Author Archives: Adrienne Fairhall

The dynamic brain!

A new method to segment brain regions by their connectivity.. examining how particular cell types participate in the cortical “chorale”.. new open-source tools to help visualize how brain regions are connected.. a data-driven model to capture how information is transformed between layers in visual cortex: these are a sampling of some of the student team projects presented on the final day of the 2016 Workshop on the Dynamic Brain.

Held at UW’s beautiful Friday Harbor campus in the San Juan Islands, this course is a joint endeavour of the Allen Institute for Brain Science and the University of Washington’s Computational Neuroscience program. With a teaching program focused on understanding cortical function, and centered on the open-access data sets and tools of the Allen Institute, students engage in an intense, hands-on learning experience that ranges from basics of neuroanatomy to theoretical models of brain function. Tutorials and problem-solving exercises working from Python notebooks get everyone up to speed and quickly engaged in developing original projects combining modeling and analyses of the Allen’s rich, unique and carefully curated data sets—including detailed connectivity maps, a wide sampling of functional properties of different cell types, and the newly released Allen Brain Observatory, recordings from many neurons while an animal is engaged in a variety of different perceptual tasks. The students, stimulated by a diverse set of lectures, are able to pose an array of novel questions that can be explored for the first time in this data.

group working

Team KART: a prize-winning collaboration.

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Team COBRA’s presentation included their team project management plan.

The progress made by course participants in these projects in two short weeks is stunning. Several factors make it possible. The course began with a Python bootcamp held at UW’s Data Sciences Studio, so that everyone hit the ground running with AIBS’ Python-based interfaces. Upon arriving at Friday Harbor, students, TAs and faculty spend all working hours together in an airy and hospitable dining hall overlooking the sea, where the buzz of activity continues into the small hours. AIBS staff and our TAs and faculty invest an enormous amount of effort preparing teaching resources for the class and are constantly on hand to assist students with accessing and manipulating data and in brainstorming project ideas. Lectures are followed up with hands-on tutorials so that students are supported while working through structured problems before proposing and launching into projects. Students bring their talent, energy and enthusiasm, and share their diverse expertise through teamwork.


Pat Churchland, Christof Koch and Blaise Aguera y Arcas field questions and discussion on consciousness in man, animals and machines.

Along with presentations from locals from UW and the Allen, lectures also highlighted forefront work being done in labs around the country; Anne Churchland (Cold Spring Harbor Labs) showed how multiple sources of information are represented and processed in the brain during complex decisions, and Rafael Yuste (Columbia) described cutting-edge optical technologies that allow one to “write in” new patterns of brain activity. Jeremy Freeman (Janelia) led an electrifying discussion and workshop on coding practices for collaborative and reproducible science that students immediately incorporated into their project teamwork. In an extended Friday night thoughtfest, philosopher Pat Churchland described the neurological origins of ethics and morality, and Google engineer Blaise Aguera y Arcas discussed developments in artificial intelligence, relationships with biological perception and creativity, and the pending social implications of AI. Christof Koch then joined the speakers in a panel and lively group discussion about machines, consciousness and ethics.

swim selfie

Students are going home with new and solid skills—Python coding, data analysis and modeling tools, familiarity with the datasets and atlases, and ideas and work practices that they can immediately inject into their research at home. But the most exciting aspect of the course is that students have access to TB upon TB of data—brain images and neuronal activity patterns—never before analyzed and seen by a human eye. The projects vividly demonstrated the new insights waiting to be extracted from the Allen Institute resources.

All participants are deeply grateful to Paul Allen for funding the course, and to the Simons Foundation for additional support.

fhl2016 party

So much talent!

UW hosts CRCNS meeting

In the last week of September, UW hosted the 2015 meeting of the recipients of NSF Collaborative Research in Computational Neuroscience grants. These awards support theorists working with experimentalists to develop and test theories of brain function.  Talks covered topics as diverse as models of sequence learning in hippocampus, network instantiations of neural integrators and deciphering whole-brain representations of natural speech.  Plenary speakers were Anne Churchland, from Cold Spring Harbor Labs, describing her work on cortical representations of multisensory integration in decision-making; Surya Ganguli of Stanford University, discussing the computational power of complex synapses; and Jesse Goldberg of Cornell who showed new results on basal ganglia dynamics during songbird learning. The meeting was also an opportunity to learn about new funding opportunities for theory from NSF, NIH and the BRAIN Initiative.

