Seeing with Helium Atoms

Dr. Andrew Jardine

Department of Physics, University of Cambridge


Dr Andrew Jardine is a University Lecturer in Physics at the Cavendish Laboratory, University of Cambridge, and a Fellow and Director of Studies at Fitzwilliam College, Cambridge. He gained his MSci degree in Physics from the University of Nottingham in 1998 and his PhD from the University of Cambridge in 2002. He held Oppenheimer and Royal Society University Research Fellowships prior to his current appointment.

Dr Jardine was part of a research group that were given a £1.3 million EPSRC grant to design and build the next generation of scanning helium microscopes to establish the field.

His other projects involve studying atoms and molecules in materials.


First there were optical microscopes, then electron microscopes, now with just three in the world, helium atom microscopes present a novel view at the microscopic scale. Helium atoms are neutral, they don’t damage the sample that you are investigating, and you don’t need to prepare the sample in advance. But neutral atoms present a challenge – how do you focus a beam of neutral atoms? What resolution can you achieve? During this lecture Dr Jardine explained how school physics is applied in this cutting-edge research in order to see what organic samples, like shark skin, look like in a helium microscope image.

Below is a link to the lecture

The following are notes from the on-line lecture. Even though I could stop the video and go back over things there are likely to be mistakes because I haven’t heard things correctly or not understood them. I hope Dr Jardine, and my readers will forgive any mistakes and let me know what I got wrong.

Microscopes are very important in science and engineering whether you are looking at the fundamental properties of materials, inspecting devices, investigating biological specimens such as the famous virus, Covid-19 (bottom left), or the silicon chips (bottom right) in your smart phone


Being able to see what you are doing or what is happening is vitally important. If you can’t see what you are doing it can be difficult to work and if you can’t measure you can’t build ad you can’t make progress.

The talk was about new types of microscope which will give new insights into different materials. Dr Jardine started by discussing some of the main types of microscopes in order to show how the helium microscope fits in.

Optical devices

1) The original optical device for us is the human eye. It isn’t a microscope but it is an incredible optical device.


The human eye is a paired sense organ that reacts to light and allows vision. Rod and cone cells in the retina are photoreceptive cells which are able to detect visible light and convey this information to the brain. Eyes signal information which is used by the brain to elicit the perception of colour, shape, depth, movement, and other features. The eye is part of the sensory nervous system.

The human eye’s non-image-forming photosensitive ganglion cells in the retina receive light signals which affect adjustment of the size of the pupil, regulation and suppression of the hormone melatonin, and entrainment of the circadian rhythm


The cornea and lens of an eye act together to form a real image on the light-sensing retina, which has its densest concentration of receptors in the fovea and a blind spot over the optic nerve. The power of the lens of an eye is adjustable to provide an image on the retina for varying object distances. Layers of tissues with varying indices of refraction in the lens are shown here. However, they have been omitted from other pictures for clarity.

Optical resolution describes the ability of an imaging system to resolve detail in the object that is being imaged.

Resolving power is the ability of the eye, or an optical instrument, to differentiate between two points or lines.

The human eye can easily resolve objects that are 50mm apart at close distances (about 0.05mm). In order to look at smaller objects we need to use microscopes.

2) Optical microscopes

The optical microscope, also referred to as a light microscope, is a type of microscope that commonly uses visible light and a system of lenses to generate magnified images of small objects. Optical microscopes are the oldest design of microscope and were possibly invented in their present compound form in the 17th century. Basic optical microscopes can be very simple, although many complex designs aim to improve resolution and sample contrast.

The earliest microscopes were single lens magnifying glasses with limited magnification which date at least as far back as the widespread use of lenses in eyeglasses in the 13th century.

Compound microscopes first appeared in Europe around 1620 and one exhibited in Rome in 1624.

The actual inventor of the compound microscope is unknown although many claims have been made over the years.

Christiaan Huygens, another Dutchman, developed a simple 2-lens ocular system in the late 17th century that was achromatically corrected, and therefore a huge step forward in microscope development. The Huygens ocular is still being produced to this day, but suffers from a small field size, and other minor disadvantages. (below left)


Christiaan Huygens FRS (14 April 1629 – 8 July 1695), also spelled Huyghens, was a Dutch physicist, mathematician, astronomer and inventor, who is widely regarded as one of the greatest scientists of all time and a major figure in the scientific revolution. Above centre

Robert Hooke FRS (1635 – 3 March 1703) was an English scientist and architect, a polymath, recently called “England’s Leonardo”,[2] who, using a microscope, was the first to visualize a microorganism.

Antonie van Leeuwenhoek (1632–1724) is credited with bringing the microscope to the attention of biologists, even though simple magnifying lenses were already being produced in the 16th century. (Above right)

Antonie Philips van Leeuwenhoek FRS (24 October 1632 – 26 August 1723) was a Dutch businessman and scientist in the Golden Age of Dutch science and technology.


Above left: Cell structure of cork by Hooke, Micrographia, 1665. Above centre left: Hooke’s microscope, from an engraving in Micrographia Above centre right: Hooke’s drawing of a flea. Above right: A microscopic section of a one-year-old ash tree (Fraxinus) wood, drawing made by van Leeuwenhoek

All modern optical microscopes designed for viewing samples by transmitted light share the same basic components of the light path. In addition, the vast majority of microscopes have the same ‘structural’ components.

Below centre: Diagram of a compound optical microscope with a lens close to the object being viewed to collect light (called the objective lens) which focuses a real image (image 1) of the object inside the microscope. That image is then magnified by a second lens or group of lenses (called the eyepiece) that gives the viewer and enlarged inverted virtual image (image 2) of the object. The lines represent light rays.

The whole image may be seen in one go, either to a screen or camera (or during my A level biology days – a pathetic attempt at drawing a diagram on paper with an inevitably blunt pencil).

image image

Eyepiece (ocular lens) (1)

Objective turret, revolver, or revolving nose piece (to hold multiple objective lenses) (2)

Objective lenses (3)

Focus knobs (to move the stage)

Coarse adjustment (4)

Fine adjustment (5)

Stage (to hold the specimen) (6)

Light source (a light or a mirror) (7)

Diaphragm and condenser (8)

Mechanical stage (9)

The resolution of an optical microscope is proportional to the wavelength of light that is being used. Typically, it is about λ/2 or 0.3mm. It is limited by diffraction.

