This repository contains code to support the download of images and metadata from two free and publically available datasets.
Example notebooks for how to use the provided code can be found under the example_notebooks subfolder of this repository.
To install the tools provided by this repository simply:
# Feel free to change /tmp/open_dataset_tools to whatever location works best for you
> git clone https://github.com/AllenInstitute/open_dataset_tools /tmp/open_dataset_tools
# Don't forget to activate the python environment you want to install this package into
# The following example creates an environment using Anaconda Python
# See: https://docs.conda.io/en/latest/miniconda.html
> conda create --yes --name open_dataset_tools python=3.8
> conda activate open_dataset_tools
> cd /tmp/open_dataset_tools
> pip install .[full]
Once you've installed the package you can access and try running the example notebooks with:
> conda activate open_dataset_tools
> cd /tmp/open_dataset_tools/example_notebooks
> jupyter notebook
The Allen Mouse Brain Atlas is now hosted on AWS.
The Jupyter notebook Accessing_Allen_Mouse_Brain_Atlas_Data.ipynb demonstrates all of the helper functions necessary to download and view images from the atlas. It also demonstrates functions for downloading metadata and loading them as python data structures for easy searching, so that users can identify the images that will be most helpful in their research.
This module uses the open source boto3 API to interface with AWS S3.
The Jupyter notebook Accessing_Ivy_Glioblastoma_Atlas_Project_Data.ipynb demonstrates how to programmatically search, download, and interact with images from the Ivy Glioblastoma Atlas Project.
This module is provided as a means to give the broader neuroscience community access to the data generated by the Allen Institute. As such, we are very interested in maintaining the code so that it remains useful. Please file any bug reports through GitHub. We will consider pull requests, so long as they do not conflict with internal Institute policies regarding software.