3D Biology: From The Microscope To The Printer.

EMpics 930x357 3D Biology: From The Microscope To The Printer.

This is a guest post by Louise Hughes who currently has a Kickstarter campaign for Human Chromosome Jewellery

Microscopy is a staple technology in the biological sciences and is not only informative but often quite beautiful. There are now numerous different types of microscopy used to study biology, the main ones using a beam of light or electrons (light and electron microscopy respectively) or a mechanical probe (focused ion beam microscopy). Micrographs (the images produced by a microscope) often contain a great deal of information, but are two dimensional representations of three dimensional samples. This can be problematic when attempting to correctly interpret structural information. In recent years the advent of three and four dimensional imaging has been used to address some of these issues.

Electron Microscopy

Electron microscopy is an area that has shown a significant boom in 3D imaging. Electrons behave in a similar way to light when accelerated through a vacuum and are focused using electro-magnetic lenses. Transmission electron microscopes (TEM) shine the beam of electrons through a thin slice (usually 50-70nms thick) of tissue. Electrons are deflected by structures and stains in the sample. A CCD camera or film records the resultant, x-ray-like image. Scanning electron microscopes (SEM) use a beam of electrons that is focused to a point or spot. That spot scans across the surface of an object. The beam electrons penetrate into the sample and interact with the atoms, either reflecting the main beam electrons back (backscattered electrons) or exciting atomic electrons, causing them to be emitted (secondary electrons). SEM results in an image that appears to be three dimensional but doesn’t contain any useful and quantifiable data in the z-axis, even using stereo-paired images (created by tilting the sample slightly between taking two separate images).

What is 3D Electron Microscopy

3D electron microscopy was developed for the TEM in the 1950’s using a technique called serial sectioning. Several sections of a sample are cut, positioned on a support surface (a grid) and imaged. The images are combined and a 3D model is built from the data. With the advance of computing technology this technique is relatively simply today, although it must have been quite a challenge several decades ago. Other, more recent, 3D TEM techniques include single particle analysis and tomography. Single particle analysis involves taking numerous 2D images of randomly orientated samples (for example, viruses) and analysing their three dimensional structure. Tomography involves taking a series of 2D images and tilting the sample between images over a large range of angles (for example, every 1° over 140° range). This essentially recreates a CT scan inside the microscope. Scanning electron microscopy also has a range of 3D techniques including FIBSEM (focused ion beam SEM), SBFSEM (serial block face SEM) and array tomography. Each of these techniques involves cutting serial sections and either imaging the sample after each cut (FIB and SBFSEM) or the sections themselves (as with serial section TEM).

3dEM3 930x719 3D Biology: From The Microscope To The Printer.

Microscopy and Printing

3D microscopy presents an interesting problem. Most publications require 2D images or figures. There is an emerging and relatively recent technology that appears to be an ideal solution for the type of data we produce. 3D electron microscopy data volumes are constructed as a series of slices. We can display this data by generating a surface model and take snapshots or create movies of the model. 3D printing also uses data broken down into slices and can generate 3D models of samples, magnifying biological structures by several million times! It seems that the two techniques are an ideal match, 3D data turned into physical 3D models, vastly improving our ability to correctly interpret and present 3D biological structures. It is also an extremely helpful teaching aid, the ability to hold and handle data creates an instant connection in a way that difficult to interpret micrographs cannot.

If you have access to a 3D printer (or you can use one of the online 3D printing companies), there is a simple way to try this out for yourself. The electron microscopy data bank (http://www.ebi.ac.uk/pdbe/emdb/) has 3D models available to download. These file types can be opened in UCSF Chimera (a freely available software with plenty of information about how to use it) and converted into .stl files (a file type that most free 3D printer software can use). You may have to reduce the surface resolution and file size (the default measurement in these files is Angstroms, whereas the default size for 3D printer software is either mm or inches). I find Netfabb studio basic and Blender very good, free programs that enable you to adjust files to the volume you desire.

The combination of 3D techniques has led to interesting and exciting access to microscopic worlds and it has even spread to the fashion industry! A new jewellery collection was recently launched on Kickstarter, combining microscopy data with 3D printing to create jewellery from the shape of human chromosomes. https://www.kickstarter.com/projects/1627392371/human-chromosome-jewellery-collection

Bronze and silver rings, pendants, earrings, bracelets and cufflinks feature the full human karyotype (all the chromosomes) as well as xx, xxy and trisomy 21 designs. As 3D technology develops further, in the microscopy and printing fields, I have no doubt that we will see an increase in applications both for science and general interest.


  1. […] Hughes shared: “From the microscope to the printer – a guest post I did about 3D electron microscopy and printing. It includes a brief section […]

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