Explained: Scanning Electron Microscope


The invention of the Electron Microscope has taken microscopy to a whole new level. Two types are most commonly used: the scanning electron microscope and the transmission electron microscope. In this blog, I’m setting in to explain the functioning of an SEM.

What It Means

As the name implies, an SEM works with a beam of electrons, that scan across the sample to be analyzed. The signals received are then analyzed, and that’s all it takes to build up an image of the sample.

An image from a Scanning Electron Microscope. Such images have a very distinctive depth-of-field. Image Credit: Wikimedia Commons

Sample Preparation 

You just can’t put in any sample just like that in an SEM to view it, unlike with optical microscopes. Preparation of samples is an integral part of electron microscopy using an SEM.

To begin with, you have to ensure that the specimen is of the correct size, such that it can be mounted on the specimen stub

Using a sample in an SEM requires the specimen to be electrically conductive. Electric conductivity is just a test of another property of the atoms of the specimen: the presence of free electrons. 

An SEM works on the principle of analyzing the reflected electrons from its incident electron beam, and also by analyzing the electrons emitted by the atoms of the specimen, which were excited by the incident electron beam.

So, the atom should have enough free electrons to be emitted, for the detectors on the SEM to detect the signals, and render the image.

Electrical conductivity indicates the presence of free electrons. 
Therefore, electrical conductivity is used as a test whether a sample is eligible to be analyzed by an SEM.

It must also be ensured that the sample is electrically grounded, to prevent the buildup of electric charge on its surface; which affects imaging; since electron beams are being used.

Metallic Objects: They do not require much of a sample preparation. The only procedure is the conventional cleaning, which is characteristic for optical microscopes too. 

Non-Metallic Objects: However, life is not so easy for non-metallic objects. Since they have no free electrons to reflect back, their surface has to be coated with an electrically conductive metal.

Various metals like gold, osmium, iridium, tungsten, and graphite are used for coating the samples. However, it is no always easy to coat biological samples.

A spider coated in gold, to be viewed under a Scanning Electron Microscope.    Image Credit: Wikimedia Commons

Biological samples which cannot be coated have to be viewed by a specially-modified SEM, known as an environmental scanning electron microscope. I’m not going into the details of ESEM. 

The Scanning Process

We know that the imaging medium for an SEM is a flow of electrons. So, the first obvious step would be to generate an electron beam. 

The process used to generate the electron beam is very much similar to that big, bulky CRT Monitor that you once used for your PC. 

The place where the electrons are created is known as the electron gun. It consists of a tungsten filament. 

The reason why tungsten is used is that it has a very high melting point, and a meagre vapour pressure.

A schematic diagram explaining the working of an SEM. Image Credit: Wikimedia Commons

The tungsten filament is heated by passing electricity through it, which makes it give out a stream of electrons. This property is known as thermionic emission. 

The emitted electron beam may have an energy ranging from anything between 0.2 keV to 40 keV. The wide stream of electron has to be focused into a beam. That is done by 2 pairs of lenses, known as condenser lenses. 

But can you use an optical lens to bend an electron beam? Sorry, you can’t. Therefore, the “lenses” used for focusing electron beams are magnetic and electric fields, since the electron being a charged particle and having its own magnetic field, interacts with both of these.

The job of the third lens, the objective lens, is to make the electron beam follow a raster scan pattern. There are two pairs on coils, each pair corresponding to positioning the beam of the X, Y axis.

The more electric current to provide to the three lenses, the stronger the magnetic and electric fields, and therefore, stronger the deflection.

In a raster scan pattern, the electron beam scans the first pixel in the first row, then the second, then the third, and so on, until it is done with all the pixels in that row.

Next, it moves on to the second row, and scans it. Once done with the second row, it moves on to the next row. It repeats this sequence until it has scanned every point in the field of view.

Once focused, the electron beam converges at a point which can be 0.4 to 5.0 nanometres in size.

In an optical microscope, you resolve the image by light reflected back from the specimen. Light is actually a stream of photons.
In an electron microscope, instead of using light, you use electrons.

The electron beam falls on each point, and certain electrons, along with electromagnetic radiation, is reflected back.

  • Backscattered High-Energy Electrons: Some of the electrons from the electron beam that had struck the sample are reflected back. They are characterised by high energy, which was characteristic of the electron beam, and a shallow reflection angle. 
  • Emitted Secondary Electrons: When the electron beam falls on the specimen, it imparts some energy to the atoms and pushes them into an excited state. When the atoms fall back to their normal state, they emit electrons in order to ward of that energy which was gained. These electrons are detected as the secondary electrons.
  • Electromagnetic Radiation: In the same way secondary electrons are emitted from the sample, electromagnetic radiation is also emitted from the sample. Of interest here is the ER in the X-ray range of the electromagnetic spectrum.

All these three kinds of reflection are analyzed by the backscatter electron detector, secondary electron detector, and the X-Ray Detector. 

Certain electrons are also absorbed by the specimen. These may also be taken into account while rendering an image of the specimen.

Each of the detectors are positioned such that each pixel on the detectors correspond to an actual “pixel” on the specimen.

The electronic input is too small, and therefore, is first amplified. Thus, you get an distribution map of the signal for each pixel. The image is then rendered accordingly.

Areas with a higher signal appear brighter, while areas with a lower signal appear darker.


An SEM can gain a magnification starting from 10x to anything about 50,000x.

Image Credit: Wikimedia Commons


EM images are rendered in grayscale, since the image is a proportional rendering of the signal present on each pixel.

However, EM images may be colorized later, while post-processing.

  • Contour/Feature Plotting Software: Certain automated software may be used to map contours or features, and colour them according to the user’s choice.
  • Special Purpose Software: Often, a colour is assigned to the image created from the three types of detectors, so that when the three inputs are combined, the colour-coding helps determine the source of each part of the image. Similar such colour characteristics may be added to various types of attributes, usually for scientific analysis later.
  • Post-Processing Software: Photoshop and paint-brush tools are always there! In these cases, adding colour is all about aesthetics, and giving the image a real feel.
An SEM image of Tradescantia pollen and stamens, colorized for aesthetics and ease of understanding. Image Credit: Wikimedia Commons

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