Uses point locations, in 3D coordinates of the Allen Brain Atlas, to create different visualisations for these locations:
📚 See documentation here
Clone this repo
Optional: create a virtual environment
In your terminal, navigate to the folder where you cloned it and run:
pip install .
Download supporting data (e.g. atlas) from
Put it inside the data folder.
All the scripts work with a text file that specifies the coordinates of the points you want to display (e.g. tip of a fiber). This file looks like the one in the example:
data/example_locations.txt
The coordinates in this example are the pixel locations of the 25um/px Allen Brain Atlas. You can generate similar files by registering your brain to the atlas (e.g. see brainreg), and annotating the x, y and z coordinates of the tip of the fiber.
Important: edit the main path (main_path) variable in the configuration file data/example_config.json to specify the absolute path to your data folder. Do the same with the locations_file variable if you want to use the example locations file.
The scripts use the configuration file to get all the variables and files (e.g. the fiber locations), and that would be the main place for you to customise the figures to your liking. The generated plots would be saved whenever your configuration file is located.
To generate the plots you should provide as argument the path to the configuration file. In your terminal, run the generate_all_figures.py script. Assuming you are in brain_locations_visualizer folder, run:
python generate_all_figures.py path/to/your/config/file.json
To generate the plots for the example data, run:
python generate_all_figures.py
Which will automatically use the configuration file in data/example_config.json.
This script will generate all the plots in the data folder.