Guide to Electron Microscope

Guide to Electron Microscope

If you are into microscopy at any level, you may have heard of electron microscopes. 

Electron microscopes are instruments that produce magnified images of objects using a beam of electrons.

While typical light microscopes use photons to collect data, these kinds of microscopes use electrons. 

Since electron microscopes are highly specialized pieces of machinery, they are very expensive and are uncommon to find in school classrooms and basic university laboratories. 

If you are interested in learning more about the topic, you have come to the right place.

This guide will cover everything you need to know about electron microscopes, including what they are and how they work. 

We will also describe what you can see with one of these instruments and explain how to use one.

Furthermore, find out what the different types of electron microscopes are and how they are used. 

Let’s get started.

What Is an Electron Microscope


An electron microscope is a type of microscope that uses electrons to produce a magnified image of a specimen. 

In these models, a beam of electrons replaces the job of an illuminator (a beam of light) that other common microscopes use, such as the compound microscope. 

In standard microscopes, particles called photons are responsible for collecting information about the specimen.

In electron microscopes, electrons take over this job and collect data about the composition and structure of the specimen to produce the final magnified image.

Electron microscopes can handle a much higher magnification level than other light microscopes.

While most light microscopes have a max of 20,000x, some electron microscopes can magnify an image up to 1,000,000x.

Due to the unique characteristics of electron microscopes, these machines produce images with much higher resolutions, making it easy to generate crisp images of small objects.

Many different scientific fields take advantage of this technology. Scientists use electron microscopes to study both non-biological and biological specimens.

People working in the biomedical research field use these instruments to study cells, organelles, tissue samples, and macromolecular structures.

How Does an Electron Microscope Work

How Does an Electron Microscope Work

At first glance, electron microscopes may look like extremely complicated machines.

However, the entire process only contains a few basic steps. Let’s take a look at how electron microscopes work. 

  • A stream of electrons is formed. The first step of the process involves a high voltage stream of electrons being formed. A component called a field emission or heated tungsten filament does this. After the machine forms the electrons, a vacuum accelerates them towards the specimen.
  • The microscope focuses the electrons into a thin beam. A series of parts, including magnetic lenses and metal apertures, focus the collection of electrons into a thin, neat beam of electrons. 
  • The beam hits the specimen. After the microscope converts the electrons into a thin beam, the magnetic lens then focuses that beam onto the specimen. 
  • The electrons and specimen interact. When the electrons hit the specimen, these two components interact and form data. 
  • The microscope collects the data and forms a final magnified image. Once the microscope processes the data, it can then produce the final image. The microscope typically sends this image to a computer.

What Can You See With an Electron Microscope


Electron microscopes are very powerful machines. Since they can support a magnification power of up to 1,000,000x, you will be able to study objects very close up with one of these microscopes. 

The first thing you will notice when viewing an electron microscope image is the lack of color. Particles called photons are responsible for generating color.

However, photons come from light, which is something that this kind of microscope does not use.

For this reason, the images that electron microscopes produce are black and white. 

Even though it does not support color images, you can see a high amount of detail with electron microscopes.

These models can magnify very small objects at incredibly high resolutions.

You can see and study things such as large molecules, biopsy samples, microorganisms, crystals, and metals.

One of the main attributes that differ an electron microscope from a light microscope is how much of the structure you can see.

With an electron microscope, you will be able to view the ultrastructure of a specimen. 

An ultrastructure refers to the internal structure of an organism that you can only view with an electron microscope.

A typical light microscope does not have the same power as an electron microscope and can not magnify a single specimen near as much.

With these instruments, you can view subcellular compartments and structures within various organisms, compared to simply viewing the surface or the main structure of a cell. 

How To Use an Electron Microscope

Electron microscopes are complex machines. Perhaps you will be working with one soon or are simply curious about how they work.

In this section, we will cover how to use an electron microscope. 

It is important to note that this guide should not be your sole source of instructions; each machine is different.

Furthermore, many institutions will require you to receive training before being able to handle this expensive and complex instrument.

Refer below for the basic steps of using an electron microscope.

  • Prepare your sample. The first thing you need to do is prepare and load your sample. The sample should be clean, dry, and securely attached to the aluminum stub. 
  • Let air into the vacuum chamber. After loading your sample, you will need to click on the “vent” button on the computer. This action will let air into the vacuum chamber.
  • Open the chamber door and load your specimen. Once the venting process is complete, open the chamber door and load your specimen onto the sample holder.
  • Hold the chamber door closed and hit the “pump” button. After you load and adjust the height of the sample, click the “pump” button and hold the chamber door closed.
  • Choose a detector. After the microscope has finished the pumping process, choose a detector. The most common detector is “SE.”
  • Choose an accelerating voltage. You will have a few options when it comes to voltage. The correct voltage will depend on what material your specimen is. 
  • Choose a spot size. The lower the spot size you choose, the more detail and noise you will see. Five is generally a good spot size to start with. 
  • Turn the beam on and focus your sample. After setting your voltage and spot size, turn the beam on and focus the image of your specimen. 
  • Adjust the focus and scan rate. After seeing the image on the screen, take a few moments to adjust the focus to get the clearest image possible. You should also choose whether you want a slow or fast scan rate to scan the image and find areas of interest. 
  • Turn the electron beam off and vent the chamber. After studying the image, make sure to turn the electron beam off and vent the microscope’s vacuum chamber. Remove the sample after you do this, and click the “pump” button to return the chamber to normal. 

