Take a Ride on a Root Canal: The VR Tooth Tour Story

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About

Hello, I am Graham Davis, Professor of 3D X-ray imaging in the Dental Institute at Queen Mary University of London at their Mile End campus. I started work in this area in 1989. I’m not a dentist, my background is in electronic engineering. I work on the design and application of micro-CT, a miniaturised form of CT that is used to scan small objects at microscopic scales. The scanners I have designed here are specifically optimised for dental research where we study the processes that go on in teeth when they are subject to things like the acid attack in dental caries, or the reverse process where mineral is reformed in the tooth (we use donated extracted teeth for this purpose). Sometimes I have gone a little “off-piste” and looked at some more exotic things like ancient scrolls and decomposing 16mm film, but most of the work involves looking at tooth and bone samples.

Micro-CT

A couple of years ago I started investigating possible use of virtual reality for teaching and public engagement, using it as a means of visualising complex biological structures. This is how I first became interested in Sketchfab. I had expected either to have to learn a whole lot of new programming skills, or else try and get the funding to get someone else to do the VR coding. But having encountered Sketchfab at a symposium, it was great to discover that someone else had already done the hard work for me. That being said, micro-CT scanners are not like the surface scanners that would be more familiar to most people on Sketchfab. With microCT, you end up with a complete volume image made up of 3-dimensional pixels, called voxels. Each voxel represents the X-ray attenuating property of the corresponding point in the sample being scanned. The next image shows a slice through a 3D volume image of a second molar:

In this image, the brighter areas indicate higher mineral content; thus, we can clearly distinguish between the highly mineralised outer enamel and the less mineralised dentine. You can even see early signs of caries (decay) in the enamel where there are slightly darkened regions. In fact, flicking through all the slices of this data set, you could get a pretty good idea of the tooth’s life history. As it is, this data set is not appropriate for visualising on Sketchfab, or any other surface 3D viewing software for that matter; we need to go from this 3D volume image to a surface image. In other words, we need a means of creating surfaces that represent the boundaries of the dentine and enamel.

Creating 3D Models of Teeth

The great thing about working with tomography data is that we are not just limited to the externally visible surfaces, we can also look at internal surfaces. To do this, we use Ajay Limaye’s (Australian National University) excellent (and free) Drishti application. Firstly, this allows us to volume render the data where we can assign colours according to the mineral content thereby giving us a chance to see what the tooth looks like. We can not only spin this around and resize it, but also cut it open; so it’s quite a useful tool.

Using the magic of Ajay’s 2D transfer functions (see here if you want to know about this), we can separate out the dentine and enamel. Having defined the transfer functions for enamel and dentine, we’re ready to create the surface meshes and we do this with Drishti’s built-in mesh generator plugin, saving a ‘.ply’ surface mesh with coloured vertices.

At this point, we have two meshes, one for enamel and one for dentine. Loading the dentine mesh into Meshlab (a well-known free mesh manipulation package) tells us that it contains around 4.5 million vertices and 9 million faces. That’s not as bad as some of our bone meshes that can have hundreds of millions of faces, but it’s still a bit on the complex side. A bit of cleaning, smoothing and decimation in Meshlab gets this down to 260 thousand vertices and 520 thousand faces; a bit more manageable.

At this point, we could do the same with the enamel mesh and add that on top, but there’s one more trick. Inside it would be nice to have the pulp and root canal system in red. I tried painting this with Meshlab, but it’s a tedious and frustrating process. My patience would run out long before I could colour any number of teeth. Instead I wrote a couple of utilities to make matters easier. The first one is used to create a copy of the dentine mesh with a red tint (tinting rather than painting leaves a bit of variation in the vertex colours, giving a textured appearance). Then, again using Meshlab, I paint the outside of the tinted dentine green (this is much easier than trying to paint an internal surface and can be done with a very broad brush). The second utility replaces any green vertices with the original untinted colour. Now the enamel is added and the tooth is ready to be uploaded onto Sketchfab.

Sketchfab

Once in Sketchfab it’s time to start seeing how this looks in VR. Over in the VR tab of the 3D Settings I started experimenting with scale. Life-size it looks a bit lost. Blow it up to the size of a person and you have a great educational resource. You can move your head through the surfaces to see internal detail (requires 6 degrees of freedom in VR, so not appropriate for phones or the Oculus Go). The fun really starts when you go bigger. Make it the size of a building and you have a ready-made VR experience.

Since first toying with this, we have shown the VR tooth tour at a few public engagement experiences, including our own Festival of Communities, demonstrating to young and old alike, and heard plenty of “wow”s and “awesome”s. What’s great about this is that something as mundane as a tooth suddenly has universal appeal and we find ourselves talking to all sorts of people about dental anatomy and pathology. If you have VR to hand, try it here:

We prefer to do this as a guided tour, so whilst someone is wearing the VR headset, an operator will talk them through the tour and advance them through the annotations using the ‘k’ key. Self guided tours work too, but make sure you keep the annotations in sight (don’t teleport down a root canal or you won’t get back up again), and don’t change the scale! The favourite “wow” inducing view is at the bottom of the root looking upwards:

Is it educational or just a big gimmick? I think both. Which are you more likely to remember, looking at the page of a dental anatomy book or teetering on the edge of a giant root canal?

VR Bone Climb Challenge

Before signing off, there’s one last trick I’d like to share with you. Did you know you can climb in Sketchfab VR? You can generally only teleport to a not-too-steep surface that is below the controller. Hold the controller high, point it down to a point above your foot level (as long as you can see the teleport circles it should work) click to teleport and you gain a bit of height.

The second VR experience has not yet been unleashed at public events; it’s called the bone-climb challenge. Ever wondered what the inside of a bone looks like? Well now you can teleport your way around inside (or walk if you have the space). When I first created this model, the VR view could get a bit confusing because it was too easy to put your head through the bone walls and see the wrong surface. Single-sided rendering did not help, it still got messed up when you were inside the bone struts (trabeculae). In the updated version, do this and everything goes dark; you’ll have to move your head around to navigate your way out. This makes the climbing challenge much more fun, if a little claustrophobic; can you make your way to the top or will you get stuck in a dead-end? If you want to know how this dark interior is done, the model has two superimposed duplicate surfaces. One of them has had the faces inverted and coloured black; Sketchfab is then set to only show only the outward faces.

Climbing around inside a giant bone may sound a little frivolous, but if it makes bone architecture appeal to a wider audience that has to be a good thing; certainly better than shooting zombies (seemingly the most popular use of VR) to my mind.

Take the challenge here:

A big thank you to Sketchfab for making it so easy to share these models and experiences.

 

About the author

Graham Davis

Graham Davis is Professor of 3D X-ray imaging in the Dental Institute at Queen Mary University of London. He works on the development of micro-CT and its application in the study of biological hard tissue.


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