Python Bootcamp: August 19 & 20, 2017

Summer Workshop on the Dynamic Brain: August 20 – September 3, 2017



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, Adrienne Fairhall, Michael A. Buice, and Shawn Olsen.

This intensive, two-week, projects-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 include data analyses, Python and other software boot-camps, and lectures, taught by faculty from the University of Washington and the Allen Institute for Brain Science, 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, Allen Institute for Brain Science
  • Adrienne Fairhall, Department of Physiology and Biophysics, University of Washington
  • Wyeth Bair, Biological Structure, University of Washington
  • Anitha Pasupathy, Biological Structure, University of Washington
  • Rafael Yuste, Columbia University
  • Rajesh Rao, Computer Science & Engineering, University of Washington
  • Michael Buice, Allen Institute for Brain Science
  • Hongkui Zeng, Research Science, Allen Institute for Brain Science
  • Shawn Olsen, Neural Coding, Allen Institute for Brain Science
  • Blaise Aguera y Arcas, Google


Brain Observatory:

The Brain Observatory 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, natural images, and movies.  Along with raw imaging, data sets will include extracted fluorescence traces from segmented ROIs, eye-tracking, and running speed.

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.