Informed baseline subtraction of proteomic mass spectrometry data aided by a novel sliding window algorithm

Proteomic matrix-assisted laser desorption/ionisation (MALDI) linear time-of-flight (TOF) mass spectrometry (MS) may be used to produce protein profiles from biological samples with the aim of discovering biomarkers for disease. However, the raw protein profiles suffer from several sources of bias or systematic variation which need to be removed via pre-processing before meaningful downstream analysis of the data can be undertaken. Baseline subtraction, an early pre-processing step that removes the non-peptide signal from the spectra, is complicated by the following: (i) each spectrum has, on average, wider peaks for peptides with higher mass-to-charge ratios (m/z), and (ii) the time-consuming and error-prone trial-and-error process for optimising the baseline subtraction input arguments. With reference to the aforementioned complications, we present an automated pipeline that includes (i) a novel `continuous' line segment algorithm that efficiently operates over data with a transformed m/z-axis to remove the relationship between peptide mass and peak width, and (ii) an input-free algorithm to estimate peak widths on the transformed m/z scale. The automated baseline subtraction method was deployed on six publicly available proteomic MS datasets using six different m/z-axis transformations. Optimality of the automated baseline subtraction pipeline was assessed quantitatively using the mean absolute scaled error (MASE) when compared to a gold-standard baseline subtracted signal. Near-optimal baseline subtraction was achieved using the automated pipeline. The advantages of the proposed pipeline include informed and data specific input arguments for baseline subtraction methods, the avoidance of time-intensive and subjective piecewise baseline subtraction, and the ability to automate baseline subtraction completely. Moreover, individual steps can be adopted as stand-alone routines.Comment: 50 pages, 19 figure

Speckle Reduction with Attenuation Compensation for Skin OCT Images Enhancement

The enhancement of skin image in optical coherence tomography (OCT) imaging can help dermatologists to investigate tissue layers more accurately, hence the more efficient diagnosis. In this paper, we propose an image enhancement technique including speckle reduction, attenuation compensation and cleaning to improve the quality of OCT skin images. A weighted median filter is designed to reduce the level of speckle noise while preserving the contrast. A novel border detection technique is designed to outline the main skin layers, stratum corneum, epidermis and dermis. A model of the light attenuation is then used to estimate the absorption coefficient of epidermis and dermis layers and compensate the brightness of the structures at deeper levels. The undesired part of the image is removed using a simple cleaning algorithm. The performance of the algorithm has been evaluated visually and numerically using the commonly used no-reference quality metrics. The results shows an improvement in the quality of the images. Keywords: Optical coherence tomography (OCT), Skin, Image enhancement, Speckle reduction, Attenuation compensation

An Improved Algorithm for Eye Corner Detection

In this paper, a modified algorithm for the detection of nasal and temporal eye corners is presented. The algorithm is a modification of the Santos and Proenka Method. In the first step, we detect the face and the eyes using classifiers based on Haar-like features. We then segment out the sclera, from the detected eye region. From the segmented sclera, we segment out an approximate eyelid contour. Eye corner candidates are obtained using Harris and Stephens corner detector. We introduce a post-pruning of the Eye corner candidates to locate the eye corners, finally. The algorithm has been tested on Yale, JAFFE databases as well as our created database

A Cosmic Watershed: the WVF Void Detection Technique

On megaparsec scales the Universe is permeated by an intricate filigree of clusters, filaments, sheets and voids, the Cosmic Web. For the understanding of its dynamical and hierarchical history it is crucial to identify objectively its complex morphological components. One of the most characteristic aspects is that of the dominant underdense Voids, the product of a hierarchical process driven by the collapse of minor voids in addition to the merging of large ones. In this study we present an objective void finder technique which involves a minimum of assumptions about the scale, structure and shape of voids. Our void finding method, the Watershed Void Finder (WVF), is based upon the Watershed Transform, a well-known technique for the segmentation of images. Importantly, the technique has the potential to trace the existing manifestations of a void hierarchy. The basic watershed transform is augmented by a variety of correction procedures to remove spurious structure resulting from sampling noise. This study contains a detailed description of the WVF. We demonstrate how it is able to trace and identify, relatively parameter free, voids and their surrounding (filamentary and planar) boundaries. We test the technique on a set of Kinematic Voronoi models, heuristic spatial models for a cellular distribution of matter. Comparison of the WVF segmentations of low noise and high noise Voronoi models with the quantitatively known spatial characteristics of the intrinsic Voronoi tessellation shows that the size and shape of the voids are succesfully retrieved. WVF manages to even reproduce the full void size distribution function.Comment: 24 pages, 15 figures, MNRAS accepted, for full resolution, see http://www.astro.rug.nl/~weygaert/tim1publication/watershed.pd