Introduction to Fluorescence Microscopy
Fluorescence is a phenomenon that takes place when a substance absorbs light at a given wavelength and emits light at another wavelength. Fluorescence occurs as an electron, which has been excited to a higher, and more unstable energy state, relaxes to its ground state and gives off a photon of light. The light that is responsible for excitation, or moving the electron to a higher energy state, is of shorter wavelength and higher energy than the fluorescence emission, which has a longer wavelength, lower energy, and different color.
Fluorescence microscopy combines the magnifying properties of the light microscope with fluorescence technology that allows the excitation of- and detection of emissions from- fluorophores - fluorescent chemical compounds. With fluorescence microscopy, scientists can observe the location of specific cell types within tissues or molecules within cells.
The main components of the fluorescent microscope overlap greatly with the traditional light microscope. However the 2 main differences are the type of light source and the use of the specialized filter elements.
Fluorescence microscopy requires a very powerful light source such as a xenon or mercury arch lamp like the one shown here. The light emitted from the mercury arc lamp is 10-100 times brighter than most incandescent lamps and provides light in a wide range of wavelengths, from ultra-violet to the infrared. This high-powered light source is the most dangerous part of the fluorescence microscope setup as looking directly into unfiltered light can seriously damage your retinas and mishandling the bulbs can cause them to explode.
The principle behind fluorescence microscopy is simple. As light leaves the arc lamp it is directed through an exciter filter, which selects the excitation wavelength.
This light is reflected toward the sample by a special mirror called a dichroic mirror, which is designed to reflect light only at the excitation wavelength. The reflected light passes through the objective where it is focused onto the fluorescent specimen. The emissions from the specimen are in turn, passed back up through the objective – where magnification of the image occurs –and now through the dichroic mirror.
This light is filtered by the barrier filter, which selects for the emission wavelength and filters out contaminating light from the arc lamp or other sources that are reflected off of the microscope components. Finally, the filtered fluorescent emission is sent to a detector where the image can be digitized, or it’s transmitted to the eyepiece for optical viewing.
The exciter filter, dichroic mirror, and barrier filter can be assembled together into a component known as the filter cube. Different filter cubes can be changed during specimen viewing to change the excitation wavelength, and a series of diaphrams can be used to modify the intensity of excitation.
When it comes to performing fluorescence microscopy, the fluorophore can be just as important as the microscope itself, and the type of fluorophore being imaged dictates the excitation wavelength used and emission wavelength that’s detected. The excitation wavelengths contain a small range of energies that can be absorbed by the fluorophore and cause it to transition into an excited state. Once excited, a wide range of emissions, or transitions back to the lower energy state, are possible resulting in an emission spectrum.
The difference between the peak of the absorption, or excitation curve and the peak of the emission curve is known as Stoke’s Shift. The greater the distance in this shift, the easier it is to separate the two different wavelengths. Additionally, any overlapping spectrum needs to be removed by the components of the filter cube for reduced background and improved image quality.
Exposure of the fluorophore to prolonged excitation will cause it to photobleach, which is a weakening or loss of fluorescence. To reduce photobleaching, you can add an anti-fade mounting medium to the slide and seal the edges with nail polish. The slide should also be kept in the dark when not being imaged.
To begin fluorescence imaging, turn on the xenon or mercury light source and allow it to warm up for as long as 15 minutes in order for it to reach constant illumination.
Next, place your sample on the stage and secure it in place. Then, turn on the white light source of your microscope. Focus on your sample using the lowest powered objective by adjusting the coarse and fine focus knobs. Then, use the stage adjustment knobs to find your area of interest.
Next, turn off the white light source, as well as any unnecessary room lights to reduce background.
Select the correct filter cube for the dye you are imaging and open the shutter to illuminate your sample.
Finally, make fine focus adjustments and direct the output light to the imaging camera. You will likely need to make adjustments to the exposure time for each different fluorophore or fluorescent dye used. However, it is important to keep the exposure time constant when comparing features with the same dye on different samples.
