Inverted Fluorescent Microscope – Principle, Protocol, Parts, Uses

What is Inverted Fluorescent Microscope?

  • An inverted fluorescent microscope is a specialized tool used in scientific research to study specimens, particularly living cells, using fluorescence. What sets this microscope apart is its unique arrangement of components, which are positioned in an inverted manner compared to traditional microscopes.
  • The inverted fluorescent microscope shares many common parts with other microscopes but with a different configuration. In this microscope, the objective lenses are situated above the stage, while the condenser and the light source are positioned below the stage. This inversion allows the microscope to observe specimens, such as cells at the bottom of a petri dish or tissue cultures, with ease and convenience.
  • To illuminate the specimen, a halogen lamp is employed as the light source. The light enters the microscope and encounters a dichroic mirror, which reflects certain wavelengths while allowing others to pass through. Ultraviolet (UV) light is reflected upward to the specimen by the dichroic mirror. As the UV light interacts with the molecules in the specimen, it induces fluorescence, generating light at a specific fluorescent wavelength. This fluorescent light is then collected by the objective lens for further examination.
  • The inverted fluorescent microscope utilizes fluorescence to study specimens, specifically living cells in various contexts. By introducing fluorescent dyes, known as fluorophores, the microscope can selectively label molecules of interest. These fluorophores absorb light at a specific excitation wavelength and subsequently emit light at a longer emission wavelength. This technique enables researchers to identify different fluorescent molecules simultaneously, even at low concentrations, making it a powerful tool in scientific investigations.
  • The halogen lamp in the microscope serves a dual purpose: it acts as both the excitation light source and the illuminator for the sample. The same objective lens that detects the emitted light from the specimen also delivers the excitation light. To eliminate interference from the excitation light, a fluorescence filter cube is employed. This cube separates the light based on its wavelength, allowing only the emitted light to be imaged and analyzed.
  • In summary, an inverted fluorescent microscope is a specialized instrument used in scientific research to study specimens, particularly living cells, through the use of fluorescence. Its inverted arrangement of components facilitates the observation of samples at the bottom of containers such as petri dishes. By utilizing fluorescent dyes, researchers can selectively label molecules of interest and study their behavior, allowing for detailed investigations and discoveries in the field of biological research.

Principle of Inverted Fluorescent Microscope

The principle of an inverted fluorescent microscope lies in its ability to utilize fluorescence to visualize and study specimens, particularly living cells. This unique microscope operates based on several key principles.

To begin, a halogen lamp serves as the primary light source for illuminating the specimen. The light emitted by the halogen lamp enters the microscope and encounters a dichroic mirror. This mirror possesses the property of selectively reflecting specific wavelengths of light while allowing others to pass through. As a result, certain wavelengths, including ultraviolet (UV) light, are reflected upwards towards the specimen by the dichroic mirror.


Upon reaching the specimen, the UV light interacts with the molecules present, inducing a phenomenon known as fluorescence. This means that the molecules within the specimen absorb the UV light and subsequently emit light at a specific fluorescent wavelength. The fluorescent light emitted by the specimen is then collected by the objective lens of the microscope. The objective lens plays a crucial role in focusing and magnifying the fluorescent light emitted by the specimen.

To further refine the fluorescence imaging process, the emitted fluorescent light travels through another dichroic mirror and an emission filter. The dichroic mirror separates the fluorescent light from any residual excitation light, ensuring that only the emitted light is directed towards the eyepiece. The emission filter further eliminates any unwanted wavelengths, allowing only the fluorescent light of interest to pass through.


Finally, the fluorescent light, filtered and refined, reaches the eyepiece of the microscope, where it forms a visual representation or image of the targeted specimen. This image can then be observed, analyzed, and captured for further examination or documentation.

In summary, the principle of an inverted fluorescent microscope revolves around the use of fluorescence to visualize specimens, particularly living cells. By utilizing a halogen lamp as the light source, specific wavelengths, including UV light, are directed towards the specimen through a dichroic mirror. The UV light induces fluorescence in the molecules of the specimen, resulting in the emission of fluorescent light. This emitted light is collected by the objective lens, and after passing through additional optical components such as a dichroic mirror and an emission filter, it reaches the eyepiece, forming a visual representation of the specimen.


