SANA Quick Start

This quick start guide shows you how to install SANA and get started with quantifying histology images.

Prerequisites

Create a virtual environment which will contain SANA and the python dependencies:

# change username to your username and/or preferred location
mkdir -p /home/username/sana
cd /home/username/sana
python3 -m venv .venv

Activate the environment (this must be done once per terminal session):

cd /home/username/sana
source .venv/bin/activate

Next, install SANA:

python3 -m pip install pdnl_sana

If a different version of SANA is desired, you can install SANA through git. First, clone the source code:

git clone https://github.com/penndigitalneuropathlab/sana.git /home/username/sana

Optionally, switch to the desired branch:

git checkout experimental

Create a shell script env.sh in the directory /home/username/sana with the contents below, modified to fit your installation

#!/bin/bash
source .venv/bin/activate

export PYTHONPATH=/home/username/sana/src:$PYTHONPATH

Create a virtual environment which will contain SANA and the python dependencies:

# change username to your username and/or preferred location
cd /home/username/sana
python3 -m venv .venv

Activate the environment (this must be done once per terminal session)::: cd /home/username/sana source env.sh

Next, install SANA dependencies:

python3 -m pip install -r src/pdnl_sana/requirements.txt

Run this command to ensure that everything installed properly:

python3 -c "import pdnl_sana.image; import pdnl_sana.slide"

If you are having issues with OpenSlide, follow instructions here to get the binaries.