Diffraction refers to various phenomena that occur when a wave encounters an obstacle or opening. It is defined as the bending of waves around the corners of an obstacle or through an aperture into the region of geometrical shadow of the obstacle/aperture. The diffracting object or aperture effectively becomes a secondary source of the propagating wave.

An optical system with resolution performance at the instrument’s theoretical limit is said to be diffraction-limited.

The observation of sub-wavelength structures with microscopes is difficult because of the Abbe diffraction limit. Ernst Abbe found in 1873 that light with wavelength λ, traveling in a medium with refractive index n and converging to a spot with half-angle θ will have a minimum resolvable distance of


The portion of the denominator nsinθ is called the numerical aperture (NA) and can reach about 1.4–1.6 in modern optics, hence the Abbe limit is d = λ/2.8. Considering green light around 500 nm and a NA of 1, the Abbe limit is roughly d = λ/2 = 250 nm (0.25 μm), which is small compared to most biological cells (1 μm to 100 μm), but large compared to viruses (100 nm), proteins (10 nm) and less complex molecules (1 nm). To increase the resolution, shorter wavelengths can be used such as UV and X-ray microscopes. These techniques offer better resolution but are expensive, suffer from lack of contrast in biological samples and may damage the sample.


Ernst Karl Abbe HonFRMS (23 January 1840 – 14 January 1905) was a German physicist, optical scientist, entrepreneur, and social reformer.

The absolute best resolution is about 0.3mm but in practise we could go down to 1mm with a typical microscope.

An optical microscope is about 50 to 100 times better than the naked eye. It is relatively cheap consisting of a couple of lenses fixed together in a tube.

Optical microscopes are important in microbiology, engineering, materials science, geology and other subjects.

Electron microscopes

These are needed if you want to resolve things smaller than 1mm

An electron microscope is a microscope that uses a beam of accelerated electrons as a source of illumination. As the wavelength of an electron can be up to 100,000 times shorter than that of visible light photons, electron microscopes have a higher resolving power than light microscopes and can reveal the structure of smaller objects. A scanning transmission electron microscope has achieved better than 50 pm resolution in annular dark-field imaging mode and magnifications of up to about 10,000,000× whereas most light microscopes are limited by diffraction to about 200 nm resolution and useful magnifications below 2000×.

Electron microscopes use shaped magnetic fields to form electron optical lens systems that are analogous to the glass lenses of an optical light microscope.

Electron microscopes are used to investigate the ultrastructure of a wide range of biological and inorganic specimens including microorganisms, cells, large molecules, biopsy samples, metals, and crystals. Industrially, electron microscopes are often used for quality control and failure analysis. Modern electron microscopes produce electron micrographs using specialized digital cameras and frame grabbers to capture the images.

The link below is a previous blog where I wrote something about the electron microscope.

The first working electron microscope was produced in 1931 by the physicist Ernst Ruska and the electrical engineer Max Knoll. (below left)


Ernst August Friedrich Ruska (25 December 1906 – 27 May 1988) was a German physicist who won the Nobel Prize in Physics in 1986 for his work in electron optics, including the design of the first electron microscope (Above right)

Max Knoll (17 July 1897 – 6 November 1969) was a German electrical engineer.


There are different types of electron microscope

Transmission electron microscope (TEM) Serial-section electron microscopy (ssEM) Scanning electron microscope (SEM) Reflection electron microscope (REM) Scanning transmission electron microscope (STEM) Scanning tunnelling microscopy (STM)

The original form of the electron microscope, the transmission electron microscope (TEM), uses a high voltage electron beam to illuminate the specimen and create an image. The electron beam is produced by an electron gun, commonly fitted with a tungsten filament cathode as the electron source. The electron beam is accelerated by an anode typically at +100 keV (40 to 400 keV) with respect to the cathode, focused by electrostatic and electromagnetic lenses, and transmitted through the specimen that is in part transparent to electrons and in part scatters them out of the beam. When it emerges from the specimen, the electron beam carries information about the structure of the specimen that is magnified by the objective lens system of the microscope. The spatial variation in this information (the “image”) may be viewed by projecting the magnified electron image onto a fluorescent viewing screen coated with a phosphor or scintillator material such as zinc sulfide. Alternatively, the image can be photographically recorded by exposing a photographic film or plate directly to the electron beam, or a high-resolution phosphor may be coupled by means of a lens optical system or a fibre optic light-guide to the sensor of a digital camera. The image detected by the digital camera may be displayed on a monitor or computer.


An image of an ant in a scanning electron microscope

The basis of an electron microscopy is that electrons can have wave-like behaviour as well as particle behaviour. The idea that particles could have wave-like behaviour is due to Louis de Broglie

Louis Victor Pierre Raymond de Broglie, 7th duc de Broglie (15 August 1892 – 19 March 1987) was a French physicist and aristocrat who made groundbreaking contributions to quantum theory. In his 1924 PhD thesis, he postulated the wave nature of electrons and suggested that all matter has wave properties. This concept is known as the de Broglie hypothesis, an example of wave–particle duality, and forms a central part of the theory of quantum mechanics.


Matter waves are a central part of the theory of quantum mechanics, being an example of wave–particle duality. All matter exhibits wave-like behaviour. For example, a beam of electrons can be diffracted just like a beam of light or a water wave. In most cases, however, the wavelength is too small to have a practical impact on day-to-day activities. Hence in our day-to-day lives with objects the size of tennis balls and people, matter waves are not relevant.

Matter waves are referred to as de Broglie waves.

The de Broglie wavelength is the wavelength, λ, associated with a massive particle (i.e., a particle with mass, as opposed to a massless particle) and is related to its momentum, p (= mv = mass x velocity), through the Planck constant, h:

λ = h/p = h/mv

Because electrons can be considered to have a wavelength and because they can be given a lot of energy, they travel very fast and can have a very small wavelength. Large momentum of the electrons means a small wavelength

As with the optical microscope the resolution of the electron microscope is proportional to the wavelength, but the de Broglie wavelength is considerably smaller than the visible light wavelength. The practical resolution for an electron microscope is about 1nm, but it depends on the sample.

