Developed Resources and Tools

We are developing a two-photon miniature fiber-coupled microscope that uses electrowetting lens technology for three dimensional neural imaging in freely moving animals. We are currently working to disseminate the technology to five beta users for testing in different animal models.

Contact Name/Position: Emily Gibson, Associate Professor

Alliance Affiliation: National Institutes of Health, National Science Foundation

Micro-scale EMG arrays for recording single- and multi-unit activity from muscle populations, and algorithms for analyzing the resulting data.

Contact Name/Position: Sam Sober, Associate Professor

Alliance Affiliation: IEEE Brain

The Allen Brain Cell (ABC) Atlas provides a platform for visualizing and analyzing multimodal single cell and spatial transcriptomics data across the whole mammalian brain in multiple datasets simultaneously. This open science resource, developed by the Allen Institute as part of the Brain Knowledge Platform, allows unprecedented insights into the enormous diversity of cell types in the brain and where they are. The ABC Atlas will enable the neuroscience community to identify more cell types in the brain, investigate the spatial location of cell types, investigate gene expression and co-expression patterns in cell types, and refine boundaries and knowledge of brain regions defined by gene expression. The Allen Institute and its collaborators continue to add new modalities, species, and insights to the ABC Atlas opening up endless possibilities for discoveries and breakthroughs in neuroscience.

Contact Name/Position: Elysha Fiabane, Product Manager III

Alliance Affiliation: Allen Institute for Brain Science

BCI2000 provides a portable open-source platform to implement the most common scenarios of adaptive neurotechnology research. BCI2000 acquires, synchronizes, and stores signals from a wide range of data acquisition systems, and translates these signals into useful outputs in real-time.

Contact Name/Position: Peter Brunner, Associate Professor

Alliance Affiliation: National Institutes of Health

BossDB (Brain Observatory Storage Service and Database, https://bossdb.org) is a cloud-based data ecosystem for large-scale volumetric 3D and 4D neuroimaging data. BossDB focuses primarily on storing volumetric Electron Microscopy (EM) and X-Ray Microtomography (XRM) datasets generated as a part of the BRAIN Initiative. BossDB stores high resolution, multi-channel image data with registered segmentations, annotations, and meshes, and connects to a number of community resources for data access and data visualization. BossDB also stores connectomics datasets and contains a number of software tools and interfaces for querying and searching connectomes.

Contact Name/Position: Brock Wester, PI

Alliance Affiliation: None

The Brain Image Library (BIL) is an NIH-funded public resource serving the neuroscience community by providing a persistent centralized repository for brain microscopy data. Data scope of the BIL archive includes whole brain microscopy image datasets and their accompanying secondary data such as neuron morphologies, targeted microscope-enabled experiments including connectivity between cells and spatial transcriptomics, and other historical collections of value to the community. The BIL Analysis Ecosystem provides an integrated computational and visualization system to explore, visualize, and access BIL data without having to download it.

Contact Name/Position: Alexander Ropelewski, Principal Investigator

Alliance Affiliation: None

The Brain Modeling Toolkit (BMTK), SONATA, and Visual Neuronal Dynamics (VND) are mutually integrated software tools that are particularly suited to support large-scale bio-realistic brain modeling, but are applicable to a variety of neuronal modeling applications. BMTK is a suite for building and simulating network models at multiple levels of resolution, from biophysically-detailed, to point-neuron, to population-statistics approaches. The modular design of BMTK allows users to easily work across different scales of resolution and different simulation engines using the same code interface. The model architecture and parameters, as well as simulation configuration, input, and output are stored together in the SONATA data format. Models and their output activity can then be visualized with the powerful rendering capabilities of VND.

Contact Name/Position: Anton Arkhipov, Associate Investigator

Alliance Affiliation: None

brainlife.io is a free and secure reproducible neuroscience analysis platform. The platform support data preprocessing, visualization and analysis. Users can analyze data on brainlife.io by either uploading or importing it from public archives. Over 400+ pre-processing apps are available to build your custom workflows. Thousands of jobs can be submitted using shared clusters or on your own computer. Perform group-level statistical analysis or apply machine learning methods using Jupyter notebooks. Publish your full workflow from raw data to published figures in an integrated bundle with a single DOI.

