3D brain atlas - RICE UNIVERSITY Building a 3D Atlas of the...

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Unformatted text preview: RICE UNIVERSITY Building a 3D Atlas of the Mouse Brain by Tao Ju A Thesis Submitted in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy Approved, Thesis Committee: Joe Warren, Professor Computer Science Ron Goldman, Professor Computer Science Richard G. Baraniuk, Victor E. Cameron Professor Electrical and Computer Engineering Lydia Kavraki, Noah Harding Professor Computer Science Houston, Texas April, 2005 Building a 3D Atlas of the Mouse Brain Tao Ju Abstract Building and studying 3D representations of anatomical structures, such as the brain, plays an important role in modern biology and medical science. While 3D imaging methods such as MRI and CT have been widely applied, 2D imaging methods such as optical microscopy typically generate images with much higher resolution. In this thesis I describe how to construct a high-resolution 3D atlas of the mouse brain from 2D microscopic images. In particular, I focus on using computer graphics techniques, such as image registration to correcting tissue distortions and polygonal modeling to build surfaces representing the partitioning of anatomical regions. The methods are being applied to construct a high-quality polygonal atlas of an adult mouse brain from 350 histological tissue sections. While the resulting brain atlas will contribute to a larger project of building a spatial database of gene expressions over the mouse brain, the methods described in this thesis are well suited for the general purpose of building polygonal atlases of arbitrary anatomical structures from tissue sections. Acknowledgements I would like to express my greatest thanks to my advisor, Dr. Joe Warren, whose broad knowledge and dynamic thinking guided me throughout the process of research and thesis writing. I would like to thank Dr. Ron Goldman for his valuable sugges- tions on both the contents of the thesis and my presentation skills. I would also like to thank Dr. Richard Baraniuk and Dr. Lydia Kavraki, who have spent their valuable time reading this work and attending the defense. I would like to thank my collaborators at Baylor College of Medicine and University of Houston: Dr. Carson, Dr. Chiu, Dr. Gregor Eichele Dr. Thaller, Dr. Kakadiaris and Musodiq Bello. Without their help I could not have finished this work. I would like to give my special thanks to my wife Ming whose patient love enabled me to complete this work. ii Contents Abstract i List of Illustrations vi List of Tables xii 1 Introduction 1 1.1 Brain Atlases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 1.2 Brain Atlases in Gene Expression . . . . . . . . . . . . . . . . . . . . 2 1.2.1 Background . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 1.2.2 2D brain atlas . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 1.2.3 3D brain atlas . . . . . . . . . . . . . . . . . . . . . . . . . . . 8 1.3 Atlas Creation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 2 Data Collection 12 2.1 Cryo-sectioning . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .2....
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3D brain atlas - RICE UNIVERSITY Building a 3D Atlas of the...

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