An atom is between 0.1 and 0.3nm and some electron microscopes do have atomic resolution.

Electron microscopes are much more complicated machines than optical microscopes and are computer controlled now.

Sometimes the image can be projected and be seen in one go but sometimes the electron beam is focused on to a point and scanned backwards and forwards across the sample, with the image built up by computer.

Electron microscopy is a very expensive technique. £50000 is a typical cost of a good cheap electron microscope.

There is a huge range of applications in science, engineering and microbiology

Scanning probe microscope

These have the ultimate resolution in terms of existing microscopes.

Scanning probe microscopy (SPM) is a branch of microscopy that forms images of surfaces using a physical probe that scans the specimen. SPM was founded in 1981, with the invention of the scanning tunnelling microscope, an instrument for imaging surfaces at the atomic level. The first successful scanning tunnelling microscope experiment was done by Gerd Binnig and Heinrich Rohrer. The key to their success was using a feedback loop to regulate gap distance between the sample and the probe.

Many scanning probe microscopes can image several interactions simultaneously. The manner of using these interactions to obtain an image is generally called a mode.

The resolution varies somewhat from technique to technique, but some probe techniques reach a rather impressive atomic resolution. This is due largely because piezoelectric actuators can execute motions with a precision and accuracy at the atomic level or better on electronic command. This family of techniques can be called “piezoelectric techniques”. The other common denominator is that the data are typically obtained as a two-dimensional grid of data points, visualized in false colour as a computer image.


Above left: Schematic diagram of a scanning tunnelling microscope.

A scanning tunnelling microscope (STM) is an instrument for imaging surfaces at the atomic level. Its development in 1981 earned its inventors, Gerd Binnig and Heinrich Rohrer, then at IBM Zürich, the Nobel Prize in Physics in 1986. STM senses the surface by using an extremely sharp conducting tip that can distinguish features smaller than 0.1 nm with a 0.01 nm (10 pm) depth resolution. This means that individual atoms can routinely be imaged and manipulated. Most microscopes are built for use in ultra-high vacuum at temperatures approaching zero kelvin, but variants exist for studies in air, water and other environments, and for temperatures over 1000 °C

STM is based on the concept of quantum tunnelling. When the tip is brought very near to the surface to be examined, a bias voltage applied between the two allows electrons to tunnel through the vacuum separating them. The resulting tunnelling current is a function of the tip position, applied voltage, and the local density of states (LDOS) of the sample. Information is acquired by monitoring the current as the tip scans across the surface, and is usually displayed in image form.

In other words when the sharp tip presses down on the sample surface and moves back and forth a current is produced between the tip and the surface. This is caused by a process called quantum tunnelling where electrons are jumping from the tip through a “forbidden region” into the surface of the sample. This quantum mechanical process means there is a strong variation of current with distance, which gives a very sensitive measure of the separation between tip and surface. If the tip is moved very accurately and can finish on a single atom then images can be generated with atomic resolution (Below left)

The typical STM image of Si(111)-7 × 7-reconstructed complex lattice surface (a), where the inset was the high magnification. During all scanning process, the bias voltage and tunnelling current was kept at 1.5 V and 0.19 nA, respectively.


Above right: Image of surface reconstruction on a clean Gold (Au (100)) surface, as visualized using scanning tunnelling microscopy. The individual atoms composing the material are visible. Surface reconstruction causes the surface atoms to deviate from the bulk crystal structure, and arrange in columns several atoms wide with regularly spaced pits between them. Technical details: Atomically resolved STM image of clean Au (100). This image is made with an Omicron Low Temperature STM and RHK Technology electronics by Erwin Rossen, Eindhoven University of Technology, 2006. Parameters: p<1e-11 mbar, T is 77 K, I_setpoint is 6 nA, V_bias is 1 mV, Au (100) surface is Ar sputtered (1,5 kV, 2uA, 30 minutes) and annealed (500°C, 30 minutes).

The images are built up by a computer as the tip scans over the surface. This is quite different from the way optical microscopes work.

Quantum tunnelling is the quantum mechanical phenomenon where a wavefunction can propagate through a potential barrier. (below left)


Gerd Binnig (born 20 July 1947) is a German physicist. He is most famous for having won the Nobel Prize in Physics jointly with Heinrich Rohrer in 1986 for the invention of the scanning tunnelling microscope (above right)

Heinrich Rohrer (6 June 1933 – 16 May 2013) was a Swiss physicist who shared half of the 1986 Nobel Prize in Physics with Gerd Binnig for the design of the scanning tunnelling microscope (STM).

Scanning probe microscopes provide the ultimate resolution. They can actually show up individual atoms.

The sharp top scans over the surface, measuring the tunnelling current. A computer uses the tunnelling currents to create an image.

This method of microscopy is used in nanoscience research; new materials research and processes. It looks at new materials at the atomic level and investigates the processes involved with them.

What is the problem with the above methods?

Why do we need new types of microscopes?

Modern microscopes are fantastic so why are new ones necessary? After all they generate lots of images.

Because there are still major challenges and in particular overcoming damage to delicate materials.

The bleaching effect of visible light has been known about for a very long time. Ancient Egyptians were said to be experts on whitening their materials. They would use the sun to whiten all of their cloths. The energy of the photons would break up the dirt molecules (Below left)


Optical microscopes use visible light but the lenses focus it, thereby concentrating the energy into a beam (Above right). This does have a heating effect towards the red end of the spectrum and an ionising effect towards the violet end of the spectrum and these effects can damage delicate materials and bleach the dyes in some materials. The dye molecules actually get broken down.

Electron microscopes enable us to view atoms and molecules but again the electrons get concentrated into a beam. The electron beam carries a great deal of energy so as it scans backwards and forwards across the sample, in order to build up an image using a computer, all of that energy is concentrated onto a tiny spot and can do a great deal of damage to the surface of the sample. In fact, sometimes little burnt in rectangles can be seen on the surface where the beam has been moving backwards and forwards.

E-beam damage: Haemoglobin NPs

The following images are stills from a video showing the effect of electron beams on haemoglobin molecules

30nm hexangonal haemoglobin particles images by a 120kV TEM image

The small black dots are 2nm gold nanoparticles Radiation damage in single-particle cryo-electron microscopy: effects of dose and dose rate


The images show that the particles get damaged almost immediately by the energy of the beam. Very quickly all trace of what they originally looked like has disappeared.

