Video Bioinformatics: From Live Imaging to Knowledge

ISBN-13: 9783319237237 / Angielski / Twarda / 2015 / 381 str.

Bir Bhanu; Prue Talbot

Opis

This unique text/reference presents a selection of innovative computational techniques to enable the efficient analysis of biological processes in large video sequences and databases. Examples are drawn from numerous topics of significant current interest, such as 2D/3D live imaging, mild-traumatic brain injury, human embryonic stem cells, the growth of pollen tubes, cell tracking, and cell trafficking. To address various challenges, multiple imaging modalities are proposed at varying spatial and temporal resolutions, in conjunction with novel computational methods for video mining and knowledge discovery.Topics and features: provides a detailed introduction to the field of video bioinformatics; examines the analysis and visualization of injured brain tissue in rodent models, using magnetic resonance imaging and optical coherence tomography; discusses segmentation of stem cell colonies and analysis of individual stem cells; describes the application of commercially available software to solve problems in video bioinformatics related to stem cell behavior in vitro; reviews video bioinformatics problems and solutions in plant and fungus biology; presents a high throughput method for quantifying DNA damage in cells, and a method that uses optogenetics to regulate protein transport in cultured cells; surveys the various software tools and databases available for use with video bioinformatics problems.This pioneering volume is essential reading on the emerging, interdisciplinary field of video bioinformatics. The text will be of great benefit to researchers and graduate students from a wide range of different areas, including bioinformatics, bioengineering, plant sciences, cell, molecular and developmental biology, genetics and genomics.

Spis treści

Part I: Video Bioinformatics: An Introduction

Live Imaging and Video Bioinformatics
Bir Bhanu and Prue Talbot

Video Bioinformatics Methods for Analyzing Cell Dynamics: A Survey
Nirmalya Ghosh

Part II: Organismal Dynamics: Analyzing Brain Injury and Disease

High and Low Level Contextual Modeling for the Detection of Mild-Traumatic Brain Injury
Anthony Bianchi, Bir Bhanu and Andre Obenaus

Automated Identification of Injury Dynamics after Neonatal Hypoxia-Ischemia
Nirmalya Ghosh, Stephen Ashwal and Andre Obenaus

A Real-Time Analysis of Traumatic Brain Injury from T2 Weighted Magnetic Resonance Images using a Symmetry-Based Algorithm
Ehsan T. Esfahani, Devin W. McBride, Somayeh B. Shafiei and Andre Obenaus

Visualizing Cortical Tissue Optical Changes during Seizure Activity with Optical Coherence Tomography
Melissa M. Eberle, Carissa L. Rodriguez, Jenny I. Szu, Yan Wang, Mike S. Hsu, Devin K. Binder and B. Hyle Park

Part III: Dynamics of Stem Cells

Bio-Inspired Segmentation and Detection Methods for Human Embryonic Stem Cells
Benjamin X. Guan, Bir Bhanu, Prue Talbot and Jo-Hao Weng

A Video Bioinformatics Method to Quantify Cell Spreading and Its Application to Cells Treated with Rho-associated Protein Kinase and Blebbistatin
Jo-Hao Weng, Rattapol Phandthong and Prue Talbot

Evaluation of Dynamic Cell Processes an

d Behavior Using Video Bioinformatics Tools
Sabrina C. Lin, Henry Yip, Rattapol Phandthong, Barbara Davis and Prue Talbot

Part IV: Dynamic Processes in Plant and Fungal Systems

Video Bioinformatics: A New Dimension in Quantifying Plant Cell Dynamics
Nolan Ung and Natasha V Raikhel

Understanding Growth of Pollen Tube in Video
Asongu L. Tambo, Bir Bhanu, Nan Luo and Zhenbiao Yang

Automatic Image Analysis Pipeline for Studying Growth in Katya Mkrtchyan, Anirban Chakraborty, Min Liu and Amit Roy-Chowdhury

Quantitative Analyses using Video Bioinformatics and Image Analysis Tools During Growth and Development in the Multicellular Fungus Neurospora Crassa
Ilva E. Cabrera, Asongu L. Tambo, Alberto C. Cruz, Benjamin X. Guan, Bir Bhanu and Katherine A. Borkovich

