Getting Started

Welcome to the MIA Lab! This guide will help you set up your development environment and get ready for the course.

On this section

• Schedule (Autumn 2026) - dates, deadlines, and which pages go with each lecture
• Installation - Python, git, and MATLAB setup
• Tools - the software and libraries used in the course
  • IDE - PyCharm, VS Code, and MATLAB
  • Ubelix HPC - running experiments on the university cluster
• Report writing with LaTeX - templates and tips for the final report
• Visualization for figures and presentations - making figures worth reading

Installation

To participate in the laboratory, you'll need to set up your development environment with the necessary tools and libraries.

Prerequisites

• Python 3.8 or higher
• Git for version control
• A modern IDE (VS Code, PyCharm, or similar)

Required packages

The main packages you'll work with include:

• SimpleITK: for medical image I/O and processing
• NumPy: for numerical computations
• scikit-learn: for machine learning algorithms
• matplotlib: for visualization

For detailed installation instructions, see the installation guide.

Tools

You'll use various tools throughout the course:

• IDE: integrated development environment for coding
• Ubelix HPC: high-performance computing cluster (if needed for computationally intensive tasks)
• Git and GitHub: version control and collaboration
• LaTeX: for report writing

The tools page has the full list, including image viewers, literature managers, and SSH/FTP clients.

Schedule

See the course schedule for:

• Lecture dates and topics
• Assignment deadlines
• Presentation dates
• Office hours

Documentation and visualization

Learn best practices for:

• Report writing with LaTeX: creating professional scientific reports
• Visualization: creating figures for presentations and reports

Next steps

1. Complete the installation of required software
2. Familiarize yourself with the tools
3. Review the course schedule
4. Start with the first exercise when it's released