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Tomography: CT Scans to 3D Printing

This article briefly covers the history and some applications of the x-ray portion of the electromagnetic spectrum while describing how humans are able to manipulate the fundamentals of particle physics to advance our understanding of the natural world. Within the past few decades the use of x-rays in medical science has evolved from being able to create 2-dimensional representations of internal structures, to the construction of sophisticated 3-dimensional models using Computerized Tomography (CT). Radiology is widely used by physicians from various sub-fields to diagnose internal issues without the need for invasive surgeries. With additive manufacturing (e.g. 3D printing) becoming financially feasible in the past decade, some scientists are experimenting with coupling the two technologies to create highly accurate models with features below 1 micron in size. Unfortunately for the hobbyist within the maker community, CT machines are costly to use and do pose a risk of radiation exposure and therefore are not easy to gain access to. On the bright side, more researchers and institutions are recognizing the potential of these machines and make their data easily accessible to the public for experimenting with; for a list of websites with free data downloads see the bottom of this page.

This sample comes from the patient dubbed ‘Adam’; the original file is composed of 245 cross-sectional views of the cranium. Using the open-source medical imaging software InVesalius, I toggled with the density thresholds to remove soft, muscle and fat tissue to be left with a model representing the dense(r) bone and enamel. Data credit - The Visible Human Project

Many associate the term 'radiation' with a negative connotation that carries with it the chance of tumors and cancer. On the contrary, much of the electromagnetic spectrum (EMS) is non-ionizing, meaning it does not contain enough energy to be harmful to humans (specifically our DNA). Radiation is emitted from atoms when their orbiting electrons are ‘excited’ by an outside energy source (collision with other particles) causing it to leave its stable ground state and move to a higher orbiting shell. While residing in this new excited state for approximately zero seconds, the electron carries with it the energy it obtained from the impact with the outside energy source. After its excitement, it returns to the previous orbiting shell and releases that excess energy as a photon in the process. The resulting photon that is radiated from the atom will contain the amount of energy that is required for the electron to advance from its ground state to the higher orbital shell. To emit radiation containing higher energy, outer electrons need to jump further from their ground state to an excited state and closer to the nucleus of the atom so that during their de-excitement the resulting photon will contain more energy.

X-rays are a form of radiation within the EMS that travel in wavelengths between .01 – 10 nanometers; this places them between the Ultraviolet (UV) portion and actually overlaps with the Gamma ray portion indicating energy levels high enough to be ionizing. Because of their wavelengths, x-rays are able to easily pass through some thinner and less dense materials, but due to their high frequency, they attenuate rather quickly and cannot pass through denser materials such as bones, teeth and metals. This makes the use of x-rays or, radiology, extremely useful in the field of medicine as it allows for the viewing of bones and some harder tissues in a non-invasive manner.

A hand drawn illustration depicting one of the ways radiation can be formed: a particle of a certain wavelength with enough kinetic energy passes its energy to an electron of an atom temporarily exciting it to another orbital. Almost instantly, the electron returns to its previous orbit, emitting a photon in the process. The wavelength of the photon emitted is dependent on the distance from the excited state to its original ground state. Photo credit - Nrao

A cartoon diagram illustrating the electromagnetic spectrum (EMS). Scientist set the boundary between ionizing and non-ionizing radiation with energies between 10-33 electron-volts (eV). This puts the boarder inside the UV portion of the spectrum. Rule of thumb: the shorter the wavelength of light, the higher amount of energy it can carry, but the faster it attenuates in the medium it travels through. When exposed to enough ionizing radiation, you increase the chances of damage to DNA which could lead to mutations in cell biology and potentially cancer. Humans are exposed to about 3.65 millisieverts (mSv) per day just from background radiation alone; it would require 2200x that amount in a single dose to be fatal, or, about 81,632,654 bananas worth of radiation. Photo credit - Mini Physics

X-rays were originally discovered by Professor Wilhlem Roentgen while researching at Wurburg University in 1895. Roentgen like many at the time, were experimenting with cathode ray tubes, when he accidentally made the discovery of a new portion of the electromagnetic spectrum. While introducing electrons into the vacuumed tube to interact with different types of metal, he noticed some crystals in his office were radiating fluorescent light even after he covered his tube with a thick paper. He later came to realize that whatever this new light may be, it was able to pass through thin materials but were absorbed by denser ones; without a name, he dubbed them ‘X-Rays’.


