PhD course Microscopy - online version (to be taken anytime)







This course will get you introduced with the basics of microscopy. Starting from the physics behind the microscope moving from basic light microscopy, through contrast enhancing techniques. Ending with the nowadays omnipresent fluorescence microscopy, and shortly discussing the advanced possibilities with these techniques. Finally, the course concludes with an introduction in image analysis to learn the basics of FIJI, the most used program for analyzing microscopic images.

This microscopy course is adapted to be taken by yourself (online). It consists of 6 lectures covering various topics and several practicals that you can try yourself (though they won’t be adopted to your own microscope per se).

The course takes about 3 days to complete, and you can get a certificate for 3 GSCs (graduate school credits).

Course material
All course material can be found at this link, including lecture Powerpoints and practical assignments. The lectures are also presented in an interactive way online:

  1. Physics of light:
  2. The microscope:
  3. Contrast techniques:
  4. Histology and sample preparation:
  5. Fluorescence microscopy:
  6. Image analysis:
Certificate of participation
For obtaining a certificate of participation, please complete this online quiz (a minimum of 162 points should be obtained). Furthermore, provide proof that you did the image analysis part by following the steps below. 
  1. Install FIJI;
  2. Go to: >Help >Update;
  3. Apply all needed changes;
  4. Restart FIJI;
  5. Repeat steps 2-4 until you get the message "Your ImageJ is up to date!".
    NOTE: Sometimes you get an error message, just repeat the steps, it should work the 2nd time;
  6. Click OK;
  7. Click 'Manage Update Sites';
  8. Select 3D ImageJ Suite, ImageScience, and Leiden University;
  9. Click Apply Changes;
  10. Restart FIJI;
  11. Go to: Plugins >LeidenUniv >Teaching >Interactive Tutorial;
  12. Finish all five assignments to get the Image analysis certificate;
  13. Email the proof to