ONWAR

Graduate School Neurosciences

Join ONWAR

2027 – Python for Science

The aim of this course is to learn the fundamentals of programming in Python and to apply them to neuroscience-related problems. By the end of the course, participants will be able to interact with Jupyter notebooks, load, manipulate, visualize, and analyze data, and apply Python tools to neuroimaging, electrophysiology, calcium imaging and network neuroscience. The course combines lectures with hands-on sessions, covering topics from basic coding practices to medical image processing, patch-clamp analysis, calcium imaging, and brain network analysis.

Date

15-19 March, 2027 

Organizer

Dr. Ismail Koubiyr

Duration

44 hrs / 1.6 ECTs

Location

VU, TBA

Course access

Current Status

Pre-enroll (11 places remaining)

Price

Free

Get Started

Log In to Enroll

Course details

Introduction

The aim of this course is to learn the fundamentals of programming in Python and to apply them to neuroscience-related problems. By the end of the course, participants will be able to interact with Jupyter notebooks, load, manipulate, visualize, and analyze data, and apply Python tools to neuroimaging, electrophysiology, calcium imaging and network neuroscience. The course combines lectures with hands-on sessions, covering topics from basic coding practices to medical image processing, patch-clamp analysis, calcium imaging, and brain network analysis.

What you’ll learn
  • Import and work with numerical and tabular data
  • Apply good coding practices: clean code, modularity, commenting, and efficient programming
  • Gain hands-on experience with medical image processing (MRI, CT, microscopy)
  • Analyze electrophysiological patch‑clamp recordings with Python notebooks
  • Explore calcium imaging data (widefield and two‑photon microscopy)
  • Explore brain network analysis using graph theory, connectivity matrices, and statistical methods
Course format

The course runs over five full days (09:00–17:00). Each day combines short introductory lectures with mostly hands-on coding exercises in small groups. Participants are expected to bring their own laptop. The participant is required to be present during the entire course (exceptions are possible if specifically requested).

Course content
  • Python basics, functions, packages, and data frames
  • Importing and visualizing data
  • Univariate statistics and regression
  • Good coding practices and writing efficient code

 

Neuroscience topics that will be covered:

  • Medical image processing
  • Brain network analysis, based on functional and diffusion MRI
  • Patch-clamp
  • Calcium imaging
Requirements

No prior experience with Python is required, but participants should have some programming experience or a strong interest in learning programming concepts. Participants with (almost) no prior Python coding experience, are strongly recommended to complete a few online modules to prepare for the course. A few weeks before the course, all participants will receive an access to a short datacamp introductory course to Python that they should follow before the course starts.

Downloads & extra recourses

  • Dr. Ismail Koubiyr (Amsterdam UMC, Coordinator)
  • Dr. Tommy Broeders (Amsterdam UMC)
  • Dr. David Cabrera (NIN)
  • Dr. David van Nederpelt
  • Dr. Mario Tranfa