheres in non-human primates (NHP) recovering from a stroke. The results may inform development of therapeutic techniques for stroke-related motor dysfunction, while improving our understanding of neuromodulation.

Positron Emission Tomography (PET) has the potential to be an important tool in understanding the human brain. However, current PET systems used in oncology are expensive and lack the level of resolution necessary for human neuroimaging studies. Drs. Hunter and Coulis plan to combine a novel detector technology with innovative system architecture for commercial production of a cost-effective PET brain imaging system (Neuro-PET HD). In the Phase I STTR, PET/X LLC will create and validate the performance of a new PET detector ring system before generating a full commercial prototype. The goal is to reduce system cost, while providing a significantly more compact, mobile system that provides rigorously accurate images of brain function.

Despite their vital roles in the brain, glial cells have been understudied in the past due to a lack of tools to precisely target and manipulate these cells. Drs. Hong and Chen plan to combine a new single-cell RNA sequencing tool, Act-seq with novel AAV-based CRISPR techniques to build a toolbox for profiling and manipulating specific mouse glial populations in vivo. Act-seq will permit transcriptional profiling of diverse glial cells, as well tracking of changes following perturbation. AAV-based CRISPR will enable tagging, labeling, and functional manipulations. By combining their expertise, the groups hope to open new avenues to study glial cell composition, function and interaction with neurons for better understanding of myriad neural circuits and complex behaviors.

Star-shaped astrocytes are the most abundant non-neuronal cells of the brain. Their thin processes envelop neuronal synapses and critically shape their formation and function. In this project, BRAIN Initiative-funded researchers, Drs. Eroglu and Soderling, will develop and use a novel chemicogenetic approach called iBioID enabling the capture of astrocyte processes and the identification of the key proteins that form the interface between neurons and astrocytes. The team will use this technique in combination with gene editing to study how these proteins regulate the growth and maintenance of synapses in the healthy brain and explore what role they may play in neurological disorders.

Our ability to genetically target diverse non-neuronal cell types in research and therapeutics has remained quite limited due to a lack of specific genetic tools. Dr. Greenberg and his team aim to advance the development of cell type-specific adeno-associated viral (AAV) drivers for non-neuronal cell populations and their distinct subtypes in mice. This group will use single-cell profiling, high-throughput screening, and validation with in vivo characterization to develop AAVs that expand genetic access to astrocytes, oligodendrocytes, microglia, and endothelial cells. The AAV drivers should retain utility across species for future experimental studies.

When used in conjunction with transgenic animals to restrict expression to cell populations of interest, adeno-associated viruses (AAVs) can provide well-tolerated, targeted transgene expression enabling long-term behavioral, in vivo imaging, and physiological experiments. From previous BRAIN Initiative funding, Gradinaru’s team developed a method that allows systemic delivery of viral vectors capable of crossing the blood brain barrier, circumventing the need for transgenic animals. Here the team proposes to improve on this methodology by enabling select AAV variants to anterogradely cross synapses. This will be achieved through targeted evolution of AAVs. This ability to cross synapses with cell-specificity will also provide neural connectivity information. One could envision eventually being able to deliver therapeutics systemically that target disrupted circuitry with cell-specificity.

Dr Sur’s lab plans to develop innovative tools to probe astrocyte gene expression, intracellular signal transduction, and glutamate uptake with enhanced spatiotemporal regulation. The team will use CRISPR/Cas9 to target multiple genes using a single virus Multi-gRNA, Cys4-mediated, Universal Targeting System (MRCUTS) in cultured astrocytes, comparing its efficacy to CRE-LoxP methods. The team will also develop optogenetically activated G-protein receptors to probe astrocyte signal transduction in vitro and in vivo.  In addition, the researchers will develop an in vivo method to optogenetically disrupt astrocytic glutamate uptake using a light-gated ion channel, ChromeQ in mouse brain slices. The tools developed may further our ability to investigate and understand astrocyte-neuron crosstalk with enhanced spatial and temporal precision.

Neurophysiology research, which focuses on recording brain cell activity, produces enormous amounts of complex data that are difficult to manage. Drs. Rubel and Ng will build upon the Neurodata Without Borders: Neurophysiology project to create a system that will allow for standardizing, sharing, and reusing neurophysiological data. The team will design an open source software system; develop methods to establish a consistent vocabulary for defining cell types, measurements, and behavioral tasks; and create tools to help the community adopt these new resources and standards. The proposed system will help accelerate neurophysiological discoveries as well as reproducibility studies.

