The Allen Institute for Brain Science 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 dicsovers fundamental brain properties through integration of experiments, modeling and theory.

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

The Allen Institute on Github

The Allen Institute Github organization hosts software packages that support public access to Institute resources and data sets.

Allen SDK

The Allen Institute for Brain Science has published the Allen Software Development Kit (SDK), which houses source code for reading and processing Allen Brain Atlas data. The Allen SDK focuses primarily on the Allen Cell Types Database, Mouse Connectivity Atlas, and Brain Observatory. Functionality relevant to other atlases is planned for future releases.

Allen Brain Atlas API

The Allen Institute for Brain Science offers access to its published data through an application programming interface (API). The API, documentation, and sample applications are made available to the community under the Allen Institute's Terms of Use in hopes of facilitating discovery. The Allen SDK provides Python classes and code samples to facilitate API access.

DiPDE

DiPDE (dipde) is a simulation platform for numerically solving the time evolution of coupled networks of neuronal populations. Instead of solving the subthreshold dynamics of individual model leaky-integrate-and-fire (LIF) neurons, dipde models the voltage distribution of a population of neurons with a single population density equation. In this way, dipde can facilitate the fast exploration of mesoscale (population-level) network topologies, where large populations of neurons are treated as homogeneous with random fine-scale connectivity.

NWB API

The NWB API is a Python libary that was used to write Allen Cell Types Database experiments' details to the Neurodata Without Borders: Neurophysiology (NWB) file format. This API is designed to work with a variety of neurophysiology data, including intracellular and extracellular electrophysiology experiments, optical physiology experiments, as well as tracking and stimulus data.