Within a few frames all trace of the hexagonal structures has gone. Over time the damage gets worse and worse and eventually the sample is completely destroyed by the electron beam. The energy being put in is causing a real problem.

Why image with atoms?

How much energy is the problem? In order to answer this question, the chemical bond energies need to be compared with the energy of the respective beams.

Typically, chemical bonds have an energy of 1eV. This is the amount of energy released when a bond is made or the amount of energy required to break a bond. The electrons in an electron microscope beam typically have energies between 1000 and 100000eV. So, the electrons have the scope to do a great deal of damage to a 1eV chemical bond.

Visible light photons have energies between 1 and 2 eV so there is still scope for them to affect chemical bonds which is why visible light causes slow changes in. dye molecules.

The photon is a type of elementary particle. It is the quantum of the electromagnetic field including electromagnetic radiation such as light and radio waves, and the force carrier for the electromagnetic force. Photons are massless, so they always move at the speed of light in vacuum, 299792458 m/s.

Like all elementary particles, photons are currently best explained by quantum mechanics and exhibit wave–particle duality, their behaviour featuring properties of both waves and particles.

Helium atoms used in imaging only have about 0.05eV of energy so they won’t cause damage to chemical bonds.

(eV is a small unit of energy. To convert it to joules you multiply the charge on an electron by the accelerating p.d. 1eV = 1.6 x 10-19C x 1V =1.6 x 10-19J)

So, the solution to reducing damage is to image with atoms

Sending an electron or a photon into a chemical bond delivers enough energy to effect/damage/break the bond when it is scattered from the surface.


However, the atom has such a low energy it can scatter off the surface of the sample without causing damage to the bonds.


Why neutral helium atoms?

Helium microscopes do not have as good a resolution as the best electron microscopes but they are better than optical microscopes.

They can extend up to the mm scale with a large depth of field

The depth of field (DOF) is the distance between the nearest and the farthest objects that are in acceptably sharp focus in an image.

They can image ultra-delicate materials. The beam does not do any damage.

The atoms are neutral. The samples do not have to be electrically conducting like the samples examined with an electron microscope. No conducting layer is needed to be added in order to image the sample, i.e. no charging or sample preparation required.


How is a microscope that images with atoms made?

The research groups needed to understand how to produce a beam of neutral helium and how to use them in the microscope.


Supersonically expand helium (~100bar) through a fine nozzle (~10mm) into a vacuum (~10-3mbar)

Firstly, everything needs to be done in a vacuum because any air molecules present would scatter helium atoms in the beam almost immediately. In fact, you wouldn’t be able to form a beam in the first place.

A supply of helium is connected to the nozzle (see above image), which is inside a vacuum. The nozzle has a small hole (~10mm in diameter). The helium expands through the hole and spreads out. As it does this, all of the random motion in the gas is transferred into the forward direction (as shown by the red arrows pointing right on the above diagram). At the quitting surface the atoms start travelling in straight lines and continue travelling in straight lines because they don’t interact with anything. The skimmer separates out the centre of the expansion and the atoms pass through the rest of the machine and forms the beam of helium that goes to the sample. So, there is a nice well defined/well controlled beam of helium and the energy is controlled by the temperature of the nozzle.

The random motion, which is associated with the gas being at a particular temperature, is converted to kinetic energy of the helium atoms and they travel with a speed of 1000m/s.

KE of a gas = (3/2)kT where k is the Boltzmann constant and T is the temperature in kelvin. The kinetic energy is also = (1/2)mv2 so there is a direct relationship between the temperature of the gas and its average velocity (m is the mass).

Once the beam has been created the researchers needed to know something about how it interacts with a surface.

Interaction with surfaces.


The green circle in the above image represents the helium atom, which is directed onto the surface. The wavy lines/contours represent the outer electrons of the surface atoms of the sample. The electrons delocalise on the surface. This means the electrons are no longer associated with a single atom or a covalent bond.

The helium atom comes in and as it approaches the surface it starts to feel an attractive Van der Waals force.

In molecular physics, the van der Waals force, named after Dutch scientist Johannes Diderik van der Waals, is a distance-dependent interaction between atoms or molecules. Unlike ionic or covalent bonds, these attractions do not result from a chemical electronic bond; they are comparatively weak and therefore more susceptible to disturbance. The van der Waals force quickly vanishes at longer distances between interacting molecules.

If no other force is present, the distance between atoms at which the force becomes repulsive rather than attractive as the atoms approach one another is called the van der Waals contact distance; this phenomenon results from the mutual repulsion between the atoms’ electron clouds. The van der Waals force has the same origin as the Casimir effect, which arises from quantum interactions with the zero-point field.

The term van der Waals force is sometimes used loosely for all intermolecular forces.


Johannes Diderik van der Waals (23 November 1837 – 8 March 1923) was a Dutch theoretical physicist and thermodynamicist famous for his pioneering work on the equation of state for gases and liquids

An attractive Van der Waals interaction forms between the helium atoms and the atoms on the sample’s surface and the helium beam bends towards the surface a little bit. But when the beam and gets really close to the sample the electrons in the helium and the sample start repelling each other. This cause the helium beam to be “reflected” or diffracted off the surface. Alternatively, the helium could get trapped in a resonance state or vibrate vibrations in the surface of the sample

A resonance is the peak located around a certain energy found in differential cross sections of scattering experiments. Cross-section is a measure of the probability that a specific process will take place.

The thing the researchers need to focus on is the elastic scattering (reflection like scattering) from the surface.

Elastic scattering is a form of particle scattering in scattering theory, nuclear physics and particle physics. In this process, the kinetic energy of a particle is conserved in the centre-of-mass frame, but its direction of propagation is modified (by interaction with other particles and/or potentials). Furthermore, while the particle’s kinetic energy in the centre-of-mass frame is constant, its energy in the lab frame is not. Generally, elastic scattering describes a process in which the total kinetic energy of the system is conserved.

So, the researchers now have their beam and they know how it interacts with the surface of the sample.