Magnetic Resonance Imaging (MRI) technology is being used to identify biomarkers in the central nervous system of children 6 months of age with Autism Spectrum Disorder (ASD). A potential promising group of biomarkers include data derived from both structural and functional MRI data acquired on infants. Dr. Bower’s group seeks to translate existing academic clinical research into a commercial product for potential clinical adoption by developing software that is a single, integrated, easy-to-use solution for MRI data collection, processing, and analysis for objectively evaluating a young child’s risk for ASD.

To leverage the public investment in the BRAIN Initiative, the sharing of data produced by its myriad projects is paramount. Dr. Podrack’s project extends the recently released OpenNeuro, which was developed based on the well-established and successful OpenfMRI, for an archive of neuroimaging data. The extended archive encompasses a broader range of neuroimaging data including EEG, MEG, diffusion MRI and others. The archive also implements easy-to-use data submission, semi-automated curation and advanced data processing workflows, which run directly on the cloud platform. The archive allows to share the results alongside the data, federate with other relevant repositories, and accessible to all researchers.

The brain consists of hundreds of molecularly, physiologically, and anatomically distinct cell types. Recently-developed methods can measure gene expression in tens of thousands of single cells, to help identify and classify many new types of brain cells. However, existing technologies capture only one aspect of gene regulation – mRNA levels. Dougherty’s team will develop a method to enable the parallel analysis of transcription factor binding and mRNA expression levels in mice to create single-cell Calling Cards, generating novel data and analysis tools. If successful, this project would contribute to neuroscience by providing a broadly useful technology for understanding brain function and development, in health and disease.

Deep brain stimulation (DBS) is currently used in children with dystonia, epilepsy, and Tourette Syndrome, and this use is expanding to other neuropsychiatric conditions. In doing so, there are several challenging ethical issues, and no consistent guidance on the use of DBS in pediatric populations. To address this challenge, Dr. Gabriel Lazaro-Munoz and team will examine neuroethics issues and decisional and informational needs of families by conducting interviews with pDBS stakeholders (minors, caregivers, and clinicians). These interviews will inform the development of a decision aid for caregivers considering DBS for dystonia, the most common use of pDBS. This project will provide key information about the ethical issues facing families, minors, and clinicians alike when considering pDBS, as well as develop a clinical decision aid for making informed, patient-centered decisions surrounding the clinical use of invasive neuromodulation in minors.

Many orofacial behaviors critical for survival, such as chewing, drinking, and breathing, require motor command modulation based on information from proprioceptors. However, since many previous studies of proprioceptors were not performed in awake, behaving animals, our understanding of this system is lacking. Dr. Olson aims to target and record from mouse jaw-innervating proprioceptors in the mensencephalic trigeminal (MeV) nucleus, while the animals perform orofacial behaviors. Using advancements in in vivo physiology, behavioral analysis, and computational techniques, the study will entail recording from these neurons and mapping the functional organization of the area. The findings may improve our understanding of how the brain controls jaw movements in real-time.

Though current implantable devices which can record neuronal activity in awake, behaving animals exist, Goodell and colleagues seek to increase the size and number of brain circuits that can be both measured and manipulated long-term. The group plans to engineer and implement a system that can control hundreds of implanted electrodes to record activity from cells at any location in the brain of non-human primates, and will couple this advancement with optogenetic technologies to control neuronal firing as well. These experiments, when applied to behaviors like visual discrimination, would dramatically enhance the ability of researchers to systematically map and characterize cortical function.

Exploration of the neural basis for behavior necessitates the development of new, anatomically rigorous methods for capturing activity patterns across the whole brain. However, current tools are underdeveloped and hamper the development of new brain therapeutics. Working with Translucence Biosystems, Dr. Damian Wheeler and a team of investigators have produced an antibody to Npas4, a gene whose expression is exquisitely tuned to neural activity. To map activity using Npas4 across the whole brain, the group will take advantage of recent advances in tissue clearing, fluorescence light sheet imaging, computational brain alignment and automated cell detection. The success of this project will lead to an assay that will provide 3D images of whole brain activity with unprecedented resolution and fidelity.

