Center for Bio-Image Informatics

NSF Site VisitMarch 22/23, 2006

B. S. Manjunath & Robert Murphy

UCSB/CMU

NSF Information Technology Research ProjectProgram Director: Dr. Kamal Shukla.

March 22, 2006

ITR Goals..

......While explicit categories will not be used in FY 2003, ITR will continue to support new awards in these previously targeted areas and will additionally emphasize the fundamental relationship between the acquisition and utilization of knowledge and the information tools needed to acquire, organize, and interpret that knowledge. The intent in FY 2003 is to stimulate research on the fundamental challenges facing the continued expansion and utilization of IT across the sciences and engineering, creation of novel use and development of IT, the interaction of IT with society at large, and the use of IT to enhance security and reduce the vulnerabilities of our society to catastrophic events, whether natural or man-made.

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March 22, 2006

Participating Institutions

• UCSB

• UC Berkeley

• CMU

• Education/Outreach Partners★ California State University San Bernardino★ California State University Fresno★ California State University Dominguez Hills*★ Universidad Metropolitana, Puerto Rico★ University of Virgin Islands

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March 22, 2006

CMU Team

Faculty Ph. D. Students

Ting ZhaoElvira Garcia OsunaJuchang HuaShann-Ching ChenJustin NewbergAmol ShanbhagCharles JacksonStaff

Dan Willard

Robert F. MurphyJelena KovacevicChristos FaloutsosGeoff GordonTom Mitchell

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March 22, 2006

California State University at San Bernardino

• Prof Arturo Concepcion

• Prof Yasha Karant

• Prof Keith Schubert

• Graduate Students: J. Curnutt and J. Tafas

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March 22, 2006

UCSB TeamBiology

Stu FeinsteinSteve FisherLes Wilson

Mark VerardoAustin Peck Tapas MannaMaura Jess

Kathy KamathGeoff LewisKen Linberg

Brian Matsumoto

Melvin Rabena, Shirly Feng, Ran Halleluyan

EngineeringSanjoy Banerjee

S. R. Jammalamadaka (statistics)Arun Majumdar (Berkeley)

B. S. ManjunathKenneth RoseAmbuj Singh

A. Altinok; A. Bhattacharya; J. Byun; S. Frame; D. Fedorov; V. Ljosa; M. El Saban*; M. A. Siddiqi;

T. Kuo; N. Vu; A. Black; R. Kumar; S. Jagdish; S. Jagannath; A. Black; W. Smith

Z. Bi; T. Can*; K. Kvilekval; B. Piorek*; B. Sumengen*; P. Markiewicz, A. Mechler*

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March 22, 2006

Advisory Board• Phil Bernstein

Microsoft Corporation One Microsoft Way http://research.microsoft.com/~philbe/philbe@microsoft.com

• Mark H. Ellisman, Ph.D.Director, National Center for Microscopy and Imaging Research (NCMIR)Professor, Neurosciences and Bioengineeringhttp://ncmir.ucsd.edu/Contact/Personnel/mark_Ellisman.htmmark@ncmir.ucsd.edu

• Andrew F. LaineDirector, Biomedical Imaging LabColumbia Universityhttp://bil.bme.columbia.edu/people.htmlaine@columbia.edu

• David W. Piston, Ph.D.Professor of Molecular Physiology and Biophysics, Director FEL CenterMolecular Physiology & Biophysicshttp://www.vanderbilt.edu/fel/dave.piston@vanderbilt.edu

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Research Thrusts

Research Activities

LearningImaging,

Image Processing & Analysis

Pattern Recognition, Modeling

Image Databases

Focus onTissue and Cell Biology (Vertebrate Retina)Sub-cellular OrganizationDynamic Cellular Processes (Microtubules)

Goal: Develop Generic tools and methods for a broad range of bio-images

March 22, 2006

Focus on Vertebrate Retina•Images of vertebrate retina offer a fertile collection of data from sub-cellular, cellular

and tissue levels that are representative of the bio-informatics challenges presented by modern bio-molecular research

Different antibodies or antibodycombinations provide informationabout specific cell types and their reaction to retinal injury

Photoreceptors labeled with antibody combinationsConfocal image projection files:

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March 22, 2006

Focus on Microtubule ImagesImages of dynamic microtubules in living cells provide an excellent collection for the development of improved data acquisition, image analysis tools and statistical modeling for many dynamic cellular processes

Immunofluorescence images: MCF-7 cells, showing co-localization of microtubules (green) and microtubule-associated protein tau (red).

