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Python and Jupyter Notebook for Medical Image Analysis

Workshop at OpenMR Benelux 2020

In this workshop, you will learn the basics of Jupyter notebook, python, and SimpleITK

Set up

  • See the video below:

    Video

  • Or follow the instructions below:

    1. Download Anaconda, a python platform:
    • Go to anaconda.com/distribution and click on Download
    • Select your operating system and click on Download
    • Once downloaded, install anaconda as you would do for any software.
    1. Download the material from GitHub:
    • In this page, click on the green Clone or downloadbutton above, and then Download Zip. Download the files in a folder of your choice.
    • Once downloaded, unzip the files
    1. Install a few python packages that we will need and download the images that we will use:
    • Open Anaconda by double-clicking on it
    • Launch JupyterLab
    • In the left panel, navigate to the folder you downloaded from GitHub
    • Double click on the file 0_setup.ipynb to open it
    • Run the cells by going to Run -> Run All Cells
    • Go to your workshop folder and unzip the downloaded images.

If you have any issue during the installation, go to the top of this page, click the tab Issue, and open an new issue. I will be happy to reply to you.

Content

There are two jupyter notebooks and their correspoding solutions:

  • 1_jupyter_and_python.ipynb and 1_jupyter_and_python_solutions.ipynb
  • 2_SimpleITK.ipynb and 2_SimpleITK_solutions.ipynb

In addition there is a list of links that can help you get familiar with the Jupyter environment, python, and SimpleITK:

  • Resources.md

Video

The content of the notebook 1_jupyter_and_python.ipynb is explained in the YouTube series
Jupyter notebook and Python for scientists:

image