Seeing Atoms!

Jun 19, 2019

Cell-phone manufacturers today constantly advertise the specs of their cameras. It is not uncommon for phones to be able to zoom in by 10x and click a great picture. But what if you wanted to zoom in more, like a lot more? What if you wanted to zoom in so much that you could see atoms? Well, you would need a very fancy camera - the electron microscope.

It is said that seeing is believing. About twenty-five hundred years ago, the Greek philosopher Democritus coined the word ‘atom’, meaning uncuttable. Democritus believed that all objects were built up of indivisible units called atoms, and that the properties of an object were a manifestation of the atoms that composed it. It took almost twenty-five hundred years for humans to actually ‘see’ atoms, and it is worth looking at some of the technology that has made this possible today.

The resolution of the naked eye is around 50 microns, which is about the thickness of a very thin hair. Most bacteria are about 1 micron in size, which is why it took humans a long time to figure out that they can cause diseases – we just couldn’t see them until about three hundred years ago when Dutch microscopist Antonie van Leeuwenhoek used a homemade optical microscope to see bacteria for the first time. Optical microscopes are routinely used today to analyse human tissue and diagnose diseases (Figure 1).

Figure 1. Human stem cells viewed using dark field optical microscopy. The colours are due to fluorescent molecules that are used to tag different parts of the cells. The scale bar at the bottom reads 10 microns, which is well below the resolution of the naked eye. Image courtesy of Dhiraj Indana, Chaudhuri Lab at Stanford University.

Optical microscopes are limited in resolution by the wavelength of light, which is about half a micron for visible light. As shown below, two closely spaced objects cannot be resolved optically because an optical system cannot collect all the light scattered by the two objects. The partially collected light forms a distorted image due to the wave nature of light (Figure 2).

Figure 2. Resolution limit of an optical system due to scattering/diffraction effects

It took about two hundred years after the invention of the optical microscope for humans to surpass the optical resolution limit. In the 1920’s, the wave nature of electrons (and all matter) was realized with the advent of quantum mechanics. At that time, German scientists Ernst Ruska and Max Knoll were working on cathode ray tubes for imaging large objects (these devices were basically primitive electron microscopes whose resolution was worse than optical microscopes). When Ruska and Knoll learned that the wavelength of electrons was many orders of magnitude smaller than light in 1932, it became clear to them what great potential lay in using electrons to image matter. In theory at least, it was possible to image atoms using electrons! Ruska quickly created a design for an electron microscope and in 1933, the resolution of the optical microscope was surpassed.

Over the next few decades, electron microscopy was advanced by research groups and companies mostly based in the UK, USA and Japan. In the 1970s, Albert Crewe of the University of Chicago pioneered major innovations in the electron microscope and obtained the first atomic resolution images using an electron microscope.

Figure 3. Albert Crewe’s image of Thorium atoms

Electron microscopes have come a long way since Ruska’s time. Modern electron microscopes routinely achieve atomic resolution images and have the capability to perform various chemical measurements at the atomic level. The fundamental design of an electron microscope, however, has changed very little since its inception. Figure 4 below shows how an electron microscope works relative to an optical microscope and as one can see, the similarities are striking. Essentially there is an electron source followed by optics that condense/spread the electron beam. The electron beam then travels through a thin specimen and goes on to form an image.

Figure 4. Light microscopy v/s electron microscopy

Despite this seemingly simple working principle, the electron microscope looks a lot more complex and intimidating than the humble optical microscope (Figure 5). This is largely because electron optics dictates that the microscope column be about a meter long. In addition to this, the walls of the electron microscope need to be thick enough to shield users from harmful x-rays that are emitted as a result of electron-matter interactions.

Figure 5. Optical microscope (left) v/s electron microscope (right). The difference in size and complexity is striking, given the very similar principle of operation.

Now that we are done talking about the scientific history of the electron microscope, let us look at some images of atoms! (These are images I recently captured with one of the electron microscopes at Stanford)

Shown below is an atomic resolution image of a Germanium crystal (Germanium is a semiconductor, just like Silicon that’s used to make the chips in your devices). Each dot is an atom! One can see the structural arrangement of atoms, i.e., the crystal structure very clearly. Also seen is the scalebar, which reads 10 nanometers.

Up next we have an amorphous carbon film! ‘Amorphous’ means that atoms are randomly oriented, and that’s exactly what is seen below.

And finally, we have some nanoparticles! The image below shows Cadmium Telluride nanoparticles (commonly called ‘quantum dots’) circled in yellow sitting on an amorphous carbon film.

And the same image zoomed in… one can clearly see the contrast between the amorphous carbon and crystalline quantum dots.

Isn’t this amazing? You are able to see the very constituents of all matter in the universe, right in front of you!

Electron microscopes have been one of the driving forces for the nanotechnology revolution over the past few decades. There is no doubt in my mind that this will continue, with newer electron microscopes being able to do high resolution imaging and analysis along with in-situ studies in parallel. The only downside is that electron microscopes are very expensive – a new high resolution microscope can easily cost more than a million dollars (that’s 7 crore rupees!) and there are no manufacturers in India. Hopefully this will change in the coming decades as India continues to advance in scientific research and instrumentation development.