To image multiple dyes on the same sample, change the filter cube to match each fluorophore and record the new image.
After each dye in the sample has been imaged, individual images can be overlaid and merged.
Many different types of experiments can make use of fluorescent microscopy and involve different types of fluorophores One of the most common applications of fluorescent microscopy is the imaging of proteins that have been labeled with antibodies that are attached to, or “conjugated” to fluorescent compounds.. Here, an antibody towards leptospiral surface proteins was detected using a secondary antibody conjugated to alexafluor-488, which fluoresces green when excited.
Another way to highlight a specific feature with fluorescence is to integrate the code for a fluorescent protein such as green fluorescent protein, or GFP, into the DNA of an organism. The gene for GFP was originally isolated from jellyfish and can be expressed, or produced, by cultured cells in response to specific triggers or as part of a specific cell type like the tumor cells shown glowing in this image
Another application of fluorescence imaging is Fluorescence Speckle Microscopy which is a technology that uses fluorescently labeled macromolecular assemblies such as the F-actin network seen here, to study movement and turnover kinetics of this important cytoskeletal protein.
An advanced technique known as Fluorescence recovery after photobleaching, or FRAP, is performed by intentionally photobleaching a small region of a sample in order to monitor the diffusion rate of fluorescently labeled molecules back into the photobleached region.
You’ve just watched JoVE’s introduction to Fluorescence Microscopy.
In this video we learned about the concept of fluorescence, how fluorescence microscopy differs from light microscopy, and how to take a fluorescence image through the scope. We also learned about some basic and advanced applications that use fluorescence. Thanks for watching and don’t forget while photobleaching looks great on your teeth it’s not so good for your samples.
Fluorescence microscopy is a very powerful analytical tool that combines the magnifying properties of light microscopy with visualization of fluoresce…
Fluorescence is a phenomenon that takes place when a substance absorbs light at a given wavelength and emits light at another wavelength. Fluorescence occurs as an electron, which has been excited to a higher, and more unstable energy state, relaxes to its ground state and gives off a photon of light. The light that is responsible for excitation, or moving the electron to a higher energy state, is of shorter wavelength and higher energy than the fluorescence emission, which has a longer wavelength, lower energy, and different color.
Fluorescence microscopy combines the magnifying properties of the light microscope with fluorescence technology that allows the excitation of- and detection of emissions from- fluorophores - fluorescent chemical compounds. With fluorescence microscopy, scientists can observe the location of specific cell types within tissues or molecules within cells.
The main components of the fluorescent microscope overlap greatly with the traditional light microscope. However the 2 main differences are the type of light source and the use of the specialized filter elements.
Fluorescence microscopy requires a very powerful light source such as a xenon or mercury arch lamp like the one shown here. The light emitted from the mercury arc lamp is 10-100 times brighter than most incandescent lamps and provides light in a wide range of wavelengths, from ultra-violet to the infrared. This high-powered light source is the most dangerous part of the fluorescence microscope setup as looking directly into unfiltered light can seriously damage your retinas and mishandling the bulbs can cause them to explode.
The principle behind fluorescence microscopy is simple. As light leaves the arc lamp it is directed through an exciter filter, which selects the excitation wavelength.
This light is reflected toward the sample by a special mirror called a dichroic mirror, which is designed to reflect light only at the excitation wavelength. The reflected light passes through the objective where it is focused onto the fluorescent specimen. The emissions from the specimen are in turn, passed back up through the objective – where magnification of the image occurs –and now through the dichroic mirror.
This light is filtered by the barrier filter, which selects for the emission wavelength and filters out contaminating light from the arc lamp or other sources that are reflected off of the microscope components. Finally, the filtered fluorescent emission is sent to a detector where the image can be digitized, or it’s transmitted to the eyepiece for optical viewing.
The exciter filter, dichroic mirror, and barrier filter can be assembled together into a component known as the filter cube. Different filter cubes can be changed during specimen viewing to change the excitation wavelength, and a series of diaphrams can be used to modify the intensity of excitation.
