The first book to review the emerging interdisciplinary field of video bioinformatics
Includes links to example videos in each chapter
Presents quantifiable experimental results on computational methods for a range of biological problems
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.
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 & C omputer 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.
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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.
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 TalbotPart 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 BhanuUnderstanding 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
Theadvances of live cell video imaging and high-throughput technologies forfunctional and chemical genomics provide unprecedented opportunities tounderstand how biological processes work in subcellular and multicellularsystems. The interdisciplinary research field of Video Bioinformatics isdefined by Bir Bhanu as the automated processing, analysis, understanding, datamining, visualization, query-based retrieval/storage of biologicalspatiotemporal events/data and knowledge extracted from dynamic images andmicroscopic videos. Video bioinformatics attempts to provide a deeperunderstanding of continuous and dynamic life processes.
Genomesequences alone lack spatial and temporal information, and video imaging ofspecific molecules and their spatiotemporal interactions, using a range ofimaging methods, are essential to understand how genomes create cells, howcells constitute organisms, and how errant cells cause disease. The book examinesinterdisciplinary research issues and challenges with examples that deal withorganismal dynamics, intercellular and tissue dynamics, intracellular dynamics,protein movement, cell signaling and software and databases for videobioinformatics.
Topics and Features
- · Covers a set ofbiological problems, their significance, live-imaging experiments, theory and computationalmethods, quantifiable experimental results and discussion of results.
- · Provides automatedmethods for analyzing mild traumatic brain injury over time, identifying injurydynamics after neonatal hypoxia-ischemia and visualizing cortical tissuechanges during seizure activity as examples of organismal dynamics
- · Describes techniques forquantifying the dynamics of human embryonic stem cells with examples of celldetection/segmentation, spreading and other dynamic behaviors which areimportant for characterizing stem cell health
- · Examines and quantifiesdynamic processes in plant and fungal systems such as cell trafficking, growthof pollen tubes in model systems such as Neurospora Crassa and Arabidopsis
- · Discusses the dynamicsof intracellular molecules for DNA repair and the regulation of cofilin transportusing video analysis
- · Discusses software,system and database aspects of video bioinformatics by providing examples of 5Dcell tracking by FARSIGHT open source toolkit, a survey on available databasesand software, biological processes for non-verbal communications andidentification and retrieval of moth images
Thisunique text will be of great interest to researchers and graduate students ofElectrical Engineering, Computer Science, Bioengineering, Cell Biology,Toxicology, Genetics, Genomics, Bioinformatics, Computer Vision and PatternRecognition, Medical Image Analysis, and Cell Molecular and DevelopmentalBiology. The large number of example applications will also appeal toapplication scientists and engineers.
Dr. Bir Bhanu isDistinguished Professor of Electrical & Computer Engineering, Interim Chairof the Department of Bioengineering, Cooperative Professor of Computer Science& Engineering, and Mechanical Engineeringand the Director of the Center for Research in Intelligent Systems, at theUniversity of California, Riverside,California, USA.
Dr.Prue Talbot is Professor of Cell Biology & Neuroscience and Director of theStem Cell Center and Core at the University ofCalifornia Riverside, California, USA.
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 subcellularand multicellular systems. The interdisciplinary research field of Video Bioinformatics is defined by BirBhanu as the automated processing, analysis, understanding, data mining, visualization, query-basedretrieval/storage of biological spatiotemporal events/data and knowledge extracted from dynamic imagesand microscopic videos. Video bioinformatics attempts to provide a deeper understanding of continuousand dynamic life processes.Genome sequences alone lack spatial and temporal information, and video imaging of specific moleculesand their spatiotemporal interactions, using a range of imaging methods, are essential to understandhow genomes create cells, how cells constitute organisms, and how errant cells cause disease. The bookexamines interdisciplinary research issues and challenges with examples that deal with organismal dynamics,intercellular and tissue dynamics, intracellular dynamics, protein movement, cell signaling and softwareand databases for video bioinformatics.Topics and Features- Covers a set of biological problems, their significance, live-imaging experiments, theory andcomputational methods, quantifiable experimental results and discussion of results.- Provides automated methods for analyzing mild traumatic brain injury over time, identifying injurydynamics after neonatal hypoxia-ischemia and visualizing cortical tissue changes during seizureactivity as examples of organismal dynamics- Describes techniques for quantifying the dynamics of human embryonic stem cells with examplesof cell detection/segmentation, spreading and other dynamic behaviors which are important forcharacterizing 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 cofilintransport using video analysis- Discusses software, system and database aspects of video bioinformatics by providing examples of5D 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 imagesThis unique text will be of great interest to researchers and graduate students of Electrical Engineering,Computer Science, Bioengineering, Cell Biology, Toxicology, Genetics, Genomics, Bioinformatics, ComputerVision andPattern 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 & C omputer Engineering, Interim Chair of theDepartment of Bioengineering, Cooperative Professor of Computer Science & Engineering, and MechanicalEngineering 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 atthe University of California Riverside, California, USA.
