5 Ways to Make Fluorescence Microscopy A More Approachable Topic

Akanksha Saxena

Introduction: Fluorescence Microscopy

Among the most groundbreaking discoveries in the history of science, one highly regarded one is “Microscopy”. The way this technique of visualizing objects at the microscopic level works has amazed students and scientists alike over the years. There is a range of different microscopy techniques that have been developed for different uses and better resolving powers.

Fluorescence microscopy is one such amazing technique.

It shows the phenomenon of fluorescence whereby light of a particular wavelength holds the capability to excite the electrons of a substance to higher states. When those electrons return to their normal state, they display the phenomenal event of fluorescence.

Based on this event, traditional microscopy has been advanced to fluorescence microscopy. When the pictures and snapshots of the first fluorescently-tagged cells or cell organelles are shown to students, it counts as one of the most spellbound moments of their academic journey.

The technique becomes troublesome and mechanical when the theory of this topic is taught in class. Educators face trouble keeping the students actively engaged and interested in learning the handling of this microscopy technique. 

Lack of a deeper understanding of how a fluorescence microscope is built, its primary components and their respective roles, the optimization, and calibration of the instrument, etc are some topics that students tend to fear a lot. 

Read on to learn more about how you can ease the process of explaining the fluorescence microscopy technique to students in your next class. We try to highlight all the issues encountered by students when dealing with different aspects of this topic. We also list some practical solutions to solve the same. By the end, we’ll convince you why a virtual lab simulation will prove useful not only for your students but also for you as an educator to deliver concepts more efficiently.

3 reasons why Fluorescence Microscopy can be tricky to teach or learn

There are 3 reasons why students sometimes struggle with the topic of the Fluorescence Microscopy technique. Acknowledging these issues is the first step toward making the topic more approachable. 

1. Confusion in basics

This is the most common reason why students confuse this microscopy technique with the others. Not knowing how the sample is specifically prepared for this technique and how the basic phenomenon of fluorescence works could be possible hurdles. Many students fail to comprehend the reason and rationale behind excitation and emission spectrums. They don’t understand basic physics topics like the “energy states of electrons” of an atom. To explain to them how electrons go from a lower energy state to a higher energy state and emit fluorescence while returning to a lower energy state is an ignored job by many teachers. This eventually portrays challenges when the working of this microscope is perplexing for half of the class.

2. Too many details

Fluorescence microscopy is no doubt a complex and technical topic for high school students. The basic principles and practical aspects of this microscopy are quite different and new to students who have dealt only with a light microscope in their lab sessions. There are too many components that need to be in sync to produce a highly resolved image. There are several available options for fluorophores amongst which we have to choose the best one. There are some limitations of this technique that need to be calculated against the benefits and accordingly the technique’s use has to be determined.  There are specific intricacies with the sample preparation and staining in this technique. 

3. The dearth of demonstrations and visualization tools

Since fluorescence microscopes are quite costly, they aren’t always available to students in academic setups. This makes the classes too theoretical with no interesting activity. Students are expected to remember all the details without ever seeing or handling the instrument. This demotivates them to learn the techniques and deprives them of knowing its potential use in their work. Further, there aren’t many video or visual tools at the teacher’s disposal to demonstrate the technique to students. 

5 ways to make Fluorescence Microscopy a more approachable topic to understand

To address the blocks encountered while teaching the Fluorescence Microscopy technique, educators can engage the under-listed solutions in their classes. These can clarify many instrumental aspects of the technique and its operation. Not only can they make teaching easier for educators like you but will also make lessons clearer and easier to assimilate for your students.

1. Chalk out the most important aspects of fluorescence microscopy

A systematic and methodical introduction to a technique is the best way to engage participation in classroom teaching and inculcate the habit of critical thinking in students. The same applies to this topic of fluorescence microscopy. Educators should try to start with the basics and then advance to the complexities of the technique. 

  • Explaining the different parts of a fluorescence microscope could be a good starting point. 
  • Explain to your students the similarities and dissimilarities of fluorescence microscopes to a light microscope that can open the horizons of critical thinking skills.
  • Explain the concept of wavelengths, visible light spectrum, excitation versus emission spectrums, energy states of electrons, fluorescence and phosphorescence phenomena, etc to strengthen their basic understanding.

Handling the core concepts well is the first and the most important step in building a good understanding of this technique amongst your students. 

Natural fluorescence phenomenon virtual lab

Figure: An image from the Fluorescence Microscopy simulation by Labster demonstrating the role of different parts of the microscope. Full simulation is available for High School, Professional, and University / College classes. 

