A 3-D visualization system for serial microscope images

Date

2018-07-18

Authors

Li, Jianping

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Abstract

A three-dimensional (3-D) visualization system for serial microscope images is developed with special reference to its application in microscopy and cell biology. The 3-D visualization system involves three process stages, namely data acquisition, volume data modeling and object rendering. The data acquisition part deals with collecting serial microscope images and is carried out by optical sectioning which records serial microscope images from the top to the bottom of a specimen. A new algorithm is proposed to computationally remove out-of-focus information from each recorded image of a specimen. This algorithm processes serial images independently and thus avoids computationally expensive 3-D convolution and 3-D Fourier transforms. Further, an extensive study of imaging properties of defocused microscopes is carried out in the thesis. The defocused point spread functions and optical transfer functions of transmitted light microscopes have been analyzed. An extensive comparison of the two approaches of obtaining these functions, namely direct measurements and theoretical calculations. is conducted. An interesting observation is made that the results of these two approaches correspond well with each other only for low magnification and low numerical aperture objective lenses. Modeling of serial microscope images is carried out by an isosurface modeling algorithm. This algorithm is based on the marching-cube algorithm with two modifications proposed in the thesis. One modification is to detect and prevent the redundancy existing in the original marching-cube algorithm. The other modification is to use the middle-point algorithm to avoid linear interpolation to locate the vertex of a polygon. Results show that the modified marching-cube algorithm proposed in the thesis significantly reduces the number of polygons generated and thus greatly increases the computation efficiency for surface generation and object rendering. Object rendering, which is to generate a realistic image, is carried out by using a C library SImple Polygon Processor (SIPP). A graphic user-interface is designed and implemented to facilitate the modeling and rendering processes. It offers various user-friendly functions, such as rotation, zooming and cutting, for close examination of the objects under study and can be used for visualizing various volume data. The interactive system together with the data acquisition algorithm form a 3-D visualization system for serial microscope images. The results of visualization show that the 3-D visualization system developed in this thesis realistically and efficiently reconstructs objects of interest from serial microscope images as well as from various volume data such as Computer Tomography (CT) and Magnetic Resonance Imaging (MRI) medical images.

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Keywords

Imaging systems, Three-dimensional display systems

Citation