Advanced course of Light and Electron Microscopy

Volumetric imaging methods of different sized living and fixed specimens.

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BCO Light Microscopy (LM) and Electron Microscopy (EM) Core Facility Laboratories



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1.5 ETCS


Health and Biosciences Doctoral Programme and Oulu BioImaging, Biocenter Oulu, University of Oulu


Students get acquainted with advanced light and electron microscopy volumetric imaging methods of living and fixed specimens of different sizes. Students learn how to apply suitable techniques for image analysis. LM part includes intravital imaging of brain vasculature and confocal fluorescence and multiphoton microscopy with fluorescence lifetime imaging (FLIM). EM part focuses on serial section imaging (Array Tomography). The course consists of lectures, microscopy demonstrations and computer-based image analysis workshops.


Veli-Pekka Ronkainen / Ilkka Miinalainen, Biocenter Oulu, tel: +358 294 486114 / +358 294 486145, e-mail: veli-pekka.ronkainen(at) / ilkka.miinalainen(at)


Lectures are open for all without registration. Registration for the demonstrations is obligatory and preference will be given to doctoral researchers and researchers whose project benefits the topics carried out during the course. Due to space limitations only 18 participants can be accepted to the course. The application with a short description of the applicant’s project should be submitted. It is recommended that Basic course on Light and Electron microscopy is passed before this course.

Wednesday, Jun 12st, 2024. Lecture hall F202 (Pharmacology)


9.00-9.05 Opening words and introduction

9.05-10.00 Principles of advanced fluorescence microscopy techniques, Veli-Pekka Ronkainen, BCO

10.00-10.15 Coffee break

10.15-11.15 Volumetric imaging methods in electron microscopy, Ilkka Miinalainen, BCO

11.15-12.15 Lunch break

12.15-13.15 Sample and image processing techniques for 3D light microscopy samples, Veli-Pekka Ronkainen

13.15-13.30 Break

13.30-14.30 Volumetric imaging methods in electron microscopy part II, Ilkka Miinalainen, BCO

14.30-15.30 Intravital imaging, Mika Kaakinen, BCO

Thursday, Jun 13th, 2024

8.55 Gathering in the meeting room 487B (Kieppi Building 4th floor, Aapistie 5A)

9.00-16.00 Demonstrations, 3 groups

  • Demo 1. Laser scanning confocal and multiphoton microscopy, Room 419A. Confocal fluorescence and multiphoton microscopy with fluorescence lifetime imaging (FLIM), Veli-Pekka Ronkainen.
  • Demo 2. Intravital imaging, Room 492B and 493B. Instrument and facility demonstrations. Preparation of an animal for multiphoton imaging. Imaging of cerebral vasculature through cranial window in a mouse. Mika Kaakinen.
  • Demo 3. Sample sectioning for array tomography and imaging, Room 320A and 488B
    How section ribbons are prepared and collected on a substrate and how data acquisition is done using Atlas 5 software, Ilkka Miinalainen.
Friday, Jun 14th, 2024. Room 337B and Computer Class KT285

9.00-10.00 Image processing and analysis, Data management, Room 337B, Mika Kaakinen, Antti Viklund, BCO

10.00-10.15 Coffee break

10.15-11.15 Machine learning and deep learning in bioimage analysis, Room 337B, Jeena Ainikkal Velayudhan, BCO

11.15-12.15 Lunch break

12.15-13.45 Computer-based processing and analysis of light microscopy images, Computer Class KT285, Veli-Pekka Ronkainen, Antti Viklund, Mika Kaakinen

13.45-14.00 Coffee break

14.00-15.30 Computer-based processing and analysis of volume-EM data sets, Computer Class KT285, Ilkka Miinalainen, Antti Viklund, Mika Kaakinen

15.30 Concluding remarks

Last updated: 8.4.2024