Monday 4th May 2026
- 09:00–12:00 Lecture hall 2
Biomedicum 1 (Haartmaninkatu 8)- 09:00 What is an image?
- 09:45 Basics of Imaging
- 11:00 Image processing workflow
- 13:00–15:15 Haartman sali 2
(Haartman Institute, Haartmaninkatu 3)- 13:00 Machine Learning
- 14:15 TBA
Wednesday 6th May 2026
-
Faculty club
Biomedicum 1 (Haartmaninkatu 8)- 8:30-10.30 coLoc The Game (group1)
- 11:00-13.00 coLoc The Game (group2)
Coloc The Game is a collaborative board game to teach co-localization analysis, in which the players, a.k.a The Scientists, team up against the game master , a.k.a Reviewer 3.
Speakers
- Romain Guiet (BioImaging and Optics Platform, Ecole Polytechnique Fédérale de Lausanne (EPFL), Switzerland)
- Antti Isomäki (Biomedicum Imaging Unit, University of Helsinki)
- Lassi Paavolainen (Bioimage profiling, Institute for Molecular Medicine Finland (FIMM))
- TBA
5th - 13th May 2026
Mix and Match! Apply for the workshops you like and we will send you your individual schedule.
Our workshops will give you the opportunity to get your hands on a wide range of image‑analysis tools. All the software we introduce is either free & open‑source or available for you to use on the BIU image‑analysis workstations.
CellProfiler:
Automate your image analysis with CellProfiler. Learn how to build and run image analysis pipelines for quantitative analysis of biological images. If you are doing high-throughput experiments, Cellprofiler is a particularly useful tool for you.
Co-loc:
Learn how to perform colocalization analysis all the way from preprocessing to quantitative evaluation using FIJI or related tools. We’ll wrap up with time for you to dig into your own colocalization questions and get feedback.
Fiji:
Get started with Fiji and learn how to handle and process your files, how to count and characterize cells and how to make your analysis faster and more reproducible with macro recording.
Ilastik:
Learn how to segment and analyze your structures of interest by annotating them with Ilastik’s interactive and intuitive machine‑learning tools.
Imaris basic:
General purpose 3D microscopy visualization and data analysis with Imaris for beginners.
Learn how to import and handle your files, how to visualize your data and generate videos and how to detect surface spots.
Imaris advanced:
3D microscopy data analysis with Imaris for advanced Imaris users. Creating Workflows, pixel segmentation, how to use Machine learning in Imaris, Stitching of tiles, 3D time series, neurons, batch processing, statistic visualization and more. Exact topics will be adapted depending on the participants needs.
Please notice that the duration of the Imaris advanced workshop is 6 hours (including breaks)!
Microscopy Image Browser (MIB) (half-day):
Get started with MIB, a versatile tool for processing and segmenting multidimensional microscopy datasets. In this hands-on workshop, you’ll practice the basics of segmentation and then take the next step by exploring deep learning workflows for analyzing both light and electron microscopy data.
QuPath:
Learn beginner and intermediate steps for analyzing and quantifying large 2D fluorescence and histology images. We will cover topics ranging from simple tissue and cell detection to more advanced topics such as using deep learning (AI) segmentation tools and batch analysis for scalable image analysis tasks.
Registration deadline: 29.03.2026
For PhD students that want to earn 1ECTS:
For every one else:
Attendance on the lecture day (4.5.2026), one CoLoc interactive lecture (6.5.2025 ca. 2h) and three hands-on workshops (3-4h each) are required for credits (1 ECTS).
The course is organized by the Biomedicum Imaging Unit, University of Helsinki. Most of the course will take place in Biomedicum 1,Haartman Institute & Terkko Health Hub. However some parts might be at the city center campus. Locations will be send to all workshop attendees in advance.