Automated morphometry of transgenic mouse brains in MR images
Scheenstra, A.E.H.
Citation
Scheenstra, A. E. H. (2011, March 24). Automated morphometry of transgenic mouse brains in MR images. Retrieved from https://hdl.handle.net/1887/16649
Version: Corrected Publisher’s Version
License: Licence agreement concerning inclusion of doctoral thesis in the Institutional Repository of the University of Leiden
Downloaded from: https://hdl.handle.net/1887/16649
Note: To cite this publication please use the final published version (if applicable).
Colophone
About the cover
The displayed mouse is a C57BL/6J mouse, which is the most widely used inbred strain and the first to have its genome sequenced. The mirrored image of the mouse represents its genetically modified relative, which has the same genome except for one gene that codes for a certain disease.
Automated morphometry of transgenic mouse brains in MR images Scheenstra, Alize Elske Hiltje
Printed by Ipskamp Drukkers, Enschede, The Netherlands
ISBN-13: 978-90-9026004-4
©2011 A.E.H. Scheenstra, Leiden, The Netherlands
All rights reserved. No part of this publication may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying, record- ing, or any information storage and retrieval system, without permission in writing from the copyright owner.
Automated morphometry of transgenic mouse brains
in MR images
Automatische morfometrie van transgene muizenhersenen in MR beelden
Proefschrift ter verkrijging van
de graad van Doctor aan de Universiteit Leiden,
op gezag van de Rector Magnificus Prof. mr. P.F. van der Heijden , volgens besluit van het College voor Promoties
te verdedigen op donderdag 24 maart 2011 klokke 16:15 uur
door
Alize Elske Hiltje Scheenstra geboren te Gouda
in 1981
Promotiecommissie
Promotor: Prof. dr. ir. J.H.C. Reiber Co-promotor: Dr.ir. J. Dijkstra
Overige leden: Prof. dr. M. van Buchem
Prof. dr. D. Rueckert (Imperial College London ) dr. L. van der weerd
This work was carried out in the ASCI graduate school.
ASCI dissertation series number 229.
I want an empty line here
This work was supported by funds from CYTTRON within the BSIK program (Besluit subsidies investeringen kennisinfrastructuur).
Voor Riena van Rijn - Haasnoot I want an empty line here Ter nagedachtenis aan Hiltje Scheenstra - Betlehem
Contents
1 Introduction 1
1.1 Transgenic mouse models . . . 1
1.2 Mouse brain anatomy . . . 3
1.3 High resolution magnetic resonance imaging . . . 3
1.4 Aim of the thesis . . . 5
1.5 Thesis outline . . . 6
2 Morphometry on rodent brains 7 2.1 Introduction . . . 9
2.2 Volumetry . . . 9
2.3 Automated morphometry . . . 9
2.4 Method comparison . . . 11
2.5 Limitations to automated morphometry . . . 12
2.A Multiple-test correction . . . 13
3 Early detection of Alzheimer’s disease in MR images 15 3.1 Introduction . . . 17
3.2 Alzheimer mouse models . . . 17
3.3 Relaxometry . . . 19
3.4 Analysis and models of plaque burden . . . 23
3.5 Cerebral amyloid angiopathy . . . 24
3.6 Volumetric methods . . . 26
3.7 Texture analysis . . . 27
3.8 Discussion and conclusion . . . 28
3.A The most commonly used AD mouse models . . . 32
Contents
4 Automated segmentation of mouse brains 35
4.1 Introduction . . . 37
4.2 Materials and methods . . . 38
4.3 Results . . . 42
4.4 Discussion . . . 47
4.5 Conclusion . . . 49
5 The generalized Moore-Rayleigh test 51 5.1 Introduction . . . 53
5.2 The Moore-Rayleigh test . . . 54
5.3 The two-sample test . . . 62
5.4 Results . . . 67
5.5 Discussion . . . 71
5.A The Fisher distribution . . . 73
6 The 3D Moore-Rayleigh test as tool for brain morphometry 77 6.1 Introduction . . . 79
6.2 Method . . . 81
6.3 Results . . . 84
6.4 Discussion . . . 92
7 Quantitative morphometry on migraine mouse models 95 7.1 Introduction . . . 97
7.2 Materials and methods . . . 98
7.3 Results . . . 100
7.4 Discussion . . . 104
8 Summary and conclusions 107 8.1 Summary and conclusions . . . 107
8.2 Future work . . . 109
9 Samenvatting en aanbevelingen 111 9.1 Samenvatting en conclusies . . . 111
9.2 Aanbevelingen . . . 113
Bibliography 115
Publications 137
Acknowledgements 139
Curriculum vitae 141
List of Figures 143
List of Tables 149
List of Abbrevations 151
viii
