PHYS8721

Part 2: Tomography
Topic
Introduction to three forms of 3D imaging: Optical Coherence Tomography, Optical
Projection/Transmission Tomography, and X-ray micro-tomography. OCT is a “direct” 3D measurement
technique, in which each measurement is of a point/region in 3D space. In contrast, OPT and XCT are
“indirect” techniques, where a number of measurements of the whole object are reconstructed into a
3D model. We will cover image formation, the mathematical basis of image reconstruction, and
applications.

Learning Goals
 The difference between direct and indirect methods of 3D imaging.
 Contrast mechanisms driving image formation in OCT, OPT, and XCT.
 OPT and XCT:
o share common theoretical underpinnings …
o but are wildly different in application.
 The factors limiting resolution in OCT, OPT, and XCT.
 Artefacts, and the practical factors that may lead to their formation.
 The relative strengths and weaknesses of each imaging method, and how they influence their
domain of application.

Week two: Optical Projection Tomography

Key questions
 What sample property is measured in projection tomography? (i.e. attenuation,
coherent/incoherent scattering, etc.)
 What is the mathematical description of the measurement process in OPT (and XCT)?
 How can that process be inverted to describe the sample, from the measurements?
 Why are the application domains of OPT and XCT fundamentally different?
 What factors influence/limit resolution and volume size in OPT?
 What are some artefacts that may arise in OPT, and how are they formed?
 Putting the above together, what sort of samples might OPT be ideal for? What samples would
be unsuitable?

Papers
See material on Wattle.

Start with Ch 03 from Kak and Slaney (also available for free online, here:
https://www.slaney.org/pct/pct-toc.html). This describes the fundamental mathematics that underlies
OPT and XCT. Then, take a look at Sharpe’s paper. As always, use the videos to supplement as-needed,
they can be effective as an introduction to the papers.
Videos (optional)
Optical Coherence Tomography
https://www.youtube.com/watch?v=2lYEnA-OBZ0&ab_channel=LecturesofYoshiakiYasuno

This is a long series, that covers a lot of ground. It’s very detailed, covering things like “how do you
calibrate this machine”, etc. etc. Probably not the best starting point.

https://www.youtube.com/watch?v=FKzIH7o8zTA&ab_channel=AndrewBerger

This video and its sequel provide a good explanation of time and frequency domain OCT image
formation, starting from the basic physics (i.e. “what happens if we put a monochromatic wave into our
system”, then moving on from there).

https://www.youtube.com/watch?v=dtcq5b0R65w&ab_channel=HuygensOptics

This one gives a thorough overview of temporal coherence (in more detail than we need!), if you’re
looking for a reference for that.

https://www.youtube.com/watch?v=dd0hdPbozJU&ab_channel=InsightOphthalmology

This video is a decent overview, though it’s worth noting that the table of numbers they give is (I think)
application-specific!

Optical Projection Tomography

https://www.youtube.com/watch?v=f0sxjhGHRPo&ab_channel=Kolibril

A slow, thorough introduction to the basic theory of X-ray and optical parallel-beam tomography.

https://www.youtube.com/watch?v=BPJQL_JXvzY&ab_channel=Labroots

This talk doesn’t explain much about how OPT works, but it does go through where it fits in the
biomedical imaging landscape, so it’s a very useful example of how someone in that field might compare
and contrast different techniques.

X-ray micro computed-tomography

https://www.youtube.com/watch?v=liVAgLJmq8g&ab_channel=AIFNCStateUniversity

A quick introduction to XCT. The discussion of reconstruction around 3:20 has an error: backprojection
alone does not produce the results they describe, a filtration step (or iterative reconstruction) is
necessary.