CRCNS workshop

A highlight of the meeting was the final workshop, a lively discussion about what machine learning might be able to tell us about the brain and how studies of the brain can inform machine learning algorithms in the future. Speakers/panelists included UW faculty Emily Fox and Wyeth Bair along with Odelia Schwartz (U. Florida) and two industry researchers, Blaise Aguera y Arcas  (Google Seattle) and Greg Corrado (Brains group, Google Mountain View).

Thinking of studying Comp Neuro and Neural Engineering at UW?

Thinking of applying for PhD studies in Computational Neuroscience and Neural Engineering at UW?

The University of Washington has a rich, active and highly collaborative community of researchers in the field of computational neuroscience and neural engineering. The University of Washington is a vibrant research university with a beautiful campus in a spectacular urban setting, with an ERC Center for Sensorimotor Neural Engineering, the UW Institute for Neuroengineering, close connections to the local tech industry and the Allen Institute for Brain Science. UW is also a major data sciences center with interdisciplinary interactions coordinated through the eSciences Institute. The city is a short distance from wilderness and outstanding summer and winter outdoor adventure.

While faculty advisors belong to a wide range of different departments, researchers come together regularly for seminars, journal clubs and a yearly retreat. Many student funding opportunities exist through multiple training grants, UWIN and the CSNE. Doctoral programs encourage collaborative research projects across departmental boundaries, but admissions and first-year course work and formal requirements are handled by graduate programs individually. Students interested in this area should apply to the program that best fits their background, interests and career goals.

 Relevant programs, websites and application deadlines include:

Faculty include:

  • Wyeth Bair (Neuro, CSE): Computer modeling of visual cortical circuits
  • Geoff Boynton (Neuro, Psychology): Functional imaging of vision
  • Beth Buffalo (Neuro): Navigation and memory in primates
  • Bing Brunton (Biology, Data Sciences): High dimensional neural data
  • Howard Chizeck (CSE, Neuro): Performance metrics for neural interfaces
  • Tom Daniel (Neuro, Biology): Sensorimotor integration and flight control
  • Horacio de la Iglesia (Neuro, Biology): Circadian rhythms
  • Marcel den Nijs (Physics): Statistical mechanics of brain function
  • Adrienne Fairhall (Neuro, BPSD, Physics): Adaptive neural coding, sensorimotor integration
  • Eb Fetz (Neuro): Motor control and brain-computer interfaces
  • Ione Fine (Neuro, Psychology): Human visual psychophysics and imaging
  • David Gire (Neuro, Psychology): Mammalian olfaction
  • Bertil Hille (Neuro, BPSD): Biophysics of neuronal signal transduction
  • Greg Horwitz (Neuro): Cortical color processing
  • Nathan Kutz (A Math): Nonlinear dynamics and dimensionality reduction
  • Adrian KC Lee (Neuro, Speech and Hearing): Auditory scene analysis with imaging
  • Chet Moritz (Neuro, Rehab Medicine): Neural prosthetics
  • Sheri Mizumori (Neuro, Psychology): Neurobiology of decisions, learning, and memory
  • Bill Moody (Neuro, Biology): Cortical development
  • Scott Murray (Neuro, Psychology): Visual neuroimaging
  • Jay Neitz (Neuro): Color vision
  • Jeff Ojemann (Neuro, Neurology): Human neural function and neuroprosthetics
  • Anitha Pasupathy (Neuro): Neurobiology of visual shape processing
  • David Perkel (Neuro, Biology, S&H): Neural mechanisms of vocal learning
  • Steve Perlmutter (Neuro): Motor control
  • Chantal Prat (Neuro, Speech and hearing): Auditory processing
  • Nino Ramirez (Neuro): Neural control of rhythmic activity
  • Rajesh Rao (Neuro, CSE): Computational modeling and brain-computer interfaces
  • Fred Rieke (Neuro, Physics, BPSD): Sensory signal processing in the retina
  • Jeff Riffell (Neuro, Biology): Neuroecology and chemosensation
  • Ed Rubel (Neuro, BPSD, S&H): Development of the auditory system
  • Jay Rubinstein (Neuro, BioE, S&H): Biophysics and engineering of cochlear implants
  • Eric Shea-Brown (Neuro, A Math): Nonlinear dynamics in neural computation and coding
  • Bill Spain (Neuro, BPSD): Biophysics of neuronal computation
  • Kat Steele (Mec Eng): Human movement
  • Emo Todorov (Neuro, A Math, CSE): Optimal motor control


Tech Sandbox winner continues to shine

larsCrawfordLars Crawford, graduate of the Neurobiology/Computational Neuroscience program’s class of 2014, was recently accepted into the Technology Commercialization Fellowship Program at the University of Washington’s Center for Commercialization for his work on a virtual home rehabilitation system called vHAB. A kinematic hand sensor and custom EMG sleeve controls a set of dynamic games that emulate traditional upper extremity therapy tasks and is designed to keep patients motivated in their home rehabilitation while collecting usage and ability data over time. The vHAB concept was a winner in the Center for Sensorimotor Neural Engineering’s Tech Sandbox course/competition in which Lars’ team, also including bioengineering graduate students Brian Mogen and Tyler Libey, created the system. The team has continued to work on the project to push it toward market and help to improve lives. The fellowship is intended to provide personal funding and mentorship to help Lars realize this goal. Congratulations!

