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  • Rights: The University of Waikato Te Whare Wānanga o Waikato
    Published 16 March 2021 Referencing Hub media

    Function: Lets users look at thin ‘slices’ in a sample while keeping sample intact. Lets you look specifically at parts of a cell (such as individual proteins) by labelling them with fluorescence.

    Maximum magnification: Approximately 2,000x.

    Best for:

    Looking at living cells.

    Understanding relationships between cells.

    Highlighting individual components of cells.


    Low resolution compared to electron microscope.

    See only fluorescent objects – no other structures visible.

    Fluorescence can cause artefacts.

    Video: University of Otago experts Allan Mitchell and Rebecca Campbell briefly explain how a confocal microscope is able to use cross-sections of a sample to generate a 3D image. Learn more about confocal microscopy in Confocal microscopy of neurons and Making connections in the brain.


    Allan Mitchell

    In a conventional microscope, we have the light shining right through the sample, which means all the information inside the thickness of that sample is superimposed on top of itself. However, with the confocal microscope, we are able to select the particular levels within that section and just focus on those. The information above that level and below that level is discarded from the image.

    Associate Professor Rebecca Campbell

    So I explain this to my students as if the tissue were a stack of pancakes, we can image each individual pancake without having to take them apart and so then we can put them back together to generate a 3D image of the pancake stack or we can look at the individual pancakes at the different focal planes.

    Allan Mitchell, University of Otago
    Associate Professor Rebecca Campbell, University of Otago

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