2026 Bioimage Analysis Course
Course announcement page
Lecture Material
What is an image? | Kirstin Vonderstein (Biomedicum Imaging Unit, University of Helsinki) | What is an Image? - Please give your feedback here! |
|
Basics of Imaging | Elnaz Fazeli (Biomedicum Imaging Unit, University of Helsinki) | Basic of Imaging - Please give your feedback here! | |
| Image processing workflow | Antti Isomäki (Biomedicum Imaging Unit, University of Helsinki) | Image processing workflow - Please give your feedback here! | |
| Seeing is not Believing | Kristin Gallik (Biomedicum Imaging Unit and Light Microscopy Unit, University of Helsinki) | Seeing is not Believing - Please give your feedback here! | |
Machine Learning | Lassi Paavolainen (Bioimage profiling, Institute for Molecular Medicine Finland (FIMM)) | Machine Learning - Please give your feedback here! | |
Colocalisation The Game | Romain Guiet (BioImaging and Optics Platform, Ecole Polytechnique Fédérale de Lausanne (EPFL), Switzerland)
| Colocalisation The Game - Please give your feedback here! |
Further reading:
https://bioimagebook.github.io/index.html (a whole book introducing you to image anlaysis in a easy way, highly recommended!)
https://courseware.epfl.ch/courses/course-v1:EPFL+IPA4LS+2019_t3/about
Hands-on workshops
| CellProfiler | Ábel Szkalisity | Cellprofiler Feedback | |
| Co-loc | Romain Guiet (BioImaging and Optics Platform, EPFL, Switzerland) Mikko Liljeström (Biomedicum Imaging Unit, University of Helsinki) | go.epfl.ch/biu-biac26-coloc | Coloc Feedback |
| Fiji | Romain Guiet (BioImaging and Optics Platform, EPFL, Switzerland) | Fiji workshop Feedback | |
| Ilastik | Romain Guiet (BioImaging and Optics Platform, EPFL, Switzerland) | go.epfl.ch/biu-biac26-ilastik | Ilastik Feedback |
| Imaris basic | Julia Schweizer (Oxford Instruments GmbH) | Imaris Basic Feedback | |
| Imaris advanced | Julia Schweizer (Oxford Instruments GmbH) | Imaris advanced Feedback | |
| Microscopy Image Browser (MIB) | Ilya Belevich (Electron Microscopy Unit, University of Helsinki) | MIB feedback | |
| QuPath | Kristin Gallik (Biomedicum Imaging Unit and Light Microscopy Unit, University of Helsinki) | https://github.com/kgallik/QuPath_Workshop_UH_2026 | QuPath Feedback |
Feedback for the whole course