Install Guide¶

This guide is a resource for using the Allen SDK package. It is maintained by the Allen Institute for Brain Science.

Attention

As of October 2019, we have dropped Python 2 support. The Allen SDK is developed and tested with Python 3.6 and 3.7. We do not guarantee consistent behavior with other Python versions.

Quick Start Using Anaconda¶

The Allen SDK comes packaged with the Anaconda Python distribution platform.

From the Anaconda downloads page, download the Python 3.7 version for your operating system and run the installer.

After the installation is complete, download one of our many Jupyter Notebook examples.

Open up a terminal (in Windows open Anaconda3).
Navigate to the directory where you downloaded the Jupyter Notebook example and run the following command:
jupyter notebook
Your browser should open and you should see the Jupyter Notebook example. Enjoy using the Allen SDK!

Quick Start Using Pip¶

First ensure you have pip installed. It is included with the Anaconda distribution.

pip install allensdk

To uninstall the SDK:

pip uninstall allensdk

Other Distribution Formats¶

The Allen SDK is also available from the Github source repository.

Required Dependencies¶

NumPy

SciPy

matplotlib

h5py

pandas

pynrrd

Jinja2

Optional Dependencies¶

pytest

coverage

Installation with Docker (Optional)¶

Docker is an open-source technology for building and deploying applications with a consistent environment including required dependencies. The AllenSDK is not distributed as a Docker image, but example Dockerfiles are available.

Ensure you have Docker installed.
Use Docker to build one of the images.
Anaconda:
docker pull alleninstitute/allensdk
Other docker configurations are also available under docker directory in the source repository.
Run the docker image:
docker run -i -t -p 8888:8888 -v /data:/data alleninstitute/allensdk /bin/bash
cd allensdk
make test
Start a Jupyter Notebook:
cd allensdk/doc_template/examples_root/examples/nb
jupyter-notebook --ip=* --no-browser