2. Simplify the instrument’s structure, staining, and underlying principle

Structure: Knowing the names of the different parts of an instrument is of no use if a student doesn’t know its role in the functioning of the instrument. On the same note, teachers must educate their students about the overall functioning of the fluorescence microscope as they introduce the students to its specific parts. Explaining the importance of filters (excitation filter and emission filter), dichroic mirror, fluorophores, light source (laser), objective lens, eyepieces, and/or camera is crucial before teaching them the complex procedures using this technique.

Staining: Explaining the importance of the “optimal choice of fluorophores” is yet another instrumental aspect of teaching the topic in class.  Teachers should emphasize the fact that this choice depends on the ‘type of filters installed in the fluorescence microscope.

Microscopy 2

Figure: Display of vibrantly colored cells in the Microscopy simulation from Labster. You can see the different parts of a cell stained with different stains. The DAPI staining as demonstrated in the picture stains the nuclei in strong blue fluorescence. Image Source

Underlying principle: Explaining the importance of the natural fluorescence phenomenon that is exploited in this technique can be beneficial for students in the long term. You can quote examples of natural fluorescence occurrences like fluorescent marine organisms that can generate interest in your students to read beyond what is taught in class to them.


Figure: Natural fluorescence phenomenon as observed in fluorescent marine organisms. Image Source

3. Educate about its real-world applications

Educating your students about the real-world applications of fluorescence microscopy can fill them with enthusiasm while learning the tough aspects of the subject. This can render them with ideas to utilize the knowledge system that they are building today.

This is very underrated yet important advice as many students in their graduate research know the techniques but don’t know how and when to utilize them in their research work.

Some of the real-world applications of fluorescence microscopy are:

  • In microbial studies (for tagging very small living organisms)
  • For studying 3D structures with precision in cell biology
  • In immunology studies (for tagging antibodies and tracking them)
  • For studying the localization of small molecules in cells
  • For studying both live and dead (fixed) biological samples
  • For studying multiple features of a cell or tissue at once (tag with different fluorophores)
  • Tracking viruses in different parts (organs) of the human body 
Explore Fluorescence Microscopy Virtual Lab Simulation 2

Figure: An image from the Fluorescence Microscopy simulation from Labster demonstrating the use of the fluorescence microscopy technique to trace the location of the virus in the intestinal cells of chicken. Full simulation is available for High School, Professional, and University / College classes. 

4. Use more colorful visuals to show the power of fluorescence microscopy

Since fluorescence microscopy is a powerful technique to tag and differentiate between different cell organelles at once, using different types of fluorophores is recommended while practical lab handling. Now since the costs involved are high, we advise educators to incorporate more illustrations, flowcharts, and figures to entice the students with the splendid vibrancy of this technique. A few examples of fluorophores that can be introduced in the class are green fluorescent protein (GFP), red fluorescent protein (RFP), phycoerythrin, fluorescein, quantum dots, allophycocyanin, AMCA, and rhodamine. 

Fluorescence rainbow

Figure: Different fluorescent dyes used in fluorescence microscopy. Image Source

Explore Fluorescence Microscopy Virtual Lab Simulation

Figure: An  from the Fluorescence Microscopy simulation from Labster explaining the fluorescence phenomenon. Full simulation is available for High School, Professional, and University / College classes. 

5. Use virtual lab simulations

Since fluorescence microscopy is a broad topic with many intricacies from different types of fluorophores, different roles of specific parts of the instrument, different wavelengths of light used, etc, it can sometimes be difficult to demonstrate all of it in a single class. 

Even though educators and teachers are passionate to demonstrate these aspects fall short due to the multitude of practices in the techniques. Sometimes the lab and fund resources also restrict the demonstration of high-end fluorescence microscopy techniques. 

We, at Labster, understand these issues for educators like you. Therefore, we bring virtual laboratory simulations that can ease your process of lecture delivery as well as lab handling sessions. You can make more insightful points as students are rendered with better visual options. The 3D simulations help them better understand the intricacies of operating different types of microscopes. 

Your students don’t have to struggle to imagine different colors of fluorophores as our interactive Fluorescence Microscopy simulation along with gamification elements come to the rescue. By using this way of active and immersive teaching, our virtual learning platform takes an advent in the field of Science to make the upcoming scientists thorough with the “basics of their respective subjects”. 

Figure: An image from the Fluorescence Microscopy simulation from Labster. Full simulation is available for High School, Professional, and University / College classes.

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