Python Boot-camp: August 24 & 25, 2019

Summer Workshop on the Dynamic Brain: August 25 – September 8, 2019


Announcing the Summer Workshop on the Dynamic Brain, co-hosted by the Allen Institute for Brain Science and the Computational Neuroscience Center at the University of Washington and directed by Drs. Michael Buice, Shawn Olsen, Christof Koch, and Eric Shea-Brown.

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, coding, and neural population dynamics. In addition, the course makes extensive use of data science tools for team-based projects and computational tools for analysis of large-scale and multi-modal neural data sets.

The workshop will include a Python boot-camp and other software tutorials. Scientific lectures will be 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 neuroanatomy and neurophysiology of cortex, neuronal cell types and cortical layers, connectomics, optical and electrophysiological methods for measuring cell populations, theories and modeling of neocortex and associated structures, big data approaches, and perceptual and behavioral neuroscience (with a focus on vision).

The workshop will feature large-scale data sets generated by the Allen Institute including the Allen Brain Observatory ( Pre-release Neuropixel electrophysiological and behavioral datasets will also be explored at the workshop.  Other Allen Institute resources will be available for interested students, including data sets featured in previous workshops and as well as modeling tools.

Students will have the opportunity to carry out computational neuroscience and data science research projects 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, University of Washington
  • Shawn Olsen, Allen Institute for Brain Science
  • Michael Buice, Allen Institute for Brain Science
  • Anne Churchland, Cold Spring Harbor Laboratory
  • Jeremy Freeman, Chan Zuckerberg Initiative
  • Wyeth Bair, University of Washington
  • Anitha Pasupathy, University of Washington
  • Rajesh Rao, University of Washington
  • Hongkui Zeng, Allen Institute for Brain Science
  • Blaise Aguera y Arcas, Google
  • Daniela Witten, University of Washington
  • Eric Shea-Brown, University of Washington


Allen Brain Observatory:

The Allen 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.

Pre-release data on Behavior and Electrophysiology:

This year’s Workshop will feature pre-release data on behavioral and electrophysiological experiments that will be included in future Allen Institute data products.

Data sets from a dense connectomic reconstruction of mouse visual cortex:

The Allen Institute for Brain Science large scale electron microscopy project, in collaboration with Baylor College of Medicine and Princeton University, is producing detailed neuronal morphologies and connectivity measurements between 100,000 neurons where there is also functional imaging from those neurons. This year’s workshop will feature a pilot release of data from this project, where students can explore the patterns in neuronal morphology, ultrastructure, and connectivity. 

Code repositories from 2018 and 2017 reflect material and projects from past workshops.

Partial funding is provided by The Simons Foundation and IBRO.