The main types of microscopes at a glance
A microscope is defined less by its magnification than by what it uses to probe the sample. Photons, electrons and a physical tip interact with matter in very different ways, and that sets the limit on what each instrument can resolve.
| Type | Probe | Best resolution (approx.) | Living samples? | Typical uses |
|---|---|---|---|---|
| Compound light (brightfield) | Visible light | ~200 nm | Yes | Teaching, histology, blood smears, microbiology |
| Stereo (dissecting) | Visible light, two light paths | Micrometres | Yes | Dissection, insects, electronics inspection |
| Phase contrast, DIC | Visible light | ~200 nm | Yes | Unstained live cells, cell culture |
| Fluorescence and confocal | Laser or LED excitation | ~200 nm; super-resolution down to tens of nm | Yes | Labelled proteins, organelles, tissue sections |
| Scanning electron (SEM) | Focused electron beam scanned over the surface | Around 1 nm | No | Surface topography, materials, fractures, coatings |
| Transmission electron (TEM) | Electron beam passing through a thin sample | Below 0.1 nm in corrected instruments | No | Crystal structure, viruses, cell ultrastructure |
| Scanning probe (AFM, STM) | Sharp tip scanned over the surface | Sub-nanometre height; atomic in STM | AFM: yes, in liquid | Surface roughness, single molecules, nanomaterials |
For a direct comparison of the two families most people meet first, see light microscope vs electron microscope.
Light microscopes: the most common types of microscopes
Optical microscopes form an image with glass lenses and visible light. Their resolution is capped by diffraction at roughly half the wavelength of light, so about 200 nm laterally with a good oil-immersion objective. In exchange they are relatively cheap, quick to use and work on living cells.
Compound microscope
The classic school and laboratory instrument combines an objective and an eyepiece, giving useful magnifications up to about 1000x. Stained samples are viewed in brightfield, where the specimen absorbs part of the transmitted light. The parts and their functions are covered in compound light microscope parts labeled, and the arithmetic in how to calculate total magnification.
Stereo microscope
A stereo or dissecting microscope sends a separate image to each eye, which produces a three-dimensional view of whole objects at low magnification. It is used where hands need to work under the lens: dissection, sorting insects, soldering or inspecting circuit boards.
Contrast techniques: phase contrast, DIC, darkfield and polarized light
Many cells are almost transparent. Phase contrast converts small differences in refractive index into differences in brightness, which makes unstained live cells visible. Differential interference contrast (DIC) gives a relief-like image with sharper edges. Darkfield lights the specimen from the side so that only scattered light reaches the objective, and polarized light microscopy reveals birefringent materials such as minerals, crystals and some fibres. The principle behind the first of these is explained in phase contrast microscopy explained.
Fluorescence, confocal and super-resolution microscopes
Fluorescence microscopy illuminates the sample with light of one colour and records the light of a longer wavelength that labelled molecules emit. Because only the labelled structures glow, a single protein type can be followed inside a living cell. Filter choice and common artefacts are discussed in fluorescence microscopy: fluorophores, filters and pitfalls.
- Widefield fluorescence lights the whole field at once. It is fast and gentle, but out-of-focus light blurs thick samples.
- Confocal microscopy scans a laser point and uses a pinhole to block out-of-focus light, giving thin optical sections and 3D stacks. See how the confocal pinhole works.
- Light-sheet microscopy illuminates the sample from the side with a thin sheet of light, which suits long imaging of embryos and cleared tissue.
- Multiphoton microscopy uses infrared pulses that penetrate deeper into scattering tissue.
- Super-resolution methods such as STED, SIM and PALM/STORM get past the diffraction limit. They are compared in super resolution microscopy: STED, SIM and PALM/STORM.
Rule of thumb: if the question involves living cells and specific molecules, start with fluorescence or confocal. If it involves structures smaller than about 200 nm and the sample can be fixed, move to super-resolution or electron microscopy.
Electron microscopes: SEM, TEM and cryo-EM
Electrons have a far shorter wavelength than visible light, so electron microscopes resolve detail down to the nanometre and below. The price is a vacuum chamber, careful sample preparation and instruments that cost several orders of magnitude more than a teaching microscope.
Scanning electron microscope (SEM)
An SEM scans a focused beam across the sample and collects secondary and backscattered electrons to build an image of the surface with a large depth of field. With an X-ray detector it can also map elemental composition. Read more in how SEM works, SEM sample preparation and energy dispersive X-ray spectroscopy.
Transmission electron microscope (TEM)
A TEM sends electrons through a sample usually thinner than about 100 nm. It reveals internal structure: organelles, viruses, crystal lattices and defects in materials. Aberration-corrected instruments resolve individual atomic columns. See transmission electron microscopy explained.
Cryo-electron microscopy
Cryo-EM images biological samples frozen so fast that water forms glass instead of ice. Averaging thousands of particle images yields protein structures close to atomic resolution, work recognised by the 2017 Nobel Prize in Chemistry. The method is described in cryo-EM explained.
Scanning probe microscopes: AFM and STM
Scanning probe microscopes do not use lenses at all. A sharp tip moves across the surface and a feedback loop records its height or the current flowing through it.
- Scanning tunnelling microscope (STM), developed in 1981, measures the tunnelling current between tip and a conductive sample and can image individual atoms.
- Atomic force microscope (AFM), introduced in 1986, measures the force between tip and surface, works on insulators and can image biomolecules in liquid. Details are in atomic force microscopy explained.
Types of microscopes in biology and microbiology classes
School and introductory courses often ask for “the two types of microscopes”. The expected answer is light and electron microscopes, compared by magnification, resolution, cost and whether living specimens can be viewed. Courses that ask for three or four types usually add stereo microscopes and split electron microscopes into SEM and TEM.
In microbiology, brightfield microscopy with Gram staining is the everyday method for identifying bacteria, phase contrast shows motility of unstained cells, fluorescence detects labelled organisms, and electron microscopy reveals viruses and fine bacterial structures such as flagella.
How to choose the right type of microscope
- Define the smallest feature you need to see. Above a few hundred nanometres, light microscopy is usually enough.
- Decide whether the sample must stay alive. Live imaging points to light, fluorescence or AFM in liquid.
- Ask whether you need the surface or the interior. SEM and AFM describe surfaces, TEM and confocal sections show internal structure.
- Check what contrast the sample provides. Transparent cells need phase contrast, DIC or fluorescent labels.
- Consider chemical information. Elemental maps need SEM or TEM with X-ray spectroscopy.
- Weigh access and cost. Electron and super-resolution instruments are typically shared in core facilities, so preparation time and booking matter as much as resolution.
Conclusion
The different types of microscopes are complementary rather than competing. Light microscopes cover everyday imaging of cells and tissues, fluorescence and confocal systems add molecular specificity, electron microscopes reach the nanometre and atomic scale, and scanning probe instruments measure surfaces directly. Many studies combine several of them, using a light microscope to find a region of interest and an electron or probe microscope to examine it in detail.