GridWeaver: A Fully-Automatic System for Microarray Image Analysis Using Fast Fourier Transforms

Experiments using microarray technology generate large amounts of image data that are used in the analysis of genetic function. An important stage in the analysis is the determination of relative intensities of spots on the images generated. This paper presents GridWeaver, a program that reads in images from a microarray experiment, automatically locates subgrids and spots in the images, and then determines the spot intensities needed in the analysis of gene function. Automatic gridding is performed by running Fast Fourier Transforms on pixel intensity sums. Tests on several data sets show that the program responds well even on images that have significant noise, both random and systemic

Gridding Spot Centers of Smoothly Distorted Microarray Images

We use an optimization technique to accurately locate a distorted grid structure in a microarray image. By assuming that spot centers deviate smoothly from a checkerboard grid structure, we show that the process of gridding spot centers can be formulated as a constrained optimization problem. The constraint is equal to the variations of the transform parameter. We demonstrate the accuracy of our algorithm on two sets of microarray images. One set consists of some images from the Stanford Microarray Database; we compare our centers with those annotated in the Database. The other set consists of oligonucleotide images, and we compare our results with those obtained by GenePix Pro 5.0. Our experiments were performed completely automatically

Microfluidics and Nanofluidics Handbook

The Microfluidics and Nanofluidics Handbook: Two-Volume Set comprehensively captures the cross-disciplinary breadth of the fields of micro- and nanofluidics, which encompass the biological sciences, chemistry, physics and engineering applications. To fill the knowledge gap between engineering and the basic sciences, the editors pulled together key individuals, well known in their respective areas, to author chapters that help graduate students, scientists, and practicing engineers understand the overall area of microfluidics and nanofluidics. Topics covered include Finite Volume Method for Numerical Simulation Lattice Boltzmann Method and Its Applications in Microfluidics Microparticle and Nanoparticle Manipulation Methane Solubility Enhancement in Water Confined to Nanoscale Pores Volume Two: Fabrication, Implementation, and Applications focuses on topics related to experimental and numerical methods. It also covers fabrication and applications in a variety of areas, from aerospace to biological systems. Reflecting the inherent nature of microfluidics and nanofluidics, the book includes as much interdisciplinary knowledge as possible. It provides the fundamental science background for newcomers and advanced techniques and concepts for experienced researchers and professionals

Subseafloor Biosphere Linked to Hydrothermal Systems: TAIGA Concept

Oceanography; Biogeosciences; Geochemistr