Allen SDK

What is Allen SDK?

The Allen Software Development Kit hosts the source code for reading and processing allen brain atlas data. The Allen SDK focuses on the Allen Brain Observatory, cell types database, and mouse brain connectivity atlas.

Allen Brain Observatory

Allen Brain Observatory is a data resource for understanding sensory processing in the mouse's visual cortex. This study systematically mediates visual responses in multiple cortical areas and layers using calcium images of two photons of neurons labeled with GCaMP6 targeted using Cre driver lines. Response characterizations include orientation adjustment, spatial and temporal frequency adjustment, temporal dynamics, and spatial receptive field structure.

The average fluorescence traces for all segmented cells are available in the Neurodata Without Borders (NWB) file format. These files contain standardized descriptions of visual stimuli to support stimulus-specific adjustment analysis. The Allen SDK provides code for:

• download and organize the experimental data according to the cortical area, image depth and Cre line
• remove the contribution of the neuropil signal from fluorescence traces
• access (or compute) traces dF/F based on the traits corrected by neuropil
• perform stimulus-specific tuning analysis (e.g., adjustment of the direction of the shunt grid)

Allen Cell Types Database

The Allen Cell Types Database contains electrophysiological and morphological characterizations of individual neurons in the mouse's primary visual cortex. The Allen SDK provides Python code to access electrophysiology measurements (NWB files) for all neurons and morphological reconstructions (SWC files) for a subset of neurons.

The database also contains two classes of models suitable for this data set: biophysical models produced using the NEURON simulator, and generalized integration and trigger models (GLIFs) produced using custom Python code provided with this toolkit.

The Allen SDK provides sample code demonstrating how to download neuronal model parameters from the Allen Brain Atlas API and run your own simulations using Allen Cell Types Database stimuli or custom current injections:

• Biophysical models
• Generalized LIF models

Allen Mouse Brain Connectivity Atlas

The Allen Mouse Brain Connectivity Atlas is a high-resolution map of neural connections in the mouse's brain. Built on a matrix of genetically modified transgenic mice to target specific types of cells, the Atlas comprises a single compendium of projections of selected neuronal populations throughout the brain. The primary atlas data consist of high-resolution images of axonprojections that target different anatomical regions or various types of cells using Cre-dependent specimens. Each dataset is processed through a computer data analysis pipeline to obtain spatially mapped quantified projection information.

The Allen SDK provides Python code to access experimental metadata along with projection signal volumes recorded in a common coordinate structure. This framework has structural annotations, which allow users to calculate signal statistics at the structure level.

System requirements

Minimum Windows Configuration:

• Operating System: Microsoft Windows 7
• CPU: Intel Core Duo or AMD 1.8GHz
• System memory: 1GB
• Video Card: OpenGL 3D Hardware Accelerated AGP or PCI Express with 64MB RAM
• Screen: 1024 x 768, 32-bit core
• Hard Drive: 200MB of free space

Minimum Mac configuration:

• Operating System: OS X 10.6.8
• CPU: 1.8 GHz from Intel
• System memory: 1GB
• Graphics card: compatible with 3D with 64 MB of RAM
• Screen: 1024x768, 32-bit colors
• Hard Drive: 200MB of free space