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NLM-SMU. Visible Human TransPacific Demonstration

Author: Michael Gill
11/5/99
Email: Home Page: http://archive.nlm.nih.gov/proj/bita/bita.php


Start Power Point Presentation

Table of Contents and HTML version:

NLM-SMU.Visible Human TransPacific Demonstration
Content
National Library of Medicine.[www.nlm.nih.gov]
PPT Slide
Application Objective
Visible Humans
PPT Slide
PPT Slide
PPT Slide
Demonstration Procedure
PPT Slide
Demonstration Procedure
Test Plan Schedule
Demonstration Timeline
Demonstration Timeline
References

Slide 1: NLM-SMU. Visible Human TransPacific Demonstration

Michael Gill
Communications Engineering Branch
Lister Hill National Center for Biomedical Communications
National Library of Medicine (NLM)
National Institutes of Health
Dr. Haruyuki Tatsumi,
tatsumi@sapmed.ac.jp
Sapporo Medical University (SMU)
JUSTSAP Millenium Workshop
Princeville Resort
Princeville, Kauai, Hawaii
November 8-12, 1999

Slide 2: Content

National Library of Medicine
Demonstration Overview
Application Objective
Application Status
Test Plan Introduction
Demonstration Procedure
Schedule
Timeline
References

Slide 3: National Library of Medicine [www.nlm.nih.gov]

  • The world's largest biomedical library.
  • 5 million items--books, journals, technical reports, manuscripts, microfilms, photographs and images.
  • Producer and distributor of MEDLINE and 40 other biomedical databases.
  • Producer of GENBANK and other biotechnology information sources.
  • Divisions include library operations, R&D centers, and international centers for database distribution.
  • Communications Engineering Branch R&D (archive.nlm.nih.gov) produces
    • DocView (document delivery via the Internet)
    • MARS (automated data entry system to create MEDLINE)
    • WebMIRS (multimedia biomedical databases of x-rays and text

Slide 4: Demonstration Overview

  • Uses a prototype Telemedicine application
    • Gathers information useful in the design and operation of Interactive Biomedical Image Collaboratories
      • Such Collaboratories would use large datasets across broadband international networks
  • Proposed demonstration will attempt to gather information
    • Using large images, application includes:
    • Interactive biomedical image segmentation
    • Labeling
    • Classification
    • Indexing using large images.

Slide 5: Application Objective

  • Interactive biomedical image segmentation, labeling classification, indexing using large images (Visible Human Dataset, VH)
    • Calculates and fills areas in the segment with metaballs and renders them
    • Attachment of anatomical terms using Unified Medical Language System
    • Creation of multilingual object database
    • VH data transferred to/from researcher
  • Motivation
    • Centralized repository, database management more easily done
    • Updates in one place ensuring authenticity and reliability.
    • Biomedical image libraries (in number and size) are sure to grow
    • Current licensees of VH dataset number 1000+ worldwide

Slide 6: Visible Humans

Slide 7

  • Dataset size/International importance
    • Multilingual labeling of the dataset proposed
  • Investigators
    • Sapporo Medical University
    • Others potential exist in Europe
  • Future online access of segmented human anatomy
    • Worldwide vital resource
  • One model use
    • NLM developed browser software
      • Selecting a cropped volumetric subset (e.g. the heart).
      • Client receives volume of interest, all labels
      • Future generic client rendering tool

Application Objective

Slide 8

  • Present: Application currently in a beta
    • Viewer module
    • Displays, sagital and longitudinal, coronal sections of a human body
    • Runs under Apple Openstep environment on several platforms
    • Annotation Module part of the architecture
  • Future: SGI-based version
    • Enhanced features: viewing at any angle
    • Beta form in about six months

Application status

Slide 9

  • Visible Human Viewer software (ver. 1.0): Between client workstation at SMU and a Sun server at NLM
    • Version 1.0 runs under Apple OpenStep Enterprise on NT.
    • Version 1.2 runs under Apple OpenStep OS on an Intel platform
    • Version 1.3 runs under Apple OS X on a G3 platform
  • Objective: Make a very rough measure of the activities of a user of the Visible Human Viewer software from a remote site
    • Repeatable USER PROFILE defined and use is approximately measured
      • Typical set of common operations a remote anatomist follows using the Visible Human Viewer software.

