How microscopes work
by Chris Woodford. Last updated: December 5, 2020.
The plant on your windowsill is buzzing with life, turning
sunlight into sugar all day long. Mold is slowly gobbling up the
apples in your fruit bowl. Your bed is creeping with dust mites. The
air is packed with pollen...
It's a truly amazing thought: there are
zillions of things happening all around us, all the time, that are
far too tiny for our eyes to see! But never fear, because we have an
equally amazing way to get around it. Powerful microscopes shed
new light on the teeny tiny and make the invisible, visible. They've
played an enormous part in science by taking us deep into worlds
we've come to think of as "microscopic." Just as telescopes scale
us up to meet the planets and stars, so microscopes scale us down
into the tiny world of atoms and cells. Let's
take a closer look at how they work!
Photo: This looks like an ordinary optical microscope, but it's
actually a fluorescence microscope (a Nikon Eclipse) designed to produce higher-contrast images.
Exactly how it works is described below. Photo by Stephen Ausmus courtesy of US Department of Agriculture: Agricultural Research Service (USDA-ARS).
Why do we need microscopes?
Photo: A scientist studies leaves for traces of ticks. Photo by Scott Bauer courtesy of
US Department of Agriculture: Agricultural Research Service (USDA-ARS).
Lots of things are invisible, but that doesn't mean they're not
there. Radio and TV broadcasts are constantly whistling through your
head from powerful transmitters, but unless you happen to have a
cunning piece of electronic equipment at your disposal—namely a
radio or TV
set—you won't be able to understand them. We're used to
the world being the totality of things we can see; that there are
worlds out there our eyes aren't tuned into is both a physical
problem and a philosophical conundrum.
Imagine if your eyes were as powerful as microscopes and you could
see all the germs crawling about on your hands. Your brain would be
so busy boggling that you wouldn't be able to concentrate on bigger
things at a more meaningful scale. Through millions of years of
evolution, our eyes and brains are programmed to worry about the
things that matter most—things on a similar scale to
our bodies. We simply don't have the time or the brain capacity to
worry about absolutely everything that's going on. If you were
constantly staring at the bugs on your fingers, you could easily get
so distracted that you'd walk straight under a bus!
Don't understand? Let's put it this way. The smaller
the things you look at, the more there is to see, the more information
there is to process, and the longer it takes. If you could see
microscopically all day long, you'd have to react much more slowly
to the world around you—and that extra reaction time would threaten your life.
This, then, is what invisible means: our bodies are finely tuned to the
business of day-to-day living on a human scale and efficiently designed to ignore
Once upon a time, we used to ignore things we couldn't see. But
thanks to modern science, we know there's a whole lot happening on
the microscopic scale that can help us to live our lives more
effectively. Scientists have known since the 17th century that the
insides of living things are made up of tiny functioning factories
called cells; understanding how they work helps us to tackle sickness
and disease. More recently, during the 20th century, scientists
figured out how materials are made of atoms and how atoms themselves
are built from smaller "subatomic" particles; understanding
atomic structure paved the way for all kinds of amazing inventions,
from electronic transistors to nuclear power.
How microscopes work
Photo: Most microscopes have several different objective lenses that turn around on a thumb-wheel to give different levels of magnification. Going from right to left, the lenses you can see here magnify by twenty times (20x), forty times (40x), and a hundred times (100x). Photo by Stephen Ausmus courtesy of
US Department of Agriculture: Agricultural Research Service (USDA-ARS).
Microscopes are effectively just tubes packed with lenses, curved
pieces of glass that
bend (or refract) light rays passing through them.
The simplest microscope of all is a magnifying glass made from a single convex lens, which
typically magnifies by about 5–10 times. Microscopes used in homes, schools, and professional laboratories are actually compound microscopes and use at least two lenses to produce a magnified image. There's a lens above the object (called the objective lens) and another lens near your eye (called the eyepiece or ocular lens). Each
of these may, in fact, be made up of a series of different lenses.
Most compound microscopes can magnify by 10, 20, 40, or 100 times, though professional ones can
magnify by 1000 times or more. For greater magnification than this, scientists generally use
Photo: Ordinary microscopes are "powered" by light. When light shines on the specimen at the bottom, it travels straight through or reflects off the surface, passing up through the lenses into the eyepiece. Microscopes that use light are called optical microscopes to distinguish them from electron microscopes, which use electrons for seeing instead of light. Photo by Peggy Greb courtesy of US Department of Agriculture: Agricultural Research Service (USDA-ARS).
So what does a microscope actually do? Imagine a fly sitting on the table in front of you. The big, fat, compound eye on the front of its head is just a few millimeters across, but it's made up of around
6000 tiny segments, each one a tiny, functioning eye in miniature. To
see a fly's eye in detail, our own eyes would need to be able to process
details that are millimeters divided into thousands—millionths of a
meter (or microns, as they're usually called). Your eyes may be good,
but they're not that good. To study a fly's eye really well, you'd
need it to be maybe 10–100 cm (4–40 in) across: the sort of size
it would be in a nice big photo. That's the job a
microscope does. Using very precisely made glass lenses, it takes the
minutely separated light rays coming from something tiny (like a fly's eye) and spreads
them apart so they appear to be coming
from a much bigger object.
