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Label-free Bioimaging 2018

Course code: MATR340

Scope: 5 credits.

General info

The course provides state-of-the-art optical methods for label-free imaging. Special attention in bioimaging.


08.01.2019: Updated exam date and place
3.12.2018: Instructions for the FDTD excercise added
26.11.2018 Link to the lecture slides added
16.11.2018 Second problem set uploaded
9.11.2018 First problem set uploaded
1.11.2018: Link to the angora homepage added.
30.10.2018: Webpage created

Lecturer: Doc. Ivan Kassamakov, C318, email: ivan dot kassamakov at helsinki dot fi.
Assistants: Göran Maconi , C204a, email: goran dot maconi at helsinki dot fi and Miikka Järvinen, B228,email: miikka dot jarvinen at helsinki dot fi.

Exam: Monday 21.1.2019, 11:00-15:00, Physicum D114

Lectures: Thursdays in
Physicum D115, 01.11.-29.11.18 at 10:15-12:00.
Physicum D115, 13.12.18 at 10:15-12:00
Exercises: Thursdays in
Physicum C106, 01.11.-08.11.18 at 12:15-14:00.
Physicum D115, 15.11.-29.11.18 at 12:15-14:00
Physicum D115, 13.12.18 at 12:15-14:00

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

Lecture notes: Link to lecture notes

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.

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.


Problem set 1

Problem set 2

There will be exercises which uses the Angora FDTD simulation package, you can find more information about this in here.

Homework for the second FDTD demo, 13.12.18:

  • Most of these steps were already done during the first FDTD demo, 29.09.2018, but for those who didn’t attend, you can do it on your own
  • Download the template config and job files: link
  • Familiarize yourself with the markup and structure of 1um_pitch_grating.cfg (open it in a text editor, like notepad++). Complete documentation of the format can be found here.
  • Modify the .cfg file so that the line widths and spacings correspond to an optical disc of your choosing.
  • Modify the name of the output folder so it has your name in it.
  • In the job file ( edit the job name (row 2) to have your name in it. Also, if you changed the name of the .cfg file, make sure to change it on row 21.
  • Log into with sftp (e.g. WinSCP). Use your ad account credentials. This has to be done from inside the university network. You can use either one of the publicly available computers, or log in from the outside using a virtual desktop. It is also possible to use an SSH tunnel.
  • Transfer the two files to kale using sftp.
  • Open an SSH session to This can be done in WinSCP, by pressing Open Terminal (Ctrl + T). Add your job to the queue with the command “sbatch”
  • You can check that your job was added to the queue, using the command “squeue -l -u <yourusername>”
  • The job should be finished the next day, make sure to download the resulting files. We will analyze them during the excercise session (Using MATLAB).