PhD Course microscopy - online version (to be taken anytime)



This course 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). 

All Powerpoints and practical information can be found here

The lectures are also presented in an intereactive 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 the following quiz (will be available during the course)

Furthermore provide proof that you did the image analysis part by following the steps below


FIJI image analysis practical


  • 1.     Install FIJI
  • 2.     Go to: >Help>Update
  • 3.     Apply all needed changes
  • 4.     Restart FIJI
  • 5.     Repeat step 2 to 4 till 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 round
  • 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


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