This is a test homepage

Semi Automatic Neuropath Analysis (SANA)

Installation

Python

• Install Python 3.9

  • IMPORTANT: Make sure to check the advanced options and include Python in PATH environment variables
  • You can test if python is installed properly by opening a command line and typing python3 -V

    OpenSlide

• Download OpenSlide Windows binaries

• Unzip, and place in a location such as C:\Users\yourname\openslide

• Add this location to your PATH environment variable

  • Search environment variables
  • Edit PATH variable under User environment
  • Append the C:\Users\yourname\openslide location to the end

    pip packages

• Copy/paste each of the following lines into your command line, be sure that each of them succeeds

  • python3 -m pip install scipy
  • python3 -m pip install pytorch
  • python3 -m pip install tqdm
  • python3 -m pip install xlrd
  • python3 -m pip install numba
  • python3 -m pip install shapely
  • python3 -m pip install matplotlib
  • python3 -m pip install pyefd

• If any of these fail, feel free to google the error message, or reach out to Noah

  SANA code

• Following steps to create an ssh key after making your github account

• Open command line and Change Directory (cd command) into a location to store the code
  • cd ~/
• git clone git@github.com:penndigitalneuropathlab/sana.git
• cd ~/sana/scripts
• python ./sana_process.py
  • If everything installed properly, you should get a USAGE message
  • If you get a package not found, you can try running python3 -m pip install PACKAGENAME or google "how to pip install PACKAGENAME"
  • Any other errors reach out to Noah

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