CIBC Collaboration

"Technology push" and "biomedical science pull"

The early years of the Center were marked by a desire to push technology. Recently, there has been a shift to a situation in which biomedical scientists see the potential of computing and work with the Center to pull some of that technology into specific applications in biomedicine.

We have implemented a new design that places each collaboration into a management process we call a "collaboration life cycle". The motivation for this comes from the challenge of providing adequate and appropriate attention to each of a number of parallel projects and ensuring that each progresses as it should. Our past collaborations have provided crucial guidance in directing the technical path of the Center in creating and extending BioPSE and map3d. This new approach will allow us to effectively manage a large number of quality collaborations. Our new process will allow us to adjust the level of attention the Center pays to a particular project, add new projects, and perhaps even minimize the ongoing support of a project.

The general role of the collaborators is to give focus and motivation to the Center's technological research and development. Collaborations also allow us to work with practicing scientists to develop techniques, algorithms, and software that are very well linked to their application to biomedicine. The feedback we receive from collaborators is invaluable in helping us identify the strengths and weaknesses of our approach and in ensuring efficient and effective interactions with the larger scientific community.

The Collaboration Pipeline

pipeline

 


Current CIBC Collaborators
Past CIBC Collaborators


Collaborating PI: Charles DiMarzio
Institution: Department of Electrical and Computer Engineering
Collaborating PI: Milind Rajadyhaksha
Institution: Dermatology Service, Northeastern University, Boston, MA
Collaborating PI: Memorial Sloan
Institution: Kettering Cancer Center, New York, NY
Title of Project: Confocal Imaging of Skin and the Oral Cavity

Collaborating PI: Rok Hren
Institution: Institute of Mathematics, Physics and Mechanics, University of Ljubljana, Slovenia
Title of Project: Evaluation of Inverse Solution Approaches

Collaborating PI: Miriam Leeser, Ph.D.
Institution: Electrical and Computing Engineering, Northeastern University
Title of Project: Middleware layer for seamless runtime porting of SCIRun computations to streaming architecture

Collaborating PI: Sinan Muftu, Associate Professor
Institution: Department of Mechanical and Industrial Engineering, Northeastern University, Boston, MA
Title of Project: Biomechanical Modeling of the Mandible and Teeth

Collaborating PI: Vasilis Ntziachristos
Institution: Technical University of Munich, Germany, Department of Mechanical and Industrial Engineering, Northeastern University, Boston, MA
Title of Project: Molecular Imaging with Individualized Priors

Collaborating PI: Joe Piven, M.D.; Heather Hazlatt, Ph.D.
Institution: Department of Psychiatry, University of North Carolina
Title of Project: Morphological analysis of neuroimages in pediatric autism

Collaborating PI: Petr Stovicek
Institution: Charles University Hospital, Prague, Czech Republic
Title of Project: Clinical Application of Electrocardiographic Inverse Solution

Collaborating PI: Martin Styner, Ph.D.
Institution: Departments of Computer Science and Psychiatry, University of North Carolina Chapel Hill
Title of Project: Cortical Correspondence Using Entropy-Based Particle Systems and Local Features

Collaborating PI: Raimond Winslow, Ph.D.
Institution: Johns Hopkins University
Title of Project: Identifying and Quantifying Shape Features of Human Left Ventricular Remodeling
Collaborating PI: Carsten Wolters, Ph.D.
Institution: University of Münster
Title of Project: Technical Collaboration for Brain Source Localization Software





Collaborating PI: Dr. John Bridge
Institution: University of Utah
Title of Project: Confocal Fluorescence Microscopy of Cardiac Myocytes
Resource personnel: Frank Sachse and Rob MacLeod
Dates (start/finish) 2005–2006

Collaborating PI: Dr. George Chen
Institution: Harvard Medical School
Title of Project: Advanced Four-Dimensional Visualization and Imaging for Radiation Oncology
Resource personnel: Dana Brooks
Dates (start/finish) Ongoing

Collaborating PI: Chi-Bin Chien, Ph.D.
Institution: Department of Neurobiology and Anatomy
Title of Project: Interactive visualization of multichannel confocal microscopy data in neurobiology research

