Artyom M Grigoryan | PubMed Health

PubMed2006

Fast splitting alpha-rooting method of image enhancement: tensor representation.

In the tensor representation, a two-dimensional (2-D) image is represented uniquely by a set of one-dimensional (1-D) signals, so-called splitting-signals, that carry the spectral information of the image at frequency-points of specific sets that cover the whole domain of frequencies. The image enhancement is thus reduced to processing splitting-signals and such process requires a modification of only a few spectral components of the image, for each signal. For instance, the alpha-rooting method of image enhancement can be fulfilled through processing separately a maximum of 3N/2 splitting-signals of an image (N x N), where N is a power of two. In this paper, we propose a fast implementation of the a-rooting method by using one splitting-signal of the tensor representation with respect to the discrete Fourier transform (DFT). The implementation is described in the frequency and spatial domains. As a result, the proposed algorithms for image enhancement use two 1-D N-point DFTs instead of two 2-D N x N-point DFTs in the traditional method of alpha-rooting.

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PubMed2002

Morphological spot counting from stacked images for automated analysis of gene copy numbers by fluorescence in situ hybridization.

Fluorescence in situ hybridization (FISH) is a molecular diagnostic technique in which a fluorescent labeled probe hybridizes to a target nucleotide sequence of deoxyribose nucleic acid. Upon excitation, each chromosome containing the target sequence produces a fluorescent signal (spot). Because fluorescent spot counting is tedious and often subjective, automated digital algorithms to count spots are desirable. New technology provides a stack of images on multiple focal planes throughout a tissue sample. Multiple-focal-plane imaging helps overcome the biases and imprecision inherent in single-focal-plane methods. This paper proposes an algorithm for global spot counting in stacked three-dimensional slice FISH images without the necessity of nuclei segmentation. It is designed to work in complex backgrounds, when there are agglomerated nuclei, and in the presence of illumination gradients. It is based on the morphological top-hat transform, which locates intensity spikes on irregular backgrounds. After finding signals in the slice images, the algorithm groups these together to form three-dimensional spots. Filters are employed to separate legitimate spots from fluorescent noise. The algorithm is set in a comprehensive toolbox that provides visualization and analytic facilities. It includes simulation software that allows examination of algorithm performance for various image and algorithm parameter settings, including signal size, signal density, and the number of slices.

Algorithms↗