Python for BioImage Analysis (3-Day Distributed Course)
Python scripting provides a general and flexible toolset for researchers to quantify and analyse digital images acquired from microscopy or clinical imaging. It enables researchers to automate image processing and connect their workflows with downstream processes like statistical testing and data visualisation.
This 3 day workshop begins with an introduction to python language essentials and uses image data to familiarise participants with core programming concepts in a research-relevant manner. Participants will learn to use popular python libraries such as scikit-image, matplotlib and pandas to visualise, interact with and extract quantitative data from digital images. The course will also cover the use and programmatic access to Napari, a powerful n-dimensional viewer.
Over the course, participants will be familiarised with practical bioimage analysis techniques, the foundation of elementary image processing operations and how they can be combined into functional image analysis workflows. You will learn how to segment images (identify object of interest in their images), using classical methods as well as machine learning solutions. Finally, you will be able to quantify and visualise biologically interesting properties such as object count, intensity statistics and morphology measurements.
Course Information
Format: This is a distributed course taught simultaneously at the University of Copenhagen (KU) and at Pompeu Fabra University (UPF, Barcelona), with common interactive lectures delivered by teachers at each location and broadcasted to the remote classroom, together with hands-on support by local teachers. Lectures will be followed by in-class practical exercises and discussions facilitated by local classroom teachers. On the last day, participants will form groups to solve a bioimage analysis project and present their group’s results to the class.
Scope: The workshop is directed at life scientists and graduate students with relevant image analysis needs, and bioimaging facility staff planning to support their users in image analysis.
Requirements: Participants are expected to bring a laptop. Further instructions to install relevant software packages will be sent in course instructions about one week before the workshop. No prior programming knowledge required!
Catering: Coffee breaks & lunch will be catered for all days.
Registration
Graduate Students — Register by 1 March 2025
The course is free of charge for PhD students at Danish universities (except Copenhagen Business School), and for PhD students at NorDoc member faculties. All other participants must pay the course fee.
Academic Staff (e.g. PIs, Postdoc, AC-TAPs) — Register by 21 March 2025
Registration Fee: 2000 DKK
Programme
31 March (Monday)
| 09:00 - 10:30 | Introduction to Basic Python Programming |
| 10:30 - 10:45 | Coffee break |
| 10:45 - 12:15 | Image Handling and Global Measurements |
| 12:15 - 13:15 | Lunch |
| 13:15 - 14:45 | Classical Image Analysis Workflows - Part I |
| 14:45 - 15:00 | Coffee break |
| 15:00 - 17:00 | Classical Image Analysis Workflows - Part II |
1 April (Tuesday)
| 09:00 - 09:30 | Introduction to U-Cloud and Environment Set-up |
| 09:30 - 10:30 | Napari for Bioimage Analysis - Part I |
| 10:30 - 10:45 | Coffee break |
| 10:45 - 12:15 | Napari for Bioimage Analysis - Part II |
| 12:15 - 13:15 | Lunch |
| 13:15 - 14:45 | Napari for Bioimage Analysis - Part III |
| 14:45 - 15:00 | Coffee break |
| 15:00 - 17:00 | Image to Data |
2 April (Wednesday)
| 09:00 - 10:30 | Machine Learning for BIA - Part I |
| 10:30 - 10:45 | Coffee break |
| 10:45 - 12:15 | Machine Learning for BIA - Part II |
| 12:15 - 13:15 | Lunch |
| 13:15 - 14:30 | Machine Learning for BIA - Part III |
| 14:30 - 17:00 | Group projects and presentations (Coffee break included) |
Location
Panum Building, Room 13.2.48
3B Blegdamsvej
University of Copenhagen (North Campus)
About the Organisers
DBI Infra IACF
The Danish Bioimaging Infrastructure (DBI-Infra) Image Analysis Core Facility (IACF) provides open services in image analysis to life scientists and medical researchers. We offer both in-person and remote support, helping you to visualize, analyze, and extract quantitative information out of your bioimaging datasets from anywhere.
Our team of experts is here to discuss your image analysis needs, guide and train you in the most suitable software solutions, or develop a complete image analysis workflow tailored to your scientific project. We leverage an extensive hardware and software infrastructure designed for remote image analysis, including a pool of latest-generation workstations, innovative High Performance Computing and data exchange services, and a broad range of bioimage analysis software tools.
Sébastien Tosi (Biophysics in Cell Biology Group, UPF)
Sébastien Tosi (Biophysics in Cell Biology Group, Pompeu Fabra University) previously headed Danish Bioimaging Infrastructure image analysis core facility (DBI-INFRA IACF) and worked at the IRB Barcelona Advanced Microscopy Core Facility (ADMCF). He collaborates with life scientists to help them optimize their imaging experiments for quantitative analysis and tailor image analysis software tools to extract relevant information backing their research hypotheses. He published several open bioimage analysis source software tools and organized international courses on the topic, especially as a core member of NEUBIAS (the Network of European BioImage Analysts).
External Teachers
Chong Zhang (IRB Barcelona)
Dr. Chong Zhang is senior research officer at the Advanced Digital Microscopy Core Facility of Institute for Research in Biomedicine, Barcelona. Her daily work involves developing image analysis solutions, providing image analysis training and technical support for users. Her experience spans across biomedical as well as life science research problems.