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README.md

GBM8378

Polytechnique Montreal course "Principes d'imagerie biomédicale".

This repository includes the lab material for the course

Documentation and Ressource

To get started with Python, we recommend this excellent tutorial (in French) made by Guillaume Sheehy.

Getting started (with Binder)

Click on the Binder badge: Binder

Wait for Binder to finish building the environment (can take 5-10 minutes), then click on the Jupyter notebook. E.g.: under lab3-irm/gbm8378-lab3-irm.ipynb.

Warning: After 10 minutes of inactivity, binder will stop working and you will have to launch it again. Save your work before closing it or it will be lost !

Getting started (on local station)

1) You will need to install miniconda in order to set-up your python environment.

2) Clone this GitHub repository on your computer:

git clone https://github.com/jcohenadad/GBM8378.git
cd GBM8378
  • For Windows user, you might need to install git prior to clone the repository.
  • If git clone is not working, you can download the zipped version of the repository and unzip it locally on your computer.

3) Once miniconda is installed and the repository is cloned, run the following commands in order to create your virtual environment and start the jupyter notebook:

Then, run the following to create a virtual environment and start the notebook:

conda env create -f environment.yml # Only do it once in order to create the environment (might take a few minutes)

# Start the jupyter notebooks:
conda activate env-gbm8378  # Do it everytime you wish to run the notebook
jupyter notebook  
  • Make sure that your prompt is currently on the GBM8378 folder when you call the environment.yml file.
  • For Windows user, you might need to type these commands in Anaconda Prompt if cmd does not recognize conda.

Make sure that you have the last version of the files by pulling the repo before every new lab (git pull). Move your Notebooks elsewhere if you don't want them to be overwritten by the new clone.

Create PDF

While on the jupyter notebook, print the page and export/save as PDF.

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Polytechnique Montreal course "Principes d'imagerie biomédicales"

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