When it comes to performing fluorescence microscopy, the fluorophore can be just as important as the microscope itself, and the type of fluorophore being imaged dictates the excitation wavelength used and emission wavelength that’s detected. The excitation wavelengths contain a small range of energies that can be absorbed by the fluorophore and cause it to transition into an excited state. Once excited, a wide range of emissions, or transitions back to the lower energy state, are possible resulting in an emission spectrum.
The difference between the peak of the absorption, or excitation curve and the peak of the emission curve is known as Stoke’s Shift. The greater the distance in this shift, the easier it is to separate the two different wavelengths. Additionally, any overlapping spectrum needs to be removed by the components of the filter cube for reduced background and improved image quality.
Exposure of the fluorophore to prolonged excitation will cause it to photobleach, which is a weakening or loss of fluorescence. To reduce photobleaching, you can add an anti-fade mounting medium to the slide and seal the edges with nail polish. The slide should also be kept in the dark when not being imaged.
To begin fluorescence imaging, turn on the xenon or mercury light source and allow it to warm up for as long as 15 minutes in order for it to reach constant illumination.
Next, place your sample on the stage and secure it in place. Then, turn on the white light source of your microscope. Focus on your sample using the lowest powered objective by adjusting the coarse and fine focus knobs. Then, use the stage adjustment knobs to find your area of interest.
Next, turn off the white light source, as well as any unnecessary room lights to reduce background.
Select the correct filter cube for the dye you are imaging and open the shutter to illuminate your sample.
Finally, make fine focus adjustments and direct the output light to the imaging camera. You will likely need to make adjustments to the exposure time for each different fluorophore or fluorescent dye used. However, it is important to keep the exposure time constant when comparing features with the same dye on different samples.
To image multiple dyes on the same sample, change the filter cube to match each fluorophore and record the new image.
After each dye in the sample has been imaged, individual images can be overlaid and merged.
Many different types of experiments can make use of fluorescent microscopy and involve different types of fluorophores One of the most common applications of fluorescent microscopy is the imaging of proteins that have been labeled with antibodies that are attached to, or “conjugated” to fluorescent compounds.. Here, an antibody towards leptospiral surface proteins was detected using a secondary antibody conjugated to alexafluor-488, which fluoresces green when excited.
Another way to highlight a specific feature with fluorescence is to integrate the code for a fluorescent protein such as green fluorescent protein, or GFP, into the DNA of an organism. The gene for GFP was originally isolated from jellyfish and can be expressed, or produced, by cultured cells in response to specific triggers or as part of a specific cell type like the tumor cells shown glowing in this image
Another application of fluorescence imaging is Fluorescence Speckle Microscopy which is a technology that uses fluorescently labeled macromolecular assemblies such as the F-actin network seen here, to study movement and turnover kinetics of this important cytoskeletal protein.
An advanced technique known as Fluorescence recovery after photobleaching, or FRAP, is performed by intentionally photobleaching a small region of a sample in order to monitor the diffusion rate of fluorescently labeled molecules back into the photobleached region.
You’ve just watched JoVE’s introduction to Fluorescence Microscopy.
In this video we learned about the concept of fluorescence, how fluorescence microscopy differs from light microscopy, and how to take a fluorescence image through the scope. We also learned about some basic and advanced applications that use fluorescence. Thanks for watching and don’t forget while photobleaching looks great on your teeth it’s not so good for your samples.
Fluorescence is a phenomenon that takes place when a substance absorbs light at a given wavelength and emits light at another wavelength. Fluorescence occurs as an electron, which has been excited to a higher, and more unstable energy state, relaxes to its ground state and gives off a photon of light. The light that is responsible for excitation, or moving the electron to a higher energy state, is of shorter wavelength and higher energy than the fluorescence emission, which has a longer wavelength, lower energy, and different color.
Fluorescence microscopy combines the magnifying properties of the light microscope with fluorescence technology that allows the excitation of- and detection of emissions from- fluorophores - fluorescent chemical compounds. With fluorescence microscopy, scientists can observe the location of specific cell types within tissues or molecules within cells.
