Summer Workshop on the Dynamic Brain

Summer Workshop on the Dynamic Brain: Datasets and Code

Students will explore open datasets from the Allen Institute for Brain Science through the course. The datasets also form the basis for the course project that students will develop over the second week of the course.

Allen Brain Observatory: Visual Coding

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.

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Allen Brain Observatory: Neuropixels

The Allen Brain Observatory Neuropixels dataset was released in late 2019. This dataset includes spiking activity in the mouse visual system and beyond.

Pre-release data 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.

Python Boot Camp

The Python boot camp is held in Seattle all day on Saturday, August 22, and the morning of Sunday, August 23, before all workshop participants depart for Friday Harbor, WA. Students who wish to get a start on the Python boot camp can work through the boot camp material and resources from 2019, see documentation from Python, or complete introduction to Python exercises by Code Academy or Google.

Code repositories

Code repositories from past workshops reflect materials and projects included in the workshop curriculum.

08/22/2020 to 09/06/2020