A web interface to query experiment data from the Allen SDK mouse connectivity project and helps identifying region of interest (ROI) for fiber crossing in the brain.
This application was developed with the help of my supervisor Joël Lefebvre for my internship during summer 2020.
- Anaconda 3 or Miniconda
- Python 3
- A git client to clone the repository, and pull the latest version.
- Linux and Mac user can use the command line git client
- Recommended clients for Windows are Github Desktop or Sourcetree
- Install Anaconda (Python 3.7 version)
- Launch a terminal (or the
Anaconda Prompt
on Windows) - Go to the source directory, and create a conda environment with:
conda env create -f environment.yml
- Activate your virtual environment with:
conda activate xtract
- Install the missing dependecies with
pip install -r requirements.txt
- On Linux or Mac, Open a terminal. On Windows, open the application
Anaconda Prompt
- Go to the repository directory
- Update the environment with:
conda env update -f environment.yml
- To run the web application locally, you need to execute the file
__init__.py
with yourpython
executable.- Launch a terminal
- Execute the file (from project root):
- On Unix:
python web/__init__.py
- On Windows:
:: Depending or your python version python web\__init__.py :: or python3 web\__init__.py
- In the folder
web
is the fileconfig.py
. From it, easily configure the application and daemon cleaner. - Access the application by opening your browser of choice at the address and port in
config.py
(ex: 127.0.0.1:5000 or localhost:5000)
Developer | Supervisor / Developer |
---|---|
github.com/lemphi97 |
github.com/joe-from-mtl |