The main components of the fluorescent microscope overlap greatly with the traditional light microscope. However the 2 main differences are the type of light source and the use of the specialized filter elements.
Fluorescence microscopy requires a very powerful light source such as a xenon or mercury arch lamp like the one shown here. The light emitted from the mercury arc lamp is 10-100 times brighter than most incandescent lamps and provides light in a wide range of wavelengths, from ultra-violet to the infrared. This high-powered light source is the most dangerous part of the fluorescence microscope setup as looking directly into unfiltered light can seriously damage your retinas and mishandling the bulbs can cause them to explode.
The principle behind fluorescence microscopy is simple. As light leaves the arc lamp it is directed through an exciter filter, which selects the excitation wavelength.
This light is reflected toward the sample by a special mirror called a dichroic mirror, which is designed to reflect light only at the excitation wavelength. The reflected light passes through the objective where it is focused onto the fluorescent specimen. The emissions from the specimen are in turn, passed back up through the objective – where magnification of the image occurs –and now through the dichroic mirror.
This light is filtered by the barrier filter, which selects for the emission wavelength and filters out contaminating light from the arc lamp or other sources that are reflected off of the microscope components. Finally, the filtered fluorescent emission is sent to a detector where the image can be digitized, or it’s transmitted to the eyepiece for optical viewing.
The exciter filter, dichroic mirror, and barrier filter can be assembled together into a component known as the filter cube. Different filter cubes can be changed during specimen viewing to change the excitation wavelength, and a series of diaphrams can be used to modify the intensity of excitation.
When it comes to performing fluorescence microscopy, the fluorophore can be just as important as the microscope itself, and the type of fluorophore being imaged dictates the excitation wavelength used and emission wavelength that’s detected. The excitation wavelengths contain a small range of energies that can be absorbed by the fluorophore and cause it to transition into an excited state. Once excited, a wide range of emissions, or transitions back to the lower energy state, are possible resulting in an emission spectrum.
The difference between the peak of the absorption, or excitation curve and the peak of the emission curve is known as Stoke’s Shift. The greater the distance in this shift, the easier it is to separate the two different wavelengths. Additionally, any overlapping spectrum needs to be removed by the components of the filter cube for reduced background and improved image quality.
Exposure of the fluorophore to prolonged excitation will cause it to photobleach, which is a weakening or loss of fluorescence. To reduce photobleaching, you can add an anti-fade mounting medium to the slide and seal the edges with nail polish. The slide should also be kept in the dark when not being imaged.
To begin fluorescence imaging, turn on the xenon or mercury light source and allow it to warm up for as long as 15 minutes in order for it to reach constant illumination.
Next, place your sample on the stage and secure it in place. Then, turn on the white light source of your microscope. Focus on your sample using the lowest powered objective by adjusting the coarse and fine focus knobs. Then, use the stage adjustment knobs to find your area of interest.
Next, turn off the white light source, as well as any unnecessary room lights to reduce background.
Select the correct filter cube for the dye you are imaging and open the shutter to illuminate your sample.
Finally, make fine focus adjustments and direct the output light to the imaging camera. You will likely need to make adjustments to the exposure time for each different fluorophore or fluorescent dye used. However, it is important to keep the exposure time constant when comparing features with the same dye on different samples.
To image multiple dyes on the same sample, change the filter cube to match each fluorophore and record the new image.
After each dye in the sample has been imaged, individual images can be overlaid and merged.
Many different types of experiments can make use of fluorescent microscopy and involve different types of fluorophores One of the most common applications of fluorescent microscopy is the imaging of proteins that have been labeled with antibodies that are attached to, or “conjugated” to fluorescent compounds.. Here, an antibody towards leptospiral surface proteins was detected using a secondary antibody conjugated to alexafluor-488, which fluoresces green when excited.