Contact Name/Position: Franco Pestilli, Associate Professor

Alliance Affiliation: None

CaMPARI (Calcium Modulated Photoactivatable Ratiometric Integrator) – a fluorescent protein-based integrator of calcium for permanent marking of neuronal activity, Voltron – a chemigenetic fluorescent voltage indicator for in vivo recording of electrical activity. Primary use cases are marking/monitoring of neuronal activity in vivo in model organisms. Goal is to disseminate as broadly as possible, primarily via publicly-accessible repositories, to enable new biology.

Contact Name/Position: Eric Schreiter, Group Leader

Alliance Affiliation: None

We have developed carbon fiber electrode arrays that can be optimized for either electrophsiology or the detection of dopamine. In addition, we have implemented tip sharpening techniques for better penetration into tissue such as nerves and ganglia. We wish to continue distributing these electrodes to existing collaborators and expand to new labs, with an overall emphasis on electrode customization per the user’s needs.

Contact Name/Position: Paras Patel (Assistant Research Scientist)
Cynthia Chestek (Associate Professor)

Alliance Affiliation: None

The Cell Type Knowledge Explorer (CTKE) is a publicly accessible web application to browse data associated with the multimodal cell census and atlas of primary motor cortex, developed in close collaboration with the BRAIN Initiative Cell Census Network (BICCN). The CTKE includes access to single-cell transcriptomic and epigenomic profiling of human, marmoset, and mouse primary motor cortex, with additional data sets assessing the spatial distribution, cell morphology (shape), and electrical properties of these cell types. All data powering the CTKE is provided to encourage cell exploration by scientists, students, and educators through the browser and linked resources.

Contact Name/Position: Mike Hawrylycz, Investigator

Alliance Affiliation: None

CellREADR (Cell access through RNA sensing by Endogenous ADAR) is a new class of RNA sensing technology to achieve genetic access of cell types and cell states. It leverages RNA editing mediated by ADAR (adenosine deaminase acting on RNA) to couple the detection of cell-defining RNAs with translation of effector proteins. CellREADR enables monitoring and manipulating of animal cells in ways that are specific, simple, versatile, programmable, and generalizable across organ systems and species.

Contact Name/Position: Z. Josh Huang, Professor

Alliance Affiliation: None

Utilizing recent 3D nanoparticle printing advances, we provide exceptionally broad, dense ephys sampling across neural volumes. The CMU Array attains previously impossible densities (>6000 electrodes/cm2). More importantly, probes are fully-customizable. Any combination of positions, lengths, and impedances are possible. One-off probes are produced in hours, not weeks – and at a fraction of the cost. Even the probe platform is customizable –including curved and flexible substrates. We are currently exploring printed optogenetic waveguides and microfluidic drug delivery.

Contact Name/Position: Eric Yttri, Assistant Professor

Alliance Affiliation: None

We have developed (1) robotic platforms for automated cranial microsurgeries. (2) transparent polymer skulls for cortex-wide neural interfacing. (1) is currently being setup at multiple groups and we are helping these groups beta test. (2) is being shared via material transfer agreement to several groups at the NIH, Stanford, MIT, Johns Hopkins, UC Boulder and Princeton. We provide starter kits – with fully assembled implants, and raw materials for making dozens more. We hope to use STTR funds soon to be provided by the BRAIN Initiative to develop commercial versions of both.

Contact Name/Position: Suhasa Kodandaramaiah, Assistant Professor

Alliance Affiliation: None

cytoNet provides a mathematical, web-based tool to rapidly characterize multiscale networks from images. To study complex tissue, cell and subcellular topologies, cytoNet integrates vision science with graph theory to quantify environmental effects on network topology. cytoNet applications include: (1) characterizing how pain sensation alters neural circuit activity in vivo, (2) quantifying patterns in how diverse brain cells respond to neurotrophic stimuli, & (3) uncovering cell cycle synchronization of differentiating neural stem cells. Awareness of cytoNet as a resource for the BRAIN Initiative community is a dissemination goal.

Contact Name/Position: Amina Ann Qutub, Cathy Burzik Professor in Engineering Design, University of Texas San Antonio

Alliance Affiliation: None

DANDI is the BRAIN Initiative supported data archive for publishing and sharing
neurophysiology data including electrophysiology, optophysiology, and
behavioral time-series, and images from immunostaining experiments. The archive
supports a broad range of users with different levels of expertise by providing
a spectrum from web-based to programmatic mechanisms to access and upload data
and helps improve the expertise through training of the scientific user base
through tutorials and workshops. All aspects of DANDI infrastructure are
developed with an adherence to open software, explicit licensing, and community
standards.

