NCRR Report 2001
Outline

Dave and Rob

1 Summary of Research Progress

• Main focus was on the software development and distribution.
• With the first software release, we have now selected subset of collaborators to implement and test
• Also progress on scientific components, especially bioelectric field problems
• Next major milestone is renewal application, October 1.

2 Highlights

2.1 BioPSE(Dave/Rob)

1. Releases
   1. Core
      1. Versions
      2. Platforms
      3. Packages
      4. Installation script
      5. Third party installation
   2. Docs
      1. FAQ
      2. User
      3. Developer
2. Download and Code Management
   1. User support
      1. How many people have downloaded the code?
      2. How many users are on the mailing list?
      3. Where are the users distributed?
      4. We have not yet made out Big Announcement - we will in July
      5. Download wizard
      6. Track usage statistics
   2. Repository
      1. Code
      2. Documentation
      3. Datasets
      4. Nets

3. Modules and Data Structures
   1. Fields enhanced
      1. Added support for dynamic compilation
      2. Added generalized interpolation
   2. Lead Fields implemented
      1. Modules to build element- and node-based lead fields
      2. Modules use lead fields for faster forward projection and focusing
   3. Vis Pipeline (sample-based vis): generalize pipeline into generate/evaluate/display
      1. Generate: construct field of samples
      2. Evaluate: determine the values at the sample locations
      3. Display: graphically represent all of the samples (iconic or direct)
      4. Within each stage, supported methods are often interchangeable
   4. Matrices unified
      1. Converters between derived types (Sparse, Dense, Column)
      2. Field transforms implemented
      3. Unary and binary operation modules added
   5. PetSc support integrated, demonstrated in SolveMatrix module

4. Core Software Enhancements
   1. Network Editor Enhancements
      1. Additional File Options: Save, Save As..., Insert, Clear
      2. Module Interactions: Process ID, Port and Pipe tracker
   2. Bridging
      1. MPEG Encode
      2. libimage
      3. Matlab: socket data transfer and compiled into SCIRun module source code
      4. GENESIS via SQL server
   3. Data Import and Export
      1. Data filters and converters
      2. Dynamic compilation and loading of import/export code
      3. XML resource files for specifying third-party formats
   4. Installable SCIRun
      1. One instance of SCIRun installed and shared among users
      2. Each user can extend SCIRun with their own local package
   5. Dynamic Compilation/Loading
      1. On-the-fly compiles for templatized modules
      2. Reduces template code bloat
      3. Compiled versions cached for reuse

5. Application Networks
   1. Focusing inversion
   2. Source localization
   3. Parameterized conductivity inversion
   4. GENESIS realistic source modeling

2.2 Geometric modeling (Rob/Dave/Xinlong)

1. Focus on surface mesh generation
2. Surface feature extraction from point clouds

2.3 Simulation (Chris/Dave)

1. Algebraic multigrid for forward and inverse problems
2. Focusing inversion
3. Neural source localization
4. GENESIS simulations?

2.4 Visualization (Rob/Dave)

1. New version of map3d released
2. Number of users, range of institutions
3. Vis features in BioPSE, e.g., seed point placement and streamline generation

2.5 External Links (Dave/Rob)

1. EAB
   1. Met in March 2. Received very positive, useful feedback 3. Details are in their report

2. Collaborators
   1. Just ramping up on collabs (need infrastructure first)
   2. Henriquez: Starting to work on Finite Volume
   3. McCarley: Source localization implemented
   4. CVRTI: i. Electric field visualization (seed based on current density), ii. Import/export data

3. Dana Brooks: 1. Tikhonov module

2.6 Web site (Dave/Rob)

1. Distribution of software
2. Datasets
   1. Brain/Heart
   2. Low Res / High Res
   3. Volume / Surface
   4. Anatomic / Functional
3. Resource for bioelectric field research

3 Personnel and Administration (Greg)

1. List of personnel activity
2. Training of Center staff
3. NCRR Seminars

4 Forms and Abstracts for Program Activities (Greg/Allyne)

5 EAB Report (Greg/Allyne)

6 Allocation of Resource Access (Greg/Allyne)

7 Bibliography

About this document ...

NCRR Report 2001
Outline

This document was generated using the LaTeX2HTML translator Version 99.2beta6 (1.42)

Copyright © 1993, 1994, 1995, 1996, Nikos Drakos, Computer Based Learning Unit, University of Leeds.
Copyright © 1997, 1998, 1999, Ross Moore, Mathematics Department, Macquarie University, Sydney.

The command line arguments were:
latex2html -split 3 -no_white -link 3 -no_navigation -no_math -html_version 3.2,math -show_section_numbers outline

The translation was initiated by Rob MacLeod on 2001-06-18