Welcome to the training materials for the NL-BioImaging Advanced Image Analysis course, held 21-24 September 2026 at Erasmus MC in Rotterdam.
Course information and registration: https://
Getting started¶
Before the course, work through the preparation page. It explains how to install Python, git and the course environments.
Already have git and conda installed? Get the materials with:
git clone https://github.com/NL-BioImaging/NL-BioImageAnalysis-course2026.gitProgram¶
Day 1 - Foundations & tools (Monday 21 September)
Python ecosystem, Jupyter notebooks and image analysis libraries
Image processing concepts: filters, thresholding and more
Day 2 - Data access & AI introduction (Tuesday 22 September)
OMERO and OME-Zarr: accessing, managing and analyzing image data
Computer vision & AI
Day 3 - AI segmentation & training (Wednesday 23 September)
Image annotation with napari
BiaPy: accessible deep learning for bioimage analysis
Preparing data and fine-tuning AI models
Day 4 - Reproducibility & wrap-up (Thursday 24 September)
Fractal: FAIR bioimage analysis at scale with OME-Zarr
Agentic AI for developing image analysis workflows
Data challenge and flash presentations
License¶
The course content (text, notebooks, images) is licensed as CC-BY 4.0 by the contributors unless mentioned otherwise. Code (scripts, code cells) is licensed under the BSD 3-Clause License.