The Bernard M. Gordon Center for Subsurface Sensing and Imaging

Systems

The Bernard M. Gordon Center for Subsurface Sensing and Imaging

Systems

Overview of Image and Data Information

Management R3-Thrust

David Kaeli, NU

This work was supported by in part by the Gordon Center for Subsurface Sensing and Imaging Systems, under the Engineering Research Centers Program of the National Science Foundation (Award # EEC-9986821).

CenSSIS Image and Data Information Management CenSSIS Image and Data Information Management

Addressing key research barriers in computational efficiency, embedded computing and image/sensor data management

Exploiting hardware/software acceleration/parallelization and Grid resources to enable new discovery in SSI applications

Producing an image/data repository and software-engineered Subsurface Sensing and Imaging Toolsets

Developing enabling tools targeting system-level projects • Near real-time reconstruction and visualization• FPGA-based phase unwrapping and registration

Addressing key research barriers in computational efficiency, embedded computing and image/sensor data management

Exploiting hardware/software acceleration/parallelization and Grid resources to enable new discovery in SSI applications

Producing an image/data repository and software-engineered Subsurface Sensing and Imaging Toolsets

Developing enabling tools targeting system-level projects • Near real-time reconstruction and visualization• FPGA-based phase unwrapping and registration

MVT

R1

R2

System Level Impact of R3 ActivitiesSystem Level Impact of R3 Activities

FundamentalScienceFundamentalScience

ValidatingTestBEDsValidatingTestBEDs

L1L1

L2L2

L3L3

R3Image and Data

InformationManagement

S1 S4 S5S3S2

Bio-Med Enviro-Civil

R3 ResearchersR3 Researchers

Faculty/Staff George Chen – MGH James Hale – Spelman Shawn Hunt - UPRM David Kaeli - NU Miriam Leeser – NU Steve Jiang – MGH Luis Jimenez - UPRM Waleed Meleis - NU Wilson Rivera - UPRM Samuel Rosario – UPRM Nayda Santiago – UPRM Greg Sharp - MGH Charles Steward – RPI Miguel Velez - UPRM Furong Yang – NU

Faculty/Staff George Chen – MGH James Hale – Spelman Shawn Hunt - UPRM David Kaeli - NU Miriam Leeser – NU Steve Jiang – MGH Luis Jimenez - UPRM Waleed Meleis - NU Wilson Rivera - UPRM Samuel Rosario – UPRM Nayda Santiago – UPRM Greg Sharp - MGH Charles Steward – RPI Miguel Velez - UPRM Furong Yang – NU

Graduate students Malak Alshawabkeh – NU Fatemeh Azmandian - NU Burak Erem – NU Carolina Gerardino – UPRM Evangelous Kanoulos - NU Avi Kelman - RPI Diego Rivera – NU Maria E. Sanchez-Castro - UPRM Dana Schaa – NU Alejandra Umana - UPRM Yijian Wang – NU Gehua Yang - RPI Jaime Yeckle – UPRM Juemin Zhang - NU

Graduate students Malak Alshawabkeh – NU Fatemeh Azmandian - NU Burak Erem – NU Carolina Gerardino – UPRM Evangelous Kanoulos - NU Avi Kelman - RPI Diego Rivera – NU Maria E. Sanchez-Castro - UPRM Dana Schaa – NU Alejandra Umana - UPRM Yijian Wang – NU Gehua Yang - RPI Jaime Yeckle – UPRM Juemin Zhang - NU

R3 ResearchersR3 Researchers

Undergraduate students Carolyn Andrews - NU Kelli Crosby – NU Nicholas Dedual - NU Danielle Edwards – Spelman Buffy Johnson - Spelman Rafal Norton - NU Jason Selwyn – NU

Undergraduate students Carolyn Andrews - NU Kelli Crosby – NU Nicholas Dedual - NU Danielle Edwards – Spelman Buffy Johnson - Spelman Rafal Norton - NU Jason Selwyn – NU

Goals for Year 7Goals for Year 7

Focus on sustainability - Won sustaining proposals, developed new industrial ties, submitted new proposals NSF STTR, NSF MRI, NSF IGERT,NIH, industry