Another way to highlight a specific feature with fluorescence is to integrate the code for a fluorescent protein such as green fluorescent protein, or GFP, into the DNA of an organism. The gene for GFP was originally isolated from jellyfish and can be expressed, or produced, by cultured cells in response to specific triggers or as part of a specific cell type like the tumor cells shown glowing in this image
Another application of fluorescence imaging is Fluorescence Speckle Microscopy which is a technology that uses fluorescently labeled macromolecular assemblies such as the F-actin network seen here, to study movement and turnover kinetics of this important cytoskeletal protein.
An advanced technique known as Fluorescence recovery after photobleaching, or FRAP, is performed by intentionally photobleaching a small region of a sample in order to monitor the diffusion rate of fluorescently labeled molecules back into the photobleached region.
You’ve just watched JoVE’s introduction to Fluorescence Microscopy.
In this video we learned about the concept of fluorescence, how fluorescence microscopy differs from light microscopy, and how to take a fluorescence image through the scope. We also learned about some basic and advanced applications that use fluorescence. Thanks for watching and don’t forget while photobleaching looks great on your teeth it’s not so good for your samples.
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Q1: What is fluorescence and how does it occur at the molecular level?
Fluorescence occurs when a fluorophore absorbs light at a specific wavelength, exciting an electron to a higher energy state. As the electron relaxes back to its ground state, it emits a photon of light at a longer wavelength and lower energy than the absorbed light. This emission enables visualization of fluorescently labeled structures in microscopy applications.
Q2: How does fluorescence microscopy differ from light microscopy?
Fluorescence microscopy combines magnification with fluorescence detection, requiring specialized components beyond traditional light microscopy. Key differences include a powerful xenon or mercury arc lamp that is 10-100 times brighter than incandescent sources, specialized exciter and barrier filters, and a dichroic mirror to separate excitation and emission wavelengths. These additions enable detection of fluorescently labeled molecules within cells and tissues.
Q3: What is Stokes Shift and why does it matter in fluorescence microscopy?
Stokes Shift is the difference between the peak absorption wavelength and the peak emission wavelength of a fluorophore. A larger Stokes Shift makes it easier to separate excitation and emission wavelengths using filters, reducing background noise and improving image quality. This separation is critical for obtaining clear fluorescent images without contaminating light from the microscope components.
Q4: What causes photobleaching and how can you prevent it?
Photobleaching occurs when prolonged excitation weakens or eliminates a fluorophore's ability to fluoresce. To reduce photobleaching, add anti-fade mounting medium to slides and seal edges with nail polish. Additionally, keep slides in the dark when not being imaged to minimize unnecessary light exposure and preserve fluorescence intensity for accurate imaging.
Q5: What are the main components of a fluorescence microscope and their functions?
The exciter filter selects the excitation wavelength, the dichroic mirror reflects excitation light toward the sample while allowing emission light to pass through, and the barrier filter selects emission wavelength while blocking contaminating light. These three components can be assembled into a filter cube, which can be changed during imaging to accommodate different fluorophores and their specific wavelength requirements.
Q6: How do you prepare and image a fluorescence microscopy sample?
Allow the xenon or mercury light source to warm up for 15 minutes to reach constant illumination. Place the sample on the stage and focus using the lowest objective. Turn off room lights to reduce background, select the appropriate filter cube for your fluorophore, and open the shutter to illuminate the sample. Adjust exposure time as needed, keeping it constant when comparing samples with the same dye.
Q7: What are common methods for labeling samples in fluorescence microscopy?
Common labeling methods include conjugating fluorescent compounds to antibodies that target specific proteins, integrating fluorescent protein genes like GFP into organism DNA for expression in specific cell types, and labeling macromolecular assemblies such as the F-actin cytoskeletal network. Each method enables visualization of different cellular structures and molecular components for research and diagnostic applications.
Chapters in this video
0:00
Introduction to Fluorescence Microscopy
1:19
Principles and Components of the Fluorescent Microscope
2:21
Basic Principles of Fluorescence Microscopy
5:25
Fluorescence Microscopy Imaging
6:59
Applications
8:45
Summary
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