Segmentation and Deconvolution of Fluorescence Microscopy Volumes
thesisposted on 14.08.2019 by Soonam Lee
In order to distinguish essays and pre-prints from academic theses, we have a separate category. These are often much longer text based documents than a paper.
Recent advances in optical microscopy have enabled biologists collect fluorescence microscopy volumes cellular and subcellular structures of living tissue. This results in collecting large datasets of microscopy volume and needs image processing aided automated quantification method. To quantify biological structures a first and fundamental step is segmentation. Yet, the quantitative analysis of the microscopy volume is hampered by light diffraction, distortion created by lens aberrations in different directions, complex variation of biological structures. This thesis describes several proposed segmentation methods to identify various biological structures such as nuclei or tubules observed in fluorescence microscopy volumes. To achieve nuclei segmentation, multiscale edge detection method and 3D active contours with inhomogeneity correction method are used for segmenting nuclei. Our proposed 3D active contours with inhomogeneity correction method utilizes 3D microscopy volume information while addressing intensity inhomogeneity across vertical and horizontal directions. To achieve tubules segmentation, ellipse model fitting to tubule boundary method and convolutional neural networks with inhomogeneity correction method are performed. More specifically, ellipse fitting method utilizes a combination of adaptive and global thresholding, potentials, z direction refinement, branch pruning, end point matching, and boundary fitting steps to delineate tubular objects. Also, the deep learning based method combines intensity inhomogeneity correction, data augmentation, followed by convolutional neural networks architecture. Moreover, this thesis demonstrates a new deconvolution method to improve microscopy image quality without knowing the 3D point spread function using a spatially constrained cycle-consistent adversarial networks. The results of proposed methods are visually and numerically compared with other methods. Experimental results demonstrate that our proposed methods achieve better performance than other methods for nuclei/tubules segmentation as well as deconvolution.
NATIONAL INSTITUTES OF HEALTH (NIH)
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