Internal:CNF Workshop

08/19/19 Presentations

Slides https://odu.app.box.com/s/4yfdokkhyyqge2zx1jlv8gctw4zw6w2q

Nikos Chrisochoides

• Leverage from computational methods from medical imaging for processing phase space distributions in Nuclear Femtography
• Enable next generation process simulations
• Bring jobs to Virginia
• “Usefulness of Useless Knowledge” by Flexner
  • Look for standards and learn lessons

Bob McKeown

• Femtography 2019 ML & Revealing the internal structure of Nucelon & Nuclei
• See pic JLab Mission
• Nuclear Femtography
  • High luminosity
  • Polarized beams and targets
  • Sophisticated detector systems
• Nature publications
  • Ultrafast Nucleons in Asymmetic Nuclei
  • …
• Virginia Center for Nyclear Femtography
  • 7/14 joint lab/university initiatives funded
• Proposed JLab electron Ion Collider (see pic)
• EIC Users Group (see pic)
• EICUG 2019
• Current Status and Path forward of EIC (see pic
• JLab has electron collider, NY Brookhaven has ion collider
  • Both need to construct the other half
• Imaging the Nucleon is the future of Nuclear Physics

Gail Dodge

• Partnership between ODU and JLab in 90’s
• 12 tenure track faculty
• 6 JLab professors
• ODU faculty intellectual leadership in research programs in JLab
• Bring together scientists from different fields
  • Bridging the gap between physics, math, and computer science to reach the potential
• ODU has hired ~6 data science faculty
• Need help to learn how to involve people from different disciplines
  • Different fields working on analyzing data, imaging protons/neutrons, and extracting scientific insights

David Richards

• “Understanding the Glue That Binds Us All: The Next QCD Frontier in Nuclear Physics”
• See slide 6 for those that submitted proposals
• Dealing with incomplete data and the importance of visualization
• Synergy across fields
  • Astrophysics
  • Visualization
  • Machine Learning
• Call for proposal late September
  • External Evaluation Committee
• CNF Symposium at ODU early 2020

Christian Weiss

• Imaging technologies in computation
• Subnuclear systems
  • Scales
  • Scattering experiments
• Workflow inmeasurements
• Tesselation
• Scales
  • Organisms- Cells
  • Molecular - Atoms
  • Nuclear - Subnuclear
• Mission: Explore subnuclear systems
  • Strong interaction : quarks,gluons
  • Understand proton neutron as emergent phenomena
    • interacting large systems develop complex structure that is not present in parts
• Interest
  • Basic building blocks of matter
  • nuclear structure and reactions, nuclear energy
• Subnuclear systems
  • Unusual dynamical system
    • contents of proton can't be localized because they are in "perpetual movement"
  • Relativity: Energy = mass - relativity, conversion processes. Proton is ‘cauldron’ filled with radiation energy and matter/antimatter
  • Only average properties are measurable: densities,correlations
    • formulation/visualization possible with appropriate tools
• Scattering experiments
  • Electrons collide on protons
  • Scatterings are gathered from detectors
  • Incident energy determines spatial resolution
  • JLab 12GeV accelerators
    • needed for resolving proton's internal structure
    • 1GeV is typical spatial size of a proton
  • Information Recorded:
    • Distribution based on type and momentum -> Phase space distributions
    • The “expression” of proton’s internal structure
    • 10^6 - 10^9 experiments in JLab
• Workflow: Measurements
  • Theory: Model of proton structure (parameters that need to be verified experimentally)
  • Predictions for scattering probabilities (cross section)
  • Phase space distributions (meeting ground between theory and experiments)
  • Reconstruction based on the raw data (detector effects)
  • Scattering Experiments -> Raw Data (kinematic coverage statistics)
  • Simulations (can be run with actual or mock data to test reconstruction /feasibility)
  • Modify theoretical model based on observations
  • "Final" picture of proton from synthesis of multiple experiments and theoretical models
• Phase space distributions
  • Use imaging techniques(e.g tessellation, slicing, viewing)
  • 10^6 -10^9 experiments
  • View distributions, projections, cuts, features
  • Compare distributions
  • Interpolate refine distributions for simulations
  • With ODU
    • Tesselated representation
    • compact memory-efficient representations
    • Efficient interpolation/refinement for MC simulations
    • Visualize the gamma ray points that were detected by the detector + the density of energy
• Proton Structure:
  • Imaging for vizualitation of subnuclear system
  • Image concept for relativistic quantum system
  • Synthetic image from theory and multiple experiments
  • Spatial size, internal motion of quarks
  • Tesselated representation