Parts of Inverted Fluorescent Microscope

The inverted fluorescent microscope comprises several essential components that facilitate the observation and analysis of specimens. These parts are strategically arranged to accommodate the inverted configuration of the microscope. Here are the key parts of an inverted fluorescent microscope:

  1. Stage: The stage is a flat surface where the specimen is positioned. It is typically constructed of glass or metal and often features a gridded surface to assist with specimen positioning.
  2. Objective Lenses: The objective lenses are situated beneath the stage and serve to magnify the image of the specimen. In an inverted fluorescent microscope, there are typically 4-6 objective lenses, each with varying magnification powers to allow for versatile observation.
  3. Eyepiece: Located at the top of the microscope, the eyepiece is used to view the magnified image of the specimen. Most inverted fluorescent microscopes have a single eyepiece, although some models offer dual eyepieces for stereo viewing.
  4. Condenser: Positioned below the stage, the condenser is responsible for focusing the light onto the specimen. It commonly includes an iris diaphragm that can be adjusted to regulate the amount of light reaching the specimen, enhancing image clarity and contrast.
  5. Light Source: The light source is typically situated above the stage and functions to illuminate the specimen. In the case of inverted fluorescent microscopes, a halogen lamp is frequently used as the primary light source.
  6. Dichroic Mirror: The dichroic mirror is located between the condenser and the objective lenses. Its role is to reflect light of a specific wavelength (the excitation wavelength) downward to the specimen, while allowing light of other wavelengths (the emission wavelengths) to pass through to the eyepiece or camera.
  7. Excitation Filter: Positioned in the light path above the dichroic mirror, the excitation filter blocks all light except for the excitation wavelength required for the specific fluorophore under investigation. It ensures that only the desired excitation light reaches the specimen.
  8. Emission Filter: Placed in the light path below the dichroic mirror, the emission filter blocks all light except for the emission wavelengths emitted by the fluorophore. This filter allows only the fluorescent light of interest to be transmitted to the eyepiece or camera for observation.
  9. Camera: An inverted fluorescent microscope may be equipped with a camera that can be attached to the microscope to capture images or record videos of the specimen. This enables documentation and further analysis of the observed fluorescence patterns.

In addition to these fundamental components, some inverted fluorescent microscopes may incorporate additional features such as a motorized stage, which enables precise and smooth specimen movement for alignment with the objective lenses, a computer interface for controlling microscope settings and displaying images on a computer monitor, and specialized software programs for image analysis and measurement of cell size and shape.


By utilizing these parts and their specific arrangement, the inverted fluorescent microscope enables researchers to explore and study fluorescent specimens in various biological and biomedical applications.

Protocol of Inverted Fluorescent Microscope

To effectively utilize an inverted fluorescent microscope, a protocol is followed to ensure proper setup and observation. Here is a step-by-step guide outlining the protocol for using an inverted fluorescent microscope:

  1. Preparation: Place the microscope on a stable and solid table or surface. Ensure that the power supply is readily available and turn on the power button of the microscope.
  2. Specimen Placement: Insert the slide or glass container containing the specimen onto the specimen stage of the microscope. Ensure that the specimen is properly positioned and secured on the stage for stability during observation.
  3. Stage Adjustment: Keep the specimen stage stationary and adjust the position of the stage knobs to center the specimen. Use the coarse adjustment knobs to bring the specimen into rough focus initially.
  4. Focus Adjustment: Use the fine adjustment knobs on the objective and condenser lenses to refine and fine-tune the focus of the specimen. Make small adjustments until the image becomes clear and in focus. Pay attention to the different magnification levels offered by the objective lenses and choose the appropriate one for the desired level of detail.
  5. Observation: Once the specimen is in focus, the image can be observed through the ocular lens (eyepiece) or displayed on a connected computer screen if the microscope is equipped with a camera and digital imaging system. Adjust the eyepiece or camera settings for optimal image quality and clarity.
  6. Additional Observations: If required, adjust the illumination intensity using the brightness control of the light source. This can help enhance the visibility of the fluorescence signals emitted by the specimen.
  7. Image Capture and Analysis: If desired, capture images or record videos of the observed fluorescence patterns using the camera connected to the microscope. These images can be further analyzed and processed using specialized software for measurements, annotations, or additional image enhancements.
  8. Cleaning and Maintenance: After completing the observation, ensure that the microscope is turned off and disconnected from the power supply. Clean the objective lenses and any other optical components with lens cleaning paper or a gentle lens cleaner solution to remove any residue or debris. Properly store the microscope to protect it from dust or damage.