Making a helium microprobe

So, the next thing the researchers need to do is make their microscope. To do this they need to make sure the beam is focused down to a spot and that they can move the spot to scan the surface of the sample. It is the spot size that gives the resolution.

Normally in an optical microscope lenses are used to focus the light beam and in an electron microscope electromagnetic lenses are used to focus the charged electrons.

The electron microscope lenses use the electrical interaction between the electric field of the lens and the charge on the electron in order to focus the beam.

Helium atoms can’t be focussed like electrons because they are neutral.

There are several focussing options, but they are very difficult.

One option is to use a curved mirror (A, B, C, D and E in the image below)


It is incredibly hard to produce the mirrors and get them to work reliably and consistently.

Another option is to use Fresnel zone plates. They look a bit like a bullseye.

A Fresnel plate is a series of rings and it focuses by diffraction. It does work with neutral helium but it is very challenging to make them. It has been shown that they can focus helium, but getting to the first step is very difficult.


Another option is to use a Fresnel zone plate

A zone plate is a device used to focus things exhibiting wave character. Unlike lenses or curved mirrors, zone plates use diffraction instead of refraction or reflection. Based on analysis by French physicist Augustin-Jean Fresnel, they are sometimes called Fresnel zone plates in his honour. The zone plate’s focusing ability is an extension of the Arago spot phenomenon caused by diffraction from an opaque disc.

A zone plate consists of a set of concentric rings, known as Fresnel zones, which alternate between being “opaque and transparent”. Waves hitting the zone plate will diffract around the opaque zones. The zones can be spaced so that the diffracted wave constructively interferes at the desired focus, creating an “image” there.

Due to quantum mechanics, matter waves can be focused this way. Wave plates have been used to focus beams of neutrons and helium atoms.


Augustin-Jean Fresnel (10 May 1788 – 14 July 1827) was a French civil engineer and physicist whose research in optics led to the almost unanimous acceptance of the wave theory of light, excluding any remnant of Newton’s corpuscular theory, from the late 1830s until the end of the 19th century.

In optics, the Arago spot, Poisson spot, or Fresnel spot is a bright point that appears at the centre of a circular object’s shadow due to Fresnel diffraction.

Cambridge’s approach is simpler

Cambridge’s approach


Schematic diagram (not to scale) illustrating the path of helium through the SHeM. The neutral helium atom beam generated by the free-jet expansion is progressively collimated by the skimmer and pinhole apertures, resulting in a pencil beam that strikes the sample surface. The intensity of backscattered helium atoms passing through the detector aperture (located to collect specular reflections) is recorded as the sample is rastered in two dimensions underneath the beam (see red arrows). Insets show an illustrative example of image formation in the SHeM, highlighting the effects of both occlusion and projection distortion by means of a simple geometric sample. The final produced SHeM micrograph of a 3D-printed analogue of the sample is also shown for completeness. Scale bar 500 μm, 2.6 seconds dwell per pixel.


Take the nozzle (above image) and expand helium through it.


The gas expands in the apparatus shown above and the skimmer selects some of it to form the beam.


The helium beam is collimated with a very fine pin hole, 1mm in diameter, (they are hoping to make it smaller in the future) which provides the resolution. This produces a micron sized beam that shines on the surface. They are hoping to replace the pinhole with a zone plate at some point in the future in order to increase the resolution.


The atoms scatter from the sample’s surface in all directions. Some of them are sampled by the detector aperture and passed into the mass spectrometer detector.


Mass spectrometry (MS) is an analytical technique that measures the mass-to-charge ratio of ions. The results are typically presented as a mass spectrum, a plot of intensity as a function of the mass-to-charge ratio. Mass spectrometry is used in many different fields and is applied to pure samples as well as complex mixtures.

A mass spectrum is a plot of the ion signal as a function of the mass-to-charge ratio. These spectra are used to determine the elemental or isotopic signature of a sample, the masses of particles and of molecules, and to elucidate the chemical identity or structure of molecules and other chemical compounds.

In a typical MS procedure, a sample, which may be solid, liquid, or gaseous, is ionized, for example by bombarding it with electrons. This may cause some of the sample’s molecules to break into charged fragments or simply become charged without fragmenting. These ions are then separated according to their mass-to-charge ratio, for example by accelerating them and subjecting them to an electric or magnetic field: ions of the same mass-to-charge ratio will undergo the same amount of deflection. The ions are detected by a mechanism capable of detecting charged particles, such as an electron multiplier. Results are displayed as spectra of the signal intensity of detected ions as a function of the mass-to-charge ratio. The atoms or molecules in the sample can be identified by correlating known masses (e.g. an entire molecule) to the identified masses or through a characteristic fragmentation pattern.

The atoms are scattered in the mass spectrometer detector as the sample is scanned backwards and forwards to build up the image.

The final piece of the design is to have a really good detector in order to make the pinhole really small. This means a small number of atoms reaching the sample so a really sensitive mass spectrometer detector is needed.

Ultra-sensitive helium detector

Commercial helium detectors are not quite good enough for the required application. They only detect one in a million helium atoms because helium is so difficult to detect.

The researchers built their own.


It is essentially a more sensitive mass spectrometer. The helium enters from the left. There are lots of electrons inside the solenoid (the thin tube coloured blue in the above image). The solenoid produces a magnetic field which causes the electrons to move in a little helical path and they collide with the helium atoms, which become ionised to form helium ions.

The helium ions get extracted and passed into some electron optics. To the right of the solenoid the helium ions are separated from any other ions that might have crept in to the apparatus.


The curved magnet (magnetic sceptre) shown in the above diagram (found at the right of the apparatus) is used to do the separation and then the atoms are counted (near where the copper object is in the image below).


The MklV Cavendish detector is very big and it is about 1% efficient.

The efficiency will be improved but it is still better than the commercial version and can give very good images.

Cavendish’s first helium microscope



The source creates the beam


The sample goes in the sample chamber


The detector

A tour through the microscope – a fly through

The following images are stills from a simulation tour of the helium microscope


A look inside the source


The sample chamber


Yellow cone is the nozzle


Gas flowing out of the nozzle and passing into the skimmer


From the source to the sample chamber


The very fine micro beam shines onto the sample

image image

And some of those atoms scatter and pass through this aperture into the detector

Stills form a video showing the inside of the microscope working



Sample is placed where the little hand is pointing.