Contact Name/Position: Satrajit Ghosh, Principal Research Scientist

Alliance Affiliation: None

DABI is a web-accessible data archive that captures, stores, and curates human invasive neurophysiology data from BRAIN Initiative proposals. These data are aggregated, organized, and disseminated to the research community to accelerate the pace of discovery in the neurosciences. In addition to its archival and organization services, DABI also integrates novel analytical tools for cohort discovery and preliminary analyses.

Contact Name/Position: Arthur Toga, Professor

Alliance Affiliation: None

DataJoint Elements provides an efficient approach for neuroscience labs to create and manage scientific data workflows: the complex multi-step methods for data collection, preparation, processing, analysis, and modeling that scientists must perform in the course of an experimental study. The work is derived from the developments in leading neuroscience projects and uses the open-source DataJoint framework for interfacing databases and automating computations.

Contact Name/Position: Dimitri Yatsenko, CEO

Alliance Affiliation: National Institutes of Health, Intelligence Advanced Research Projects Activity, Simons Foundation

Quantifying behavior is crucial for many applications in neuroscience, genetics, and biology. Videography provides easy methods for the observation and recording of animal behavior in diverse settings, yet extracting particular aspects of a behavior for further analysis can be highly time-consuming.

DeepLabCut offers an efficient method for marker-less pose estimation based on transfer learning with deep neural networks that achieves excellent results (i.e. you can match human labeling accuracy) with minimal training data (typically 50-200 frames). Its versatility has been demonstrated by tracking various body parts in multiple species across a broad collection of behaviors. The package is open source, fast, robust, and can be used to compute 3D pose estimates. It is actively maintained.

Contact Name/Position: Alexander Mathis, Assistant Professor

Alliance Affiliation: None

Diesel2p is a custom two-photon microscope system with dual scan engines that can operate completely independently. Each arm has optical access to the same large imaging volume (~25 mm^2 FOV) over which subcellular resolution is maintained in scattering tissue to typical 2-photon imaging depths. Each arm can use multiple sources simultaneously, for example, in imaging and photoactivation experiments.

Contact Name/Position: Spencer Smith, Associate Professor

Alliance Affiliation: None

We are developing genetically encoded indicators for monitoring voltage in vivo (GEVIs). Our tools can use the same wavelengths and equipment as used for imaging calcium indicators. We are open to new collaborators to deploy or benchmark these indicators for new applications, model systems, and/or imaging modalities.

Contact Name/Position: Francois St-Pierre, Assistant Professor

Alliance Affiliation: None

We have developed new genetically-encoded reagents for fluorescence-synapse labeling and connectivity analysis in brain tissue designed for high-throughput, compartment-specific localization of synapses across diverse neuron types in the mammalian brain. High-resolution confocal image stacks of sparsely-labeled, virally-transduced neurons can be used for 3D reconstructions of postsynaptic cells, automated detection of synaptic puncta, and multichannel fluorescence alignment of dendrites, synapses, and presynaptic neurites to assess cell-type specific connectivity. We are using these fluorescence-based reagents to quantitatively evaluate changes in synaptic connectivity during learning and in mouse models of neurological disorders. The vast number of fluorescently-labeled, input- and target-specified synapses we are collecting offers new and exciting opportunities for data analysis and machine learning.

Contact Name/Position: Alison Barth, Professor

Alliance Affiliation: National Institutes of Health

Gray Matter Research designs and manufactures large-scale microdrive systems to enable semi-chronic recording of neural activity from large numbers of independently moveable microelectrodes to record neural circuit activity in behaving non-human primates. Recent innovations include a larger number of electrodes and longer travel distances, flexibility to curve electrode trajectories, ability to register the electrodes to post-op scans and improved reliability. Our microdrive systems are used in over 50 laboratories worldwide. We also developed a prosthetic instrument expanding the scope and reliability of a new generation of microdrives using multi-channel laminar probes. This class of instrumentation is under development and in use in multiple laboratories. These tools provide unprecedented capabilties for reseachers to measure the activity in distributed neural circuits in behaving non-human primate performing cognitive tasks.

