1. The main innovation projects
Июль 2013
Center for Biomedicine and
Computational Technologies
http://biomedcompcenter.ru/
Participant № 1120499

2. Laboratory of High-Performance Computing on Cluster Systems
2
Victor Gergel,
D.Sc. Prof. (CV)
Iosif Meerov,
Ph.D. (CV)
Project:
«Global Expert» - software system of decision-making support
Goal: Development of decision support software system (i.e. choice of optimal parameters ) based on
solving multicriterion multiextremal problems as a most general model of choice. Software is oriented
on the HPC-clusters as far as in real-world applications even estimation of one combination of
parameters is time-consuming.
Purpose of a scientific-technical product: Parallel software system of decision support «Global Expert».
Main parameters:
Software system of decision-making support that integrates the following:
1) multiparameter optimization (hundreds of parameters);
2) multicriterion optimization (tens of criterions);
3) mixed discrete – continuous optimization;
4) constrained optimization (hundreds of constraints);
5) correction of problem statement during optimization process;
5) using of system on supercomputers (thousands of processors);
6) remote access to the system through the Internet (сsystem as a cloud service).
Characteristics of software must correspond to foreign analogues systems, e.g., LGO system
developed by Pintér Consulting Services, Inc. http://www.pinterconsulting.com/.

3. «Global Expert» - software system of decision-making
support
3

4. «Global Expert» - software system of decision-making
support
4

5. «Global Expert» - software system of decision-making
support
5
Project:
History
Project is proposed as a result of long-term researches carried out by research team of UNN supported by Russian
Foundation of Basic Research (RFBR), grants of the President of Russian Federation, Russian Federal Program
"Scientists and Educators in Russia of Innovations". Well-known in Russia and abroad scientific school was formed
during the years of investigations.
Developing Dynamics
As a result of the RFBR project (2011-2012) it was develop the experimental prototype of the system «Global Expert».
This prototype has no analogs in Russia and abroad by many indicators (number of variable parameters, number of
using processors).
Supporting by federal grants
1) Federal Program "Scientists and Educators in Russia of Innovations": proposal 2012-1.1-12-000-1005-033 (2012-
2013), 5.1 mln. rub. (financing confirmed)
2) RFBR: grant № 11-01-00682-а (2011-2013), 0.75 mln. rub.
3) grants of the President of Russian Federation: grant № НШ-1960.2012.9 (2012-2013), 1 mln. rub.
Project Status
1) Parallel optimization algorithms has been developed, theoretical analysis of its efficiency has been carried out.
2) Prototype of system has been developed. This prototype has the part of proposed indicators (solution of
multiparameter continuous global optimization problems with nonconvex constraints)

6. Laboratory of Scientific Visualization
projects: http://biomedcompcenter.ru/?id=lab01&jd=projects
6
Prof. Gregory
Nielson (USA) (CV)
Dr.of Sci. Vadim
Turlapov (CV)
Project:
Virtual 3D tomograph - anatomical table
Objective: Creation a modern competitive on the world-market product via fusion in one software
package and complementarities of two products: of electronic atlases and 3D-reconstructors of
tomograms. 3D-visualization will be realized for geometric models of human organs with normal
anatomy and with standard pathologies, and also for the current state of the patient organs across his CT
scans, seamlessly stitched with geometric models. In perspective the results of all types of diagnostics
will be fused in a single three-dimensional model in order to increase the accuracy of diagnosis, and
treatment quality. Removing the risk of commercialization, and reaching of competitive price for the
product.
Appointment of scientific and technological product: software for the clinician work place ("Virtual 3D
tomograph"), and also for the work place of teacher (or student) - an interactive dissection table ("Virtual
anatomical table").
The main technical parameters:
Features of the product must meet or exceed unique today foreign analog, created by
Anatomage - Anatomy Imaging Software (http://www.anatomage.com/), Interactive
Anatomy Dissection Table (http://www.youtube.com/user/Anatomage), and premiered
in May 2011 at Stanford University (http://youtu.be/28XhiI2bG3g).

