Label-free Bioimaging 2022

Course code: MATR340

Scope: 5 credits.

Lecturer: Doc. Ivan Kassamakov, C318, email: ivan dot kassamakov at helsinki dot fi.


M.Sc. Joonas Mustonen, joonas.mustonen at

Pyry Palmen, pyry.oe.palmen at

M.Sc. Göran Maconi, goran dot maconi at helsinki dot fi

General info

The course covers state-of-the-art optical methods for label-free imaging, special attention in bioimaging. The course is structured to provide practical skills via exercise sessions for using optical microscopes for imaging real samples and guidance to use Zemax OpticStudio for optical simulations.

Latest update: 27/12/2022

NB! This course page contains the updated and the most exact information about the course practicalities – please, follow the updates actively and on a regular basis during the course.


27-12-22: Lecture notes added

08-12-22: Exam time & place information added

07-12-22: Rest of the exercise sessions are held in ZOOM

28-11-22: Exercise session 1.12. in held in ZOOM & report instructions added

15-11-22: Lecture (not exercises) 24.11. is held in ZOOM

09-11-22: Lectures (not exercises) 10.11. and 17.11. are held in ZOOM

07-11-22: Exercise topics added

02-11-22: Welcome-email sent (if you have not received, ask Joonas via email a.s.a.p.)

Literature: Douglas B. Murphy & Michael W. Davidson: Fundametals of light microscopy and electronic imaging (2nd edition or older), Online version available in Helka

Exam: Friday 20.01.2023 between 10:00 – 14:00 at D105 (Physicum)

Timing in studies: 1st-2nd year.

Grading: The course grade will be based on (40%) attendance and participation in the exercise/demo sessions and (60%) an exam at the end of the course.

Exercise grading:

2p. / participating in microscope demo session
1p. / participating in Zemax simulation demo session
3p. / written report about results of using Zemax OpticStudio

Prerequisites: First year classes in electromagnetism and calculus (MAPU). The optics and photonics courses will help to understand the principles taught in the course but are not compulsory.

Lecture Notes


Th 03.11.2022: 10.15–12.00 Physicum, D115

Th 10.11.2022: 14.15–16.00 ZOOM

Th 17.11.2022: 14.15–16.00 ZOOM

Th 24.11.2022: 14.15–16.00 ZOOM

Th 01.12.2022: 10.15–12.00 Physicum, D115

Th 08.12.2022: 10.15–12.00 Exactum, B119

Th 15.12.2022: 10.15–12.00 Physicum, D115



Th 03.11.2022: 14.15–16.00 ZOOM (Link in the email)

Introduction to OpticStudio

Th 10.11.2022: 10.15–12.00 Physicum, C106 (Microscope classroom)

Basics of Using Light Microscopes (mineral/rock samples)

Th 17.11.2022: 10.15–12.00 Physicum, C106 (Microscope classroom)

Imaging with and without dyeing bio-samples

Th 24.11.2022: 10.15–12.00 Physicum, C106 (Microscope classroom)

Imaging CD and DVD tracks

Th 01.12.2022: 14.15–16.00 ZOOM

OpticStudio: Simulating ideal lens system

Th 08.12.2022: 14.15–16.00 ZOOM

OpticStudio: Imaging 3D-scanned Zebrafish geometry

Th 15.12.2022: 14.15–16.00 ZOOM

OpticStudio: 3D-imaging with interferometry

Simulation report instructions