Ron Kikinis

• Making data machine readable
  • Critical for effective/accessible data
• DICOM (standard for medical images)
• 3D Slicer
• Browser based versions
  • ohif.org
  • openanatomy.org
• Look at data from different vantage points
• SlicerAstro
  • colors to show data most helpful to doctors, students, etc.
  • Use of Slicer3D in astronomy
• Punzo et al 2015

Alexandra Golby

• In the past doctors would infer where the problem wass by the symptoms. They would then open the brain and see if they were right
• Now: Brain organization -> functional connectivity
• Functional MRI measures blood flow
• Diffusion Tensor Imaging the only method for imaging tensors
• Combine fMRI with MEG or fMRI with MRI
• VR to prepare for operation
• AR to help annotate points of interest on the brain
• The relationship in the brain of where things are locate and how they relate to other places in the brain is important

Steve Pieper

• New software - Keep using the best software we have
• Open source - Reproducible science
• 3D Slicer with
  • Python
  • Tensorflow
  • Numpy, pandas, scipy…
  • Wrapper API
  • Extensions marketplace
  • VR Support
  • Remote Rendering
  • Jupyter Notebook support
• OHIF Viewer
  • Browser based medical image viewer
  • VTK.js
  • Crowds-cure.org
  • GPU Segmentation (Grow cut algorithm)

Tina Kapur

• Discourse Forum
• Project Week Event
  • projectweek.na-mic.org
  • upcoming one takes place January 20-24, 2020 in Las Palmas, Gran Canaria, Spain
  • next one takes place June 22-26,2020 at MIT in Boston, USA

Andriy Fedorov

• “Your source code is your data”, NVIDIA CEO
  • For reproducibility for example
• National Cancer Institutr Quantitative Imaging Network
  • Goal: Transalte quantitative imaging methods and algorithms as clinical decision support tools into clinical utility
• DICOM includes metadata that can help to interpret images
  • Unique identifiers
  • Helps to query your data
  • TCIA (Cancer Imaging Archive) :Collection of medical images
    • can submit image sets for analysis
    • need big data to be accessible
• NCI Cancer Research Data Commons

08/20/19 Presentations

Nikos Chrisochoides

• Lessons from yesterday
  • DICOM type
  • 4D Meshes for JLab, Medical imaging
  • Very nice presentation by Christian Weiss
  • Cross-department funding for another workshop?

James V. Koch

• Risk: You know the probabilities
• Uncertainty: You don’t
• Privately profitable vs. society
• Recent inovations started from individuals, not big companies
• National Labs work better when in cooperation with universities
• Lesson learnt: Get people together and let them work on what they think
• Profit motive makes people more productive
• When to sell intellectual property, since imitations will arise soon
• Lessons
  • Outside funders are skeptical
    • they look at the diffusion curve (uncertainty)
    • they want equity
  • Need substantial amount of equity to participate
  • Very high discount rates because of uncertainty
  • Investors require control
  • Try to get some benefits for the decision makers early on since they will not be there for too long
    • Don't sell out before benefits

James Cheng

• VA institutions very spread around
• Companies also
• Angel investments recently appeared in south VA
  • 757 Angels - Hampton Roads Investing
  • CVA, 1717, Startup Virginia, NRV - Richmond
  • CAN, CAV Angels - Charlottesville
• Resources on the slides
  • TEConomy Study
  • SBIG - small business investments
  • VEDP
  • VRIF Awards
  • OTA - way Gov't gets funding
• Want scalable technology
  • tie software to a machine/product for intellectual property protection