Contact Name/Position: Baldwin Goodell, Owner of Gray Matter Research

Alliance Affiliation: National Institutes of Health

Magneto- and electro-encephalography (MEG/EEG) are the two methods to non-invasively record human brain activity with millisecond temporal resolution. MEG and EEG provide reliable markers of healthy brain function and disease states. However, the difficulty of relating these macroscopic signals to the underlying cellular- and circuit-level neural generators is a major, fundamental limitation that constrains using MEG/EEG to reveal novel principles of information processing or to translate the findings into new therapies for neural pathologies. To address this problem, we built the Human Neocortical Neurosolver (HNN, https://hnn.brown.edu). HNN is a user-friendly software tool designed to help researchers, and clinicians interpret the cellular and network origins of MEG/EEG data. HNN’s core is a detailed, mechanistic neural model including canonical features of a layered neocortical circuit, with layer-specific thalamocortical and cortico-cortical drive. HNN’s model is uniquely designed to account for the biophysical origin of the electrical currents generating MEG/EEG with enough detail to connect to the underlying cellular-level activity. HNN provides a user-friendly graphical user interface so that researchers can work interactively between model and data without needing to alter the underlying mathematical model or the open-source code. Tutorials on how to simulate the most commonly measured signals, including event related potentials and brain rhythms (alpha, beta, gamma), are provided. Researchers can compare simulated signals to recorded data and easily manipulate the model parameters to develop and test alternative hypotheses for the neural origin of their signals. Micro-scale features, including layer-specific responses, cell spiking activity, and somatic voltages, can be visualized and used to guide validation of model predictions with a variety of invasive and non-invasive methods. HNN is being developed with best practices in open source software design and is also distributed with a python interface and corresponding python tutorials. The ability of HNN to associate signals across scales makes it a unique tool for translational neuroscience research.

Contact Name/Position: Stephanie R Jones, Associate Professor

Alliance Affiliation: None

We have developed micro-coil that can be implanted into the cortex and used to magnetically stimulate cortical neurons. Coils have two important advantages over conventional micro-electrodes. First, the magnetic fields they induce are less susceptible to changes in the surrounding environment, e.g. due to foreign body responses, and second, the fields they induce can be shaped to selectively target specific types of neurons.

Contact Name/Position: Shelley Fried, Associate Professor

Alliance Affiliation: None

MapMyCells is a web tool that allows scientists worldwide to assign cell types to their own transcriptomics and spatial data by comparing their data to massive mammalian brain reference taxonomies derived by the Allen Institute for Brain Science and the BRAIN Initiative Cell Atlas Network (BICAN). Researchers follow a simple process to map their gene expression: (1) upload a cell by gene matrix, (2) choose from available reference taxonomies and mapping algorithms, (3) download the reference cell type assignments for their data when the mapping is complete. Methods and data used in this tool will be publicly accessible for code-based applications as well.

Contact Name/Position: Elysha Fiabane, Product Manager III

Alliance Affiliation: Allen Institute for Brain Science

BARseq and MAPseq can map long-range projections of 1000s of neurons in a single brain area at single neuron resolution, and further correlate projections to gene expression and Cre. We achieve mapping of densely labeled neurons at single neuron resolution by cellular barcoding and sequencing. Our methods allow comparison of projections across neuronal subtypes within an animal, across individual animals, and across genotypes. We offer MAPseq service through CSHL core facility, and may offer BARseq service in the future. We also welcome other labs to adopt both methods on their own.

Contact Name/Position: Xiaoyin Chen (Postdoc)
Anthony Zador (Professor)

Alliance Affiliation: None

Our goal is to disseminate high-density micro-LED optoelectrodes for mapping circuits in the brain.

Contact Name/Position: Euisik Yoon (Professor)
Jose Roberto Lopez Ruiz (Program Manager)

Alliance Affiliation: None

Miniature micro-endoscope. The micro-endoscope presented here has a small footprint, weight, and cost making it almost disposable. It can be used to record brain activity in multiple brain areas simultaneously in mice.