7. 7
Project
Status
Virtual 3D tomograph - anatomical table
On the base of software framework InVols

8. The software package InVols for stereo and 3D-visualization and analysis has
a clinician-oriented interface:
8
Project
Status
Virtual 3D tomograph - anatomical table

9. Method of block decomposition was implemented . The dependence of the rendering performance from
the block size and the size of the data was investigated for different GPU . The record performance was
reached.
9
256х256х256
64х64х64
Размер
блока
A test dataset with record for GPU size ~2GB: 5382х512х512 (12-bit)
See http://www.youtube.com/watch?v=WIqg7yTqV0o (576 view per year)
Block sizes:
Project
Status
Virtual 3D tomograph - anatomical table

10. 10
(1) (2) (3)
Visual defects associated with the classification of data values were investigated and minimized .
Examples of data classification functions (s ϵ[-1000 HU ,3000 HU])
 (s)
C(s)
s
 (s)
C(s)
s
 (s)
C(s)
s
-1000 HU 1000 HU
0.0
1.0
Project
Status
Virtual 3D tomograph - anatomical table

11. A dependence of rendering quality from the sampling rate (number of samples per voxel ) and
PSNR (Peak Signal to Noise Ratio) as a measure of quality were investigated, and the sampling
rate was optimized.
1.2 2.2 4.3 6.9
Sampling rate
10dB
PSNR 20dB 30dB 40dB
PSNR map
1) PSNR < 30dB – noise is very noticeable
2) PSNR ϵ [30dB,40dB] – acceptable quality
3) PSNR > 40dB – almost imperceptible improvement in the quality of
11
Project
Status
Virtual 3D tomograph - anatomical table

12. The quality efficient pre-integrated rendering was studied and optimally realized.
1 frame by the pre-integrated
rendering
PSNR=36dB
Averaging 60 frames with
post-classification
PSNR=27dB
1 frame by the rendering
with post-classification
PSNR=12dB 12
Project
Status
Virtual 3D tomograph - anatomical table
Sampling rate (number of samples per voxel ) = 2

13. 13
History
The project and research team were formed during the years of investigations. Cooperation with the
medicine needed to execute the project was shaped, including: Nizhny Novgorod medical academy
(http://www.nizhgma.ru/eng/), Volga Regional Medical Center (http://www.pomc.ru/), Regional Diagnostic
Center (http://www.xn----ttbeqkc.xn--p1ai/nn/eng.html).
Supporting by federal grants
1) Federal Program "Research and Research and teaching staff of Innovative Russia" for 2009-2013:
State Contract № 02.740.11.0839 from 11.06.2010 to 15.10.2012, 3 000 000 rub
Virtual 3D tomograph - anatomical table
Project:
Project Status
1. Interactive rendering performance for
gigavoxel sizes of datasets is reached
2. Internet-accessible database of
tomograms has been organized on
resources heterogeneous computing
cluster and filled with 10,000
tomograms from Regional Diagnostic
Center.

14. 14
Global Illumination on GPU
High-performance full-GPU-renderer for virtual reality in the 3D-cinema industry
Project:
Unreal and non-polygonal fractal-object and its shadow in the polygonal environment

15. 15
Global Illumination on GPU
Project:
Full-GPU high-performance architecture of
the System with a number of new algorithms
was created. The System has special global
illumination pipeline, material subsystem and
scene-graph subsystem.

16. 16
Global Illumination on GPU
Project:
Performance of the System was completely tested and our system solutions was compared with state of art
analogues on the example of NVIDIA OptiX. Our solution (RTRays) at a trace depth = 8 surpasses OptiX 2
times.
San-Miguel (Upper Floor and Ground Floor), 10.5M triangles in each

17. Laboratory of Electrophysiology and Modeling of the Heart
projects: http://biomedcompcenter.ru/?id=lab03&jd=projects
17
PhD, Prof. Juergen
Kurths (CV)
PhD, Prof. Grigory
Osipov (CV)
Project:
"Virtual Heart"
Goal: Create modern competitive software product by synthesis of CT and MRI abilities with human heart
activity numerical modeling abilities (both healthy and diseases cases)
The appointment: Work software of cardiologist "Virtual Hears"
Technical parameters:
3D high-realistic model of main parts of human heart and software for modeling heart activity (both
healthy and diseases cases) where:
- patient individual anthropometric, CT, and MPI data will be used to have better modeling precision;
- real anatomic examples will be used in modeling
- most common pathologies modeling will be covered
- system will contain database with details description of organs and pathologies description at least in
two languages
- modeling will cover both electric and mechanic heart activities
- comparison between healthy activities and pathological changes will be implemented
- model compatibility with external systems (e.g. learning software)

18. Virtual heart
Theoretical, computational, and experimental analysis of electromechanical
activity of isolated heart
Main features
• Realistic cell models
• Multidomain models
• Virtual ECG
• 2D and 3D spatio-temporal diagrams
• Whole heart segmentation (sinoatrial
and atrioventricular
nodes, atriums, ventricles, Pirkinje
fibre etc)
• Databases of normal and arrhythmia
behavior
Project: