README.md

allen-human-brain-atlas

Setup

1. Create a python virtual environment (venv) using the following command:

   python -m venv <path_to_venv>
   

2. Activate the virtual environment by navigating to the Scripts folder, then running ./activate. To deactivate the virtual environment at any time, issue the deactivate command.

3. Install the necessary dependencies.

   3a. abagen:

   git clone https://github.com/rmarkello/abagen.git
   cd abagen
   pip install .
   

   3b. abagen + parquet (for faster conversions): pip install abagen[io]

   3c. Jupyter notebook: pip install notebook

   3d. ipykernel: pip install ipykernel

   3e. nibabel: pip install nibabel

   3f. nilearn: pip install nilearn

   3g. matplotlib: pip install matplotlib

   3h. seaborn: pip install seaborn

4. Install a new ipython kernel: ipython kernel install --user --name=<project_name>

Resolved Errors

• If you encounter a ModuleError: No module name pkg_resources message when attempting to import abagen, your Python setuptools package is likely broken. To resolve this, issue the following command: pip install setuptools.

Documentation

• Access the abagen docs here.
• Access the Allen Human Brain Atlas dataset here.