Contact Name/Position: Walter Gonzalez (Postdoc)
Carlos Lois (Principal Investigator)

Alliance Affiliation: None

The MORF strategy addresses the need for a simple, generalizable, and scalable method to sparsely label genetically-defined neuronal populations by developing reporter mouse lines conferring Cre-dependent sparse cell labeling methodology based on MOnonucleotide Repeat Frameshift (MORF) as a stochastic translational switch. The suite of MORF reporter mice labels about 1-5% of Cre+ neurons and glia distributed stochastically throughout the brain and can be imaged with endogenous fluorescence (mNeonGreen in MORF1 and EGFP in TIGRE-MORF/Ai166) or stained for a multivalent immunoreporter (Spaghetti Monster fluorescent protein V5, or smFP-V5, in MORF3). As a resource for both the BRAIN Initiative and general neuroscience communities, MORF enables the labeling and reconstruction of thousands of genetically defined cells per brain for large-scale, unbiased classification and quantitative analyses of CNS cell types brainwide.

Contact Name/Position: X. William Yang, Principal Investigator

Alliance Affiliation: None

MoSeq (or Motion Sequencing) provides a pipeline for quantifying 3D videos or keypoints from 2D/3D videos of freely behaving mice and discovering the underlying structure of mouse behavior. MoSeq automatically locates, tracks, and quantifies the mouse in each frame of the video. Unlike typical supervised behavioral classifiers that then require human labeling, the pipeline instead trains an unsupervised machine learning model to identify repeated motifs (or syllables) of behavior. The pipeline then offers a suite of visualization tools and statistical tests for understanding the discovered behaviors and comparing them across experimental conditions. MoSeq dramatically reduces human labor in exploring mouse behavior, discovers previously unknown behaviors, and allows neuroscientists to more completely relate neural activity to free behavior.

Contact Name/Position: Sandeep Robert Datta, Associate Professor

Alliance Affiliation: National Institutes of Health

The Neuroelectromagnetic Data Archive and Tools Resource (NEMAR) is a gateway to OpenNeuro for research using publicly available human NEM data (EEG, MEG, iEEG/ECoG). NEM data made available on OpenNeuro can be analyzed in place via the Neuroscience Gateway (NSG, nsgportal.org). We are building web applications to evaluate the quality of uploaded NEM data, to visualize the data, and an easy-to-use pathway to apply user-specified processing to the data via NSG, without requiring data download and re-upload.

Contact Name/Position: Scott Makeig, Director Swartz Center for Computational Neuroscience

Alliance Affiliation: None

Neurodata Without Borders: Neurophysiology (NWB) is a data standard for neurophysiology, providing neuroscientists with a common standard to share, archive, use, and build common analysis tools for neurophysiology data. NWB is designed to store a variety of neurophysiology data, including data from intracellular and extracellular electrophysiology experiments, data from optical physiology experiments, and tracking and stimulus data. NWB is more than just a file format; it defines an ecosystem of tools, methods, and standards for storing, sharing, and analyzing complex neurophysiology data. NWB provides software for data standardization and application programming interfaces (APIs) for reading and writing the data, and is supported by a growing ecosystem of data analysis and management tools.

Contact Name/Position: Oliver Ruebel, Staff Scientists, Computational Research Division, Lawrence Berkeley National Laboratory; Benjamin Dichter, CatalystNeuro

Alliance Affiliation: National Institutes of Health, The Kavli Foundation

We are building a suite of bioluminescent molecular tools for controlling cells and tracking activity, as well as hardware (most notably, microscopes) to optimize their use. The NeuroNex Bioluminescence hub systematically develops and disseminates these novel and powerful tools for brain science.

Contact Name/Position: Christopher Moore, Professor

Alliance Affiliation: National Science Foundation, National Institutes of Health

Imaging deeper, wider, and faster. Imaging multiple species using multiphoton microscope. Dissemination through meetings, campus visits, and commercial vendors.

Contact Name/Position: Chris Xu (Professor)
Joe Fetcho (Professor)
Chunyan Wu (PhD Candidate)

Alliance Affiliation: None

This resource is an open-access recombinant antibody/affinity reagent repository for the neuroscience community called Neuroscience AntiBody Open Resource (NABOR). Reliable access to affinity reagents validated for use in diverse neuroscience research applications is crucial to accomplishing numerous goals of the BRAIN Initiative. Currently available affinity reagents from companies can be variable in quality and the molecular identity of the material is completely unknown to scientists. Addgene has built an open-access library and is providing plasmids, sequences, and ready to use protein-format antibodies.