Collaborating PI: Chi-Bin Chien, Ph.D.
Institution: University of Utah
Title of Project: Serial-Section Electron Microscopy for Analysis of Organization of Retinal Axons
Resource personnel: Ross Whitaker
Dates (start/finish) 2006–2010

Collaborating PI: Ed DiBella, Ph.D.
Institution: Utah Center for Advanced Imaging Research, University of Utah
Title of Project: MRI Imaging of Cardiac Perfusion
Resource personnel Chris Johnson, Alexi Samsonov
Dates (start/finish) 2003 – 2005

Collaborating PI: Charles DiMarzio, Ph.D, and Milind Rajadhyaksha, Ph.D.
Institution: Northeastern University
Title of Project: Computational Microscopy of Skin Simulations
Resource personnel: Dana Brooks
Dates (start/finish) Ongoing

Collaborating PI: Mark Ellisman, Ph.D.
Institution: National Center for Microscopy and Imaging Research (NCMIR)
Title of Project: EM image processing and visualization

Collaborating PI: Craig Henriquez, Ph.D.
Institution: Department of Bioengineering, Duke University
Title of Project: Integration of cardiowave and SCIRun

Collaborating PI: David Isaacson, Ph.D.
Institution: Rensselaer Polytechnic Institute (RPI)
Title of Project: Torso Volume and Breast Cancer Imaging with Electrical Impedance Tomography
Resource personnel: Dana Brooks
Dates (start/finish) 2005–2006

Collaborating PI: Allan Johnson, Ph.D.
Institution: Duke University
Title of Project: Multi-dimensional Bioelectric mapping of Mouse Models of Cardiac Disease
Resource personnel: Chris Johnson
Dates (start/finish) 2005

Collaborating PI: Prof. Charles Keller
Institution: University of Texas at San Antonio
Title of Project: Computed Tomographic Imaging Blood Vessel in Transgenic Mouse Models for Human Tumors
Resource personnel: Ross Whitaker
Dates (start/finish) Promoted to primary in 2007

Collaborating PI: Dr. Dirar Khoury
Institution: Baylor College of Medicine
Title of Project: Integrated Intracardiac Ultrasound and Electrical Imaging
Resource personnel: Rob MacLeod and Dana Brooks
Dates (start/finish) 2005–2006

Collaborating PI: Ron Kikinis, M.D.
Institution: Surgical Planning Laboratory, Harvard University
Title of Project: Volume Rendering Support for Slicer

Collaborating PI: Dr. Ron Kikinis
Institution: Harvard Medical School
Title of Project: Multi-Modal Volume Rendering and Segmentation
Resource personnel: Marty Cole
Dates (start/finish) 2005–2007

Collaborating PI: David Laidlaw, Ph.D.
Institution: Brown University
Title of Project: Diffusion Tensor Imaging
Resource personnel Chris Johnson, Gordon Kindlmann
Dates (start/finish) 2004–2005

Collaborating PI: Janet Lainhart, M.D.; Mark Leppert, Ph.D.
Institution: Departments of Psychiatry and Genetrics, University of Utah
Title of Project: Image-Based, Intermediate Biological Phenotypes Associated with Autism Spectrum Disorder

Collaborating PI: Leslie Loew, Ph.D., and Ion Moraru, Ph.D.
Institution: The National Resource for Cell Analysis and Modeling (NRCAM), University of Connecticut Health Center
Title of Project: Image based modeling in cell simulations

Collaborating PI: Leslie M. Loew
Institution: University of Connecticut Health Center
Title of Project: Three-Dimensional Image Analysis and Visualization Capabilities within Virtual Cell
Resource personnel: Rob MacLeod
Dates (start/finish) Ongoing

Collaborating PI: Robert Marc, Ph.D.; Bryan Jones, Ph.D.; James Anderson
Institution: Moran Eye Center, University of Utah
Title of Project: Serial section microscopy for discovering the circuitry of the mammalian retina

Collaborating PI: Cameron McIntyre, Ph.D.
Institution: Cleveland Clinic, Lerner College of Medicine
Title of Project: Systems-Level Model of Deep Brain Stimulation