By following this protocol, users can effectively set up and operate an inverted fluorescent microscope, enabling them to visualize and analyze fluorescent specimens with precision and accuracy.

Applications of Inverted Fluorescent Microscope

The applications of an inverted fluorescent microscope are diverse and span various scientific disciplines. Some notable applications include:

  1. Cell Biology and Microbiology: Inverted fluorescent microscopes are widely used in cell biology and microbiology research. They allow for the visualization and examination of living cells and microscopic organisms in their natural environment. By labeling specific cellular components or molecules with fluorescent markers, researchers can study cell behavior, intracellular processes, and microbial interactions.
  2. Tissue Culture and Live Cell Imaging: Inverted fluorescent microscopes are particularly useful for observing cells cultured in vitro. They enable researchers to monitor cell growth, viability, and behavior over time. The microscope’s inverted configuration allows for easy access to cells at the bottom of culture vessels like tissue culture flasks and Petri dishes.
  3. Cancer Research and Drug Development: In cancer research, inverted fluorescent microscopes are used to study cellular processes involved in tumor development and progression. Researchers can visualize fluorescently labeled cancer cells, track their behavior, and assess drug responses. This information aids in drug development, evaluating drug efficacy, and understanding cellular mechanisms involved in cancer.
  4. Infectious Disease Studies: Inverted fluorescent microscopes play a vital role in studying infectious diseases and pathogenic microorganisms. They are used to investigate host-pathogen interactions, microbial colonization, and invasion mechanisms. By labeling pathogens or host cells with fluorescent markers, researchers can track infection routes, understand microbial behavior, and develop strategies for disease prevention and treatment.
  5. Micromanipulation and Microinjection: Inverted fluorescent microscopes allow for precise micromanipulation and microinjection techniques. Researchers can manipulate individual cells or subcellular structures using specialized tools, such as microinjectors or micropipettes, guided by the microscope’s imaging capabilities. This facilitates a wide range of applications, including cell sorting, genetic modification, and cellular reprogramming.
  6. Nanoparticle and Drug Delivery Studies: Inverted fluorescent microscopes are utilized in the field of nanomedicine to study nanoparticle behavior and drug delivery mechanisms. By labeling nanoparticles or drugs with fluorescent markers, researchers can track their cellular uptake, distribution, and release patterns. This information contributes to the development of targeted drug delivery systems and improved therapeutic strategies.

In summary, the inverted fluorescent microscope finds application in various scientific domains, including cell biology, microbiology, cancer research, infectious diseases, nanomedicine, and micromanipulation. Its ability to visualize and analyze fluorescently labeled specimens provides valuable insights into cellular processes, disease mechanisms, drug interactions, and nanomaterial behavior, ultimately advancing scientific knowledge and technological advancements in these fields.

Advantages of Inverted Fluorescent Microscope

The inverted fluorescent microscope offers several advantages that make it a valuable tool in scientific research. Here are the key advantages of using an inverted fluorescent microscope:

  1. Large Stage: The inverted design of the microscope provides a spacious stage, allowing for the observation of specimens in glass tubes, Petri dishes, and other larger vessels. This feature enables researchers to examine cells and tissues within their native environment, accommodating a wide range of sample sizes and formats.
  2. Sterility Maintenance: With the objective lens located above the stage, the inverted fluorescent microscope minimizes the risk of specimen contamination. The specimen remains untouched by the objective lens, ensuring its sterility and preserving the integrity of the sample for further analysis or experimentation.
  3. Versatile Specimen Holders: The microscope offers multiple specimen holders to accommodate different types of samples. These holders provide stability and ease of positioning, facilitating the observation of various specimens, including cell cultures, tissue sections, and other complex samples.
  4. Enhanced Imaging Techniques: In addition to fluorescence microscopy, the inverted microscope can be equipped with other advanced imaging techniques such as differential interference contrast (DIC) and phase-contrast optics. These techniques improve image quality by enhancing contrast and revealing fine details of the specimen, making it a versatile tool for various research applications.
  5. Compatibility with Digital Recording: The inverted fluorescent microscope can be easily connected to a wide range of digital recording devices, such as cameras and imaging software. This allows for the capture and documentation of high-resolution images or videos, facilitating data analysis, sharing, and publication.
  6. Wide-Field Eyepieces: The microscope is equipped with wide-field eyepieces that provide clear and detailed images. The fine focusing capability allows for precise adjustment, enabling researchers to visualize and examine minute details with ease. Additionally, the use of simple, achromatic objectives with a long working distance eliminates the need for a cover glass, ensuring a large view field and minimizing potential image distortions.