Brain University continues

Our Seattle Arts and Lectures series, Hacking the Brain to Reveal, Repair, Rebuild, launched on October 1 with a mind-bogglingly fun and informative talk from Phil Horner about the use of stem cells to repair spinal cord. The series continues on October 22 with a talk by Beth Buffalo on the remarkable spatial coding properties of the hippocampus, for which the 2014 Nobel Prize in Physiology was awarded, and how we may be able to intervene to enhance memory. Sneak previews promise a fascinating evening. Spread the word to family and friends!

Beth talk ad



Congratulations to Yu Hu!

The Huthesis of Yu Hu, an Applied Mathematics PhD Student advised by Eric Shea-Brown, was selected as the top-ranked thesis in mathematical sciences, physics and engineering in the competition for the 2014 UW Graduate School Distinguished Dissertation Award.  His dissertation, “Collective Activity in Neural Networks: the Mathematical Structure of Connection Graphs and Population Codes,” propelled him to a Swartz Fellowship at Harvard, where we’ll be watching to see more great findings coming down the comp neuro pipeline.

New graduate students

We are happy to announce the new graduate trainees in the Computational Neuroscience Program.

Yoni Browning, working in the Buffalo and Fairhall labs, is working on primate navigational strategies and their representation in hippocampus using virtual reality environments. Yoni is a graduate of the UW undergraduate computational neuroscience program. He will be cofunded by UW Institute for Neuroengineering.

Kaitlyn Casimo, working with neurosurgeon Jeff Ojemann, works on the measurement and characterization of ECoG signatures of resting state activity.  Kaitlyn is also cofunded by the UW Institute for Neuroengineering.

Phil Mardoum, a graduate of the University of Chicago’s computational neuroscience program, will be working with Fred Rieke and Rachel Wong on optimal filtering by synapses in the retina.

Joris Vincent, who will work with Steve Buck on computational models of lightness perception, is a graduate of University College Utrecht with a background in neuroscience and psychology.




Dispatch from Friday Harbor

We are well into the second week of our new summer Workshop on the Dynamic Brain, co-hosted by the UW Computational Neuroscience program and the Allen Institute for Brain Science. The course is held at Friday Harbor Labs, UW’s exquisitely beautiful “science camp” on the forested shores of San Juan Island.  This course has a very distinct flavor compared with other computational neuroscience courses: it is structured around the data being produced by the Allen Institute. Twenty-four students from all over the world have gathered for the opportunity to learn to use relevant tools, access new data and to start to think about constructing models for cortical function based strongly on measured anatomy and ultimately, physiology and activity data from behaving animals– all with help and advice from the people creating and curating that data for public use.  Christof Koch, Clay Reid, Shawn Olsen and Michael Buice discussed visual processing, connectomics and high-level models of cortical function while Lydia Ng, Nick Cain and David Feng introduced students to tools to explore the “projectome” using AIBS unpublished data and to click together network models using a new graphical user interface called SimViz.  Along with the Allen Institute team, speakers have included local UW faculty including Adrienne Fairhall and Eric Shea-Brown on models of neural coding, visual scientists Wyeth Bair, Anitha Pasupathy and Jay Neitz and data sciences guru Bill Howe; Google engineer Blaise Aguera y Arcas speaking on machine intelligence; and Anne Churchland, from Cold Spring Harbor Laboratory, on circuits of decision-making.

Students are busy carrying out cool projects including analyses of the topography and multisensory nature of projections into superior colliculus, building dynamical models based on the projectome connectivity matrix and developing recurrent networks for feature extraction.

As today’s highlight, Christof Koch accepted the ALS ice bucket challenge.

Christof takes the bucket!

Wyeth helps Christof accept the ice bucket challenge.

Working with projects in the mess hall

Student Alex Cayco-Gajic works with AIBS faculty Shawn Olsen, Nick Cain and David Feng.

Friday Harbor

Friday Harbor ferry terminal