CISC881

Lessons for CISC 881 - Deep Learning for Medical Imaging

Quickstart

First, clone this repository:

git clone https://github.com/med-i-lab/CISC881
chdir CISC881

create an environment for the project (we recommend anaconda), and install the requirements:

conda create --name cisc881 python=3.9
conda activate cisc881
pip install -r requirements.txt

Pytorch Basics

We use pytorch which is the most widely used framework for deep learning researchers. If you are not familiar with pytorch, that's fine! Please check out this video https://www.youtube.com/watch?v=IC0_FRiX-sw&ab_channel=PyTorch for an introduction to pytorch. We also included a "Hello world" pytorch example, which can be run using:

python basic_training_example.py

Try running the example and reading through the script to get a feel for it.

Chest X-ray Lesson

We will be using a chest X-ray dataset as the source for our lessons. We need to download the dataset, it is available at https://www.kaggle.com/datasets/prashant268/chest-xray-covid19-pneumonia. To follow along with the demo, you need to download the dataset, put it in the data/ folder, and unzip it.