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 one: Optical Coherence Tomography
Key questions
What is coherence, as a property of light?
What sample property is measured in OCT? (i.e. attenuation, coherent/incoherent scattering,
etc.)
Compare/contrast time and frequency domain OCT.
What factors influence/limit lateral resolution, depth resolution, and volume size in OCT?
What are some artefacts that may arise in OCT, and how are they formed?
Putting the above together, what sort of samples might OCT be ideal for? What samples would
be unsuitable?
Papers
See material on Wattle.
Start by trying to understand time-domain OCT. It’s probably the most straightforward method. If the
papers are intractable to begin with, then start with some of the videos below. I found the textbook
chapter more useful when read last, but others may prefer to start there and move to the review paper.
As always, the videos linked below can provide helpful introductions to things that the papers may gloss
over quickly.
Videos (optional)
Optical Coherence Tomography
[Link]
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.
[Link]
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).
[Link]
This one gives a thorough overview of temporal coherence (in more detail than we need!), if you’re
looking for a reference for that.
[Link]
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
[Link]
A slow, thorough introduction to the basic theory of X-ray and optical parallel-beam tomography.
[Link]
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
[Link]
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.
