Informatics

Project summary Over the past five years, the Allen Institute has built two unique in-house pipelines for in vivo electro- and optical-physiology: together they form the Allen Brain Observatory. We used this observatory to freely and openly share calcium imaging data from ~60,000 cells from 221 running mice viewing standard visual stimuli; in October 2019, we will release Neuropixels electrophysiology recordings from ~100,000 cells from 100 mice under the same conditions, all registered to a common anatomical coordinate system (CCFv3).

The field of neuroscience and the BRAIN Initiative in particular are amassing a wealth of informatics resources for managing, analyzing, and sharing data.

PROJECT SUMMARY The goal of this project is to build an open-access recombinant antibody/affinity reagent resource for the neuroscience community called NABOR (Neuroscience AntiBody Open Resource).

PROJECT SUMMARY/ABSTRACT This project aims to disseminate validated technologies and resources of the National Center for Microscopy and Imaging Research (NCMIR) at UC San Diego to advance the completion of strategic goals of the BRAIN Initiative.

PROJECT SUMMARY Lack of standards for neurophysiology data and related metadata is the single greatest impediment to fully extracting return on investment from neurophysiology experiments. One of the greatest questions in science today is understanding how the brain works and gives rise to thoughts, memories, perception, and consciousness.

Advancing Bio-Realistic Modeling via the Brain Modeling ToolKit and SONATA Data Format One of the major goals of the BRAIN Initiative is to distill complex, multi-modal data into predictive frameworks via theory/modeling.

Since its invention in the early 90s, functional magnetic resonance imaging (fMRI) has revolutionized our un- derstanding of the human brain. Functional MRI may be used to observe brain function during a specific motor or cognitive task, or at “rest” (resting-state fMRI). The latter produces so-called “functional connectivity” maps that may provide a new window into human cognition. There is currently a large, world-wide effort underway to discover potential research and clinical uses of such connectivity maps.

The BRAIN Viral Vector Service and Distribution Core will serve as a resource for the maintenance, propagation, and distribution of viral vectors that are used by neuroscientists for neural circuit identification and manipulation, as well as for preclinical translational studies.

Traditional file-based neuroimaging data management and integration strategies have shown increasing limitations in accommodating the meteoric growth in both the scale and complexity of today’s neuroimaging data. The sophisticated software and hardware pipelines required in many of today’s neuroimaging studies have produced numerous platform-specific data files that are increasingly difficult to parse, exchange, and understand by the broader research community.

Advances in neuroscience depend on robust in vivo and in vitro models with innovative technologies to carry out functional and mechanistic studies accompanied by advanced imaging techniques. The Human Brain Organogenesis Program (HBOP), Behavioral and Functional Neuroscience Laboratory (BFNL), Gene Vector and Virus Core (GVVC), and Neuroscience Microscopy Services (NMS) make up a platform, the Stanford Neuroscience Research Center (SNRC), for centralization and dissemination of innovative neuroscience models, reagents and methods.