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The fifth course of the series contains three video units and a textbook chapter that can be accessed free of charge at this webpage. It covers basic principles of the light and fluorescence microscope, methodologies for relevant staining techniques, and data interpretation.

Course Information

  • About

    This course focuses on the basic principles of the light and fluorescence microscope, methodologies for relevant staining techniques, and data interpretation. The course is designed for both academics and practitioners, including graduate and postgraduate students, researchers, laboratory staff, plant operators, consultants, and other sector professionals with a background in sanitary, civil, environmental or (bio)chemical engineering, environmental biotechnology or biochemistry. As the course is at graduate level, participants with knowledge of and experience with the basic concepts of biological wastewater treatment will particularly benefit from it.

  • Syllabus

    The following topics are part of the course:

    • Light microscopy;
    • Morphological investigations;
    • Examining activated sludge microscopically;
    • Fluorescence in situ hybridization;
    • Combined staining techniques.

    For a detailed table of contents please click here.



  • Objectives │ Activities │ Assessment

    Learning objectives, activities and assessment depend on the delivery mode of the course. In general, learning objectives are more complex for instructor-led courses. This is particularly true for on campus courses and tailored training because they allow for guided, hands on, laboratory exercises and assignments. To view the learning objectives, activities and assessment of this course please click here.

  • Contact


Gram staining

This video shows how to distinguish between Gram negative and Gram positive bacteria by using the Gram staining technique.

1 of 3

Neisser staining

The Neisser staning technique is presented to assess the presence of intracellular metachromatic granules, such as volutin bodies and poly-phosphate.

2 of 3

Fluorescent in situ hybridization (FISH)

The in situ identification of individual microbial cells is carried out by applying the FISH method.

3 of 3

Download the chapter

Microscopy (5.2 MB)

Available in English, Spanish and Croatian. Coming soon in Russian, Hindi, Marathi and Tamil.


This chapter is an integral part of the textbook Experimental Methods in Wastewater Treatment. It is a complementary part of the course curriculum and includes background information on the processes of interest, details on experimental set-ups, preparation and execution, as well as a results discussion and interpretation, accompanied with examples and additional information. The book is also used for teaching the MSc specialization in Sanitary Engineering at IHE Delft and several other universities worldwide. It is the product of collaborative efforts by research groups and practitioners around the world. You can download your free copy of the book in one of currently available languages.
  • Van Loosdrecht M.C.M., Nielsen P.H, Lopez-Vazquez C.M., Brdjanovic D. Ed. (2016) Experimental Methods in Wastewater Treatment. IWA Publising, pg. 350, ISBN 9781780404745 (Hardback) 9781780404752 (eBook)