The Allen Institute is dedicated to accelerating the understanding of how the human brain works in health and disease. Using a big science approach, the Allen Institute generates useful public resources used by researchers and organizations around the globe, drives technological and analytical advances, and discover fundamental brain properties through integration of experiments, modeling and theory.

GitHub Profile | Allen Institute for Brain Science | Allen Brain Atlas | Allen SDK

The Allen Brain Observatory Ecosystem on Github

The Allen Brain Observatory presents the first standardized in vivo surveys of physiological activity in the mouse visual cortex. Neural activity is recorded using two different modalities: 2-photon optical physiology and Neuropixels probes. We make all the data from our systematic surveys of the mouse visual system available to the community for further analysis and exploration. These data provide a rich testbed for theories and models of cortical computation.

The observatory currently encompasses three broad projects:

Visual Coding used a broad range of visual stimuli, ranging from gratings and noise stimuli to natural images and movies which the mice passively view. It surveys the spatial and temporal dynamics of visual representation in the mouse corticothalamic visual pathways.

Visual Behavior mice performed a visual change detection task to characterize how sensation and behavior are encoded in activity across the visual cortex and how these representations are influenced by behavior state and expectation. Both the Visual Behavior and Visual Coding projects include 2-photon and Neuropixels datasets that have slightly different implementations.

In the Learning mFISH project description

To accommodate the different neural recording modalities as well as the differences between Visual Coding and Visual Behavior, we have created several different Github repositories to facilitate data exploration and analysis across these different data variations.

Brain Observatory Overview | Visual Coding: 2-photon | Visual Coding: Neuropixels | Visual Behavior: 2-photon | Visual Behavior: Neuropixels |

Allen SDK

The Allen Institute for Brain Science has published the Allen Software Development Kit (SDK), which houses source code for reading and loading Allen Brain Observatory data. This is a public repo intended for use by both internal and external researchers.

This repo supports both Visual Coding and Visual Behavior

Brain Observatory Utilities

The Brain Observatory Utilities (BOU) repository is a utility toolkit for processing, manipulating and visualizing data from the Allen Brain Observatory data via the Allen SDK. This is a public repo intended for use by both internal and external researchers.

This repo supports Visual Behavior project data as well as newly emerging projects

Brain Observatory Analysis

The Brain Observatory Analysis (BOA) repository is an analysis toolkit focused on development of new analytical and visualization tools of Allen Brain Observatory data (Visual Behavior Ophys, Learning mFish). This is a public repo intended for use by both internal and external researchers.

This repo supports Visual Behavior project data as well as newly emerging projects

Brain Observatory QC

The Brain Observatory QC (BOQC) repository computes quality control metrics and plots for Allen Brain Observatory projects, and specifically those that utilitze 2-photon imaging. It is also a central location for for tracking data quality issues. This is a private repo and is only accessible to internal Allen Institute researchers.