Contact Name/Position: Melina Fan, Chief Scientific Officer

Alliance Affiliation: None

Neuroscience Multi-Omic Archive is a data repository focused on the storage and dissemination of -omics data generated from the BRAIN Initiative and related brain research projects.  Primary data of interest to NeMO includes both transcriptomic and epigenetic data including transcription factor binding sites and other regulatory elements, histone modification profiles and chromatin accessibility, levels of cytosine modification, and genomic regions associated with brain abnormalities and disease. Sequence-level data for human samples consented with restrictions are made available through an approval process in conjunction with the NIMH Data Archive and NeMO archive. The NeMO Archive is consistent with the principles advanced by the NIH Strategic Plan for Data Science, including FAIR Principles, documentation of APIs, data-indexing systems, workflow sharing, use of shareable software pipelines and storage on cloud-based systems.

Contact Name/Position: Owen White, Principal Investigator

Alliance Affiliation: None

The UNC Neuroscience Center NeuroTools Vector Core provides custom viral vectors tailored for neuroscience experiments. We work directly with investigators to provide optimal combinations of payloads, capsids/pseudo-types, titers, and purity. We will modify our production protocol to meet your specfic needs. We also assist with vector design and viral vector performance trouble-shooting.

Contact Name/Position: Kimberly Ritola, Director

Alliance Affiliation: None

We have made and validated these nanoparticles (as supported by the BRAIN Initiative), and shown that after an intravenous infusion of the nanoparticles, they induce drug effects only when and where focused ultrasound is applied to the brain. We have seen that the particles may be loaded with any of a variety of neuromodulatory agents. We have also validated a production and storage scheme that will allow them to be stored long term and shipped frozen to collaborator sites. We are now working on a fool-proof protocol for any lab to easily make their own particles.

Contact Name/Position: Raag Airan, Assistant Professor

Alliance Affiliation: None

The Open Ephys GUI is open-source, plugin-based cross-platform software for acquiring data from implanted electrodes, used by hundreds of labs around the world. It is available for download from open-ephys.org/gui

Contact Name/Position: Josh Siegle (Assistant Investigator)

Alliance Affiliation: National Institutes of Health, Allen Institute for Brain Science

This collection of documentation includes shared clinical protocols, IDE submission materials, FDA correspondence and meeting materials, file formats, QMS and design control background, and related reference material for groups designing and spearheading clinical studies utilizing advanced bidirectional DBS device technology.

Contact Name/Position: Phil Starr, Professor
David Borton, Asst. Professor
Tim Denison, Professor
Greg Worrell, Professor
Heather Dawes, Exec. Director

Alliance Affiliation: National Institutes of Health

This collection of software tools is geared to support research using advanced deep-brain (DBS) stimulation technology (e.g. Medtronic’s Summit RC+S system) in clinical studies. The tools have been developed and shared by OpenMind Consortim member laboratories and include read-me, explanatory videos, and other material to enable use and adaptation by users to suit their research needs. The tools encompass code for data visualization and analysis, as well as code for device programming and control via device APIs. This set of resources helps to fill a critical gap in technological capacity needed to fully utilize advanced DBS device technology in clinical studies, and brings efficiencies in cost, labor, time and knowledge-sharing to the community of advanced DBS researchers.

Contact Name/Position: Phil Starr, Professor
David Borton, Asst. Professor
Tim Denison, Professor
Greg Worrell, Professor
Heather Dawes, Exec. Director

Alliance Affiliation: National Institutes of Health

OpenNeuro is a data archive that provides the ability to openly share data from a broad range of brain imaging data types following the FAIR principles for data sharing. Uploaded datasets are made available with minimal restrictions to the public at large, in order to permit maximal reuse. OpenNeuro accepts datasets formatted according to the Brain Imaging Data Structure (BIDS) standard, a community-developed standard that aims to achieve broad coverage of neuroimaging data types while unifying metadata.

Contact Name/Position: Russell Poldrack, Professor

Alliance Affiliation: None

OpenScope opens the Allen Brain Observatory pipeline to the community, enabling theoretical, computational, and experimental scientists to test sophisticated hypotheses on brain function in a process analogous to astronomical observatories that survey the night sky. Once a year OpenScope will accept experimental proposals from external scientists, which will be reviewed by a panel of leading experts for their feasibility and scientific merit. The Allen Institute will carry out the selected experiments following verified, reproducible, and open protocols for in vivo single- and multi-area two photon calcium imaging and Neuropixels electrophysiology, making the data freely available to these scientists and to the community. This will lower barriers to testing new hypotheses about brain function, bring new computational and theoretical talents into the field, and enhance the reproducibility of results in brain research, thereby accelerating progress toward an integrated understanding of neural activity in health and disease.

