SI2009 Electron Tomography and Mesoscale Modeling

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General Information

The track is geared towards researchers in the computational biology field, who are interested in mesoscale modeling using realistic subcellular structures. Although the main examples will come from heart physiology and pathology, these techniques should be widely applicable to modeling problems in biology.

This track will begin with a review of EM instrumentation and petascale reconstruction problems in biology. Participants will learn advanced tomographic reconstruction techniques using TxBR, and the use of EM and LM in high resolution imaging of subcellular organelles beyond the diffraction limit of LM. They will also learn to use GAMER in the generation of high quality mesh representation of subcellular structures. Case studies will be provided using the T-tubular network in the simulation of CICR in cardiac myocytes.

Each session includes lectures and demonstrations or hands-on exercises.

Projected Outcome By the end of the sessions, the participants should be able to gain a working knowledge of EM tomography, and how to combine LM and EM to obtain high resolution images of subcellular structure. They will also be able to create high quality mesh representation, and conduct basic simulations of CICR in subcellular models of cardiac myocytes.

Instructors: Albert Lawrence, Ph.D., Sebastien Phan, Ph.D., Masahiko Hoshijima, M.D., Ph.D., Zeyun Yu, Ph.D., Anushka Michailova, Ph.D., Yuhui Cheng, Ph.D.

Time M-F, 9 am to 12 pm, Aug 3-7, 2009

Location PFBH PC lab Room 161

Prerequisite Familiarity with Unix is recommended but not required.

Schedule

  • Monday, Introduction to EM tomography and TxBR
    Instructor: Rick Lawrence, Ph.D., Sebastien Phan, Ph.D., James Bower, Ph.D., Alexander Kulungowski, M. S.
    • Transform Based Tracking, Bundle Adjustment and Reconstruction
    • EM Tomography and Petascale Biology
    • EM Instrumentation and Tomography
    • Advanced Computational Techniques in Tomography
    • Demonstration of TxBR on Graphics Processor Units
  • Tuesday, Introduction to EM tomography and TxBR
    Instructor: Rick Lawrence, Ph.D., Sebastien Phan, Ph.D., James Bower, Ph.D., Alexander Kulungowski, M. S.
    • Advanced Features of TxBR
    • Hands-on Reconstruction
  • Wednesday, Image processing and mesh generation
    Instructor: Zeyun Yu, Ph.D.
    Image Processing: contrast enhancement, noise reduction, segmentation, skeleton extraction
    Mesh Generation: surface and volumetric meshing from molecules (PDB/PQR) and 3D images, and surface mesh quality improvement
  • Thursday, Simulation of CICR using realistic models of cardiac myocytes
    Instructor: Masahiko Hoshijima, M.D., Ph.D., Zeyun Yu, Ph.D., Anushka Michailova, Ph.D.
    Masahiko: Introduction to heart failure and EM imaging of cardiac myocytes
    Zeyun: Multi-scale geometric modeling of ventricular myocytes
    Anushka: Finite element simulation of cardiac myocytes
  • Friday, Computational Simulations using FETK
    Instructor: Anushka Michailova, Ph.D., Yuhui Cheng, Ph.D. Lecture slides

Related Tracks from Previous SI

SI2008 Multiscale_Image_Analysis_and_Visualization

SI2008 Programming_Scalable_Scientific_Applications

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