CO4: Imaging for the Life Sciences

Git repository for the MSLS module CO4 – Imaging for the Life Sciences (Moodle)

Instructions – Overview

In the practical part, we will use Python and Jupyter notebooks to work hands-on with image data. We recommend the following setup:

• Python 3.10 or higher
• Jupyter 7.x
• Microsoft Visual Studio Code (with Python and Jupyter extensions)
• Git version control
• A set of Python packages (see requirements.txt)

We also recommend using a tool to manage different Python environments, such as venv (or Anaconda). VS Code supports both methods.

Instructions – Step by step:

• Install Python

  • There are different possibilities to install Python on your system
  • One possibility is to get the installer from: https://www.python.org/

• Install Visual Studio Code (VS Code)

  • Get the installer from https://code.visualstudio.com/

• Install the official Python extension for VS Code

  • Open VS Code
  • Click on the extensions view icon on the sidebar
    (shortcut: Ctrl/Cmd+Shift+X)
  • Search the extension "Python"
  • Click Install on the Python extension by Microsoft
  • If you are not familiar with the Python interface: Read this tutorial

• Install the official Jupyter extension for VS Code

  • Search the extension "Jupyter"
  • Click Install on the Jupyter extension by Microsoft
  • If you are not familiar with the Jupyter interface: Read this tutorial

• Install the version control system git:

  • Follow these instructions

• Clone the course repository: Open the following lines in a terminal

  # Navigate to the folder where you want to store 
  # the course materials for the CO4 module.
  #   - Use mkdir to create the folder first
  #   - Use "" if your path contains spaces!
  
  # Win:
  cd "path\to\folder"
  # Mac / Linux:
  cd "path/to/folder"
  
  # Clone this repository
  git clone https://github.com/hirsch-lab/msls-co4-ss24.git
  

• Create a virtual Python environment (venv):

  • Make sure that you are running the desired Python:

    python --version

  • Create a venv named venv-msls-co4:

    python -m venv "venv-msls-co4"

  • Activate the new environment

    # Win:
    venv-msls-co4\scripts\activate
    
    # Mac / Linux:
    source venv-msls-co4/bin/activate

  • Update the Python package installer

    python -m pip install pip --upgrade

  • Install the required packages

    # Win
    python -m pip install -r msls-co4-ss24\requirements.txt
    
    # Mac / Linux
    python -m pip install -r msls-co4-ss24/requirements.txt

• Add the Git project folder to your VS Code workspace:

  • Open VS Code
  • File $\rightarrow$ Add Folder to Workspace...
  • Choose the folder msls-co4-ss24

• Run the test notebook in VS Code:

  • Open VS Code
  • Open the notebook: notebooks/00-test-setup.ipynb
  • When running the Jupyter notebook for the first time, you need to select the correct Jupyter kernel:
    • Open the command palette: Ctrl/Cmd + Shift + P
    • Type and select: Notebook: Select Notebook Kernel
    • Choose: Select Another Kernel
    • Choose: Python Environments
    • Choose venv-msls-co4 from the drop down list
      If you don't see the new venv, you may have to restart VS Code
  • Run the notebook