Continued support of existing software toolboxes and new toolbox development Integrated 4-D visualization and image tagging (Northeastern and Spelman) Support of the SSI textbook effort with complementing tools

Expanded work on existing CenSSIS R3 projects Grid Computing – Load balancing - funded by MGH for yrs. 6 and 7 Hyperspectral Image Analysis – Acceleration/semi-automatic parallelization FPGA acceleration – QR Decomposition and phase unwrap

Increased utility of the image database (additional images and users) Provided image database user classes Continued collaboration with the S2 group on tumor tracking

Focus on sustainability - Won sustaining proposals, developed new industrial ties, submitted new proposals NSF STTR, NSF MRI, NSF IGERT,NIH, industry

Continued support of existing software toolboxes and new toolbox development Integrated 4-D visualization and image tagging (Northeastern and Spelman) Support of the SSI textbook effort with complementing tools

Expanded work on existing CenSSIS R3 projects Grid Computing – Load balancing - funded by MGH for yrs. 6 and 7 Hyperspectral Image Analysis – Acceleration/semi-automatic parallelization FPGA acceleration – QR Decomposition and phase unwrap

Increased utility of the image database (additional images and users) Provided image database user classes Continued collaboration with the S2 group on tumor tracking

Toolboxes

Sustainability Project PostersSustainability Project Posters

NSF STTR on automatic parallelization of high level languages with Interactive Supercomputing Corp. Poster R3B P5 - "Semi-Automated Parallelization Using Star-P" Utilizing CenSSIS applications to evaluate/demonstrate the efficiency of these

tools

NSF affiliated project on acceleration of sparse matrix problems Poster R3B P1 - "Characterizing the Relationship Between ILU-Type

Preconditioners and the Storage Hierarchy"

New projects on utilizing GPU technology to accelerate image reconstruction – Submitted IGERT and talking to AMD/ATI and NVIDIA Poster R3B P2 - "Digital Tomosynthesis Mammography Parallelization Using

Graphics Processors“ Poster R3A P4 – "Fast and Parallel Implementation of Image Processing

Algorithm Using CUDA”

NSF STTR on automatic parallelization of high level languages with Interactive Supercomputing Corp. Poster R3B P5 - "Semi-Automated Parallelization Using Star-P" Utilizing CenSSIS applications to evaluate/demonstrate the efficiency of these

tools

NSF affiliated project on acceleration of sparse matrix problems Poster R3B P1 - "Characterizing the Relationship Between ILU-Type

Preconditioners and the Storage Hierarchy"

New projects on utilizing GPU technology to accelerate image reconstruction – Submitted IGERT and talking to AMD/ATI and NVIDIA Poster R3B P2 - "Digital Tomosynthesis Mammography Parallelization Using

Graphics Processors“ Poster R3A P4 – "Fast and Parallel Implementation of Image Processing

Algorithm Using CUDA”

CenSSIS Toolbox PostersCenSSIS Toolbox Posters Multiview Tomography Toolbox (MVT)

C++ fddlib: January 2003 (v. 1.0) July 2003 (v. 1.1)

MATLAB mvt: October 2004 164 downloads of these tools in the past 2 years Being used in the SSI Textbook and NSF STTR project

Poster R3B P5 - "Semi-Automated Parallelization Using Star-P" Rensselaer Generalized Registration Library (RGRL)

Released September 2004 Effort has spawned a startup company

Poster R2D P5 - "New Applications and Enhancements in the Theory of the GDB - ICP Registration Algorithm"

Hyperspectral Image Analysis Toolbox (HIAT) 749 downloads in past 3 years The range of algorithms included in the toolbox have been funded by NASA, DoD,

ARMY, and NSF New work highlighted in poster:

Poster R3B P6 - "New Developments and Application of the MATLAB Hyperspectral Image Analysis Toolbox"

Multiview Tomography Toolbox (MVT) C++ fddlib: January 2003 (v. 1.0)

July 2003 (v. 1.1) MATLAB mvt: October 2004 164 downloads of these tools in the past 2 years Being used in the SSI Textbook and NSF STTR project

Poster R3B P5 - "Semi-Automated Parallelization Using Star-P" Rensselaer Generalized Registration Library (RGRL)

