Here you will find scripts to access and interact with the Allen Connectivity Atlas SDK.
For more detailed information and examples, look at:
- https://github.com/AllenInstitute/SWDB_2019/blob/master/DynamicBrain/solutions/Other/Connectivity_solutions.ipynb
- https://allensdk.readthedocs.io/en/latest/allensdk.api.queries.mouse_connectivity_api.html#allensdk.api.queries.mouse_connectivity_api.MouseConnectivityApi
- https://community.brain-map.org/c/how-to/mouse-connectivity-atlas/31
Before starting, remember to install the AllenSDK package in Anaconda.
I suggest creating a virtual environment specifically for it, as it works best with older versions of Python.
My suggestion:
conda create -n allensdk_env python=3.10
conda activate allensdk_env
pip install numpy==1.23.5
pip install allensdk
pip install notebook
pip install pandas
pip install matplotlib
pip install imageio
pip install scipy
pip install seaborn
pip install pynrrd