Collaborating PI: Scott Makeig, Ph.D.
Institution: Swartz Center for Computational Neuroscience, University of California San Diego
Title of Project: Estimation to Improve Source Localization
Resource personnel Rob MacLeod, Chris Johnson
Dates (start/finish) 2002 – 2007

Collaborating PI: Prof. Robert Marc
Institution: University of Utah
Title of Project: Serial-Section Electron Microscopy for Analysis of Ganglion Connectivity
Resource personnel: Ross Whitaker
Dates (start/finish) 2005

Collaborating PI: Andrew McCulloch, Ph.D.
Institution: University of California, San Diego
Title of Project: Modeling and Simulation with Higher-Order Finite Elements
Resource personnel: Marty Cole, Frank Sachse
Dates (start/finish) 2002–2005

Collaborating PI: Prof. Alonso Moreno
Institution: University of Utah
Title of Project: Visualization and Simulation of Activation in Transgenic Mouse Hearts
Resource personnel: Rob MacLeod
Dates (start/finish) 2005–2006

Collaborating PI: Dr. Vasilis Ntziachristos
Institution: Massachusetts General Hospital
Title of Project: Software for Fluorescence Molecular Tomography (FMT)
Resource personnel: Dana Brooks
Dates (start/finish) 2005–2006

Collaborating PI: Dr. Steven Peltier
Institution: UCSD
Title of Project: Bridging the BioPSE Environment with the Telescience Grid
Resource personnel: Chris Johnson
Dates (start/finish) 2005-2006

Collaborating PI: Andrew Pullan, Ph.D.
Institution: Auckland Bioengineering Institute, University of Aukland, New Zealand
Title of Project: Simulation of bioelectric fields

Collaborating PI: Bruno Taccardi, Ph.D.
Institution: CVRTI, University of Utah
Title of Project: Visualization of Cardiac Currents
Resource personnel: Rob MacLeod and Dana Brooks
Dates (start/finish) 2000–2006

Collaborating PI: Dr. Paul Thompson
Institution: UCLA
Title of Project: Collaborative Project on Visualization of Brain Variability
Resource personnel: Chris Johnson
Dates (start/finish) 2005-2009

Collaborating PI: Matthew Tocheri
Institution: Smithsonian Institute
Title of Project: Shape-based analysis of hominid trapezia

Collaborating PI: Art Toga, Ph.D.
Institution: USC
Title of Project: Integration of SCIRun with the LONI Pipeline

Collaborating PI: Joseph Tranquillo, Ph.D.
Institution: Biomedical and Electrical Engineering, Bucknell University
Title of Project: Non-linear Coupled Neural Models
Resource personnel: Chris Johnson, David Weinstein
Dates (start/finish) 2007

Collaborating PI: David S. Tuch
Institution: Harvard Medical School
Title of Project: Biophysical Modeling of Diffusion Anisotropy in Nerve Tissue
Resource personnel: Marty Cole
Dates (start/finish) 2005

Collaborating PI: Simon Warfield
Institution: Harvard Medical School / Massachusetts Institute of Technology
Title of Project: Pediatric Epilepsy Surgical Planning
Resource personnel: Chris Johnson and Dana Brooks
Dates (start/finish) Ongoing

Collaborating PI: Carl-Fredrik Westin, Ph.D.
Institution: Laboratory of Mathematics in Imaging, Harvard Unviersity
Title of Project: Diffusion Tensor Analysis, Tracking, and Visualization
Resource personnel: David Weinstein, Gordon Kindlmann
Dates (start/finish) 2000–2007

Collaborating PI: Dr. Stephen Wong
Institution: Harvard Medical School
Title of Project: Diffusion Tensor Image Analysis in the Study of Age-Related Neurodegeneration
Resource personnel: Dana Brooks
Dates (start/finish) 2005

Collaborating PI: Gregory A. Worrell, M.D., Ph.D.
Institution: Mayo Clinic Rochester and Mayo Clinic College of Medicine
Title of Project: Biomarkers of the epileptic brain