Information extraction on biological, organic and inorganic materials using image processing techniques

Jehangir, Muhammad (2006) Information extraction on biological, organic and inorganic materials using image processing techniques. Masters thesis, Memorial University of Newfoundland.

[English] PDF - Accepted Version Available under License - The author retains copyright ownership and moral rights in this thesis. Neither the thesis nor substantial extracts from it may be printed or otherwise reproduced without the author's permission. Download (5MB)

Abstract

Information extraction from images is essential to research in many science faculties today, from computer science to bioinformatics and medicine. My research focuses on the analysis of structural changes in biological, organic and inorganic materials under a variety of conditions. Therefore, I process images from before and after an event (such as the addition of ions) to quantify exactly how much change is occurring in the material. -- My major focus is to write code to automate finding objects/structures (in an image) and calculating their sizes, heights, orientations, and distributions. The data comes from atomic force microscope measurements, which produce multi-layered two-dimensional arrays of data (i.e. sets of three-dimensional images). The image processing involves noise reduction, background leveling, object identification, and then the calculation and display of statistical information. The code used to automate these processes and to present the features to the user is written in the IgorPro Scripting Language. -- The processing of an image proceeds iteratively, where an initial identification of objects/structures in an image leads to a definition of background and noise, which can then be adjusted to better identify the objects. Background leveling can be done vertically as well as horizontally, as per the requirements of a specific image. Distribution (spacing) of objects is calculated in different ways for isotropic versus non-isotropic arrangement of objects. The information about the objects in the images is presented in comparison graphs and summary tables.

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