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Dissertation
Rat brain variability, utility of its surface for guiding alignment and development of a structured light based brain surface scanner
Doctor of Philosophy (Ph.D.), Drexel University
1997
DOI:
https://doi.org/10.17918/00004723
Abstract
In order to achieve a better understanding of central nervous system different studies using different brains have to be correlated with each other. This can be done by aligning all brains into a single reference or atlas brain. By moving all data to a standard coordinate space one gains the possibility of employing image based arithmetic to compare data from different animals. It has been shown in this dissertation that experimental rat brains which are prepared in a certain way have a low three-dimensional variability and can be aligned effectively using their external surface as a guide. In this approach there are two critical issues: which method to use in the alignment and how to get the brain surface? The alignment method examined here is the distance map based alignment. A software package (a MATLAB toolbox) has been developed which aligns binary objects whose contours are given as a set of voxel/pixel coordinates. It uses the Euclidean distance transform and the Marquardt-Levenberg optimization algorithm to estimate the parameters of a transformation for optimal alignment. For the acquisition of the brain surface, a Brain Scanner has been developed which acquires the brain surface using an active stereo technique (Structured Light). Structured light (SL) is a modified stereo imaging system, in which one of the cameras of the regular stereo have been replaced with a projector. Surface points are gathered directly by triangulation after establishing correspondence between the projection and imaging planes. It is shown in this dissertation that adequate number of points with desired accuracy can be gathered from the surface of the brains using SL. An other contribution of this dissertation to the structured light field in general is the use of a new set of codes (perfect submaps). Methods for code generation, decoding and implementation, and some of their attractive properties especially under occluded settings have been examined.
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Details
- Title
- Rat brain variability, utility of its surface for guiding alignment and development of a structured light based brain surface scanner
- Creators
- Cengizhan Ozturk
- Contributors
- Jonathan Nissanov (Advisor) - Drexel University, Drexel University (1970-)
- Awarding Institution
- Drexel University
- Degree Awarded
- Doctor of Philosophy (Ph.D.)
- Publisher
- Drexel University; Philadelphia, Pennsylvania
- Number of pages
- xiii, 160 pages
- Resource Type
- Dissertation
- Language
- English
- Academic Unit
- Drexel University
- Other Identifier
- 991021888949204721