Below is a still of the scanning process



Start imaging


Above indicates the helium is coming through


The sample is passing backwards and forwards

Imaging a small sample of coral

Process is time consuming although they are gradually speeding up the process


Finished image

Some sample images

The aim is to look at materials that are challenging with other methods


3D structure: Polymer fibre filter.

It is challenging to image the fibres because they are not conductive. It is a 3-dimensional structure which is difficult to image through the depth of the material with an optical microscope.


Insulating material: Eroded diamond

If you want a protective coating you need to understand how that material looks after it has been doing its protecting. You need to be able to look at the surface. This would be difficult with an electron microscope as the surface is not a conducting surface.


Composite: Nanotube epoxy materials


Insulator: Diffraction enhanced LiF (Lithium fluoride crystal) image


Bio structure: Coral. A broad image with two zoomed sections at higher resolutions.


What is it useful for?

Imaging delicate materials such as wax and chocolate. Both of these will melt if you use a high energy source (such as optical or electron microscopes) to examine them, even if you could get round the charge problem.

Some materials would be affected by electrons and light. This would be important if you were making solar cells and you want to understand the structure. If the structure changes when you apply light you can’t look at it with an optical microscope. Similarly with making electronic devices out of polymer materials (organic electronics). These would be easily damaged if using high energy electrons from an electron microscope.

Transparent materials, insulators, polymers and biomaterials can also be investigated with the helium microscope.

Where does the contrast in the images come from?

Researchers need to understand the angular distribution of scattering


Looking at the 100mm image of the polymer fibre. What is it that makes part of the image brighter than others?

If thinking about light we think of it being diffusely reflected or specular reflected.

Diffuse reflection is the reflection of light or other waves or particles from a surface such that a ray incident on the surface is scattered at many angles rather than at just one angle as in the case of specular reflection.

Specular reflection, or regular reflection, is the mirror-like reflection of waves, such as light, from a surface.


Diffuse and specular reflection from a glossy surface. The rays represent luminous intensity, which varies according to the cosine law for an ideal diffuse reflector.

When using helium atoms that process could be completely different.

The researchers really need to understand how the images are formed if they are going to be able to apply the technique widely. They want to be able to examine an element of the surface of the sample and see how the helium atoms scatter.


Do they scatter in all directions or do they scatter as a reflected beam? What happens on different types of materials?

So, understanding the contrast is to understand how the images are formed.

Cosine scattering

Researchers need to measure over a series of different angles if they want to look at angular distribution. They need to be able to look at a whole range of angles.

Imaging a sphere is a really good way of doing this. Because of the shape of the surface, imaging a sphere gets all kinds of angles of incidence when moving over the surface.




The helium images above are of glass microspheres at two different working distances. They are all quite similar, although one is a bit dirty. They have the same shape


Different angles to the left and different angles to the right


This sphere has got a bit of dirt on it


There is a shadow here (this will be explained later)

For the sphere itself the pattern across each one is very similar. The researchers found that very interesting because they thought that different materials would behave quite differently.

It turns out that the scattering is all rather similar.

In fact, it looks like a cosine distribution.


The cosine distribution is based on the local surface normal. The local surface normal is the normal line perpendicular to the surface at that point


Surface normal


A normal to a surface at a point is the same as a normal to the tangent plane to that surface at that point.

A surface normal, or simply normal, to a flat surface is a vector that is perpendicular to that surface. A normal to a non-flat surface at a point P on the surface is a vector perpendicular to the tangent plane to that surface at P. The word “normal” is also used as an adjective: a line normal to a plane, the normal component of a force, the normal vector, etc. The concept of normality generalizes to orthogonality.

In the two-dimensional case, a normal line perpendicularly intersects the tangent line to a curve at a given point.

So, as you move away from the surface normal the signal drops as a cosine function and eventually reaches zero at 90o.

From the images, the researchers can’t really say they are cosine, but they look pretty close. This is interesting because they thought many surfaces would reflect in a different way.

A normal reflection would see the outgoing beam of atoms leaving the surface at the same angle as the incoming beam with respect to the normal.


Above right: Simplified schematic of a scanning helium microscope (SHeM), showing the principle of operation. The helium beam is formed in a supersonic expansion, then collimated by a skimmer and pinhole. Atoms scatter off the sample and those that enter the detector are counted. The image is formed by rastering the sample position. The close up shows the key parts of the instrument that are relevant to the current simulation framework, including the sample position and the mounting plate for both the pinhole and detector apertures. In the current Cambridge SHeM configuration a ≈ 2.1 mm.

So, the researchers were expecting that if the incoming beam was 45o to the normal then the outgoing beam would produce a scattering angle of 45o.

Instead they saw the atoms come in and seem to “lose” all memory of the direction from which they came and they scattered with the cosine distribution based on the local orientation of the surface.

That was really interesting.

Ray tracing simulations

So, the researchers used ray tracing simulations to investigate what was going on a bit more and to analyse the results.


The four possibilities at each iteration of a ray being traced. Normally, the ray will ‘continue’ to its next iteration, but can also be ‘detected’ when it hits a suitable surface, can be treated as having ‘left’ the simulation volume, or can be ‘discarded’ if it exceeds a certain number of steps or trajectory length. The incoming cone (marked in checkerboard pattern) is not included in the simulation.

The idea was to repeat the experiment in a computer. This involved creating a computer model of the helium microscope and using it to test out the different assumptions and reproduce the images.


Simulation works by taking the beam


Beam comes in here


Scatters from the sample


Scatters with a particular distribution which can be controlled


And some of the atoms goes through


To the detector

The atoms are counted and the image is built up


Alternatively, if the atoms don’t go into the detector they can be allowed to bounce around.


Bounce around multiple times in this geometry. The same geometry as the actual microscope.

If the atoms spend too long or leave the central region, they can be removed but otherwise they just bounce around until they eventually reach the detector.

So simulated images can be built up in exactly the same way as the real microscope. Based on an assumption about the scattering the researchers found that when they did the simulation and compared the result with the actual experimental result, they were remarkably similar.


Above left is the experimental results and above right are the simulated results. The simulation gives exactly the same shadow and almost the same distributions across the sphere. The experimental result had a little extra structure which isn’t in the simulation because it was dirt.

