Advanced Microscopy unit

Department of Pathology

Haartman Institute, University of Helsinki

About this web site and tutorial

This web site is running for academic purpose only, including user training, information share and administrative task. Most of the commercial products mentioned in the web pages are devices this unit have purchased, their appearance here is just for explain their usage and function, no advertisement meaning. All the brand names mentioned here are the properties of the company concerned.

The on-line confocal tutorial is revised and expanded from a PowerPoint slide show I used in the confocal microscopy user training course. The aim of this tutorial is to help those potential new user who did not participate that training course. For experienced users, this tutorial also contains some more detailed explanation, mechanism and tips for choosing some parameters, related theories and formula, etc., which can be a useful reference for them to increase their knowledge and efficiency to use the device.

This tutorial does not copy all the theoretical and technical details of confocal microscopy, instead, it delineate the outline about how confocal microscope works, and some basic concepts that are important for a user to understand or decide which button to press, which knob to turn, etc.. Some pictures are taken from the operation manuals of the devices concerned or from the web site of their manufacturers, or the technical release, tutorial materials they have published. A reference below lists their sources.

The tutorial can be freely used, printed for non-commercial purpose as long as it is remain in its original form.

Although every effort has been made to ensure the accuracy of the information provided here, the author do not assume any responsibility for the damages incurred by using information mentioned here.


  1. Robert H. Webs. Theoretical Basis of Confocal Microscopy. In Confocal Microscopy, P. Michail Conn ed. Methods in Enzymology. pp 3-20, Vol 307, 1999.
  2. S. K. Kong, et al. Practical Consideration in Acquiring Biological Signals fro Confocal Microscope. In Confocal Microscopy, P. Michail Conn ed. Methods in Enzymology.  Vol 307, pp 21-26,1999.
  3. Stefan Wilhelm, et al. Confocal Laser Scanning Microscopy : Principles. Carl Zeiss Microscopy, 1998.
  4. Anna Smallcombe.  Fluorescence bleed-through: how to reduce or avoid it. BioRad Microscopy Division: Technical paper.
  5. H. G. Kapitza. Microscopy from the very beginning. 2nd Rev. Carl Zeiss Microscopy, 1997.
  6. E. H. K. Stelzer. Contrast, resolution, pixelation, dynamic range and signal-to-noise ratio: fundamental limits to resolution in fluorescence light microscopy. Journal of Microscopy. Vol.189  pt1, pp15-24,1998.
  7. U. Tauer et al. Confocal spectro-photometry. Special issue "Confocal Microscopy ", CDR4, pp 15-27. Leica Microsystems. 2000.
  8. Leica Confocal Systems. Products and Technology Guide. Leica Microsystems. 2002.
  9. Stephen Rawlings, et al. How Microscopy Produce a Sharper image. Biophotonics International. Vol. 9.  pp 44-48, May, 2002.

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 Statement about this web and tutorial
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This page was last updated 02.04.2014