Photo: An antique
Nachet polarizing microscope, based on a design invented in 1833. This one, dating from 1880, uses two light-polarizing (Nicol) prisms, one underneath the stage and the other in the eyepiece. Photo courtesy of National Institute of Standards and Technology Digital Collections, Gaithersburg, MD 20899.
As we've just seen, a basic optical microscope uses one or more lenses to bend the light bouncing off (or traveling through) a
specimen, so fooling our brains into thinking what we're looking at is bigger than it really is. But there are other kinds of optical microscopes that work in different ways.
Ordinary light consists of waves that vibrate in every direction. If we pass light like this through a grid-like
filter, so the waves can vibrate in only one direction (plane), what we get is called polarized light (or, sometimes,
plane-polarized light). If you shine polarized light through an ordinary piece of glass, it bends in the usual way
through the process of refraction (or refringence, as it was once known). We can compare the amount by which light bends in different materials using a measurement called the refractive index. (Refraction is explained in more detail in our main article about light.)
So far so good. But other solid materials, including ice, calcium carbonate, quartz, plastics (such as cellophane),
stressed plastics, and various other crystals, change light in different ways when it travels through them in different directions. If you pass light through these materials, something much more interesting happens: it splits into two separate waves that bend by different amounts. In other words, unlike glass (which has a single refractive index), these materials have two refractive indices; that's why this effect is called birefringence (in effect, double refraction). If you collect the two waves coming out of a birefringent crystal and pass them through another polarizing filter, called an analyzer, which is set up at right angles to the first polarizing filter, they recombine, interfere with one another, and produce colorful patterns that change as you rotate the specimen.
Photo: Photoleasticity means using polarized light to study the stress patterns in a material.
In this example, I'm making some polarized light using an ordinary LCD laptop
screen, passing it through a plastic CD case, and viewing the result through polarizing sunglasses.
Polarizing microscopes work in a broadly similar way.
Polarizing microscopes are based on this idea: they're much like ordinary optical microscopes but with polarizing filters fitted above and below the specimen. We can use them to study birefringence and other properties of materials, which can help us identify minerals or figure out important things about their inner structure. Polarizing microscopes have useful applications in:
- Geology—for example, studying the mineral components of a particular rock.
- Crystallography—for identifying crystals in everything from
forensic science to art conservation.
- Materials science—such as studying the stress on certain mechanical components
- Medicine—including urinalysis (diagnosing medical problems from the substances in
Seeing things under microscopes isn't just a matter of making them look bigger; a lot
of the time, the problem is making things stand out enough so we can see them at all. In other
words, it's a matter of improving the contrast in an image.
Photo: Increasing contrast makes it easier to see an object against its background and identify what it is from its key features ("specificity").
Optical microscopy uses all sorts of
tricks—chemical and physical—for achieving this.
If you've ever used a simple microscope at school, for example, you probably used chemical stains like iodine,
which turns carbohydrates a dark brown or black, or
methylene blue (C16H18N3ClS), which shows up the shape of bacteria by coloring acids inside them a deep shade of blue. As we saw up above, polarizing microscopes achieve colorful contrast with the help of
polarized light waves. And there's another very popular, contrast-improving technique in microscopy that relies
on fluorescence—the chemical trick pulled by creatures like fireflies.
Photo: Looking at a high-contrast image of an Indian meal moth caterpillar
using a fluorescence microscope. Fluorescence from the sample is picked up by an image sensor and displayed on a computer screen. Photo by Greg Allen courtesy of US Department of Agriculture: Agricultural Research Service (USDA-ARS).
In a fluorescence microscope (like the one in the top picture), we stain the specimen with a fluorescent dye,
and bombard it with light of a particular wavelength (usually from a mercury lamp). That makes the dye give off light of a different (longer and redder) wavelength by the process of fluorescence, which produces a high-contrast
image we can look at through conventional lenses (using special filters) or record with a camera (or a light-detecting image sensor).
Fluorescence microscopes are very widely used because they have greater contrast and sensitivity than ordinary
scopes, and they help pick out the unique, functional bits and pieces in microscopic
samples that make it easier to identify things (technically, this is called greater "specificity").
Artwork: How a fluorescence microscope works.
Light from a mercury arc lamp (1) passes through a filter (2) that selects
a particular wavelength we want to excite our sample.
The beam hits a dichroic mirror (3), which reflects certain wavelengths and allows
others to pass through, and bounces down onto our specimen at the bottom (4).
The specimen fluoresces and gives off a redder beam of light (5) that
passes back through the dichroic mirror (6) and a filter into our eyepiece or image sensor (7).
Even the best microscopes have their limits: most can't magnify
more than a few thousand times. Why? One way of understanding light is
to say that it's made up of energetic particles called photons,
which behave like waves hundreds of times thinner than a human hair. But what if we
want to look at things smaller than this? In that case, we can't use
light: we have to use particles with even smaller wavelengths—namely electrons,
the tiny negatively charged particles that whizz around inside
atoms. Microscopes that work in this way are called