Part V: Dynamics of Intracellular Molecules

Quantification of the Dynamics of DNA Repair to Ionizing Radiation via Colocalization of 53BP1 and H2AX
Torsten Groesser, Gerald Fontenay, Ju Han, Hang Chang and Bahram Parvin

A Method to Regulate Cofilin Transport Using Optogenetics and Live Video Analysis
Atena Zahedi, Vincent On and Irnya Ethell

Part VI: Software, Systems and Databases

Integrated 5-D Cell Tracking and Linked Analytics in the FARSIGHT Open Source Toolkit
Amine Merouane, Arunchalam Narayanaswamy and Badrinath Roysam

Video Bioinfo

rmatics Databases and Software
Ninad S. Thakoor, Alberto C. Cruz and Bir Bhanu

Understanding of the Biological Process of Non-Verbal Communication: Facial Emotion and Expression Recognition
Alberto C. Cruz, Bir Bhanu and Ninad S. Thakoor

Identification and Retrieval of Moth Images Based on Wing Patterns
Linan Feng, Bir Bhanu and John Heraty

O autorze

Dr. Bir Bhanu is a Distinguished Professor and the Director of the Center for Research in Intelligent Systems at the University of California at Riverside, USA. His other Springer publications include the titles Distributed Video Sensor Networks, Human Recognition at a Distance in Video, and Human Ear Recognition by Computer.

Dr. Prue Talbot is a Professor of Cell Biology and the Director of the Stem Cell Center and Core Facility at the University of California at Riverside, USA. She is also the Director of the Inland Empire Stem Cell Consortium.

Blurb

The advances of live cell video imaging and high-throughput technologies for functional and chemical genomics provide unprecedented opportunities to understand how biological processes work in subcellular and multicellular systems. The interdisciplinary research field of Video Bioinformatics is defined by Bir Bhanu as the automated processing, analysis, understanding, data mining, visualization, query-based retrieval/storage of biological spatiotemporal events/data and knowledge extracted from dynamic images and microscopic videos. Video bioinformatics attempts to provide a deeper understanding of continuous and dynamic life processes.

Genome sequences alone lack spatial and temporal information, and video imaging of specific molecules and their spatiotemporal interactions, using a range of imaging methods, are essential to understand how genomes create cells, how cells constitute organisms, and how errant cells cause disease. The book examines interdisciplinary research issues and challenges with examples that deal with organismal dynamics, intercellular and tissue dynamics, intracellular dynamics, protein movement, cell signaling and software and databases for video bioinformatics.

 

Topics and Features

• ·        Covers a set of biological problems, their significance, live-imaging experiments, theory and computational methods, quantifiable experimental results and discussion of results.
  
• ·        Provides automated methods for analyzing mild traumatic brain injury over time, identifying injury dynamics after neonatal hypoxia-ischemia and visualizing cortical tissue changes during seizure activity as examples of organismal dynamics
  
• ·        Describes techniques for quantifying the dynamics of human embryonic stem cells with examples of cell detection/segmentation, spreading and other dynamic behaviors which are important for characterizing stem cell health
  
• ·        Examines and quantifies dynamic processes in plant and fungal systems such as cell trafficking, growth of pollen tubes in model systems such as Neurospora Crassa and Arabidopsis
  
• ·        Discusses the dynamics of intracellular molecules for DNA repair and the regulation of cofilin transport using video analysis
  
• ·        Discusses software, system and database aspects of video bioinformatics by providing examples of 5D cell tracking by FARSIGHT open source toolkit, a survey on available databases and software, biological processes for non-verbal communications and identification and retrieval of moth images
  

This unique text will be of great interest to researchers and graduate students of Electrical Engineering, Computer Science, Bioengineering, Cell Biology, Toxicology, Genetics, Genomics, Bioinformatics, Computer Vision and Pattern Recognition, Medical Image Analysis, and Cell Molecular and Developmental Biology. The large number of example applications will also appeal to application scientists and engineers.

Dr. Bir Bhanu is Distinguished Professor of Electrical & Computer Engineering, Interim Chair of the Department of Bioengineering, Cooperative Professor of Computer Science & Engineering, and Mechanical Engineering and the Director of the Center for Research in Intelligent Systems, at the University of California, Riverside, California, USA.

Dr. Prue Talbot is Professor of Cell Biology & Neuroscience and Director of the Stem Cell Center and Core at the University of California Riverside, California, USA.