Tutorial: Navigating the Allen Brain Observatory
This tutorial will introduce participants to the scientific foundations, data parameters, and practical skills for using the Allen Brain Observatory in computational neuroscience research.
The Allen Brain Observatory is a massive, complex open dataset that facilitates deep-dive research projects and the development of models of cortical computation and is of interest to both experimental and theoretical neuroscientists. The Allen Brain Observatory: Visual Coding project surveys physiological activity in the mouse visual cortex, measuring 2-photon calcium activity in the awake mouse while it views a diverse set of visual stimuli. This open dataset consists of recordings of over 60,000 neurons throughout the visual cortex recorded in over 450 experiments.
All data, unique visualizations, and more analysis tools are available through the Allen Brain Atlas portal. Programmatic access is available via the AllenSDK, a software kit that enables users to analyze raw data including fluorescence traces, visual stimulus information, extracted events, eye tracking data, running speed, and other features.
After attending the workshop, attendees will be prepared to fully leverage this data set for use in their own research.
A new publication on the Allen Brain Observatory is available on bioRxiv.
Thursday, February 28, 2019
Epic Sana Lisboa Hotel
Av. Engenheiro Duarte Pacheco 15
1070-100 Lisbon, Portugal
Monday, March 4
Criteria for evaluating biologically plausible learners.
Workshop: Why spikes? Understanding the power and constraints of spiking based computation in biological and artificial neuronal networks.
Tuesday, March 5
Large-scale activity mapping of the corticothalamic visual system in mice.
Workshop: Studying visual processing in rodents: where a decade of research has taken us and what is waiting ahead.
Thursday, February 28
Multi-area recordings reveal distinct functional ensembles spanning mouse visual cortex.
Xiaoxuan Jia*, Joshua Siegle, Severine Durand, Greggory Heller, Tamina Ramirez, Yazan Billeh, Shawn Olsen*.
Friday, March 1
Motion detection model predicts direction-reversing neurons as observed in the mouse visual cortex.
Yazan N. Billeh*, Ramakrishnan Iyer, Gabriel K. Ocker, Michael A. Buice, Stefan Mihalas, Anton Arkhipov, Saskia de Vries.
Saturday, March 2
A large-scale physiological survey reveals higher order coding throughout the mouse visual cortex.
Saskia de Vries*, Michael A. Buice*, Jérôme Lecoq, Gabriel Ocker, Michael Oliver, Daniel Millman, Peter Ledochowitsch, Peter Groblewski, Nicholas Cain, Clay Reid, Christof Koch.
Stimulus-driven bursting dominates neural activity measured by calcium imaging.
Peter Ledochowitsch*, Nicholas Cain, Joshua Siegle, Xiaoxuan Jia, Ulf Knoblich, Lawrence Huang, Lu Li, Gabriel Ocker, Daniel Millman, Michael Oliver, Hongkui Zeng, Shawn Olsen, Clay Reid, Stefan Mihalas, Saskia de Vries, Michael A. Buice.
Functional interactions between Vip and Sst interneurons are stimulus and state dependent.
Daniel Millman*, Gabe Ocker, Nicholas Cain, Peter Ledochowitsch, Rylan Larsen, Kevin Takasaki, Michael Oliver, Clay Reid, Michael Buice, Saskia de Vries.
Representational similarity analysis reveals population coding complexities in mouse visual cortex.
Jianghong Shi*, Gabriel Ocker, Michael Oliver, Nicholas Cain, Peter Ledochowitsch, Daniel Millman, Saskia de Vries, Eric Shea-Brown, Michael A Buice.
* Presenting author.