X-Tract Allen web interface

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.

Dependencies

• 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

Installation

• 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

Update

• 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

Usage

• To run the web application locally, you need to execute the file __init__.py with your python 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 file config.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)

Contributors

Developer	Supervisor / Developer
	)
github.com/lemphi97	github.com/joe-from-mtl

License

• Allen Institute Software License