Cell-level analysis and a proliferation of cell-type classification has transformed our understanding of the brain. While detection of protein in fixed tissues via immunohistochemistry has been a major driver of cell-type discovery, it suffers from the slow labeling rate at which reagents passively diffuse into tissue. Working with Lifecanvas Technologies Inc., Dr. Luke Bogart and team have developed SmartLabel, a whole-organ active immunostaining device that can label an entire mouse brain in a few days. The group will extend SmartLabel's capabilities to ensure its compatibility with other biomarkers, adapt the technology to work with diverse sample types including organoids, and prototype its cost-effective scalability. Project success will generate a rapid immunostaining device capable of batch-processing a wide range of sample types, facilitating whole-sample analysis techniques in neuroscience.

Electrocorticography (ECOG) allows the direct recording of a small population of neurons in human subjects, generating vast amounts of data. Dr. Beauchamp plans to develop the software RAVE (R Analysis and Visualization of Electrocorticography data) to help researchers explore such datasets. Incorporating established and successful informatics approaches that enable standardization, sharing, and re-use of neurophysiology data and analyses, RAVE includes rigorous statistical methodologies and seamless integration with existing analysis platforms. To facilitate user adoption and maximize impact, the developers plan to release RAVE 1.0 to the entire ECOG community within 6 months of the project start.

Rabies viral tools are widely used to identify cells in direct synaptic contact with a targeted group of neurons, but due to their toxicity, they cannot be used in long-term experiments. Here, Dr. Wickersham’s lab aims to develop a new generation of rabies viral vectors and monosynaptic tracing systems that will allow nontoxic fluorescent labeling, optical monitoring, and optogenetic manipulation of connected neuronal networks. The team will characterize and validate the new viral vectors through longitudinal structural and functional two-photon imaging of labeled neurons over month timescales and optimize parameters for in vivo, retrograde monosynaptic tracing in mice. This work could provide new tools to study healthy and disease conditions through longer physiological and behavioral studies in animals.

Studying how the brain works from the molecular to the circuit level is crucial for improving our understanding of how the brain functions normally, and what goes wrong in various disorders. Antibody probe techniques are effective tools that work at both of those levels. This project will develop a collection of validated, recombinant antibodies that are also highly renewable. In addition, antibodies will be miniaturized to increase binding efficiency and improve labeling precision. These resources will provide a cutting-edge, validated set of research tools to enable neuroscience research across a variety of resolutions from the intracellular to the neuronal network level.

fMRI can be a powerful tool to measure activity throughout the entire brain. But, because it is an indirect measure of activity through changes in blood oxygenation, it is subject to error based on local microstructural and microvascular properties of the cortex. Thus, Dr. Blazejewska intends to remove these biases in fMRI results, providing a framework for a more accurate representation of neural activity. Using histology of human brain specimens with advanced ex vivo and in vivo imaging, the team will map between tissue microarchitecture and fMRI results, correcting errors due to microstructure. These results should allow for a more accurate measurement of functional activity across all cortical layers, promoting a better understanding of the brain’s circuitry.

Two-photon microscopy has emerged as a key technique for studying the activity of living neural networks. However, little optimization has been performed for the associated fluorescent activity probes and sensors. Dr. Drobizhev’s research group will create a resource at Montana State University to characterize the properties of two-photon probes and make that service available to the broader research community. Given increased used of this type of resource by BRAIN Initiative investigators, the research group will also organize meetings to help other labs develop their own characterization processes.

GABAergic interneurons have a key role in regulating circuits in the brain, and their dysfunction is linked to neurodevelopmental diseases. It is known that diversity exists between classes of interneurons, but the extent and mechanisms of this diversity are unknown. Dr. Crow will explore the transcriptional, epigenetic, and developmental mechanisms that govern interneuron diversity, in a cross-species analysis. The work will leverage computational and phylogenetic models, machine learning, and advances in single cell RNA-sequencing technology to shed light on interneuron identity.

Neuroimaging techniques are advancing at a rapid rate, resulting in high resolution images of brain tissue and large datasets that can be difficult to manage. William Gray Roncal’s team propose an integration framework called SABER: Scalable Analytics for Brain Exploration Research. With a focus on techniques (e.g., electron microscopy) that produce high resolution brain images, SABER will create a unified framework by which these data types are accessible to a broader audience, can be processed in a reproducible, portable way, and can be scaled from small data volumes to large datasets. SABER has the potential to enable discoveries from high-resolution imaging techniques, making the parsing of entire brains a new reality.

