Image Processing with Python

European Molecular Biology Laboratory

14-15 January 2020

09:30 - 17:00

Instructors: Dominik Kutra, Gregor Mönke

Helpers: Toby Hodges

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: Meyerhofstrasse 1, 69117 Heidelberg. Get directions with OpenStreetMap or Google Maps.

When: 14-15 January 2020. Add to your Google Calendar.

Requirements: This workshop is open only to EMBL participants. If you'd be interested in attending another, similar workshop at EMBL in the future, please email Toby Hodges.

Participants must bring a laptop 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).

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.

Accessibility: We are committed to making this workshop accessible to everybody. The workshop organizers have checked that:

Materials will be provided in advance of the workshop and large-print handouts are available if needed by notifying the organizers in advance. If we can help making learning easier for you (e.g. sign-language interpreters, lactation facilities) please get in touch (using contact details below) and we will attempt to provide them.

Contact: Please email for more information.


Please be sure to complete these surveys before and after the workshop.

Pre-workshop Survey

Post-workshop Survey


This curriculum is under active development and hasn't been taught many times before. Subsequently, the workshop schedule may deviate from that given below. However, we will try our best to keep the breaks scheduled as listed below.

Day 2

Morning Thresholding
Morning Break
Edge Detection
Afternoon Connected Components
Afternoon Break
Evening Post-workshop survey

We will use this collaborative document for chatting, taking notes, and sharing URLs and bits of code.



To participate in a Data Carpentry workshop, you will need access to the software 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.

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