UNLABELLED: The Illumina Infinium HumanMethylation450 BeadChip is a newly designed high-density microarray for quantifying the methylation level of over 450 000 CpG sites within human genome. Illumina Methylation Analyzer (IMA) is a computational package designed to automate the pipeline for exploratory analysis and summarization of site-level and region-level methylation changes in epigenetic studies utilizing the 450K DNA methylation microarray. The pipeline loads the data from Illumina platform and provides user-customized functions commonly required to perform exploratory methylation analysis for individual sites as well as annotated regions. AVAILABILITY: IMA is implemented in the R language and is freely available from http://www.rforge.net/IMA.

Active contours are a well known segmentation toolkit and widely adopted in various forms for biological image analysis. Most techniques are commonly based on object geometry but overlapping regions cause severe problems to contour propagation. In this paper, we propose a novel active contour technique (“cellsnake”) for solving this problem with an application to cell and fibre segmentation. Given that the transparency of overlapped objects is unavailable, we present a new set of contour forces derived from a-priori knowledge of cell geometry that allows the contour to deform correctly in those regions. We combine these terms with other existing forces and we show that cellsnake gives appropriate shape estimation of the objects especially in areas ahowing overlapping.