Interactive Lung View Access 3D (ILVA 3D)
Clarence Wigfall
TNDY 405I - Data Analytical Tools, Technologies and Applications Across the Disciplines
Brian Hilton and Hovig Tchalian Instructors
Abstract
ILVA 3D is a prototype application/platform combination
that addresses the need to find a solution that allows all
lung study and imaging data-bases being to be studied and
used world-wide simultaneously by researchers. ILVA 3D
demonstrates that large lung datasets can be explored in
Real Time and used as 3D real-time interactive
visualizations through the internet. Disparate data can be
joined to allow researchers to move from one data set to
another data set seamlessly to the perception of the
researcher even when the source process to create the data
sets are different. ILVA 3D can be used as an open-access
resource to create a comprehensive Lung molecular atlas
viewable as 3D anatomical visual constructs that are true
anatomical representations.
ILVA 3D provides the prototype of a solution
Big Data Project
Making high-resolution data sets anatomical information
accessible and usable to researchers studying the lung and its
functions is a big data application that provides
Opportunity to address big data as 3D anatomical visual constructs
explored as true anatomical representations
Merge All NIH funded Lung data sets into one interactive
application that can be accessed through the internet and explored
from the gross anatomical levels through cellular anatomical levels
through genetic levels in a seamless manner by clicking through
each successive data set as a 3D visual experience
National Heart, Lung and Blood Institute (NHLBI), an Institute of The
National Institutes of Health (NIH), has funded cooperative agreement
grants creating Research Centers (RCs) to create and develop a Molecular
Atlas of Lung Development Program (LungMAP)
Creates heretofore not possible 3D visualizations
of that data that can be accessed and
manipulated by all researchers as needed in real
time
Demonstrates that it is currently possible to
make the data accessible as interactive 3D visual
representations through an internet interface
hosted on a cloud based platform
Objectives
ILVA 3D was created to address a critical need and a take advantage of the
technological advances to create 3D visualizations from high resolution
data sets generated by advanced microscopy and MRI imaging. The
critical need concerns the massive amounts of data being generated by
lung researchers in the United States and abroad. These data sets represent
the results of the most advanced microscopy imaging being used to
understand the structure of the lung.
Makes all of the data in all of the biological data
sets being created world-wide accessible
simultaneously to all researchers around the
world
Hardware – Software
Volume rendering software created by VoluMedic software is the
application that provides the real time rendering of the data sets
Microsoft Azure: Virtual Machines that run on the Azure platform as a
service provides Cloud Platform
Coupling Volumedic and the Azure platform: Multiple iterations were
necessary to bring the combined application/platform to a high level of
functionality that equals running the application on a local computer
Virtual Machine Progression
A-series general purpose machines. The combination of the early Volumedic
render and the A level machines resulted in high latency and inconsistent
control of ILVA 3D.
D-series machines were tested.
current application runs on G3 level Virtual Machines
G-series virtual machines tested to the G4 level with 16 cores and 224GB of
memory. The improvement over a G3 with 8 cores and 112GB of memory
was not enough to continue to run on a G4 and the G3 has performed as well
as having the application run locally on relatively fast computers
Real-Time Exploration of Disparate Data Sets
Centrally Maintained Application and Platform
Data sets range - megabytes -> terabytes when aggregated easily
reach past the petabyte ->exabyte -> yottabyte levels
Cannot be housed by any one research laboratory or between
multiple laboratories that store and maintain their own data sets
and create their own interactive applications.
Centrally maintained and managed application and platform to host
the data and application is critical
Demonstrates that disparate data can be joined
to allow a researcher to explore one level of
anatomy then immediately jump to a more
microscopic level of that same structure
Transdisciplinary Project
The efforts of experimental biologists including microscopy
and imaging specialists provide high resolution data sets
Application Developers
Platform Developers and Platform as a Service Applications
My particular areas of interests are: combining Experimental
Biology, Public Health, Applied Social Psychology
Translating the Convergence of advanced technologies and
communication theory to broad Array of Practical Health
Services
Ampulla of Wigfall
Never seen before
References
Demonstrates that these data sets can be
produced by different processes, i.e., microCT
scan (5 micron resolution and higher) and
confocal microscopy and still be used seamlessly
by the viewer
National Institutes of Health/Department of Health and Human Services.
(2014). Retrieved from http://grants.nih.gov/grants/guide/rfa-files/RFAHL-14-008.html
Acknowledgements
David Warburton, PI – Children’s Hospital/Saban LungMap
Research Center Grant
Rex Moats – Co-Director Translational Biological Imaging
“The overall goal of this program is to build an open-access reference
resource by creating a comprehensive molecular atlas of the late-stage
developing lung (human and mouse) with data and reagents available to
the research community…”
RESEARCH POSTER PRESENTATION DESIGN © 2012
www.PosterPresentations.com
Produces 3D Interactive Real-Time Modeling of
Data Driven Anatomically Exact Lung: Gross to
Cellular structures
Lab (SABAN)
Elmar Moelzer – Founder VoluMedic
Wei Shi and David Koos – Data Sets
William D. Crano – Advisor
Eusebio Alvaro – Second Reader