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BioImage Informatics Conference 2017

Visual coding and Allen Brain Observatory

Mike Hawrylycz, Investigator, Allen Institute for Brain Science

The Allen Brain Observatory is a comprehensive physiological survey of neural activity in the visual cortex during sensory stimulation and behavior. This project systematically measured visual responses from neurons across cortical areas and layers utilizing transgenic Cre lines to drive expression of genetically encoded fluorescent calcium sensors (GCaMP6). This dataset provides a rich resource for exploring the progressive coding of sensory stimuli through the cortical visual pathway at both the single cell and population level.  In addition to searchable data from hundreds of two-photon calcium imaging sessions across multiple visual areas and depths in the visual cortex, the Observatory contains a variety of data visualization summaries capturing visual coding properties of single cell and cell population responses to sensory stimuli, standardized spatial mapping of cellular responses to five types of rich visual stimuli, surveyed from transgenic mouse lines, and raw data and analysis modules made ready for download via an API/SDK.  These data present rich opportunities for computational image analysis.


Mike Hawrylycz has been responsible for data annotation, mapping, and analysis at the Allen Institute for Brain Science since the Institute’s inception in 2003. He received his Ph.D. from MIT in applied mathematics and has worked in a variety of areas applying data analysis and image processing to the life sciences, including the Human Genome Project at Los Alamos National Laboratory and the National Human Genome Research Institute ENCODE project. Most recently Dr. Hawrylycz will be forming a team to enhance translational applications of Allen Institute resources.