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    Explore the features of different microscopes and learn how scientists choose which ones to use in their research.

    Select a label to explore the strengths and weaknesses of eight types of microscope. Discover why individual scientists have chosen to use particular microscope types in their research. 

    To use this interactive, move your mouse or finger over any of the labelled boxes and click to obtain more information.

    Transcript

    Choosing a microscope

    When planning an experiment with microscopes, you need to think carefully about which microscope to use. It all depends on what you want to learn. What do you want to do?

    • Look at organisms, cells or tissues that are currently alive?
    • Look at the surface of a living thing?
    • Look at whole cells and how they connect in 3D?
    • Look at the surface of a sample at high resolution?
    • Look at a cross-section of a sample at high resolution?
    • Build up a 3D model from the results?
    • Avoid removing moisture from the sample?

    This interactive takes you through some of the important differences between microscopes.

    Download the image as a PDF.

    Stereomicroscope (light)

    Function: Uses visible light to illuminate the surface of a sample.

    Maximum magnification: Approximately 2,000x.

    School light microscopes that do not use oil immersion have a magnification range of 40–400x.

    Best for:

    Looking at living things.

    Looking at things without disrupting them.

    Disadvantages: Usually lower resolution than the compound light microscope.

    Video: Allan Mitchell, Technical Manager of Otago Micro and Nanoscale Imaging, discusses the benefits and limitations of the compound microscope and the stereomicroscope.

    Select here to view video transcript and copyright information.

    Compound microscope (light)

    Function: Uses visible light to illuminate a thin section of sample.

    Maximum magnification: Approximately 2,000x.

    School light microscopes that do not use oil immersion have a magnification range of 40–400x. 

    Best for:

    Looking at some living things (for example, a single cell layer).

    Looking at cells and tissues (preparation steps are less critical than for electron microscopy).

    Getting an overview of a sample. 

    Disadvantages:

    Low resolution compared to electron microscope. 

    Video: Allan Mitchell, Technical Manager of Otago Micro and Nanoscale Imaging, discusses the benefits and limitations of the compound microscope and the stereomicroscope.

    Select here to view video transcript and copyright information.

    Confocal laser scanning fluorescence microscope

    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. 

    Disadvantages:

    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.

    Select here to view video transcript and copyright information.

    Scanning electron microscope (SEM)

    Function: Lets users look at the surface of objects at high resolution.

    Maximum magnification: Approximately 500,000x. 

    Best for:

    Looking at surfaces of objects.

    Looking at objects in 3D. 

    Disadvantages:

    Resolution often not as high as the transmission electron microscope.

    Can’t be used to look at living things (samples need to be dried and coated in metal before visualising).

    Costly to run. 

    Video: Liz Girvan is a SEM expert with Otago Micro and Nanoscale Imaging. She explains how a scanning electron microscope works by knocking electrons off the surface of a sample. Understand more about SEM microscopy in Why we use SEM, Artefacts in the SEM and Sputter coating. 

    Select here to view video transcript and copyright information.

    CryoSEM

    Function: Lets users look at the surface of objects that contain liquid (avoids sample preparation steps for conventional SEM). 

    Maximum magnification: Approximately 500,000x. 

    Best for:

    Looking at biological samples in a lifelike state.

    Looking at biological samples too delicate to survive preparation for conventional SEM.

    Looking at hydrated or wet surfaces of biological samples. 

    Disadvantages:

    Resolution often not as high as the transmission electron microscope.

    Can’t be used to look at living things (sample needs to be frozen before visualising).

    Frozen water may hide important information.

    Costly to run. 

    Video: University of Otago experts Liz Girvan and Dr Bronwyn Lowe tell us why cryoSEM is best when looking at things that contain moisture, such as plants or food. 

    Select here to view video transcript and copyright information.

    Electron tomography

    Function: Lets users build up a 3D model of a sample from TEM data. 

    Maximum magnification: Approximately 5,000,000x. 

    Best for:

    Understanding relationships between objects in a sample at high resolution.

    Understanding three-dimensional structure.

    Looking at objects in very high resolution. 

    Disadvantages:

    Can’t be used to look at living things (samples need to be prepared extensively before visualising). 

    Video: Allan Mitchell, Technical Manager of Otago Micro and Nanoscale Imaging, explains how electron tomography uses an electric beam to build an image in 3D. Watch Electron tomography of the primary cilium to see why Associate Professor Tony Poole utilised electron tomography for his research.

     

    Select here to view video transcript and copyright information.

    Transmission electron microscope (TEM)

    Function: Lets users look at a very thin cross-section of an object (such as a cell). 

    Maximum magnification: Approximately 5,000,000x. 

    Best for:

    Looking at internal structure of objects.

    Looking at objects at very high resolution.

    Looking at relationships between structures at high resolution. 

    Disadvantages:

    Can’t be used to look at living things (samples need to be prepared extensively before visualising).

    Costly to run. 

    Video: The transmission electron microscope shoots a beam of electrons at a thin slice of sample. Allan Mitchell points out the components of the transmission electron microscope. Learn about why you would use this microscope over others in Why use the transmission electron microscope?

    Select here to view video transcript and copyright information.

    Scanning tunnelling microscope (STM)

    Function: Lets users study the surface of nanostructures. 

    Maximum magnification: Approximately 90,000,000x. 

    Best for:

    Looking at individual atoms.

    Looking at the surface of nanostructures. 

    Disadvantages:

    Only a few nanometres of a sample can be seen at a time.

    Requires very clean and stable surfaces. 

    Video: Professor Richard Haverkamp of Massey University explains how a scanning tunnelling microscope works, accompanied by views of the device in use.

     

    Select here to view video transcript and copyright information.

    Rights: The University of Waikato Te Whare Wānanga o Waikato Published 16 March 2021 Size: 1.7 MB Referencing Hub media