The Visible Human Project Today
Director, Michigan Center for Biological Information (MCBI)
UM Office Vice President for Research (OVPR)
Assistant Professor
Director, University of Michigan Visible Human Project
Department of Cell and Developmental Biology
University of Michigan Medical School
Ann Arbor, Michigan
http://vhp.med.umich.edu http://CTAalliance.org
September 26, 2002
Presented by
Brian D. Athey, Ph.D.
2002: NLM/NIH NGI Visible Human CollaboratoryFor Health Sciences Education and Training
StanfordUniversity
Universityof Colorado
Health Sciences
Universityof
Michigan
Pittsburgh SupercomputingCenter (PSC)
National Libraryof Medicine (NLM)
Uniformed ServiceUniversity of the Health Sciences
(USUHS)
Abilene Network
Virtual Environment – Combat Battlefield
Integrated Core – Manikin with Synchronized Anatomy from Visible
Human Project
An Early Test-bed Application: ARPA 1992-1995To Extend the DoD Medical Training Platform from WRAMC to Battlefield
Internet2 Backbone
Virtual Workbench
Dexterous Skills Training
Middleware Needed
Future:Middleware and Applications
Past: Enabling Infrastructure
Old-time (~1995-1997) VH Client-Server Application Concept
Servers
Visible Human
Applications/Tools
Development Focus: Visible Human
Project (courtesy Don Jenkins, NLM)
VISIBLE HUMAN DATASETSVISIBLE HUMAN DATASETS
Natural Biologic Natural Biologic Variation Variation
Disease and PathologyDisease and PathologyNormal VariationNormal Variation
TeachingTeaching ApplicationsApplications
Public Domain Web Public Domain Web SitesSites
National Anatomy ArchiveNational Anatomy Archive
DIGITAL HUMAN SIMULATIONDIGITAL HUMAN SIMULATION
ANCILLARY DATA SETSANCILLARY DATA SETS
MRI, CT, PETMRI, CT, PETRadiologyRadiologyAnatomicAnatomic
Structural ChangeStructural ChangeScale & ResolutionScale & ResolutionBiological Biological
Structure Structure ContinuumContinuum
EmbryologyEmbryologyGross AnatomyGross AnatomyMicro AnatomyMicro AnatomySub MicroscopicSub MicroscopicPhysiologyPhysiologyBiochemistryBiochemistry
DevelopmentDevelopmentAgingAging
Clinical PatternsClinical PatternsSigns & SymptomsSigns & SymptomsPathophysiologyPathophysiology
The Evolving Amphitheater of Human Anatomy
Vision: Medical Student User Product
Interface
Visible Human Database
Animations
Visuals
Text
Learning Materials
Labels
Simulations
Quizzes
Case Inquiry
ConceptU of M Center for Parallel Computing
U of Kiev
Local Server
U of MichiganU of Kiev
Local Server
U of Michigan
iBook
Bejing Med U
Visible Human Infrastructure Development Embraces “Cyberinfrastructure” Vision
Vision of Integrated IT and Computing ArchitectureFor Life and Health Sciences Informatics
Ontology Integration and Biological Context
NLM UMLS Ontology (Linked to 50 Others)
Digital Anatomist
Cell Cell
Proteome
Bio/SPICE (DARPA) and Others
Gene
NLM UMLS Semantic Network + the “Semantic Web”
Bioinformatics Databases and Data Standards e.g. Celera, GO
nM
M
Physiology109
Gene
Organs&
Tissues
High Throughput “Structural Biology”
Geneotype
Phenotype
Behavior(organs,
organisms)SystemsPhysiology(process
engineering)Cellular
Processes and Interactions
Years
Minutes
Seconds
Milliseconds
Microseconds
Nanoseconds
Picoseconds
Molecular Dynamics
Quantum Mechanics
0.1 nm 10nm 100nm 1um 1mm 1cm 1mAdapted from the work of Bill Goddard, Caltech
Need for Multiple Need for Multiple ScalesScales
Visible Human “Data-locator”
Navigable Volume Data
UMich Visible Human Knowledge Base Schematic
Anatomical layer
Semantic layer
Annotation layer• Hyperlinked texts• Movies• Sounds, etc
• Medical lexicons• Semantic relations• Links to regions, volumes, and
annotations
• Labels of structures• Voxel data and segmentation• Volume surfaces• Spatial relationships
System: Skeletal MuscleRegion: PelvicStructure: Sartorius
BoundariesContainsSurface AnatomyCommon AnomaliesIllustrations
ActionOriginInsertionInnervationArterialVenousBounded by
Femoral Nerve SourceBranchesMotorSensory
lumbar plexus (ventral primary rami of spinal nerves L2-L4)
Original Labeling Scenario
Database Development
Over 7000 Terminologia Anatomica(TA) terms are now available via the UMVH database.