Using currently available imaging technology, capturing a comprehensive 3D molecular snapshot of a single mouse brain takes approximately 3 years. And, to create such a map of one single human brain is estimated to potentially take 6,000 years of imaging time!  Dr. Regev’s team will develop tools based on compressed sensing, a method that uses small amounts of data to model larger images and datasets, to help accelerate the imaging timeline for brain maps. To test the tools, Dr. Regev’s group will use them to create a detailed atlas of specific areas of mouse brain, and will share all protocols and codes to help speed brain mapping across the research community.

Genetic isoforms are different types of RNA products that come from the same portion of a gene and can affect genetic activity individually or in complex units. It is unknown whether brain-region and development-specific isoforms are generated in specific cell populations. Dr. Tilgner’s group will develop novel genetic tools to closely examine distinct isoforms in 5 regions of the mouse brain at different developmental times, specifically identifying those that occur in broadly from those that appear in specific cell populations. This work could reveal distinct mechanisms for differential RNA-isoform expression, the location and timing of which may be relevant to neurodevelopmental disease.

Molecular profiling, though common in rodent models, has not been extensively applied to the brains of more evolutionarily related model organisms, like Rhesus macaques. To gain insight into what genes are turned on and off in neurons and how that activity changes across the lifespan, Drs. Snyder-Mackler, Platt, Shendure, and colleagues will develop a comprehensive, single-cell molecular atlas of the macaque brain using epigenetic and transcriptomic sequencing of 25 brain regions. This resource of over 16 millions cells will be shared with the research community to allow for more detailed mapping of macaque brains that could eventually help us to better understand human brains.

The characterization of single neurons is a major theme of research in the BRAIN Initiative Cell Census Network. Dr. Mukamel and team develop Single Neuron Analyzer (SNA), a cloud-based computer tool for interactive data exploration, analysis, and validation for single cell molecular data generated by the BRAIN Initiative. The software specifically implements machine learning and cross-validation techniques to improve the reproducibility of neuronal cell type identification.

Dopamine (DA) inputs in the midbrain influence striatal activity in the basal ganglia, and dysfunction in this system is associated with many neurological and psychiatric illnesses. Dr. Vu aims to measure dopamine release onto the dendrites of single striatal neurons in real-time using 2-photon microscopy, and map functionally-relevant dopamine release onto striatal dendrites during different behaviors in mice. This work will inform our understanding of the spatial organization of dopamine inputs onto single neurons in the striatum, as well as how these inputs affect post-synaptic cell firing.

Studying neural circuitry and function is particularly challenging in the human brain due to ethical considerations and the overall inherent experimental intractability of postmortem tissue. Furthermore, many aspects of human neurobiology are not fully recapitulated in small animal models, and research in large mammals is hindered by cost and experimental difficulties. Sestan’s team will optimize and validate a first-in-class neurotechnology, BrainEx, for the restoration of molecular and cellular functions of the postmortem large mammalian brain to allow connectivity and circuit tracing in myriad regions, as well as functional imaging. They aim to achieve this in the porcine model, in which brain size, complexity, and physiology are highly similar to human brains. These studies could establish the groundwork for the potential translation of this technology for conducting studies in the postmortem human brain.

Organoids, grown in laboratory settings to resemble parts of the developing human brain, hold great potential for shedding light on human brain function and disease. Researchers are working to achieve key bioengineering advancements, including successful vascularization of brain organoids, generating the full complement of cell types present in a human brain, and recording and modulating neural activity in organoids. These anticipated advances in bioengineered human brain modeling research may raise ethical questions about the moral status of large, complex human brain organoids and ethical boundaries on manipulating increasingly realistic engineered brain models. In this project, Dr. Hyun will lead proactive ethical discussions among ethicists and the neuroscientists conducting this cutting-edge work to develop greater awareness and understanding of these ethical implications and to inform future management of ethical issues that may be unique to this novel area of brain research.

Many organisms are capable of interval timing, as it is essential to many tasks important for survival. However, no research has determined a neural mechanism for this process.  Dr. Smart will study the neural mechanisms of interval timing in a coordinated network throughout the brain, and how these estimates of time affect behavior. The work will leverage behavioral assays, whole-brain neural activity imaging, and genetic techniques in the Drosophila brain. These findings will improve our understanding of how the brain keeps time.

Inconsistent terminologies of neuroimaging metadata prevent the precise description of the design and intent of an experiment, experimental subject characteristics, and the data acquired. Dr. Keator and colleagues aim to address this problem by developing human neuroimaging domain-specific controlled vocabularies. This will greatly improve our ability to search across datasets; to reuse, compare and integrate data across studies and sites; and to replicate neuroscience findings. They also aim to promote the adoption of the controlled vocabularies through community engagement.

Defining a complete cell atlas of the human brain, including a full molecular catalog of all its cell types and their spatial distribution, is a critical step toward understanding the human cognitive machine. Zhang’s team will expand on their previous efforts toward building a complete cell atlas of the whole human adult brain. They will systematically apply novel technologies for scalable, single-nucleus transcriptome sequencing, single-cell DNA accessibility assay, and in situ RNA imaging to MRI-scanned human brains, incorporating innovative computational approaches. If successful, the derived data will facilitate the study of molecular mechanisms underlying brain function and disorders, empowering the scientific community with a massive, readily accessible database of unprecedented scope.

Dr. Chung’s team aims to build a three-dimensional proteomic atlas of cells and neural circuits of human brains. To do this, his team plans to develop indestructible and transparent hydrogel-tissue hybrids for multi-rounds of protein labeling and imaging at subcellular resolution. They will stain the tissue via a variety of cellular and molecular labeling techniques and then use automated imaging to visualize different brain cell types, nerve fibers and synapses. The team will also create a supercomputing cloud- based framework and algorithms to analyze petabytes of high-resolution image data. This three- dimensional human brain atlas could give researchers a rapid, low cost way to discover brain cell types and the circuit problems behind neurological and neuropsychiatric disorders.

The ability to target specific glial cell populations within particular cortical and sub-cortical circuits during discrete developmental timepoints is stalled by the current lack of cell-type specific genetic markers. Dr. Allen and her team will use single-nucleus methylCytosine and Transcriptome sequencing (snmCT-seq) in the visual system of mice to profile the genetics of myriad glial cells. snmCT-seq should support identification of cell-type, region-type, and developmental stage-specific regulatory elements to improve access to glial cells. Additionally, viral tools will be developed to target and manipulate subsets of glial cells in a circuit-specific manner to further our understanding of the unique identities and roles of glial cells in neuronal circuits.

Recent advances in sequencing technology are revealing diverse cell types across the human and mouse brains, with some transient progenitor cell types found to exist only during development. In addition to this diversity of cell types, early evidence points to diversity in lipid expression and function throughout the brain. Dr. Bhaduri aims to characterize the developing human cortex across multiple regions, linking differences in transcriptomic and lipidomic data in order to understand how metabolism and transcriptional regulation interact to determine cell fate decisions in cortical progenitors. The work will offer insight into how the human brain develops.

Habituation is a form of learning by which organisms become less responsive to repetitive stimuli. While often impaired in disorders with complex cognitive symptoms, and thus has relevance to human disease, there are significant gaps in the understanding of habituation learning. To address this challenge, Dr. Nelson will study the critical role of protein modifications in habituation learning, using larval zebrafish as a model system. The project will involve training in protein modification and in vivo electrophysiology, integrating these approaches into a well-rounded system to examine learning across genes, circuits, and behavior. Success of the project may reveal how post-translational protein modifications influence synaptic plasticity within defined neural circuits as we learn.

Neuro-glio-vascular interactions are vital to nervous system activity, yet an inventory of vascular cells within defined brain regions and circuits does not exist due to the relatively low numbers of vascular cells compared to neurons and glia. Dr. Gu’s team aims to apply a refined dissociation protocol to isolate vascular cells from small specialized regions of the mouse brain. Using these new tools, they plan to build a comprehensive inventory of vascular and perivascular cells in specific brain regions, identify differences in cellular interactions, and create cell-type and region-specific markers to genetically target these cells for further study. The researchers hope to generate a neuro-glio-vascular connectome database to help researchers better understand the contribution of heterogenous non-neuronal cell types in brain structure and function.

Traumatic events can result in anxiety disorders, including post-traumatic stress disorder (PTSD), a hallmark of which is amplified expression of fear and resistance to behavioral therapies. While the ventromedial prefrontal cortex (vmPFC) is thought to have a fear-inhibiting role, activity in its subregions is also elevated in many PTSD patients. To understand this functional dichotomy, Dr. Cummings will investigate the mechanisms by which vmPFC subregions encode learned fear by using a range of approaches, including calcium imaging, circuit tracing, in vivo optogenetic manipulation, and ex vivo electrophysiology in mice. Success of the project should result in characterization of the role of vmPFC in the regulation of fear memory, which may inform existing models of fear circuitry and help elucidate the mechanisms that are recruited in fear learning.