The uses of x-rays were immediately popular in the medical field as it allowed physicians to view denser tissue in detail giving an alternative to invasive procedures such as surgery. X-rays are used with special radiographic film that is sensitive to light with x-ray wavelengths. The film, when unexposed is white, and when fully exposed is black. As x-rays are shot through the target, they are partially absorbed by the denser materials, while the remaining x-rays make an impression on the film creating what looks like a grey shadow of the target. The radiographic film is similar to photographic film in that it utilizes silver halide crystals immersed in gelatin called an emulsion layer. The crystals are made up of loose anions and cations (either silver bromide or silver chloride), which, when introduced to light (negatively charged electrons) causes the atoms of the crystals to restructure themselves forming a latent image in the process. The film is then developed by being immersed in a series of chemical baths; the latent image reacts with the solutions to create metallic silver which produces an image visible to the human eye.

All x-ray machines operate in a similar way by utilizing an x-ray tube which is a thick glass tube that is completely void of atmospheric gasses by use of vacuum and is partially surrounded by Lead or Aluminum casing to reduce harm from ionizing radiation. The system consists of a cathode emitter, an anode target attached to a rotating surface, and a difference in electrical charge between the two. To produce x-ray radiation, the cathode emitter is heated at a low intensity giving energy to its electrons and allowing them to be liberated through thermionic emission. Due to the difference in charge, the freed electrons are then accelerated towards, and collide with, the anode target which is usually a piece of reactive metal like Tungsten or sometimes Silver. The anode usually sits on top of a rotating disk which is spun to help distribute the heat energy the Tungsten gives off as it is being bombarded by high energy particles. Sometimes the anode sits in in water or oil to absorb thermal radiation for the same reason.





















Some of the electrons will approach the atoms of the anode target at high speeds before being acted upon by the electromagnetic forces. These forces either slow the electron down as it passes through the field, or completely stops it. The kinetic energy that is lost by the electron in its change in speed is either absorbed by the atom, or it’s emitted as x-rays; this is referred to as Bremsstrahlung or, Braking Radiation. This adheres to the law of conversation of energy where energy cannot be created or destroyed, instead it must transform from one form to another and maintain balance. Therefore, the wavelength of the x-ray that is emitted is dependent on how much the electron is affected by the force of the atom: the more kinetic energy the electron loses, the more energy the resulting x-ray will have and the shorter its wavelength will be. X-rays with the highest amount of energy and the shortest wavelengths are produced when electrons are completely immobilized by the atom. Because the electrons emitted from the cathode travel with such high kinetic energy, they also have the potential to knock out an electron within the target atom’s inner orbital shell. If this occurs, an electron from a lower orbital shell will jump to a much higher orbital shell in an excited state to fill in; it releases an x-ray as it de-excites back to its initial ground state.

The conventional design for a cathode (x-ray) tube: thick glass housing (H), some sort of fluid used to absorb thermal radiation (O), cathode containing a metal which is heated with low-voltage electricity to free electrons via thermionic emission (C), anode which attracts accelerated free electrons with a polar charge (A), target metal, sometimes Tungsten or Silver used to produce x-ray radiation (T), motor that rotates to cool down target metal and mitigate temperature increases from inside the container (R), open window for x-rays to be emitted from, towards the object of interest (W), vacuumed and void of atmospheric gases (E), Photo credit - Radiopedia

A diagram illustrating the portions of a typical photographic film. X-ray film works in a similar way, creating an image with the use of light sensitive silver halide crystal that are affected and leave a latent image when exposed to light. This latent image becomes pronounced after the film soaks in a series of solutions. X-ray film typically has a layer of blue tint that is added to reduce the strain on the developer's eyes when developing film for long periods of time. Picture credit - Afterness