Contact Name/Position: Jerome Lecoq, Principal Scientist

Alliance Affiliation: National Institutes of Health, Allen Institute for Brain Science

This repository hosts tools to curate PET brain data using the Brain Imaging Data Structure Specification. The work to create these tools is funded by Novo Nordisk Fonden (NNF20OC0063277) and the BRAIN initiative (MH002977-01). This tool extracts and outputs some of the additional blood and radiological data along with PET neuroimaging data into the Brain Imaging Data Structure. It is one of the few tools that exists to aid in this conversion and is being used to convert and share data on OpenNeuro.org.

Contact Name/Position: Anthony Galassi, Computer Programmer

Alliance Affiliation: None

The Polymer Implantable Electrode (PIE) Foundry is a service which provides access to polymer-based microelectrode arrays for neuroscientists, by providing training, testing, and custom-made devices. Polymer-based electrodes offer improved device lifetime compared with conventional silicon and microwire probes, but there are few commercial options. By adapting processes from semiconductor foundries, the PIE Foundry can produce made-to-order devices with a high-degree of uniformity and precision. PIE Foundry offers BRAIN community members tools and training so they can incorporate polymer-based probes and electrodes into their own research.

Contact Name/Position: Ellis Meng, Professor; Dong Song, Research Associate Professor

Alliance Affiliation: National Institutes of Health

Pinpoint is a trajectory planning tool for acute and chronic electrophysiology recordings as well as injections. Using an interactive 3D scene, Pinpoint allows researchers to plan multi-probe insertions in an intuitive environment, all in the convenience of your web browser. Users can explore different options for craniotomies and check that insertions will not interfere with other parts of a surgical implant or recording rig. During live experiments, Pinpoint can be linked to hardware micro-manipulators as well as data acquisition software, allowing you to follow along as your probes are placed into position inside the brain, and forward that anatomical information to be viewed alongside your live data.

Contact Name/Position: Daniel Birman, Postdoctoral Fellow

Alliance Affiliation: National Institutes of Health, Simons Foundation

We have developed a modular recordings system with soft, flexible polymer electrodes that makes it possible to record from hundreds of neurons distributed across many brain areas, and to do so for many months. We are currently distributing these electrodes to ~20 other labs for testing, and their feedback will be used to further refine the devices. Our long term goal is to be able to disseminate these devices to the entire community.

Contact Name/Position: Loren Frank, Professor

Alliance Affiliation: None

This new tool, a genetically-encoded voltage sensor (GEVI) was modified for enhanced sensitivity and targeted to dendrites and dendritic spines by adding a nanobody against PSD95 (FingR.PSD95). With this voltage sensor, named postASAP, we are capable to measure voltage signals under two-photon microscopy in vivo in pyramidal neurons of the mouse cortex. With postASAP, we can detect in living animals backpropagation of action potentials, dendritic activity, and isolated synaptic potentials in dendritic spines.

Contact Name/Position: Rafael Yuste, Professor of Biological Sciences

Alliance Affiliation: None

We develop, validate, and enhance community access to a diverse toolbox of renewable recombinant antibodies and affinity reagents for neuroscience research. Extensively characterized in mammalian brain samples (rat, mouse, human). These reagents include conventional and recombinant mouse monoclonal antibodies and miniaturized ScFV derivatives, and nanobodies (single chain miniaturized antibodies). The small size, solubility, and stability of ScFvs and nAbs facilitates their functional expression in mammalian cells, allowing for their use as intrabodies to target cargo including optogenetic reports and actuators to distinct subcellular sites in neurons. Their small size also enhances the resolution of light and electron microscope imaging when they are used as immunolabels, and their penetration into intact cleared samples.