In summary, the inverted fluorescent microscope offers significant advantages over other microscope designs. Its large stage, versatility in specimen holders, sterility maintenance, compatibility with various imaging techniques and digital recording devices, and the use of wide-field eyepieces contribute to its superiority in visualizing and analyzing specimens in their native environments. These advantages make the inverted fluorescent microscope a valuable tool in a wide range of research fields, including cell biology, microbiology, cancer research, and drug discovery.

Limitations of Inverted Fluorescent Microscope

While the inverted fluorescent microscope offers significant advantages, it also has certain limitations that researchers should consider. Here are the key limitations of using an inverted fluorescent microscope:

  1. Photobleaching: One of the primary limitations of fluorescence microscopy is photobleaching. Photobleaching refers to the loss of fluorescence intensity and capacity of fluorophores when exposed to light. This phenomenon limits the duration for which a sample can be effectively observed using fluorescence microscopy. To mitigate photobleaching, researchers can employ more robust fluorophores, reduce the intensity of the light source, and use photoprotective scavenger chemicals.
  2. Limited Penetration Depth: Inverted fluorescent microscopes are designed for the observation of thin specimens or samples at the surface of culture vessels. The limited penetration depth restricts the ability to image specimens located deeper within thick tissues or complex samples. For such applications, other imaging techniques like confocal microscopy or multiphoton microscopy may be more suitable.
  3. Challenging Imaging of Thick Samples: Due to the inverted configuration, imaging thick samples or three-dimensional structures can be challenging with an inverted fluorescent microscope. The necessity of focusing through a significant depth of the specimen can lead to decreased image quality and reduced resolution. Techniques like optical sectioning or Z-stack imaging may be required to overcome this limitation and obtain accurate three-dimensional information.
  4. Expensive Equipment and Maintenance: Inverted fluorescent microscopes can be more expensive than traditional upright microscopes due to their specialized design and functionality. Additionally, the maintenance and care of the microscope, including cleaning objectives and replacing bulbs, can be cost-intensive and time-consuming.
  5. Limited Compatibility with Certain Techniques: While inverted fluorescent microscopes are compatible with various imaging techniques, such as phase contrast and DIC, they may have limitations when it comes to certain specialized techniques or accessory attachments. Compatibility with advanced imaging modalities like super-resolution microscopy or total internal reflection fluorescence microscopy may vary depending on the specific microscope model and setup.
  6. Higher Sensitivity to Vibration: Inverted fluorescent microscopes, particularly those used for live-cell imaging, are more sensitive to vibrations compared to traditional upright microscopes. Vibrations can introduce unwanted artifacts and affect image quality, requiring careful isolation and stabilization of the microscope setup to minimize disturbances.

In summary, while the inverted fluorescent microscope offers significant advantages in fluorescence microscopy, it also has limitations to consider. Photobleaching, limited penetration depth, challenges with imaging thick samples, higher equipment costs and maintenance, limited compatibility with certain techniques, and sensitivity to vibrations are important factors to be aware of when using an inverted fluorescent microscope for research purposes. Understanding these limitations helps researchers make informed decisions and overcome potential challenges during experimental design and data interpretation.

Precautions of Inverted Fluorescent Microscope

When working with an inverted fluorescent microscope, it is important to follow certain precautions to ensure safety and maintain the functionality of the instrument. Here are the key precautions to keep in mind:

  1. Power Safety: Turn off the power of the microscope during installation, assembly, cable connection/disconnection, and maintenance procedures. This minimizes the risk of electric shock or damage to the microscope components.
  2. Avoid Spills: Be cautious of wet or spilled substances around the microscope. Liquids can damage the internal components, lead to malfunctions, or cause the device to overheat. Clean up any spills immediately and ensure a dry working environment.
  3. Proper Handling: When carrying the microscope, hold it firmly by the bottom front recess and the bottom rear recess. This ensures a secure grip and prevents accidental drops or damage to the microscope.
  4. Prevent Scratches: Take care to prevent scratches on optical components such as lenses and filters. Scratches can affect the focus and clarity of the microscopic image. Handle the microscope with care and avoid contact between the lenses and any abrasive surfaces.
  5. Proper Disposal: Dispose of contaminated slides or samples according to the established procedures in your facility. Adhere to the appropriate guidelines and regulations for the disposal of biohazardous materials to prevent contamination and maintain safety.
  6. Environmental Conditions: Place the microscope in an area with a suitable temperature range of 0 to 40°C and a relative humidity of 85% or less. Extremes of temperature or humidity can affect the performance and longevity of the microscope. Maintain a controlled environment to ensure optimal conditions for operation.
  7. Minimize Shocks and Vibrations: Avoid subjecting the microscope to physical shocks or vibrations. Even small shocks can degrade the accuracy and alignment of the microscope components. Handle the instrument gently and take precautions to prevent unnecessary impacts or vibrations.

