Developed Resources and Tools
BRAIN Initiative-funded scientists have been working hard to develop exciting tools that will advance the field of neuroscience. What are some of these tools and what do they do? Learn about several of these tools, and the toolmakers behind them, here, in our resource section.
FILTER BY:
| NAME | TITLE | TYPE | KEYWORDS | MORE |
|---|---|---|---|---|
| 2P-FCM | 2P-FCM: Miniature 2-photon fiber-coupled microscope for 3D neural imaging in freely moving animals | Optics / Microscopy | 3D-Neural imaging, Miniature fiber-coupled microscope, Electrowetting lens technology, BRAIN Initiative | |
| 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. | ||||
| Brain Modeling Toolkit (BMTK) | The Brain Modeling Toolkit: A Python-based software package for creating and simulating neural network models. | Software | Software package, Neural network, Model building, Computational model, BRAIN Initiative | |
| BMTK is a Python-based software package for creating and simulating neural network models at multiple levels of resolution by providing wrappers to tools such as NEURON, NEST, and diPDE. It is an open-source software development kit, developed modularly, allowing users to modify the existing functionality and easily add new extensions. Currently BMTK contains a Builder module for creating models and four simulator modules – BioNet, PointNet, PopNet, and FilterNet – for running simulations at different levels of granularity. | ||||
| CaMPARI & Voltron | Fluorescent indicators for neuronal activity: CaMPARI and Voltron | Molecural / Cellular | Fluorescent protein-based integrator, Fluorescent voltage indicator, GENIE, Calcium activity, Neuronal activity, BRAIN Initiative | |
| CaMPARI (Calcium Modulated Photoactivatable Ratiometric Integrator) - a fluorescent protein-based integrator of calcium for permanent marking of neuronal activity, and 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. | ||||
| Craniobot & See-Shells | Robotic platforms for automated cranial microsurgery and transparent polymer skulls for neural interfacing | Other Hardware Development | Robotic surgery, Polymer skull, Cranial procedure, BRAIN Initiative | |
| "We have developed (1) robotic platforms for automated cranial microsurgeries. (2) transparent polymer skulls for cortex-wide neural interfacing and (3) (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." | ||||
| cytoNet | A mathematical, web-based tool to rapidly characterize multiscale networks from images | Software | Academic software, Cell-cell interaction, Graph Theory, Topology, Image analysis, Systems biology, BRAIN Initiative | |
| 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. | ||||
| ENIGMA-Viewer & WebGIVI | Tools for data visualization and analysis: Gene data exploration; brain meta-analysis | Software | Meta-analysis, Data visualization, Data exploration, Interactive tool, Informative terms, BRAIN Initiative | |
| Brain meta-analysis tool for scientists to load their study results to compare them. A gene data exploration tool for scientists to study down-streaming up stream effects. | ||||
| Genetically Encoded Voltage Indicators (GEVIs) | "GEVIs: engineered protein-sensor to monitor the electrical dynamics of individual neurons Molecular technologies: Genetically encoded indicators for monitoring voltage in vivo (GEVIs)" | Molecural / Cellular | GEVIs, Imaging probe, Genetic probe, Protein sensor, Optical sensor, Neuroengineering, Optogenetic recording tool, Biological indicator, Optophysiology, In vivo voltage monitor, BRAIN Initiative | |
| 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. | ||||
| Graymatter Research | Hardware development for non-human primates: distributed recording systems and orthopedic implantation | Other Hardware Development | Microdrive system, Microelectrode, Neuronal activity, Non-human primate, BRAIN Initiative | |
| "Our company, Gray Matter Research, designs large-scale microdrive systems to enable semi-chronic recording of neural activity from large numbers of independently moveable microelectrodes in a behaving non-human primate (NHP). We have received two Brain Initiative grants related to this technology. The first was a three year grant under the Funding Opportunity Title “BRAIN Initiative: Optimization of Transformative Technologies for Large Scale Recording and Modulation in the Nervous System (U01)”. Optimizations that we completed include longer travel length, larger number of electrodes, flexibility to curve electrode trajectories, ability to register the electrodes to post-op scans and overall better reliability. We have sold over thirty of these systems in the last year. The second grant was a Phase 1 SBIR to develop a cranial-mounted orthopedic device for a new generation of microdrives using multi-channel laminar probes. We successfully designed and tested two devices on NHPs. We are just starting to incorporate this new platform into existing designs. We could present the design and features of a few recent projects." |