Feel free to reach out to me ( for more amazing pictures like the ones above!

Joel Martis Archives: 

By Joel Martis
Joel Martis is a PhD candidate at Stanford University working on developing new imaging techniques in electron microscopes.
To submit your article / poem / short story to Daijiworld, please email it to mentioning 'Article/poem submission for daijiworld' in the subject line. Please note the following:

  • The article / poem / short story should be original and previously unpublished in other websites except in the personal blog of the author. We will cross-check the originality of the article, and if found to be copied from another source in whole or in parts without appropriate acknowledgment, the submission will be rejected.
  • The author of the poem / article / short story should include a brief self-introduction limited to 500 characters and his/her recent picture (optional). Pictures relevant to the article may also be sent (optional), provided they are not bound by copyright. Travelogues should be sent along with relevant pictures not sourced from the Internet. Travelogues without relevant pictures will be rejected.
  • In case of a short story / article, the write-up should be at least one-and-a-half pages in word document in Times New Roman font 12 (or, about 700-800 words). Contributors are requested to keep their write-ups limited to a maximum of four pages. Longer write-ups may be sent in parts to publish in installments. Each installment should be sent within a week of the previous installment. A single poem sent for publication should be at least 3/4th of a page in length. Multiple short poems may be submitted for single publication.
  • All submissions should be in Microsoft Word format or text file. Pictures should not be larger than 1000 pixels in width, and of good resolution. Pictures should be attached separately in the mail and may be numbered if the author wants them to be placed in order.
  • Submission of the article / poem / short story does not automatically entail that it would be published. Daijiworld editors will examine each submission and decide on its acceptance/rejection purely based on merit.
  • Daijiworld reserves the right to edit the submission if necessary for grammar and spelling, without compromising on the author's tone and message.
  • Daijiworld reserves the right to reject submissions without prior notice. Mails/calls on the status of the submission will not be entertained. Contributors are requested to be patient.
  • The article / poem / short story should not be targeted directly or indirectly at any individual/group/community. Daijiworld will not assume responsibility for factual errors in the submission.
  • Once accepted, the article / poem / short story will be published as and when we have space. Publication may take up to four weeks from the date of submission of the write-up, depending on the number of submissions we receive. No author will be published twice in succession or twice within a fortnight.
  • Time-bound articles (example, on Mother's Day) should be sent at least a week in advance. Please specify the occasion as well as the date on which you would like it published while sending the write-up.

Comment on this article

  • Clement Lobo, Chickmagalur/Melbourne

    Sat, Jun 29 2019

    Hi Joel

    It’s great to see about your contribution in writing about the topics which are interesting. Wish you well and hope to see you enterprising.

    I’m keen in pushing forth in Australia about clean energy and Climate control you previously wrote which will be our future history

    Clement Lobo

  • Vincent D'sa, Dubai/Pangala Parish

    Mon, Jun 24 2019

    Good article. Try to be a regular over here. Young readers need stimulative and scientific reading content and at the moment they are fed less.

  • felix and shanthi d costa, urwa mangalore

    Sat, Jun 22 2019

    Dear Joel Martis
    thank you for your article and taking trouble in spite of your hectic schedule.
    please send such articles in future also for us
    May God bless you.

  • Jean Lobo (Benny), Mangalore

    Fri, Jun 21 2019

    Joel, all the best to you in all that you do.

  • Eric Rodrigues, Mangalore

    Fri, Jun 21 2019

    Mr Martis, congratulations and keep writing and enlighten us. Show us the nano particles which created the matter in universe which scientists are working on now. Good job Joel.

  • Tony Tauro, Mary Hill Mangalore

    Fri, Jun 21 2019

    Hi Joel....Very Impressive and Informative.. Keep Going, All the Best

  • Mercy Martis, Abu Dhabi

    Thu, Jun 20 2019

    Very Nice Joel....

  • Dr Edward Nazareth, Mangaluru

    Thu, Jun 20 2019

    Nice one, Informative article...Keep writing Joel.

  • Sunil, Mangalore

    Wed, Jun 19 2019

    Very Informative Joel , Keep it up.!!!

  • griffith, KULAI

    Wed, Jun 19 2019

    NICE ONE JOEL.....

Leave a Comment

Title: Seeing Atoms!

You have 2000 characters left.


Please write your correct name and email address. Kindly do not post any personal, abusive, defamatory, infringing, obscene, indecent, discriminatory or unlawful or similar comments. will not be responsible for any defamatory message posted under this article.

Please note that sending false messages to insult, defame, intimidate, mislead or deceive people or to intentionally cause public disorder is punishable under law. It is obligatory on Daijiworld to provide the IP address and other details of senders of such comments, to the authority concerned upon request.

Hence, sending offensive comments using daijiworld will be purely at your own risk, and in no way will be held responsible.