Enabling Shared Analysis and Processing of Large Neurophysiology Data

Project SummaryAbstract Understanding brain function is key to improving health care and advancing a number of scientific initiativesThe treatment of degenerative brain diseases such as Alzheimer sParkinson sand ALS is becoming increasingly important as the current US population ages and life expectancies increaseThe costs of Alzheimer s and other dementias is estimated at over $billion inalonenot to mention the human devastation that these diseases incurAutismaddictiondepressionepilepsytraumatic brain injuryand pain treatment are just a few more of the critically important health concerns related to brain functionCognitive science is also at the forefront of research into computational and autonomous systemswith the potential to revolutionize human computer interaction and tackle emerging global challengesAs a result of these and other significant opportunities the BRAINBrain Research through Advancing Innovative NeurotechnologiesPresidential initiative was created to improve the future health and competitiveness of the nationwith the fundamental goal of accelerating brain researchConsistent with this goalthe brain research community has developed the Neurodata Without BordersNeurophysiologyNWBfile format and specification to support large scale collaboration and researchThis open format was created inand is already making an impact on cellular based neurophysiologywith organizations such as the Allen Institute for Brain Science generating and sharing datasets such as the Allen Brain Observatory and the Allen Cell Types DatabaseAlthough this preliminary work is promisingprogress in the research community is slowed by a lack of software tools to readily browseprocessanalyseand visualize NWB datawhile promoting replicabilityThus 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 communityThe work proposed here addresses three important workflows in cellular based neurophysiologyoptical physiology to image neurons under stimulisilicon probe recordings to detect spike events from the surface of the cortex down through deepsstructuresandin vitro slice electrophysiology to record time varying stimulus and electrical response from a neuronNovel multiscale software tools will be created to enable efficient browsingprocessinganalysisand visualization of NWB based brain datalinking experimental stimuli to observed responsesConversion utilities will also be developed to convert existing data into NWB formAs the data is largecomplexand may be distributed across many sitesthe software tools will be web basedenabling researchers to remotely access and process data in a reproducible mannerand to use scalable cloud computing resourcesThe software will be released under open source licences and will be placed under formal software process to facilitate sharing across the research communityThe tools will be conceived and created with the help of Allen scientistswho will also perform final validation using these three workflows