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March 22, 2006

CMU: Focus on subcellular location

* Comparing, Classifying, Clustering Subcellular Location Patterns in Space and Time

* Difficult image analysis problems due to heterogeneity of patterns from cell to cell

* Analysis of large scale collections required (~20,000 proteins in just one cell type)

* Critical information for Systems Biology

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March 22, 2006

Information Processing Challenges

• Vast number of images generated

• very few get published

• a majority of them are not accessible to other researchers

• tools to easily manage such data are urgently needed

• basic image processing and pattern recognition tools

• database tools to manage images

• sharing and collaboration

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March 22, 2006

BISQUE (Bio-Image Semantic Query Interface)

Imageand

metadataserver

WEB

DigitalNotebook

XMLimage

search

external internal

BISQUE

XML

Research in image processing

Cell counterplug-in for

ImageJ

metadata

Research in biology

features

analysisCell counterplug-in for

ImageJ

Cell counterplug-in for

ImageJ

Nuclei Detector

plug-in forImageJ

Distributedcomputing

cluster

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March 22, 2006

Centers for Bio-Image Informatics

• Advancing the Image Informatics Technologies for bio-images

• About half way through the project

• Initial focus datasets

• to define and evaluate progress on IT

• Many of them easily generalize to a larger class of problems (e.g., basic schemas, image analysis methods, etc.)

• Actively exploring collaborations outside of the ITR participants (U. Utah, U. Tennessee, Scripps, UCSD, ..)

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March 22, 2006

Interdisciplinary Education• Biologists and Engineers engaged in

interdisciplinary research

• Engineering students attend regular biology lab meetings• Engineers trained in introductory biology and bioimaging

• industry sponsored workshop at UCSB

• Intro Biology course for engineers

• advanced bioimaging course with Engineering/CS + Bio students

• Graduate biology students exposed to Image Processing & Pattern Recognition tools

• Collaborations with industry (Asylum, Olympus)• CMU Center (CBI) University-wide Bioimaging day

event held each year to disseminate results and create new collaborations

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March 22, 2006

Education Outreach

• UCSB

• Summer undergraduate research program

• over 20 students from California State Universities

• 8 of these students continuing to graduate studies

• Expanded to include high school students in 2005

• 2006: will include both high school students and teachers

• working with other on-campus resources to actively encourage math & science education at all levels

• CMU• 13 students from minority-serving institutions• 2 undergrads won best poster awards at national meetings in 2004 and 2005

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March 22, 2006

Undergraduate research

• Two of the projects leading to further research and development

• “Bio-wall” (after UCSD): A 20 monitor display array, developed and installed in the Neuroscience Research Institute

• “Scientists Notebook”: A simple to use digital notebook to upload images to our image server.

• One student presented a poster at 2005 IEEE Bioimage symposium at Stanford

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March 22, 2006

Project Management

• Regular CMU +UCSB discussions (via phone, video conference, e-mails)

• kick-off meeting at UCSB in Dec 2003

• visit to CMU in Nov 2004

• Advisory board meeting at UCSB in March 2005

• UCSB:

• weekly project wide meetings

• subgroups meet at least once a week

• Seminars/invited speakers

• annual undergraduate research workshops

• Advisory board meeting in March 2005

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March 22, 2006

Today

• Research Presentations

• covering image informatics research in the context of cell & tissue imaging and live cell imaging

• Current state of the research infrastructure

• Education and Outreach efforts

• Poster session at 5PM with UCSB and CSUSB students

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