By following these precautions, users can ensure the safe and reliable operation of the inverted fluorescent microscope while minimizing the risk of damage or injury. It is important to prioritize safety, handle the microscope with care, and maintain a suitable working environment for optimal performance.


What is an inverted fluorescent microscope?

An inverted fluorescent microscope is a type of microscope that is designed with an inverted configuration, meaning the objective lenses are located below the stage. It is specifically used for fluorescence microscopy, allowing the observation and analysis of fluorescently labeled specimens, such as living cells, in their natural environment.

What are the advantages of using an inverted fluorescent microscope?

Some advantages of using an inverted fluorescent microscope include its ability to observe specimens in larger vessels, compatibility with different specimen holders, maintenance of specimen sterility, compatibility with advanced imaging techniques, such as phase contrast and DIC, and the option to connect digital recording devices for image and video capture.

What are the limitations of an inverted fluorescent microscope?

Limitations of an inverted fluorescent microscope include photobleaching of fluorophores, limited penetration depth for thick samples, challenges in imaging three-dimensional structures, higher equipment costs and maintenance, limited compatibility with certain techniques, and sensitivity to vibrations.

What types of samples can be observed with an inverted fluorescent microscope?

An inverted fluorescent microscope is suitable for observing a wide range of samples, including live cells in culture, tissue sections, microbial cultures, and fluorescently labeled specimens in various biological and biomedical applications.

Can an inverted fluorescent microscope be used for live-cell imaging?

Yes, inverted fluorescent microscopes are commonly used for live-cell imaging. The inverted configuration allows easy access to observe and monitor living cells in culture vessels, such as Petri dishes or multiwell plates, providing researchers with real-time insights into cell behavior and dynamics.

How can photobleaching be minimized with an inverted fluorescent microscope?

Photobleaching can be minimized by using more robust fluorophores, reducing the intensity of the light source, adjusting exposure times, and using photoprotective scavenger chemicals. Careful optimization of imaging parameters and acquisition settings can help minimize photobleaching and extend the observation time of fluorescently labeled samples.

How does an inverted fluorescent microscope work?

An inverted fluorescent microscope works by illuminating the specimen with a light source, typically a halogen lamp. The light passes through a series of filters, including excitation and emission filters, to selectively excite and capture the emitted fluorescence from the specimen. The fluorescent light is then collected and observed through the objective lenses, providing detailed imaging and analysis of the specimen.

Can an inverted fluorescent microscope be used for other imaging techniques besides fluorescence microscopy?

Yes, an inverted fluorescent microscope can be used for other imaging techniques, such as phase contrast, DIC (differential interference contrast), and brightfield microscopy. These techniques allow for visualization and analysis of samples without the need for fluorescent labeling.

What are some practical applications of an inverted fluorescent microscope?

Inverted fluorescent microscopes have diverse applications in various fields, including cell biology, microbiology, cancer research, drug development, infectious disease studies, nanomedicine, and micromanipulation. They are used for studying cellular processes, host-pathogen interactions, tumor biology, drug delivery mechanisms, and more.

What are the maintenance requirements for an inverted fluorescent microscope?

Maintenance requirements may include regular cleaning of optical components, such as lenses and filters, to ensure optimal imaging quality, as well as routine checks for proper alignment and functionality of the microscope. It is also important to follow the manufacturer’s guidelines for bulb replacement and general care of the microscope to prolong its lifespan and performance.


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  2. Sun, Y., Wang, D., Ma, Y., Guan, H., Liang, H., & Zhao, X. (2019). Elucidating Escherichia Coli O157:H7 Colonization and Internalization in Cucumbers Using an Inverted Fluorescence Microscope and Hyperspectral Microscopy. Microorganisms, 7(11), 499.

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