Image Processing with Python

Start Date

5 Jun 2023

Start Time

09:30 Europe/Amsterdam



End Date

6 Jun 2023

End Time

17:00 Europe/Amsterdam

Image Processing with Python


June 5 - 09:30 am


June 6 - 05:00 pm

Event Category:


Click to Register:

eScience Center Digital Skills Programme


Netherlands eScience Center

402 Science Park, 1098 XH Amsterdam

Amsterdam, NH, NL, 1098 XH

In this workshop participants will use Python to understand and manipulate images.

The workshop will take place at Science Park 402, 1098 XH Amsterdam. Please note that lunch (both days) and drinks (at the end of the workshop) are included. We are committed to making this workshop accessible to everybody. Unfortunately, the elevator in the building is currently broken. If this causes any accessibility problems for you, please inform and we will see how we can help you.

This workshop will teach you to about digital images and how to work with them with code. The workshop will cover the basics of digital images, manipulation with Python and the scikit-image (skimage) library. Both deeper image understanding and automation of image processing tasks will be covered.

By the end of the workshop you should be able to enhance your research with images be they from microscopy, radiology or another discipline.

The workshop is based on the teaching style of the Carpentries, and learners will follow along while the instructors write the code on screen. More information can be found on the workshop website here.


The workshop is open and free to all researchers in the Netherlands at PhD candidate level and higher. We do not accept registrations by Master students. The workshop is aimed at PhD candidates and other researchers or research software engineers.


The participants should:

  • Be familiar with Python (you should be able to write simple functions)
  • Be interested in analysis of images towards scientific goals


  • Introduction to images : Digital Image Basics
  • Working with skimage: How can the skimage Python computer vision library be used to work with images?
  • Drawing and Bitwise Operations
  • Creating Histograms: How can we create grayscale and color histograms to understand the distribution of values in an image?
  • Blurring Images: Intro to filtering and blurring
  • `Thresholding: How can we use thresholding to produce a binary image?
  • Connected Component Analysis: How to extract separate objects from an image and describe these objects quantitatively.
  • Capstone Challenge: solving a real world microscopy problem
  • Bonus session: Preparing images for machine learning (affines, other transformations and more)


This training will take place in-person at the eScience Center, Science Park 402, Amsterdam. We are committed to making this workshop accessible to everybody. Unfortunately, the elevator in our building is broken and it will take until July to fix it. Please contact us at if you cannot use the staircase.


Monday 5 June – 09:30-17:00

Tuesday 6 June – 09:00-17:00