The researchers explored other distributions that they didn’t think would work as well. If they used something like a reflective beam rather than cosine scattering, they got a result that didn’t look right.


Broad specular scattering. It doesn’t look right

So, if they have a reflective beam and it is broadened a bit to allow for the surface being a little rough it simply doesn’t look like the simulation or the experiment. They really do see the cosine distribution.

Complex structures

The idea of ray tracing is really helpful, generally. Another example of where the researchers try to use it, is to try and understand what is going on. So, they had a test sample made, which was a series of trenches machined on a microscale and placed on a substrate, and imaged it with the helium beam.


The method can explain relatively complex structures such as nano trenches of different depths

You can see towards the right a shallow trench and going towards the left there are dark patches.


The beam follows the blue arrow path but if it hits the corner the beam can’t get out to the detector. The red arrow shows the path of the beam if it was able to leave the trench.

There are particular angles that the beam can reach the detector.

As the trench gets deeper more of the atoms get trapped and the shadowing increases. On the other hand, when the trenches get really deep, they suddenly go completely grey. Initially the researchers didn’t understand why this happened until they did simulations.


This is due to multiple scatterings of the atoms when they have entered the trench

What causes the greyness is that the atoms enter the trench and bounce around and around. When they eventually leave, they are completely randomised and so the net effect is that the whole trench appears grey. The researchers were able to use this idea and repeat the experiment on the computer to really understand what was going on in the images.

Generally, this is a useful technique. Do the experiment and then run a simulation of the experiment. If the simulation doesn’t give the experimental result then modify the simulation and run it again. Keep doing this until the simulation and the experimental results match. This helps the researchers to understand what is going on in the real system.

The researchers found the discovery of the scattering cosine scattering very exciting.



The “circle” represents the cosine distribution. This means the length of an arrow to the circle represents the intensity of the beam in that direction. So, if you know that angle then you know the intensity.

So, if the researchers are expecting a cosine distribution and most of the surface seems to scatter with a cosine distribution then by measuring the strength of the beam, they know the angle at which the beam hit the sample.

The researchers can take measurements in several different directions (at least three) and work out the complete orientation of that little bit of surface that the beam is scattering from. They can work out the local surface angle.

If the researchers know the orientation of that part of the surface, they can work out the whole profile of the surface.

Example: Demonstration of the principle

The researchers essentially take a series of different images from different angles.

Below is a series of 4 images taken from 4 different quadrant directions.

They then used the cosine distribution to gain information about the local surface orientation of the pixel that corresponded to it (surface gradient for each pixel).


These 4 images here are still simulations

Integrate all the gradients in order to give the complete surface profile. So, the 4 images above were combined in order to give this complete surface profile

They are still simulations because the research group is still building the machine that will do the experiments for real in the lab,

There is an actual technique with light called photometric stereo

Photometric stereo is a technique in computer vision for estimating the surface normals of objects by observing that object under different lighting conditions. It is based on the fact that the amount of light reflected by a surface is dependent on the orientation of the surface in relation to the light source and the observer. By measuring the amount of light reflected into a camera, the space of possible surface orientations is limited. Given enough light sources from different angles, the surface orientation may be constrained to a single orientation or even overconstrained.

So, the researchers called their technique heliometric stereo

Contrast: Shadowing and masking

This is a new technique to give a complete surface profile and because helium is being used there will be no damage to the sample. This will give the true profile being looked for.

No matter how delicate the material the surface structure is being seen properly

Actually, much more going on that Dr Jardine didn’t have time to explain

Shadowing and masking

Image formation in the scanning helium microscope


If a beam of helium is sent towards a 3D structure there is a region of the surface where the beam can’t get out to the detector and there is a region of the surface the helium atoms can’t “illuminate” because the beam can’t get in or get out again. These produce shadows and masks.


The 3d structure


SHeM micrograph of a hexagonal TEM grid produced with the Mark II scanning helium microscope using a 3 micron step size (scale bar is 100 microns in length). The helium beam strikes the sample from the right side of the image, with the detector aperture sitting to the left. Suspension of the grid off the substrate with carbon tape yields the strong helium shadows observed beneath the grid.

You can see the effects outlined above in the real images of a grid (see the image above). The grid was suspended above the surface. The grid can be seen as well as the surface, the shadowing and the masking that occurs in that system.

Contrast: Quantum effects

The surface of the samples is made up of atoms

Helium “sees” a periodic array of atoms when it scatters

The helium atoms “diffract” in similar way as light from a diffraction grating. It is something that can be seen.

Observation of diffraction contrast in scanning helium microscopy – PubMed (


(a) Overview of the Cambridge scanning helium microscope. The instrument consists of a helium beam source and differential pumping stage, after which the beam is collimated using a pinhole aperture. The microprobe is incident on a sample, and scattered atoms are transferred to a high sensitivity detector. The pinhole plate defines the way in which contrast is generated. (b) Schematic showing the pinhole plate and how the sample is moved during a z scan, including those variables that are changed as the pinhole to sample distance is increased. Since the incoming beam is oriented at 45° to normal, when the sample moves in z it also needs to be shifted laterally to ensure that the same part of the surface is kept illuminated. When the sample to pinhole distance is changed, both the outgoing angle of the gas that is detected and the solid angle of the detector aperture also change.

Explaining the diffraction is a bit difficult to explain. One of the ways that the effect can be seen is to take the sample and slide it along the diagonal line indicated in the below centre image, keeping the beam pointing at the same spot on the sample surface.



Then the outgoing angles measured are changed


Above image: You can see from this point the outgoing angle, but from another point there is a different outgoing angle.

Researchers can look at the different scattering angles from the same spot on the surface and if they have a simple distribution like the cosine effect, they usually see a nice smooth variation.


Plot of a z scan taken from a sample exhibiting diffuse scattering (highly oriented pyrolytic graphite, blue points) and the change in detector aperture solid angle (orange curve) during a z scan. The specular condition is labelled with a dashed line. As the distance between the sample and pinhole is varied, the majority of the change in the detected flux is due to the change in solid angle of the detector aperture. The remaining variation is due to the change in transmission probability through the detector cone.


