Enabling Shared Analysis and Processing of Large Neurophysiology Data

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Project Summary / Abstract Understanding brain function is key to improving health care and advancing a number of scientific initiatives. The treatment of degenerative brain diseases such as Alzheimer's, Parkinson’s, and ALS is becoming increasingly important as the current US population ages and life expectancies increase. The costs of Alzheimer's and other dementias is estimated at over $200 billion in 2016 alone, not to mention the human devastation that these diseases incur. Autism, addiction, depression, epilepsy, traumatic brain injury, and pain treatment are just a few more of the critically important health concerns related to brain function. Cognitive science is also at the forefront of research into computational and autonomous systems, with the potential to revolutionize human computer interaction and tackle emerging global challenges. As a result of these and other significant opportunities the BRAIN (Brain Research through Advancing Innovative Neurotechnologies) Presidential initiative was created to improve the future health and competitiveness of the nation, with the fundamental goal of accelerating brain research. Consistent with this goal, the brain research community has developed the Neurodata Without Borders: Neurophysiology (NWB) file format and specification to support large-scale collaboration and research. This open format was created in 2014 and is already making an impact on cellular-based neurophysiology, with organizations such as the Allen Institute for Brain Science generating and sharing datasets such as the Allen Brain Observatory and the Allen Cell Types Database. Although this preliminary work is promising, progress in the research community is slowed by a lack of software tools to readily browse, process, analyse, and visualize NWB data, while promoting replicability. Thus this work aims to to produce such tools in support of the BRAIN initiative and other large-scale brain research programs by supporting and growing the NWB community. The work proposed here addresses three important workflows in cellular-based neurophysiology: o​ ptical physiology to image neurons under stimuli, silicon probe recordings to detect spike events from the surface of the cortex down through deeps​ structures, and​ in vitro slice electrophysiology to record t​ ime-varying stimulus and electrical response from a neuron​. Novel multiscale software tools will be created to enable efficient browsing, processing, analysis, and visualization of NWB-based brain data; linking experimental stimuli to observed responses. Conversion utilities will also be developed to convert existing data into NWB form. As the data is large, complex, and may be distributed across many sites, the software tools will be web-based, enabling researchers to remotely access and process data in a reproducible manner, and to use scalable cloud computing resources. The software will be released under open source licences and will be placed under formal software process to facilitate sharing across the research community. The tools will be conceived and created with the help of Allen scientists, who will also perform final validation using these three workflows.