Browsing by Author "Ju, Tao"

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    Building a 3D atlas of the mouse brain
    (2005) Ju, Tao; Warren, Joe
    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.
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    Convex contouring of volumetric data
    (2003) Ju, Tao; Warren, Joe
    In this thesis we present a fast, table-driven isosurface extraction technique on volumetric data. Unlike Marching Cubes or other cell-based algorithms, the proposed polygonization generates convex negative space inside individual cells, enabling fast collision detection on the triangulated isosurface. In our implementation, we are able to perform over 2 million point classifications per second. The algorithm is driven by an automatically constructed look-up table that stores compact decision trees by sign configurations. The decision trees determine triangulations dynamically by values at cell corners. Using the same technique, we can perform fast, crack-free multi-resolution contouring on nested grids of volumetric data. The method can also be extended to extract isosurfaces on arbitrary convex, space-filling polyhedra.