A multi-view approach to cDNA micro-array analysis

The official published version can be obtained from the link below.Microarray has emerged as a powerful technology that enables biologists to study thousands of genes simultaneously, therefore, to obtain a better understanding of the gene interaction and regulation mechanisms. This paper is concerned with improving the processes involved in the analysis of microarray image data. The main focus is to clarify an image's feature space in an unsupervised manner. In this paper, the Image Transformation Engine (ITE), combined with different filters, is investigated. The proposed methods are applied to a set of real-world cDNA images. The MatCNN toolbox is used during the segmentation process. Quantitative comparisons between different filters are carried out. It is shown that the CLD filter is the best one to be applied with the ITE.This work was supported in part by the Engineering and Physical Sciences Research Council (EPSRC) of the UK under Grant GR/S27658/01, the National Science Foundation of China under Innovative Grant 70621001, Chinese Academy of Sciences under Innovative Group Overseas Partnership Grant, the BHP Billiton Cooperation of Australia Grant, the International Science and Technology Cooperation Project of China under Grant 2009DFA32050 and the Alexander von Humboldt Foundation of Germany

Lesion boundary segmentation using level set methods

This paper addresses the issue of accurate lesion segmentation in retinal imagery, using level set methods and a novel stopping mechanism - an elementary features scheme. Specifically, the curve propagation is guided by a gradient map built using a combination of histogram equalization and robust statistics. The stopping mechanism uses elementary features gathered as the curve deforms over time, and then using a lesionness measure, defined herein, ’looks back in time’ to find the point at which the curve best fits the real object. We implement the level set using a fast upwind scheme and compare the proposed method against five other segmentation algorithms performed on 50 randomly selected images of exudates with a database of clinician marked-up boundaries as ground truth

Optimized Anisotropic Rotational Invariant Diffusion Scheme on Cone-Beam CT

Cone-beam computed tomography (CBCT) is an important image modality for dental surgery planning, with high resolution images at a relative low radiation dose. In these scans the mandibular canal is hardly visible, this is a problem for implant surgery planning. We use anisotropic diffusion filtering to remove noise and enhance the mandibular canal in CBCT scans. For the diffusion tensor we use hybrid diffusion with a continuous switch (HDCS), suitable for filtering both tubular as planar image structures. We focus in this paper on the diffusion discretization schemes. The standard scheme shows good isotropic filtering behavior but is not rotational invariant, the diffusion scheme of Weickert is rotational invariant but suffers from checkerboard artifacts. We introduce a new scheme, in which we numerically optimize the image derivatives. This scheme is rotational invariant and shows good isotropic filtering properties on both synthetic as real CBCT data

Automated reduction the speckle noise of the panoramic ultrasound images of Muscles and Tendons

Peer reviewedPublisher PD

A robust lesion boundary segmentation algorithm using level set methods

This paper addresses the issue of accurate lesion segmentation in retinal imagery, using level set methods and a novel stopping mechanism - an elementary features scheme. Specifically, the curve propagation is guided by a gradient map built using a combination of histogram equalization and robust statistics. The stopping mechanism uses elementary features gathered as the curve deforms over time, and then using a lesionness measure, defined herein, ’looks back in time’ to find the point at which the curve best fits the real object. We compare the proposed method against five other segmentation algorithms performed on 50 randomly selected images of exudates with a database of clinician demarcated boundaries as ground truth

MR coil sensitivity inhomogeneity correction for plaque characterization in carotid arteries

We are involved in a comprehensive program to characterize atherosclerotic disease using multiple MR images having different contrast mechanisms (T1W, T2W, PDW, magnetization transfer, etc.) of human carotid and animal model arteries. We use specially designed intravascular and surface array coils that give high signal-to-noise but suffer from sensitivity inhomogeneity. With carotid surface coils, challenges include: (1) a steep bias field with an 80% change; (2) presence of nearby muscular structures lacking high frequency information to distinguish bias from anatomical features; (3) many confounding zero-valued voxels subject to fat suppression, blood flow cancellation, or air, which are not subject to coil sensitivity; and (4) substantial noise. Bias was corrected using a modification of the adaptive fuzzy c-mean method reported by Pham et al. (IEEE TMI, 18:738-752), whereby a bias field modeled as a mechanical membrane was iteratively improved until cluster means no longer changed. Because our images were noisy, we added a noise reduction filtering step between iterations and used approximate to5 classes. In a digital phantom having a bias field measured from our MR system, variations across an area comparable to a carotid artery were reduced from 50% t