Automated analysis and visualization of preclinical whole-body microCT data

Citation

Baiker, M. (2011, November 17). Automated analysis and visualization of preclinical whole- body microCT data. Retrieved from https://hdl.handle.net/1887/18101

Version: Corrected Publisher’s Version

License: Licence agreement concerning inclusion of doctoral thesis in the Institutional Repository of the University of Leiden

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Automated Analysis and Visualization of Preclinical Whole-body MicroCT Data

Martin Baiker

About the front cover:

Shown is a ‘segmented’ X-ray picture of a Microsoft mouse (original image by courtesy of www.petergof.com).

About the verso:

Shown are a laughing and a weeping face, the symbols of the ancient Greek muses Thalia (comedy) and Melpomene (tragedy). Image by courtesy of www.theaterverein-thalia.de.

Automated Analysis and Visualization of Preclinical Whole-body MicroCT Data M. Baiker - Leiden, Leiden University Medical Center

PhD thesis Leiden University - with a summary in Dutch

Advanced School for Computing and Imaging

This work was carried out at the Division of Image Processing at the Leiden Univer- sity Medical Center, Leiden, The Netherlands and in the ASCI graduate school. ASCI dissertation series number 238.

ISBN-13: 978-9491098239

Printed by F&N Eigen Beheer, Amsterdam, The Netherlands

Copyright c 2011 by M. Baiker. All rights reserved. No part of this publication may

be reproduced or transmitted in any form or by any means, electronic or mechanical,

including photocopy, recording, or any information storage and retrieval system, without

permission in writing from the author.

Automated Analysis and Visualization of Preclinical Whole-body MicroCT Data

Geautomatiseerde Analyse en Visualisatie van Preklinische MicroCT Datasets van Hele Lichamen

(met een samenvatting in het Nederlands)

Proefschrift

ter verkrijging van

de graad van Doctor aan de Universiteit Leiden,

op gezag van Rector Magnificus prof. mr. P.F. van der Heijden, volgens besluit van het College voor Promoties

te verdedigen op donderdag 17 november 2011 klokke 13:45 uur

door

Martin Baiker

geboren te Stuttgart (Duitsland)

in 1978

Overige leden: Dr. ir. J. Dijkstra Prof. dr. W. Niessen

Erasmus Medical Center, Rotterdam Prof. dr. ir. M.J.T. Reinders

Delft University of Technology

This research was financially supported by the European Network for Cell Imaging and Tracking Expertise (ENCITE), which was funded under the EU 7th framework program.

Financial support for the printing of this thesis was kindly provided by (alphabetic order):

• Advanced School for Computing and Imaging (ASCI), Delft, NL

• Bontius Stichting inz Doelfonds Beeldverwerking, Leiden, NL

• Caliper Life Sciences, Hopkinton, USA

• Foundation Imago, Oegstgeest, NL

Contents

1 General Introduction 1

1.1 Molecular imaging for preclinical research . . . . 1

1.2 Image processing challenges . . . . 2

1.3 State of the Art . . . . 4

1.4 Goals of the research . . . . 8

1.5 Outline of the thesis . . . . 8

2 Articulated Atlases 13 2.1 Introduction . . . . 15

2.2 Methods . . . . 17

2.3 Applications . . . . 21

2.4 Discussion and Conclusions . . . . 27

3 Whole body segmentation 33 3.1 Introduction . . . . 35

3.2 Methodology . . . . 38

3.3 Experimental setup. . . . 48

3.4 Results . . . . 52

3.5 Discussion . . . . 53

3.6 Conclusion and Future Work . . . . 57

4 APR visualization 63 4.1 Introduction . . . . 65

4.2 Related work . . . . 67

4.3 Method. . . . 68

4.4 Implementation . . . . 76

4.5 Evaluation . . . . 77

4.6 Conclusion and Future Work . . . . 81

5 Bone Volume Measurement 85 5.1 Introduction . . . . 87

5.2 Materials and Methods . . . . 88

5.3 Results . . . . 95

5.4 Discussion . . . . 97

6.6 Conclusion . . . 113

7 CT BLI Registration 115 7.1 Introduction . . . 117

7.2 Methodology . . . 118

7.3 Experiments . . . 120

7.4 Results and Discussion . . . 122

7.5 Conclusions and Future Work . . . 122

8 Summary and Future Work 125 8.1 Summary and Conclusions . . . 125

8.2 Future work . . . 128

References 144

Samenvatting en Aanbevelingen 147

Publications 155

Acknowledgements 159

Curriculum Vitae 163

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