When the sample slides along the direction indicated in the image above and helium atoms are being diffracted something more complicated happens.


Simulated z scan on LiF using the simplified diffraction model described in the text and shown in the inset, to illustrate the general form expected with diffractive scattering. The orange curve illustrates the diffuse component of the scattered helium, while the blue curve illustrates the total scattered beam including both the diffractive and diffuse components. The peaks in the z scan correspond to different diffraction orders entering the detector aperture. The specular condition is labelled with a dashed line. (Inset) shows the representative diffraction pattern for a helium beam at 298 K with 45° incidence. The lattice is rotated anticlockwise by 14° to match the experimental setup described later. Note that diffraction peak heights are not calculated rigorously, and simply reduce in intensity around the specular beam. The large detector aperture (shown as a red circle) leads to the possibility of multiple peaks entering the detector at once. This is seen on certain surface in the microscope.

When the atoms diffract it means that as the researchers pass that particular diffraction angle that corresponds to the diffraction peak, they see peaks and troughs in the profile and there are certain surfaces that can be chosen where the effects are seen,

Diffraction contrast

If the researchers take different images under different imaging conditions they can be combined. It offers them the ability to choose which images to combine in order to pick out even more detail. Images are enhanced by diffraction


Above shows two images of the same LiF surface. Taken under different conditions, distances


Combining the images together produces an enhanced image where different features can be picked out. The bluey/purple shade shows the nice flat surfaces and pieces of surface tilted at different angles are appearing as the bright yellow regions.

The researchers are just beginning to understand how to use all the techniques.

What are the next steps?

Build a new better, faster and higher resolution microscope. Cambridge is working on this at the moment and hope to take images with it in the next few weeks.


The new microscope will allow them to use 4 detectors simultaneously to do the 3D imaging. The orange pipes shown in the inset image lead to the detectors.

At the moment research groups have to design and build the helium microscopes themselves as the current commercial ones are not good enough. The aim is to work with a company to make a decent commercial product.

Cambridge will be researching further into how the images are formed. Researching how the diffraction contrast mechanism could be used. There are several other mechanisms that are unique to helium that they can potentially use.

The group wants to gain new insight into materials by using helium microscopy.

They want to use the technique more often and encourage other scientists to use it too.


Helium microscopy is an exciting new type of microscopy.

It can be used to image surfaces that are otherwise impossible to see.

The research group are still learning how the technique works and they believe it is going to be very useful

Finding out more


You can “play” with the helium microscope yourself

Seeing with Helium Atoms (Android)

‎Seeing With Helium Atoms (Apple)

Learn more!

A lot of information can be found on the web



Matt Bergin and Sam Lambrick produced some of the images for the lecture

Glasgow made the aperture and will make the zone plates


Questions and answers

1) What is the “Quitting” surface made from?

It isn’t actually a real thing. It’s a representative surface.

It’s a line we pretend exists. It’s the position where the atoms stop interacting with each other.

It represents the transition from the atoms bouncing off each other to not bouncing off each other.

2) Why is it bad if a sample becomes charged?

If it becomes charged it stops other particles from scattering normally from the surface. So, if you are imaging with an electron microscope, when the electrons come in, they interact with the sample and then get scattered.

If the surface becomes charged the atoms can’t reach its surface. They get repelled early and the image is blurred. All of the resolution is lost from the image.

3) How does helium compare with an electron microscope? How does your microscope compare to the enormous diamond light source in resolution?

Diamond is an X-ray source, scanning transmission X-ray microscopy. It is very similar to the helium method. You can use the Fresnel zone plates to image with but if you do image with X-rays you are using very high energy electromagnetic waves. These can do a lot of damage to the surface.

There are lots of different imaging techniques and they tend to be good for different things.

X-rays are good for imaging but there is a risk of damage.

4) What about the accuracy between the different methods?

Electron microscopy can see objects as small as about 1nm.

Helium is going to almost as good. Researchers are working on improving it. They can see objects as small as 0.5 microns at the moment. This is better than a typical optical microscope. The aim is to replace the pin-hole with a Fresnel zone plate which will improve the resolution to between 10 and 50nm. Ultimately 10nm resolution is the aim. This isn’t quite as good as an electron microscope but much better than optical.

5) Why use helium atoms?

Helium is chemically inert. The danger with hydrogen is that it might react with a surface (although this might be desirable).

Whichever gas you use there is going to be some background signal with the mass spectrometer. You just need to know that the mass spec. signal is much greater than the background in order to see it. Helium has a relative atomic mass of 4 and a very low background. Nothing else has this very low background in relation to the mass. Hydrogen, in comparison, exists as a diatomic molecule (H2) with a molecular mass of 2 that unfortunately has a background signal exactly equal to its mass spec. signal. The background signal is primarily caused from other residual gases that find themselves in the detector.

Trying to detect the desired signal from the background is a relatively boring technical job.

6) How do you introduce colour into the images?

The colours are the operator’s choice. They are entirely false colours. The idea is to take two different images of the same thing. Covert one image to yellow and the other to blue, and then combine them together to give the false colour image. This provides a method of picking out different parts of the surface.

7) Why don’t you get multiple reflections in shallower trenches so they grey out?

You do get a small amount of it. If the beams hit an inside corner of the trench there is a small number of atoms that will be scattered around the trench and produce a little diffuse “illumination” around the edges but basically the primary beam comes in and the majority of the atoms are able to leave. The cosine distribution dominates.

At the deep trenches diffuse “illumination” becomes dominant.

8) Wouldn’t simultaneously beams of helium be difficult to record as they might collide with each other from different angles.

Actually, there is only one beam of helium and four detectors.

9) Are the images made up from layering two different 2D images.

No, the image is simply made up of two different images.

10) Could helium microscopy replace other types in the future and can you only get black and white images?

Colour doesn’t apply to helium. It’s not a factor in how the microscope works.

We can use false colour to pick out things but it’s not a natural colour.

Helium won’t really replace the other methods of microscopy. The electron microscope produces amazing images as does the optical microscope but there are things you just can’t do with them like imaging delicate things such as wax, which would melt in an electron microscope.

Helium is a technique in addition to others. It is used when appropriate. A typical materials science laboratory would aim to have several electron and optical microscopes and one helium microscope for the very challenging materials.

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