Types of Electron Microscopes

Types of Electron Microscopes

A few different kinds of electron microscopes include transmission electron, scanning electron, and reflection electron microscopes. 

In this section, we will briefly explain each type of electron microscope and what researchers use them for.

Transmission Electron Microscopes

Transmission electron microscopes work best for studying thin specimens since the electron beams travel through the entire specimen to generate images. 

Researchers use these machines for studying a variety of things, including the interior of a cell, the structure of protein molecules, cytoskeletal filaments, and viruses. 

Transmission electron microscopes can support a magnification level of up to 2,000,000x. You can typically find them in medical and biological fields.

Scanning Electron Microscopes

Scanning electron microscopes are effective for studying the surface of larger objects.

The process of this machine involves scanning the entire surface of an object with an electron beam and producing a black and white image from the data.

Scientists use these machines for size determination, particle counting, and process control.

Furthermore, they are popular in the material sciences field for quality control, failure analysis, and other research. 

Reflection Electron Microscopes

Reflection electron microscopes use electron beams to study crystals. These instruments can gain information on a crystal’s topography, composition, and structure. 

The instrument uses diffractive contrast to observe things such as atomic phases and other processes that occur on the surface of a crystal. 

Why Are Electron Microscopes Used

Why Are Electron Microscopes Used

There are a few reasons why electron microscopes are used. 

First of all, the electron beam that electron microscopes utilize has shorter wavelengths than photons do.

What this means is that the beam can support a much higher resolution compared to visible light. 

When you scan a sample using an electron microscope, you can see a lot more detail in the micrograph compared to your standard light microscope.

The main reason why researchers use electron microscopes is to study things at atomic levels and to learn more about cells, macromolecular structures, organelles, and tissues.

Electron microscopes have also played a big role in learning more about viruses, such as smallpox.



If you will be working with an electron microscope, it is a good idea to know how to maintain the machine.

These instruments are very expensive and highly specialized; for this reason, it is important to know how to handle them properly.

Always Hire a Professional

Before we get into the main points, it is essential to cover this first rule: always hire a professional. 

Electron microscopes are big, heavy machines that have hundreds of small working parts to them.

The average cost of these microscopes is around $300,000, so you won’t want to fiddle around with it yourself. 

Hire a professional for any sort of maintenance or repairs. If you try fixing the machine yourself, you could end up paying even more than you initially did for the machine. 

Perform Preventative Maintenance 

You should never wait until something is wrong with the machine to perform maintenance on it. When it comes to an electron microscope, performing preventative maintenance is a must. 

Make sure to call a professional and schedule preventative maintenance every six months or so. If you do this, you will rarely come across a major problem that requires an expensive repair.

Handle With Care

With a machine this expensive and complex, handling it with care should be the number one rule. 

If the microscope is in a public setting such as a university or research center, make sure to post rules of proper handling.

Furthermore, everyone who uses the machine should be properly trained.

One of the most important things to remember when handling an electron microscope is to wear gloves.

Using powder-free gloves will prevent residue from landing in the vacuum chamber. 

Always Follow the Correct Procedures

The best way to properly maintain an electron microscope is to follow the correct procedures. Even if you have used the microscope before, always double-check the posted procedures. 

It is also important to remember that not all microscopes are the same.

If you use an electron microscope at a different facility than you are used to, read over the procedures carefully and have them on-hand while using the machine. 


Electron microscopes use electron beams to scan specimens and produce black and white images from the data. 

Since these machines use electrons instead of photons, they can support a much higher resolution and magnification power.

Some electron microscopes can support up to 2,000,000x magnification power.

While electron microscopes may seem complicated, the process only contains a few basic steps. 

First of all, a stream of electrons is formed. The microscope then focuses the electrons into a thin beam and directs it onto the specimen.

When the specimen and electrons interact, the microscope collects data. Finally, the microscope then uses this data to produce a final black and white image. 

Many researchers use electron microscopes to study things at atomic levels. Since they can support higher resolutions, scientists can use these machines to observe organelles, macromolecular structures, cells, tissues, and more.

When working with an electron microscope, make sure to handle it with care. Wear powder-free gloves and follow the correct procedures.

Always hire a professional for repairs and perform preventative maintenance about every six months or so.