Released September 2004 Effort has spawned a startup company

Poster R2D P5 - "New Applications and Enhancements in the Theory of the GDB - ICP Registration Algorithm"

Hyperspectral Image Analysis Toolbox (HIAT) 749 downloads in past 3 years The range of algorithms included in the toolbox have been funded by NASA, DoD,

ARMY, and NSF New work highlighted in poster:

Poster R3B P6 - "New Developments and Application of the MATLAB Hyperspectral Image Analysis Toolbox"

HIAT

MVT

RGRL

The Image Tagging InterfaceThe Image Tagging Interface

A 2-D X-ray image is read, and then notes are entered into the

radiologist’s report

The Image Tagging InterfaceThe Image Tagging InterfaceInstead, a 3-D image can be

annotated by the radiologist with searchable tags, so the notes can be integrated with the image in a

relational database system.

Poster R3B P4 - "Online Image Tagging System"

<feature type="Ellipse" label="Tumor"> <ellipse> <xCenter>277</xCenter> <yCenter>278</yCenter> <xRadius>44</xRadius> <yRadius>34</yRadius> </ellipse></feature>

4-D Radiotheraphy – 3D + Time4-D Radiotheraphy – 3D + Time

New visualization tools to allow physicians to rapidly segment and identify regions of interest in 3D or 4D

Leverages SCI-Run (Univ. of Utah) – a visual programming problem solving environment

The total time for treatment planning can be reduced by allowing more efficient analysis of size, shape, and movement of tumors

Present work focuses on enabling accurate physical measurements in our visualization environment

New visualization tools to allow physicians to rapidly segment and identify regions of interest in 3D or 4D

Leverages SCI-Run (Univ. of Utah) – a visual programming problem solving environment

The total time for treatment planning can be reduced by allowing more efficient analysis of size, shape, and movement of tumors

Present work focuses on enabling accurate physical measurements in our visualization environment

Poster R3B P3 - "Development of Visualization Tools for 4D CT Datasets"

Parallelization and AccelerationParallelization and Acceleration

Parallelization work at NU and UPRM is focused on developing a general set of Grid level tools Tomosynthesis and classification are being used as the proof-of-

concept applications Tomosynthesis reconstruction paper in Proc. of the 2006 IEEE

International Conference on Parallel and Distributed Computing, coauthored by NU/MGH

FPGAs are being used at NU to provide real-time processing closer to the sensor Discrete Cosine Transform acceleration with the S1 project to

accelerate phase unwrapping Floating point division and square root based on Taylor series for the

variable precision floating point library

Parallelization work at NU and UPRM is focused on developing a general set of Grid level tools Tomosynthesis and classification are being used as the proof-of-

concept applications Tomosynthesis reconstruction paper in Proc. of the 2006 IEEE

International Conference on Parallel and Distributed Computing, coauthored by NU/MGH

FPGAs are being used at NU to provide real-time processing closer to the sensor Discrete Cosine Transform acceleration with the S1 project to

accelerate phase unwrapping Floating point division and square root based on Taylor series for the

variable precision floating point library

Poster R3A P3 – “Design of Workflow Scheduler" Poster R3A P5 - "Utilizing High-Performance Computing to Investigate Performance and Sensitivity of an Inversion Model for Hyperspectral Remote Sensing of Shallow Coral Ecosystems”

Poster R3A P2 - "Phase Unwrapping Using Reconfigurable Hardware"

Poster R3A P1 – “Floating-Point Divide and Square Root for Efficient FPGA Implementation of Image and Signal Processing Algorithms"

CenSSIS Image Database SystemCenSSIS Image Database System

Poster R3B – P7 "The CenSSIS Web-Accessible Image Database System"

• Over 17,000 image files online

• Offered 3 online classes to the CenSSIS research community

Impact on System Level ProjectsImpact on System Level Projects

R3 Project S Project Impact

Parallel/Grid/GPU Processing

Accelerating tomosynthesis reconstruction < 5 minutes on a $500 platform

Hyperspectral toolbox

Accelerating HIAT code by more than 25X – reducing parallel programming time by 10X

Image database Developing customized database interfaces to facilitate rapid data entry

4-D visualization Improving radiation treatment planning

S3

S4

S1

S2