Contact Name/Position: Jim Trimmer, Professor

Alliance Affiliation: None

single-cell combinatorial indexing on Microbiopsies Assigned to Positions for the Assay for Transposase Accessible Chromatin (sciMAP-ATAC). High-throughput single cell genomic assays resolve the heterogeneity of cell states in complex tissues, however, the spatial orientation within the network of interconnected cells is lost. We present a novel method for capturing spatially-resolved epigenomic profiles of single cells within intact tissue, and apply this method to generate non-neuronal cell taxonomy atlases of human and mouse cortex. This method will be made accessible through protocols.io and all data, along with single cell analyses, will be made available through the BRAIN Initiative Cell Census Network (BICCN)

Contact Name/Position: Casey Thornton (ACGME Laboratory Genetics & Genomics Fellow)
Andrew Adey (Principal Investigator)

Alliance Affiliation: None

SLEAP (Social LEAP Estimates Animal Poses) is a deep learning software framework for general purpose multi-animal limb tracking from video. This software couples a GUI for importing and annotating data with deep neural networks designed for learning to locate and associate user-specified anatomical landmarks on unmarked animals. Use cases range from kinematic studies of animal movement, to quantification of social dynamics via multi-animal part tracking.

Contact Name/Position: Talmo Pereira (Salk Fellow & PI)
Mala Murthy (Professor)
Joshua Shaevitz (Professor)

Alliance Affiliation: None

This is a toolset of multifunctional soft neural probes for simultaneous optical stimulation, optical recording, electrophysiological recording, pharmacological infusion and virus delivery. The neural probes are made of soft and stretchable hydrogel materials, which exhibit superior optical and mechanical properties. With the merit of improved material-tissue interfaces, this tool will allow for long-term neural modulation and recording through multiple modalities.

Contact Name/Position: Siyuan Rao, Assistant Professor

Alliance Affiliation: None

The Stanford Program for Integrated Neuroscience Technologies (SPrINT) aims to establish a platform for the centralization and dissemination of innovative neuroscience technologies, models, reagents, and training in order to advance neuroscience in the areas of the human brain organogenesis technology, behavioral and functional neuroscience models, viral vectors, and imaging technology. Under this program, we engage with the national neuroscience community to disseminate essential resources and emerging technologies to a growing user network through a Pilot Study Program and Annual Workshops. Collectively, our vision of SPrINT is to provide an integrated platform in which users can engage multiple modalities or can expand their research to areas outside their expertise.

Contact Name/Position: Mehrdad Shamloo, Professor/Director

Alliance Affiliation: None

Please note this tool was previously referred to as “Phase Calculator Plugin”, which is one component of the Toolkit for Oscillatory Real-Time Tracking and Estimation (TORTE).

We have built a set of open-source tools for precisely locking experimental perturbations (optical/electrical/magnetic stimulation, behavioral triggering, etc.) to the phase of ongoing LFP oscillations (probably could be used with anything that has an oscillation, e.g. whisking). They are substantially more accurate than anything in the published literature and have been adapted to work with both human and animal experimental rigs. The target use case is understanding the role of oscillatory phase in cognition, e.g. altering phase relations between structures by timed perturbation.

Contact Name/Position: Alik Widge, Assistant Professor

Alliance Affiliation: National Institutes of Health

This resource provides the service of characterization of multiphoton absorption properties and multiphoton stability to a large number of protein engineers and neuroscientists involved in the BRAIN initiative. This information is indispensable because it makes it possible to choose the best probe and best excitation conditions (wavelength, laser power, etc.) for deep high-resolution multiphoton microscopy of the brain. Although there are few laboratories around the world that are able to quantitatively characterize the multiphoton properties of organic molecules, they are either not dealing with the probes utilized in neuroscience or they are not providing the service for all interested BRAIN researchers.

Contact Name/Position: Mikhail Drobizhev, Associate Research Professor

Alliance Affiliation: National Institutes of Health

I lead the development of the open source UCLA Miniscope project. We develop the most widely used miniature microscope for neural recording in freely behaving animals. Our system is currently in about 500 labs and we look to continue expanding access to transformative tools. New miniaturized microscopes: wireless, large field-of-view, integrated with electrophysiology. We disseminate our tools on miniscope.org

Contact Name/Position: Daniel Aharoni (Assistant Professor)
Peyman Golshani (Professor)

Alliance Affiliation: None

The Floating Microelectrode Array allows stimulation and recording from the CNS and the periphery through a wireless link. This device is 5mm diameter and can interface to 16 electrodes without any wires or tethers. Power and communication is through a magnetic wireless link. The WFMA is being used for a clinical trial of cortical visual prosthesis, but has also been used for peripheral nerve (cuff) interface. Currently it is being deployed for neuroscience research through a joint effort by MicroProbes for Life Science and Sigenics, Inc.

Contact Name/Position: Philip Troyk, Professor

Alliance Affiliation: None