Part I: Video Bioinformatics: An Introduction.- Live Imaging and Video Bioinformatics.- Video Bioinformatics Methods for Analyzing Cell Dynamics.- Part II: Organismal Dynamics: Analyzing Brain Injury and Disease.- High and Low Level Contextual Modeling for the Detection of Mild-Traumatic Brain Injury.- Automated Identification of Injury Dynamics after Neonatal Hypoxia-Ischemia.- A Real-Time Analysis of Traumatic Brain Injury from T2 Weighted Magnetic Resonance Images using a Symmetry-Based Algorithm.- Visualizing Cortical Tissue Optical Changes during Seizure Activity with Optical Coherence Tomography.- Part III: Dynamics of Stem Cells.- Bio-Inspired Segmentation and Detection Methods for Human Embryonic Stem Cells.- A Video Bioinformatics Method to Quantify Cell Spreading and Its Application to Cells Treated with Rho-associated Protein Kinase and Blebbistatin.- Evaluation of Dynamic Cell Processes and Behavior Using Video Bioinformatics Tools.- Part IV: Dynamic Processes in Plant and Fungal Systems.- Video Bioinformatics: A New Dimension in Quantifying Plant Cell Dynamics.- Understanding Growth of Pollen Tube in Video.- Automatic Image Analysis Pipeline for Studying Growth in Arabidopsis.- Quantitative Analyses using Video Bioinformatics and Image Analysis Tools During Growth and Development in the Multicellular Fungus.- Part V: Dynamics of Intracellular Molecules.- Quantification of the Dynamics of DNA Repair to Ionizing Radiatio
n via Colocalization of 53BP1 and H2AX.- A Method to Regulate Cofilin Transport Using Optogenetics and Live Video Analysis.-
Part VI: Software, Systems and Databases.- Integrated 5-D Cell Tracking and Linked Analytics in the FARSIGHT Open Source Toolkit.- Video Bioinformatics Databases and Software.- Understanding of the Biological Process of Non-Verbal Communication.- Identification and Retrieval of Moth Images Based on Wing Patterns.
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.
Über den Autor
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.
Inhaltsverzeichnis
Part I: Video Bioinformatics: An Introduction.- Live Imaging and Video Bioinformatics.- Video Bioinformatics Methods for Analyzing Cell Dynamics.- Part II: Organismal Dynamics: Analyzing Brain Injury and Disease.- High and Low Level Contextual Modeling for the Detection of Mild-Traumatic Brain Injury.- Automated Identification of Injury Dynamics after Neonatal Hypoxia-Ischemia.- A Real-Time Analysis of Traumatic Brain Injury from T2 Weighted Magnetic Resonance Images using a Symmetry-Based Algorithm.- Visualizing Cortical Tissue Optical Changes during Seizure Activity with Optical Coherence Tomography.- Part III: Dynamics of Stem Cells.- Bio-Inspired Segmentation and Detection Methods for Human Embryonic Stem Cells.- A Video Bioinformatics Method to Quantify Cell Spreading and Its Application to Cells Treated with Rho-associated Protein Kinase and Blebbistatin.- Evaluation of Dynamic Cell Processes and Behavior Using Video Bioinformatics Tools.- Part IV: Dynamic Processes in Plant and Fungal Systems.- Video Bioinformatics: A New Dimension in Quantifying Plant Cell Dynamics.- Understanding Growth of Pollen Tube in Video.- Automatic Image Analysis Pipeline for Studying Growth in Arabidopsis.- Quantitative Analyses using Video Bioinformatics and Image Analysis Tools During Growth and Development in the Multicellular Fungus.- Part V: Dynamics of Intracellular Molecules.- Quantification of the Dynamics of DNA Repair to Ionizing Radiatio
n via Colocalization of 53BP1 and H2AX.- A Method to Regulate Cofilin Transport Using Optogenetics and Live Video Analysis.-
Part VI: Software, Systems and Databases.- Integrated 5-D Cell Tracking and Linked Analytics in the FARSIGHT Open Source Toolkit.- Video Bioinformatics Databases and Software.- Understanding of the Biological Process of Non-Verbal Communication.- Identification and Retrieval of Moth Images Based on Wing Patterns.
Klappentext
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
The first book to review the emerging interdisciplinary field of video bioinformatics
Includes links to example videos in each chapter
Presents quantifiable experimental results on computational methods for a range of biological problems
Includes supplementary material: sn.pub/extras
