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Python for Bioimage Analysis
Python scripting provides a generic and flexible toolset for researchers to quantify and analyse digital images acquired from microscopy or clinical imaging. It enables researchers to automate image analysis and feed the results to downstream processes like statistical testing and data visualisation.
This 3-day course starts with an introduction to Python language 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 then delves into basic image processing operations and how they can be combined into practical bioimage analysis workflows, with a special focus on identifying biological objects and extracting their relevant properties (e.g. count, intensity statistics, morphology) by classical bioimage analysis and machine learning techniques. The course also covers the use, programmatic scripting and user interface customization of Napari, a powerful multidimensional image viewer with a very active community.
Course information
Format: This is a two-site course taught simultaneously at University Pompeu Fabra (UPF) and the University of Copenhagen (KU), with shared 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
Life scientists and graduate students with relevant image analysis needs
Bioimaging facility staff planning to support their users in image analysis
Requirements
No prior programming knowledge required
Laptop (no netbook) with WIFI
Further instructions will be sent by email
Catering
Coffee breaks are catered
Students are expected to self-organize for lunches
Registration
The course is free of charge and is mostly first in first serve moderated by your own motivation and needs to attend. By registering you commit to attend the whole 3-day course.
The course is full and the registration is closed since March 1st 2025
Stay tuned for the next events!
Programme
| 9 - 10:30 | Introduction to Python |
| 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 Workflow I |
| 14:45 - 15:00 | Coffee break |
| 15:00 - 17:00 | Classical Image Analysis Workflow II |
| 9 - 9:30 | Introduction to Open OnDemand |
| 9:30 - 10:30 | Napari for Bioimage Analysis I |
| 10:30 - 10:45 | Coffee break |
| 10:45 - 12:15 | Napari for Bioimage Analysis II |
| 12:15 - 13:15 | Lunch |
| 13:15 - 14:45 | Napari for Bioimage Analysis III |
| 14:45 - 15:00 | Coffee berak |
| 15:00 - 17:00 | Image to Data |
| 9 - 9:30 | Machine Learning for BIA I |
| 10:30 - 10:45 | Coffee break |
| 10:45 - 12:15 | Machine Learning for BIA II |
| 12:15 - 13:15 | Lunch |
| 13:15 - 14:30 | Machine Learning for BIA III |
| 14:30 - 17:00 | Group projects and presentations |
Location
UPF Campus del Mar
Doctor Aiguader, 80, Barcelona
Classroom 61.226 (Second floor)
Detailed location: Building 61
Detailed location: Classroom 61.226
Organizers
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).
Danish Bioimaging Infrastructure
The Danish Bioimaging Infrastructure Image Analysis Core Facility (DBI-INFRA IACF) provides open services in image analysis to life scientists and medical researchers by offering both in-person and remote support, helping to visualize, analyze, and extract quantitative information from bioimaging datasets from anywhere.
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.
Sponsors
