Image Processing with Python



March 11 - 14, 2024

9:00 - 13:00 CET

Instructors: Candace Moore, Giulia Crocioni, Jaro Camphuijsen

Helpers: Thijs Vroegh

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General Information

Data Carpentry develops and teaches workshops on the fundamental data skills needed to conduct research. Its target audience is researchers who have little to no prior computational experience, and its lessons are domain specific, building on learners' existing knowledge to enable them to quickly apply skills learned to their own research. Participants will be encouraged to help one another and to apply what they have learned to their own research problems.

For more information on what we teach and why, please see our paper "Good Enough Practices for Scientific Computing".

Who: The course is aimed at graduate students and other researchers. You don't need to have any previous knowledge of the tools that will be presented at the workshop.

Where: This training will take place online. The instructors will provide you with the information you will need to connect to this meeting.

When: March 11 - 14, 2024, 9:00 - 13:00 CET.

Requirements: Participants must have access to a computer with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have a few specific software packages installed (listed below).

Accessibility: We are dedicated to providing a positive and accessible learning environment for all. Please notify the instructors in advance of the workshop if you require any accommodations or if there is anything we can do to make this workshop more accessible to you.

Contact: Please email or for more information.

Code of Conduct

Everyone who participates in Carpentries activities is required to conform to the Code of Conduct. This document also outlines how to report an incident if needed.



This workshop is scheduled on four separate concurrent mornings. This allows you to work on your code in between the sessions, implementing the lessons you learned during our meetings together. Please schedule dedicated work time in your calendar, so you can take full advantage of the workshop.

Day 1.

9:00 Welcome and Introduction
9:20 Image Basics
9:40 Working with the skimage library
10:30 Coffee break
10:40 Drawing +
11:40 Bitwise Operations
12:30 Wrap up
12:40 Feedback collection
13:00 END day 1

Day 2.

9:00 Welcome back
9:00 Welcome back + questions
9:15 Histograms
10:30 Blurring Images
11:30 Thresholding Images
11:30 Wrap up and summary
11:40 Feedback collection
12:00 Optional extra tutoring
13:00 END day 2

Day 3.

9:00 Welcome back
09:15 Thresholding Images II
10:15 Connected Component Analysis
12:20 Optional Challenge Introduction
12:30 Feedback collection
13:00 END day 3

Day 4.

9:00 Welcome back
9:15 Capstone Challenge
11:30 Bonus lecture: transformations, affine
12:30 Feedback collection
13:00 END day 4

All times in the schedule are in the CET timezone (Amsterdam time).


To participate in a Data Carpentry workshop, you will need access to software as described below. In addition, you will need an up-to-date web browser.

We maintain a list of common issues that occur during installation as a reference for instructors that may be useful on the Configuration Problems and Solutions wiki page.

Software setup

The setup for this workshop requires you to have both a proper environment created and the data for the workshop downloaded. The easiest way to do this is to download the workshop repository which includes both the data and setup instructions.

The setup instructions for our Data Carpentry Image Processing workshops can be found at the image processing workshop overview site


If you do not wish to use conda you can create an environment without conda with the libraries in the environment file

Install the videoconferencing client

If you haven't used Zoom before, go to the official website to download and install the Zoom client for your computer.

Set up your workspace

Like other Carpentries workshops, you will be learning by "coding along" with the Instructors. To do this, you will need to have both the window for the tool you will be learning about (a terminal, RStudio, your web browser, etc..) and the window for the Zoom video conference client open. In order to see both at once, we recommend using one of the following set up options:

  • Two monitors: If you have two monitors, plan to have the tool you are learing up on one monitor and the video conferencing software on the other.
  • Two devices: If you don't have two monitors, do you have another device (tablet, smartphone) with a medium to large sized screen? If so, try using the smaller device as your video conference connection and your larger device (laptop or desktop) to follow along with the tool you will be learning about.
  • Divide your screen: If you only have one device and one screen, practice having two windows (the video conference program and one of the tools you will be using at the workshop) open together. How can you best fit both on your screen? Will it work better for you to toggle between them using a keyboard shortcut? Try it out in advance to decide what will work best for you.
This blog post includes detailed information on how to set up your screen to follow along during the workshop.