Stanford Program for Integrated Neuroscience Technologies
Posted on July 17th, 2023
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.
Brain Image Library
Posted on September 30th, 2022
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.
BossDB – Brain Observatory Storage Service and Database
Posted on August 19th, 2022
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.
Dual Independent Enhanced Scan Engines for Large field-of-view Two-Photon imaging (Diesel2p)
Posted on June 15th, 2022
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.
OpenScope
Posted on November 5th, 2021
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.
Two-photon spectrometer
Posted on November 4th, 2021
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.
Genetically-encoded reagents for high throughput connectomics
Posted on August 13th, 2021
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.
2P-FCM
Posted on August 13th, 2021
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.
NeuroNex: Cornell
Posted on October 26th, 2020
Imaging deeper, wider, and faster. Imaging multiple species using multiphoton microscope. Dissemination through meetings, campus visits, and commercial vendors.
UCLA Miniscope
Posted on October 26th, 2020
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