2018 Data to Structural Models Program

Monday, August 13, 2018 - Atkinson Hall 4004

Title: Image Analysis and Segmentation

Introduction to NBCR image analysis and segmentation tools using deep learning. Segmenting large electron tomographic image volumes.

Instructors: Chris Churas and Matthias Haberl
Schedule

  • 08:30 – 08:50 Registration
  • 08:50 – 09:00 Welcome: Rommie Amaro and Andrew McCulloch
  • 09:00 – 09:30 Lecture: Introduction to EM modalities for big data collection and segmentation
  • 09:30 – 10:00 Hands-On: Generating ground truth data for machine learning
  • 10:00 – 10:30 Break
  • 10:30 – 12:00 Hands-On: Training a deep neural network for 3D image segmentation
  • 12:00 – 13:30 Lunch
  • 13:30 – 14:00 Hands-On: Automated segmentation using the trained network
  • 14:00 – 14:30 Lecture: Evaluation of segmentation quality
  • 14:30 – 15:00 Break
  • 14:30 – 16:00 Hands-On: Post-processing steps to enhance segmentation results
  • 16:00 – 16:30 Lecture: Saving manual time by re-using a pre-trained network and data sharing
  • 16:30 – 17:00 Hands-On: Building 3D models from the segmentation

Tuesday, August 14, 2018 - Atkinson Hall 4004

Title: Meshing with GAMer

Creating high-quality triangular and tetrahedral meshes for numerical analysis from segmented image volumes with GAMer.

Instructors: Mike Holst and Chris Lee
Schedule

  • 09:00 – 10:30 Lecture: Part 1
  • 10:30 – 10:45 Break
  • 10:45 – 12:00 Lecture: Part 2
  • 12:00 – 13:30 Lunch
  • 13:30 – 17:00 Hands-On and Consultation Session

Wednesday, August 15, 2018 - PFBH 161

Title: Blender and Continuity

Using HexBlender to generate, refine and visualize high-quality hexahedral Lagrange and cubic Hermite meshes from segmented tomographic image volumes, and least squares fitting of three-dimensional anatomic models of geometry and structure using Continuity.

Instructors: Andrew McCulloch, Eric Carruth and Kevin Vincent
Schedule

  • 09:00 – 10:30 Lecture: HexBlender: Introduction to image-based finite element meshing and installation of software
  • 10:30 – 10:45 Break
  • 10:45 – 11:45 Introduction to Continuity, cardiac fiber architecture and diffusion tensor MR imaging
  • 11:45 – 12:30 Lecture: Introduction to Blender and the HexBlender toolkit
  • 12:30 – 13:30 Lunch
  • 13:30 – 14:30 Hands-On: Creating a cardiac anatomic model from segmented human CT images
  • 14:30 – 15:30 Hands-On: Continuation of cardiac meshing from human CT images; prepare mesh for exporting to Continuity
  • 15:30 – 15:45 Break
  • 15:45 – 17:00 Hands-on: Fitting fiber architecture model to Diffusion Tensor MRI data with Continuity

Thursday, August 16, 2018 - PFBH 161

Title: SEEKR and BrownDye

Atomic scale simulations using SEEKR and BrownDye

Instructors: Gary Huber and Ben Jagger
Schedule

  • 09:00 – 09:45 Lecture: Introduction to BrownDye
  • 09:45 – 10:45 BrownDye Hands-On Session: Using Brownian dynamics to simulate associations reactions of biomolecules
  • 10:45 – 11:00 Break
  • 11:00 – 11:45 Lecture: Introduction to SEEKR
  • 11:45 – 13:30 Lunch
  • 13:30 – 14:30 SEEKR Hands-On Session: Automating the preparation and analysis of ligand-reception kinetic calculations
  • 14:30 – 15:00 Group Photo
  • 15:00 – 17:00 Hands-On and Consultation Session

Friday, August 17, 2018 - PFBH 161

Title: cellPACK and cellVIEW

Enhancing research on drug discovery, multi-scale modeling and complex biology using cellPACK and cellVIEW tools.

Instructors: Art Olson, Ludovic Autin, Michel Sanner and Brett Barbaro
Schedule

  • 09:00 – 10:00 Lecture: Introduction to cellPACK and cellVIEW tools
  • 10:00 – 10:15 Break
  • 10:15 – 12:15 cellPACK Tutorial and Demonstration (Users are welcome to bring their own systems to walk through the tutorial)
  • 12:15 – 13:00 Lunch
  • 13:00 – 17:00 Hands-On and Consultation Session