iMinds The Conference: Wim van Aarle

Wim van Aarle .

Small animal imaging with discrete tomography..

08 November 2012

Breakout session on Small Animal Imaging

iMinds the conference 2012

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Computed tomography

CT

reconstruction projection data projection

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CT in biomedical research

Osteoporosis

• “Detecting early bone changes using in vivo micro-CT in ovariectomized, zoledronic acid-treated, and sham-operated rats”, E. Perilli, V. Le, B. Ma, P. Salmon, K. Reynolds, N.L. Fazzalari, Osteoporos. Int (2010) 21:1371-1382.

- 20 female albino rats, divided in 3 groups • OVX: ovariectomized (induces loss of bone strength)

• OVX+ZOL: treated with zolendronic acid

• SHAM: sham-operation (testset)

- Longitudinal study • Week 0, 2, 4, 8, 12

- SkyScan 1076 µCT • FDK reconstructions of ROI

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CT in biomedical research

Osteoporosis

Week 0, OVX+ZOL Week 0, OVX

bone parameter value

BV/TV (%) 2.6

Tb.Th* (µm) 77

Tb.Sp* (µm) 1058

Tb.N (1/mm) 0.35

SMI 2.5

bone parameter value

BV/TV (%) 17.6

Tb.Th* (µm) 74

Tb.Sp* (µm) 255

Tb.N (1/mm) 2.41

SMI 1.9

Week 12, OVX Week 12, OVX+ZOL

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CT in biomedical research

Osteoporosis • A few important issues

- Are the bone parameters correct?

- X-rays are harmful! • Rats are animals too

• Radiation might induce bone changes

• Is it possible to draw similar conclusions with less radiation?

• Possible solution: Discrete tomography

noise, misalignment,

motion, etc.

PVE, beam hardening,

etc.

PVE, limited data,

etc.

threshold selection

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Computed tomography

limited data problem

• Ill-posed reconstruction problem - Many unknown (pixels)

- Few measurements (detectors)

0° 180° 0° 180° 0° 180° 0° 180° full angular data low angle count limited angular range truncated data

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Computed tomography

limited data problem

• Discrete Tomography Discrete Algebraic Reconstruction Technique => DART

• Assumptions - homogeneous objects

- prior knowledge: grey levels

phantom image

reconstruction from

5 projection images

segmentation

difference

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Discrete tomography

DART

iteration 1 error pixels: 9491

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Discrete tomography DART

iteration 10 error pixels: 5460

iteration 1 error pixels: 9491

iteration 50 error pixels: 233

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DART in biomedical research

Osteoporosis

DART can be applied for in-vivo bone reconstructions

- 3 homogeneous materials (air, tissue, bone)

- Prior knowledge can be obtained from a hardware phantom

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DART in biomedical research

Some results Overlay of FDK reconstruction with

- FDK segmentation (underestimated)

- DART reconstruction (slightly overestimated)

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DART in biomedical research

Some results

Trabecular Thickness

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DART in biomedical research Trabecular Separation

Some results

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In conclusion

• Computed Tomography

- is still a popular imaging modality in biomedical research

• Discrete Tomography

- allows accurate reconstructions from limited projection data

- combines segmentation and reconstruction

• Discrete Tomography in small animal imaging

- conclusions can be drawn with less radiation

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The end Thanks!

Special mention:

dr. Egon Perilli, Flinders University, Australia

dr. Elke Van de Casteele, University of Antwerp