Bioimage Analysis Course 2020

Improve your Bioimage Analysis Skills!

Please notice that the whole course will take place online because of the ongoing Corona virus pandemic!



Monday 11th May 2020  

9.00 - 17.15 EEST (=UTC+3)
online streaming

What is an image?
Marko Crivaro (Light Microscopy Unit, University of Helsinki)
Basics of Imaging
Marko Crivaro
Trustworthy image restoration is the only road to trustworthy analysis
Gitta Hamel (Scientific Volume Imaging, The Netherlands)
Expand your tool box - overview of open source tools and Fiji plugins
Anna Klemm (SciLifeLab BioImage Informatics Facility, Uppsala University, Sweden)
lunch break
Romain Guiet (BioImaging and Optics Platform, Ecole Polytechnique Fédérale de Lausanne (EPFL), Switzerland)
Cell Counting
Antti Isomäki (Biomedicum Imaging Unit, University of Helsinki)
Trust Images & Numbers
Ville Rantanen (Machine Vision Specialist at Reaktor Innovations, Helsinki)


Hands-on Workshops

12th - 19th May 2020 

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 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.

SVI Huygens (half-day):
Deconvolution with Huygens. Learn how to apply the correct restoration and analysis tools for obtaining reliable and quantifiable results from your images.

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 particular useful tool for you.

ZEN/APEER (half-day):
Are you taking your images with ZEISS microscopes? Here you learn how to process and analyze them directly in ZEN. If you want to get help with analyzing your own data, you can send them before the workshop. In addition, there will be a short introduction to APEER.


Application for hands-on workshops is closed!

Due to the amazing interest, we decided to prolong registration for the lectures until 3rd May 2020! First come, first served!

Registration for the lectures via elomake



To obtain credits, students should register via WebOodi using the enrol-link and select their preferred course through e-lomake.

Attendance on the lecture day (11.5.2020) 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 and will take place online. Participants will receive links  to the online meeting rooms prior to the lectures and hands-on workshops.



Lectures 11th May 2020

Hands-on Workshops  12th May – 19th May 2020

Application for hands-on workshops is closed!

Due to the amazing interest, we decided to prolong registration for the lectures until 3rd May 2020! First come, first served!

Registration for the lectures via elomake