Summer Workshop on the Dynamic Brain 2015

August 23, 2015 - September 6, 2015

  • Friday Harbor, WA
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Announcing the Summer Workshop on the Dynamic Brain, co-hosted by the Allen Institute for Brain Science and the Computational Neuroscience Program at the University of Washington and directed by Drs. Christof Koch and Adrienne Fairhall.

This intensive two-week, project-based interdisciplinary course aims to give advanced students in neuroscience, biology, physics, engineering and computer science a rapid introduction to the current state of understanding of the neurobiology of sensory processing, including anatomy, physiology and neural coding.

The workshop will include data analyses, Python boot camps and lectures, taught by faculty from the University of Washington and the Allen Institute, on topics focused on the mammalian cortex and closely associated satellite structures. Lecture topics will include biophysics of cortical neurons, neuroanatomy and neurophysiology of cortex, genomics, neuronal cell types, neuronal development, connectomics, network analysis, voltage- and calcium-dependent brain imaging, theories and modeling of neocortex and associated structures, big data approaches and perceptual neuroscience (with a focus on vision).

The workshop will also feature methodological and practical lectures on several Allen Institute data collections and tools, such as the mouse, monkey and human brain atlases; Brain Explorer; mouse connectivity atlas; mouse and human developmental atlas; modeling toolboxes and new neurophysiology data sets – see below for details of the novel data sets to be explored this year.

Students will have the opportunity to carry out a short informatics/computational neuroscience research project with the guidance of faculty, and will present their project to faculty and fellow participants at the conclusion of the workshop.


  • Christof Koch, Chief Scientific Officer, Allen Institute for Brain Science
  • Adrienne Fairhall, Associate Professor, Department of Physiology and Biophysics, University of Washington
  • Wyeth Bair, Assistant Professor, Biological Structure, University of Washington
  • Anitha Pasupathy, Associate Professor, Biological Structure, University of Washington
  • Rajesh Rao, Associate Professor, Computer Science & Engineering, University of Washington
  • Jeremy Freeman, Group Leader, Janelia Farm
  • Michael Buice, Allen Institute for Brain Science
  • Hongkui Zeng, Senior Director, Research Science, Allen Institute for Brain Science
  • Clay Reid, Senior Investigator, Neural Coding, Allen Institute for Brain Science
  • Shawn Olsen, Assistant Investigator, Neural Coding, Allen Institute for Brain Science
  • Eric Shea-Brown, Associate Professor, Applied Mathematics, University of Washington
  • Blaise Aguera y Arcas, Google


In Vitro Single Cell Characterization

The IVSCC pipeline is a high-throughput effort to characterize the mouse lateral geniculate nucleus (LGN) and primary visual cortex (V1) with single-neuron resolution through morphology, electrophysiology and gene expression with single-cell resolution.  Students will have access to subthreshold and spiking voltage responses of neurons in response to a battery of stimuli. Further, reconstructed axonal and dendritic morphology of neurons will be available for approximately 20% of the cells.

Cortical Activity Map

The Cortical Activity Map is a survey of physiological activity across multiple regions, layers, and cell types in the visual system of awake, behaving mice using two photon calcium imaging.  The mice are presented with visual stimulation using a wide array of stimuli:  gratings, locally sparse noise, spatio-temporal noise, natural images, and others.  Along with raw imaging, data sets will include extracted fluorescence traces from segmented ROIs, eye-tracking, running speed, and psychophysical performance.

Allen Mouse Brain Connectivity Atlas

The Allen Mouse Brain Connectivity Atlas uses enhanced green fluorescent protein (EGFP)-expressing adeno-associated viral vectors to trace axonal projections from defined regions and cell types, and high-throughput serial two-photon tomography to image the EGFP-labelled axons throughout the brain. Spatial registration of multiple experiments allows the construction of a whole-brain connectivity matrix.

Application deadline: April 1, 2015
Selected applicants will be contacted after May 1, 2015