Follow the examples described in https://github.com/davisreinaguerra/Wallace-Lab-Brain-Registration-Workflow to obtain a CSV file which contains Allen CCFv3 X, Y, and Z coordinates (* in millimeters) for all cells of a given class in a given brain. Or if you would like, use the practice data ('some_cells.csv').
In an anaconda terminal, navigate to whatever directory your python file is in, then create an environment for brainrender
(base) >conda create brainrenderenvironment
Activate your environment with:
(base) >conda activate brainrenderenvironment
Once the environment is active, install brainrender with:
(brainrenderenvironment) >pip install brainrender
In an anaconda terminal with the brainrenderenvironment active, navigate to a folder which contains both the given python file and the csv file of coordinates you want to visualize
(brainrenderenvironment) >python brainrendertest.py