Due to risk of radiation exposure, Lead is used in most protective garments and as a shield as it is a very stable element with a large nucleus and high amount of electrons within its orbital cloud. With more electrons, the cloud is denser making it much harder for fast, high energy particles to knock out an electron before being slowed down by the electromagnetic force created by the atom. Aluminum is also used as a protective tool against ionizing radiation. When x-rays are formed by the de-excitement of electrons, sometimes the photons created do not have enough energy to be useful for creating radiographic images, however they are still dangerous to the patient. Filters made of Aluminum are used to completely block low energy x-rays from reaching the patient, while still being thin enough to allow high energy x-rays to pass through.

An improvement to radiographic film and x-ray imaging is the use of Computerized Tomography (CT) which utilizes the same basic principle, however constructs a 3-dimensional model instead of just a 2-dimensional image. Before, radiographic film would only allow physicians to peer through soft tissue and all the denser objects in view would be superimposed upon one another. A CT scan corrects this issue by having an x-ray emitter stationed to a gantry which rotates around the target in 360 degrees with a receiver on the antipode collecting the data in real time. The computer can then take those cross-sectional views and construct a 3D model that can be viewed from any angle. Computer software can even remove segments of the model based on there density which is calculated by the intensity of light that was recorded during the initial scan.

A cartoon illustration depicting how CT machines work.: the target lays on a slow moving table which travels perpendicular to the gantry. The target is scanned slice by slice as they move through the opening; on the opposite side of the gantry is a receiver which acquires the remaining x-rays that are not absorbed by the denser parts of the target. The machine then relays this information in real-time to a computer which can reconstruct a 3D model allowing physicians to peer into the target. Photo Credit - Cyberphysics

The data obtained from the CT scan is stored as a series of lossless digital images (usually TIFF files to preserve the quality) in the Digital Imaging and Communications in Medicine (DICOM) format. A DICOM file binds the images of the CT scan together along with metadata associated with the patient and the scanning procedure. Using open-source medical imaging software such as InVesalius, users can construct 3D models from these images. The software can also determine the varying densities within the target allowing users to isolate or remove specific segments. Since the software's purpose is to model the target in 3D, exporting the data as a Wavefront (.obj) or STereoLithography (.stl) file is a breeze. With the exported 3D file,  all that is required is minor clean up using Blender and then it is ready to be printed using your choice of printing software.

Adam's skull is ready to be printed... once I get a printer.

CT Scanning Applied to Coral

Although CT machines are almost exclusively used by doctors in the medical fields, researchers in other fields of science also utilize this technology to increase their understanding of their subjects and to construct models of them. One application of CT scans applied to coral reef ecology helped researchers quantify how much coral is being lost due to bioturbation and acidifying ocean water. Although coral may appear healthy from the outside, scientist have found that by using CT scanners, they are able to measure how the acidity is making the structure weaker and less dense which is analogous to bones developing osteoporosis. Coral structures are created in successive layers by polyps which sequester calcium from the ocean water and secrete calcium carbonate forming vast habitats for millions of marine organisms. However, due to an increase in acidity caused by anthropomorphic climate change, polyps and other calcifying organisms are being forced to work harder than before to sequester calcium resulting in weaker structures and degrading health. You can see the video animation below or, read the article or the publication.

By knowing the initial volume of the limestone tiles, the research team were also able to quantify how much coral is lost by dissolution and bioturbators in a year by measuring the remaining amount with a CT scanner.

Another use of CT scanning technology applied to coral was done by Carlos Gonzalez Uribe supervised by Dr. James Weaver at the Wyss Institute for Biologically Inspired Engineering. With the Mediated Matter group, Uribe combined the beauty of biology and state-of-the-art technology to model and print an individual coral structure; see the CT video scan below.

© 2023 by Jordan Pierce

List of available DICOM Data
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