Microscopy: a picture is worth a thousand words


People say that a picture is worth a thousand words, and for life sciences this certainly has been true since the invention of a microscope. This resource will guide you through the fascinating field of light microscopy, starting with the basics and ending with the recent Nobel prize-winning advancements. Note that we will not cover any other forms of microscopy, such as electron or atomic force microscopy. Although they have also been extremely illuminating in our quest to understand life, especially in the last few decades, the huge advantage of light microscopy is its minimal effect on the object under study, which makes it the only technique suitable for observing living cells.

This resource includes material not only within the realm of biology. To properly understand microscopy, physics and chemistry have to be touched upon as well. This is an evident trend in modern sciences: after branching out from natural philosophy and isolating themselves for a while, they are now coming back together. Therefore, to understand the world, it is important to keep your mind open to knowledge of any kind. I hope you will enjoy this resource and will fall in love with microscopy just as I did.


The light microscope was in my opinion the single most important invention for the field of life sciences, which enabled us to understand how living systems work. The idea of using glass to magnify objects is very old - the oldest lens was found in the archaeological excavations of the Assyrian city of Nimrud and is believed to have been made between 750 and 710 BC. It took about two thousand years (at least in Europe) to go from that rough piece of thick glass to glasses, which became widely used for eyesight correction in the XIII century. Finally, after another four hundred years, the first microscopes were made in the beginning of XVII century more or less simultaneously by the Dutch spectacle-maker Zacharias Janssen, the Dutch inventor Cornelis Drebbel and the famous Galileo Galilei, whose friend Giovanni Faber coined the term "microscope".

This invention was a bomb for the scientific and even general educated public of the time, and amazing discoveries started pouring from this horn of plenty. The English polymath Robert Hooke was the first to propose that living organisms are made of tiny compartments, which he saw when observing the cross-section of cork tree under a microscope and called cells. The Dutch Antonie van Leeuwenhoek became the "mad genius" in the field. Although his initial interest was in studying the structure of fabric to examine its quality for his draper shop, he soon developed a method to craft very small, round and smooth lenses. This enabled him to make an astonishing number of discoveries, ranging from the existence of microbes to the sperm cells and red blood cells. Since he did not want to share his secret with anyone, his discovery of single-celled organisms was received with suspicion at first, but in the end the scientific community had to accept his work, and he even became a member of the Royal Society.

In the following centuries, microscopes were perfected until they reached the absolute resolution limit of light microscopy, which we will cover in the first activity. They became widespread, with scientists applying them to study small animals, plant and animal tissue slices (histology), individual cells of multi-cellular organisms, single-celled eukaryotes and prokaryotes. A new era in microscopy began with the invention of fluorescence microscopy in the beginning of the last century, which will be the topic of the second activity. In the following decades, scientists used it to understand molecular details of the inner world of the cells, as well as their interactions and organisation within organisms. Furthermore, both conventional and fluorescence microscopy also became important medical tools, used to diagnose and monitor infectious diseases, cancer, neurodegenerative diseases and others. Nowadays, light microscopy, despite being about 350 years old, is still blooming, and novel approaches, which we will discuss in the last activity, continue to expand the boundaries of our knowledge.

Let's begin our journey by taking a little quiz, and you can retake it after you go through the activities.

What can you see in a light microscope?

  • HIV virus particle
  • Atoms of carbon in human cells
  • Which neuron is active in the brain of a living mouse
  • Two proteins interacting with each other
  • Smallest cells in the world

The videos below relate to the activity sheets so download these first before watching.

Activity 1- The Resolution Limit of Light Microscopy - YouTube

Activity 2- Immunoflurescence - YouTube

Video Resource

Video Resource

Resource activities

Activity 1: Microscopy basics

This activity will introduce you to the field of microscopy. We will explore the inner workings of a typical light microscope and the principles of image formation within it, alongside the key concepts of contrast and resolution.


Activity 2: Fluorescence Microscopy

Fluorescence microscopy is perhaps the most important and widely used microscopy technique in modern molecular and cell biology. In this activity, we will learn what fluorescence is and how a fluorescence microscope works. We will then touch upon the vast variety of ways that fluorescence microscopy is used in biology.


Activity 3: Frontiers in light microscopy

The final activity will give you a taste of the capabilities of modern microscopy that the early pioneers could not even dream of. We will look in detail at two amazing techniques that are currently revolutionising the respective fields: super-resolution microscopy and miniature microscopes.


Activity questions

  • Explain the concepts of contrast and resolution. How is contrast generated in microscopy? How is resolution different from magnification, and why is there a fundamental limit for it?
  • What advantages does fluorescence microscopy offer compared to conventional methods?
  • What is the general principle of single-molecule localisation microscopy?
  • How are miniscopes able to image deep within optically dense tissues, such as brain? What possible applications does the miniscope approach open?

Reflective questions

To answer and record these questions you will need to have an account and be logged in.

Task 1

What are the key arguments, concepts, points contained within it?

Task 2

What are you struggling to understand?

What could you do to improve your understanding of these concepts/terminology etc.?

Task 3

What further questions has this resource raised for you?

What else are you keen to discover about this topic and how could you go about learning more?

Can you make any links between this topic and your prior knowledge or school studies?

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Further reading

  • Nikon's MicroscopyU Educational Resource

    A great resource for basic and advanced topics in microscopy.

  • The Carl Zeiss Microscopy Online Campus

    Another comprehensive resource for learning more about microscopy.

  • iBiology

    A stunning collection of rather in-depth talks on very different areas of biology by the world's leading experts. For the topics discussed here, check for example "Miniature Microscopes for Deep Tissue Imaging", "Super-Resolution: Localization Microscopy" or "Breakthroughs in Intracellular Fluorescent Imaging".

  • AK Lectures

    A library of free lectures, explaining scientific topics on the high school and undergraduate level. It is not directly relevant to microscopy, but it can be a great aid in understanding the necessary auxiliary topics, such as optics.

  • The Derm Review - Resource Guide on Anatomy, Biology and Structure of the Skin

    This guide highlights the anatomy, physiology of the skin, crossword puzzles, and skin lessons for kids to name a few.