High-Throughput Image Reconstruction and Analysis

by A. Ravishankar Rao, Guillermo A. Cecchi

Overview

Explore the latest developments in bioimaging, image analysis, and data mining with the first comprehensive book on innovative high-performance computing (HPC) techniques that are facilitating never-before research capabilities and applications. This unique resource demonstrates how HPC can solve the data bottleneck created by today's microscopy techniques. It provides state-of-the-art methods and algorithms for building complex models from large biological datasets and solving data analysis and interpretation problems.
This innovative volume surveys the latest image acquisition advances in serial block face techniques in scanning electron microscopy, knife-edge scanning microscopy, and 4D imaging of multi-component biological systems. The book introduces parallel processing for biological applications. You learn advanced parallelization techniques for decomposing a problem domain and mapping it onto a parallel processing architecture using the message-passing interface (MPI) and OpenMP. Case studies show how these techniques have been successfully used in simulation tasks, data mining, and graphical visualization of biological datasets. You also find coverage of methods for developing scalable biological image databases and for facilitating greater interactive visualization of large image sets.

Product Details

ISBN-13:	9781596932951
Publisher:	Artech House, Incorporated
Publication date:	01/01/2009
Series:	Bioinformatics & Biomedical Imaging
Pages:	380
Product dimensions:	7.20(w) x 10.20(h) x 0.90(d)

About the Author

A. Ravishankar Rao is a research staff member with the Biometaphorical Computing Group at the IBM T.J. Watson Research Center, Yorktown Heights, New York. He is also an associate editor of the journals Pattern Recognition and Machine Vision and Applications. Dr. Rao received his B.Tech degree in electrical engineering from the Indian Institute of Technology (Kanpur), and his M.S. and Ph.D. degrees in computer engineering from the University of Michigan, Ann Arbor. He was named a Master Inventor at IBM Research in 2004.

Guillermo A. Cecchi is a research staff member with the Biometaphorical Computing Group at the IBM T.J. Watson Research Center, Yorktown Heights, New York. Dr. Cecchi received his M.Sc. in physics at the University of La Plata, Argentina and his Ph.D. in physics and biology at The Rockefeller University. He also served as a postdoctoral fellow at Cornell University.

Table of Contents

Introduction.
Image Acquisition I: Serial Block Face Scanning Using High-Resolution Scanning Electron Microscopy.

Image Acquisition II: Knife-Edge Scanning Microscope.

Image Acquisition III: 4D Imaging of Multi-Component Biological Systems.

Utilizing Parallel Processing in Computational Biology Applications.

Introduction to High-Performance Computing Using MPI and Open MP.

4D Image Analysis I: Feature Extraction on Parallel Machines.

4D Image Analysis II: Parallel Data Mining.

gridImage Microscopy.

High-Throughput Image-Based Screening.

Laser Capture Microdissection.

Advantages of Using High-Performance Computing: A Case Studying Involving Analysis of Optical

Images of Cortical Tissue.

Applications of High-Performance Computing to Functional Magnetic Resonance Imaging (fMRI) Data.

Databases for Bioimaging.

Interactive Visualization of Large Image Datasets.

Conclusion.