Structural relationships (i.e. heirarchy) imported from UMLS/TA and linked to VH content.
Non-English Languages (e.g Chinese). Web-based querying and editing.
Navigable Volume Data
Volume/Structure/Instructional Space
Structure
UMLS MESH TA
Area VolumeUser
Request
Rotation-TranslationParameters
Arbitrary Section
Integration of VH, and Volume/Structure/Instructional Databases
User Skill Instruction Area
Dental Surgery Nursing AnatomyAlliedHealth
Video
Audio
Quizzes
Tests
XML Tagged
XML Tagged
Walter Meixner
Labels
Overview of simulation
3D rendering computation
tissue biomechanics computation
Tool tip position
deform
ation
Force sensed at tool tip
Tissue deformation observed
Force computed 1000 - 10,000 times per sec
Image computed 10 - 30 times per sec
Remote client
Server
Haptics process Display process
Internet
3D model
Parvati DevStanford University
MediaserverAccess to resources
Library of images and models – A mediaserver
Retrieval interface (general purpose)
Interface to rotate and peel through dissection images (specialized)
Interface to control a simulation (specialized)
Search and browse interface
Client Client Client Client
Parvati DevStanford University
National Test-bed Demonstration at NREN (June 2001): Four Parallel VH Streams—
Memory-to-Memory Transfer (UMich to Ames)
University of Michigan Internet Connectivity
vBNS
UM BINGigE
ITCS CAEN
DOE
NASA
DREN
Abilene
MERIT
MCIT
MichGiga PoP
Gig
EO
C-3
CAC MGrid Test sitesATLAS Physics
Michnet
Internet Qwest Cleveland POP
Research Networks Commercial Networks
FW
StarLightChicago
Gig E Gig E
MGrid Test sites
4x 100mbit/sec
UMArbor Lakes
#1 #3
Medical SchoolUM Hospital + MCAREBioinformaticsProteomics
MCBI
FW
MCIT 4x100mbit/sec
UCAIDInstitutions
Europe
Stereo Volume
Java Browser - Model View
UMich Visible Human Project NGI/I2 Network-Enabled Software Tools and Content
Pittsburgh Supercomputing Center (PSC) Segmentation Tool: To facilitate the creation of surface models, our collaboration partner the PSC has been commissioned with the development of a segmentation tool for the production of contours. This tool has been ported to Linux, Mac and Windows platforms. Data Slice - Embedded Model
View
Edgewarp: Created by Dr. F. Bookstein and Dr. W. Green as a tool for analyzing shape variation by extracting invariant geometric operations from volumes and surfaces, this software program has been extensively modified for the UM VH Project. The addition offeatures such as labeling, model display and filmstrip creation has expanded its usefulness to medical education.
Java Browser:Alexander Ade has created a set of Java-based Browsers that allows web-based volume visualization as either slices or volume-rendered scenes. The applications show anatomical labels queried from an database and displays 3-D models in either mono or stereo views.
Java Browser - stereo model view
VH Image Data Representation
• Hierarchical multi-resolution tree
• Each node is an 8*8*8 cube
• 4 levels of representation
• Volumetric compression
Implementation Approach• Avoid disk seek and network bottlenecks
• Use memory based server representations
• Apply volumetric compression techniques
• Serve volume data by client demand
• Take advantage of intelligent clients
• Minimize server computational demands
• Leverage network tuning from Web100
AnatomyDatabase
MeshServer
Voxel IdentityServer
CollaborativeServer
indirect
(NGI)
direct
…or…
Intermediate Server
Router or Hub
System Architecture
Compression Numbers• Lossy simple VQ 9.42:1 = 2.67Gbyte• Lossless TS wavelet VQ 7.03:1 =3.53Gbytes• Normal JPEG @23.3:1 = 1.06Gbytes• JPEG2000 estimated ~40:1 = ~500Mbytes• Lossless SPHIT + arith ~4.22:1• Lossless SPHIT + huffman ~4.10:1 (2x faster)• Lossy SPHIT & other EWZ useful beyond 50:1
Shared & PrivateLibraries
Shared Services
Object Libraries
Version Control
Data Library
Runtime Results
Authoring ToolsSolvers,utilities.
VisualizationUser Interface
Validation
Bug Reporting
Peer Review
A Scalable Test-bed Must Include an Open Source Mechanism Featuring a Standards-based Adaptive Middleware Environment
Middleware and Infrastructure
Users/ Applications
ETF-based Raycasting: The Next Step