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ABC - Anything But Cortex. David Kleinfeld. Reverse Engineering the Brain Stem Circuits that Govern Exploratory Behavior

Title: The adaptive atlas

Abstract:

Scientific Topic: The anatomy and function of nerve circuits in the brain stem of the mouse.

Types of data: Image stacks from a scanning microscope. This includes both brightfield imaging as well as fluorescent imaging. Different channels in the fluorescent imaging. We are developing a computation and visualization pipeline for aligning an atlas with a stack of brain sections. The result is to overlay a standardized coordinate system on the stack. The coordinate system enables experimental results from multiple brains to be related to each other. Our current focus is on projections of the rabies retrovirus from muscles to locations in the mouse brain-stem.

Open Questions: what textures (microarchitectures) can be identified reliably in the brain? How can we efficiently find the best diffeomorphism to map the atlas to a brain?

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