Bioimage Analysis Course 2022

Improve your Bioimage Analysis Skills!


Lecture slides can be found here:

Monday 7th March 2022 

9.00 - 12.0 EEST (=UTC+3)
Lecutre hall 3 Biomedicum

What is an image?
Marko Crivaro (Light Microscopy Unit, University of Helsinki)
Basics of Imaging
Marko Crivaro
Cell Counting
Antti Isomäki (Biomedicum Imaging Unit, University of Helsinki)

Tuesday 8th March 2022 

9.00 - 12.30 EEST (=UTC+3)
Lecutre hall 3 Biomedicum

Trust Images & Numbers
Ville Rantanen (Machine Vision Specialist at Reaktor Innovations, Helsinki)
Romain Guiet (BioImaging and Optics Platform, Ecole Polytechnique Fédérale de Lausanne (EPFL), Switzerland)
Machine Learning

Lassi Paavolainen (Bioim­age pro­fil­ing, Institute for Molecular Medicine Finland (FIMM))

Hands-on Workshops

9th - 15th March 2022

Mix and Match! Apply for the workshops you like and we will send you your individual shedule.
If you are a beginner to image analysis we would highly recommend that you attend the lectures as well.

Get your hands on the different tools for image analysis. All software introduced during the workshops is either open-source software or commercial software that is available to you at the BIU image analysis workstations.

Imaris basic (half-day):

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 (whole day):

3D microscopy data analysis with Imaris for advanced Imaris users. Stitching of tiles, 3D time series, neurons, batch processing, statistic visualization and more. Exact topics will be adapted depending on the participants needs.

Fiji (half-day):

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.

CellProfiler (half-day):

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.

Colocalisation (half-day):

Learn how to:

1. perform colocalisation when you can segment the objects in your sample (distinct cells, vesicles, etc.) with DiAna

2. do pixel based colocalisation when segmentation is not possible with JACOP

(If you don’t need credits you can choose to attend both parts or only the part relevant to you)

Microscopy Image Browser (MIB) (half-day):

Introduction to MIB, a versatile software for image processing and segmentation of multidimensional datasets. During the workshop, we will see various image processing workflows for both light and electron microscopy including contrast normalization (photo bleaching correction), alignment, blind classification, edge preserving filtering, batch processing and segmentation.


Registration deadline: 20.02.2022

For PhD students that want to earn 1ECTS:
Registration for the whole course (all lectures + 3 hands-on workshops) -> here

For every one else:
Mix and match as you like. Registration for lectures, hands-on workshop or both ->here


Attendance on both lecture day (7+8.32022) 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/ Terkko Health Hub, but some parts will be online. In case of any changes, we will update you as soon as possible. Participants will receive information on lecture rooms and/or links to the online meeting prior to the lectures and hands-on workshops.

Lectures 7. & 8.  March 2022

Hands-on Workshops  9.–15 . March 2022

Registration deadline 20. February 2022