Tools

This page lists software tools and libraries to be familiar with.

Python

We use Python 3.8 or later inside an Anaconda environment.

Integrated development environment (IDE)

This page has more details about IDEs.

• PyCharm: recommended (Community and Professional version are free for students).

• Visual Studio Code: great community support and plugins.

Libraries

• Numpy: Fundamental package for scientific computing with Python (a good & short tutorial).

• scikit-learn: An open-source software library for machine learning.

• SimpleITK: Suite of software tools for image analysis (examples).

• matplotlib: Plotting library.

• seaborn: Statistical data visualization.

• pymia: generic and modular code for medical image analysis (developed by your lecturers!).

• Sphinx: A Python documentation generator.

Git

• git: required base of the version control system.

• GitHub: recommended; free git repository hosting service.

• Gitlab: alternative hosting service.

GUI Clients

• GitHub Desktop: recommended [Win, Mac]

• The git client within PyCharm/Visual Studio Code: recommended

• SourceTree: [Win, Mac, Linux]

• GitKraken: [Win, Mac, Linux]

• Git Extensions: [Win]

• git-gui: Rudimentary GUI that comes with git [Win, Mac, Linux]

Image Viewer

• ITK-SNAP: Simple tool to check results and do manual corrections [Win, Mac, Linux]

• 3D Slicer: More advanced tool [Win, Mac, Linux]

• ParaView: Visualization software [Win, Mac, Linux]

Writing with LaTeX

This page has more details about LaTeX.

• LaTeX Guide: Installation, basics, elements, etc.

• Overleaf: highly recommended; Online LaTeX editor, collaborative writing, and publishing tool

• TeXstudio: Desktop editor [Win, Mac, Linux]

• Texmaker: Desktop editor [Win, Mac, Linux]

LaTeX distributions (not needed with Overleaf):

• TeX Live: [Win, Linux]

• MiKTeX: [Win]

• MacTeX: [Mac]

Literature

Search

• Google Scholar

• Scopus

• Web of Science

Management

• Mendeley: Tool to organize your references (and create your bibliography)

• Mendeley Desktop: Client for Mendeley [Win, Mac, Linux]

Organization

• Trello: Tool to organize and prioritize your projects

• Jira: Tool to manage large projects

• Asana: Task management tool

Server Transactions

See more about using Ubelix HPC here.

SSH Clients

• Putty: [Win, Linux]

• Termius: [Win, Linux, Mac]

FTP Clients

• WinSCP: [Win]

• FileZilla: [Win, Linux, Mac]