Fluorescence Microscope: Principle, Types, Applications

By Nisha Rijal •  Updated: 05/30/21 •  5 min read

Fluorescence microscopy is a type of light microscope that works on the principle of fluorescence. A substance is said to be fluorescent when it absorbs the energy of invisible shorter wavelength radiation (such as UV light) and emits longer wavelength radiation of visible light (such as green or red light). This phenomenon, also termed fluorescence, is widely used in clinical and diagnostic settings for the rapid detection of microorganisms, antibodies, and many other substances.

NOTE: Some substances have autofluorescence ability (e.g., chlorophyll) while others fluoresce after staining with fluorescent dyes such as DAPI (49,6-diamidino-2-phenylindole), acridine orange, auramine-rhodamine, Alexa Fluors, or DyLight 488.

When fluorescence microscopy is used for the detection of antigen-antibody reaction, it is known as immunofluorescence.

Components of a Fluorescence Microscope:

Fluorescence microscopes as other light microscope has a

  1. Light source: Xenon arc lamp or mercury-vapor lamp are common; power LED and lasers are used in more advanced forms.
  2. A set of optical filters: Optical filters include a set of a compatible excitation filter, emission filter, and dichroic beam splitter;
    1. An excitation filter selects the wavelengths to excite a particular dye within the specimen.
    2. A dichroic beam splitter/ dichroic mirror reflects light in the excitation band and transmit light in the emission band, enabling the classic epifluorescence incident light illumination.
    3. An emission filter serves as a kind of quality control by letting only the wavelengths of interest emitted by the fluorophore pass through.
  3. Darkfield condenser: It provides a black background against which the fluorescent objects glow.

The filters are often plugged in together in a filter cube (compound microscopes) or in a flat holder (mainly stereo microscopes).


To observe the sample through a fluorescence microscope, it should be first labeled with a fluorescent dyes/substance known as a fluorophore.

Working mechanism of Fluorescence Microscope
Working mechanism of Fluorescence Microscope
(Photo credit: Henry Mühlpfordt)

Higher energy light shorter wavelength of lights (UV rays or blue light) generated from mercury vapor arc lamp passes through the excitation filter which allows only the short wavelength of light to pass through and removes all other non-specific wavelengths of light. The filtered light is reflected by the dichroic filter and falls on the sample (i.e. fluorophore-labeled). The fluorochrome absorbs shorter wavelength rays and emits rays of longer wavelength (lower energy) that passes through the emission filter. The emission filter blocks (suppresses) any residual excitation light and passes the desired longer emission wavelengths to the detector. Thus the microscope forms glowing images of the fluorochrome-labeled microorganisms against a dark background.

To the observer, the background is dark, as there is no visible light and only the labelled specimen (cells, microorganisms etc.) appear bright (fluoresce).

Types of Fluorescence Microscopes

There are various types of fluorescence microscopes. Some of the common types are:

  1. Epifluorescence microscopes: The most common type of fluorescence microscope in which, excitation of the fluorophore and detection of the fluorescence are done through the same light path (i.e. through the objective).
  2. Confocal microscope: In this type of fluorescence microscope, high‐resolution imaging of thick specimens (without physical sectioning) can be analyzed using fluorescent-labeled dye.
  3. Multiphoton microscope: In this type of microscope, multiphoton fluorescence excitation results in the capture of high-resolution three-dimensional images of specimen tagged with highly specific fluorophores.
  4. Total internal reflection fluorescence (TIRF) microscope: Total internal reflection fluorescence microscopy (TIRFM) exploits the unique properties of an induced evanescent wave or field in a limited specimen region immediately adjacent to the interface between two media having different refractive indices. 

Applications of Fluorescence Microscope

Fluorescence microscopy is widely used in diagnostic microbiology and in microbial ecology (for enumerating bacteria in natural environments).

Fluorescent antibody-stained specimen showing numerous, Toxoplasma sp. tachyzoite
Fluorescent antibody-stained specimen showing numerous, Toxoplasma sp. tachyzoite
(Image credit: CDC)
  1. Detection of acid-fast bacilli (AFB) in sputum or CSF when stained with auramine fluorescent dye.
  2. Detection of Trichomonas vaginalis, intracellular gonococci, and other parasites when stained by acridine orange.
  3. In immunodiagnosis of infectious diseases, using both direct and indirect antibody techniques.

Limitations of Fluorescence Microscope

  1. Fluorophores gradually lose their ability to fluoresce as they are illuminated in a process called photobleaching. Photobleaching can severely limit the time over which a sample can be observed by fluorescence microscopy. However, several techniques exist to reduce photobleaching such as the use of more robust fluorophores, by minimizing illumination, or by using photoreactive scavenger chemicals.
  2. Fluorescence microscopy has enabled analysis of live cells; but fluorescent molecules generate reactive chemical species under illumination that enhances the phototoxic effect, to which live cells are susceptible.
  3. Fluorescence microscopy only allows observation of the specific structures which have been labeled for fluorescence. For example, observing a tissue sample prepared with a fluorescent DNA stain by fluorescence microscopy only reveals the organization of the DNA within the cells and reveals nothing else about the cell morphologies.

References and Further Readings

Nisha Rijal

I am working as Microbiologist in National Public Health Laboratory (NPHL), government national reference laboratory under the Department of health services (DoHS), Nepal. Key areas of my work lies in Bacteriology, especially in Antimicrobial resistance.

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