Tools#

This list summarizes software tools and libraries we are going to use or we can recommend to use.

Python#

We use Python 3.8 or newer inside an Anaconda environment.

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: pymia - generic and modular code for medical image analysis (developed by your lecturers!)
Sphinx: A Python documentation generator

Integrated development environment (IDE)#

PyCharm: Strongly recommended (Community and Professional version are free for students) [Win, Mac, Linux]

Git#

git: required base of the version control system [Win, Mac, Linux]
GitHub: free git repository hosting service

GUI Clients#

SourceTree: [Win, Mac]
GitHub Desktop: [Win, Mac]
GitKraken: [Win, Mac, Linux]
Git Extensions: [Win]
git-gui: Rudimentary GUI that comes with git [Win, Mac, Linux]
or use the git client contained in PyCharm

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]

LaTeX#

LaTeX Guide: Installation, basics, elements, etc.
Cheat Sheet

Editors#

Overleaf: Online LaTeX editor, collaborative writing, and publishing tool
TeXstudio: Desktop editor [Win, Mac, Linux]
Texmaker: Desktop editor [Win, Mac, Linux]
or pick any (list of tex editors)

Distributions#

(not needed with Overleaf)

TeX Live: [Win, Linux]
MiKTeX: [Win]
MacTeX: [Mac]

Literature#

Search#

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#

SSH Clients#

Putty: [Win, Linux]
Termius: [Win, Linux, Mac]
or pick any (list of SSH clients)

SFTP Clients#

WinSCP: [Win]
FileZilla: [Win, Linux, Mac]
or pick any (list of SFTP clients)