Slide 10: Demonstration Procedure

  • Preliminary
    • Establish NetMeeting 98 audio/video connection NLM-SMU for coordination link
    • Establish teleconference number for demonstration coordination, troubleshooting as needed
    • Verify SMU can reach NLM via ping, traceroute, and NFS over satellite
    • Record ping and traceroute results
    • SMU verifies directory listing of server data: /home2/gibn

Slide 11

  • Day X (X=1-8) of satellite link availability:
    • SMU begins first run using VH USER PROFILE procedure (see references)
    • x.1 Notify demonstration email list upon start/uses voice loop
      • Coordinate with other testing by network engineers
    • x.2 Record starting from the point at which one hits the enter key after changing the filename to the display of the first image (landmark image try #1) for Subtask 2.1 of the VH USER PROFILE
    • x.3 Record the start and stop times for each of the subsequent image viewing attempts (5) until each subtask is completed

Slide 12: Demonstration Procedure

  • x.4 Repeat x.2 and x.3 for the remaining subtasks (2.2, 2.3, 2.4) of the VH USER PROFILE
    • Stop at display of last image (identification of lower end of femur)
  • x.5 Notify demonstration email list upon stop of each testing run
  • x.6 Repeat this complete procedure x.1-x.5 as often as possible during scheduled test time (minimum twice)
  • x.7 Send results to demonstration email list after each day's runs

Slide 13: Test Plan Schedule

  • Satellite link available on or about January 24, 2000 for one month
  • Satellite link will be available two days per week between NLM and SMU 8 AM - 1 PM EST
  • Eight days (Day 1 - Day 8) total
  • Terrestrial (via STAR TAP/APAN) link will be available as backup when satellite link not available
    • Tests basic functionality at low throughput.

Slide 14: Demonstration Timeline

  • November 1999
    • MSU and NLM researchers refine VH Viewer profile procedure
    • Initial readiness testing using terrestrial link
    • SMU uses VH Viewer application and verifies client communication with NLM server
    • Record initial test runs using for comparison with the satellite connection
  • December 1999
    • Continued use of terrestrial Link by SMU for baseline data gathering
    • Continue debugging communication links if necessary

Slide 15: Preparation Timeline

  • January 2000
    • Prepare for 1/24/2000 satellite link start date
      • Initial readiness testing using satellite link dependant upon availability
      • Verify routing working with NASA, CRL and SMU technical groups
      • Turn link over to SMU for application testing.
  • February 2000
    • Continue SMU to NLM testing through February 24
    • Monitor satellite link and NLM server for readiness as it becomes available for testing each test period
    • Link is turned over to PI for application testing using Visible Human Viewer software between SMU and NLM.

Slide 16: References

  • Principal Investigator (SMU):
    • Haruyuki Tatsumi, MD, PhD, tatsumi@sapmed.ac.jp
  • Co-PIs (NLM):
    • Dr. George Thoma
    • Dr. Michael Ackerman
    • Michael Gill
  • National Library of Medicine Trans-Pacific Digital Library Demonstration Description: http://archive.nlm.nih.gov/proj/bita/trans-pacific.html
  • NLM-SMU Visible Human TransPacific Demonstration presentation at the JUSTSAP Millenium Workshop: http://archive.nlm.nih.gov/proj/bita/justsap-workshop.html
  • Visible Human Viewer User Profile-draft, http://archive.nlm.nih.gov/proj/bita/vhuser-pro.html
  • Communications Engineering Branch- http://archive.nlm.nih.gov
  • NIH- http://www.nih.gov
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