2017 Data to Structural Models Program

Monday, August 7, 2017 - Atkinson Hall 5302

Title: Image Analysis and Segmentation

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

Instructors: Matthias Haberl and Chris Churas
Schedule

  • 08:30 – 08:50 Registration
  • 08:50 – 09:00 Welcome: Profs. Amaro and McCulloch
  • 09:00 – 10:30 Lecture – Introduction to EM modalities for big data collection and segmentation
  • 10:30 – 10:45 Break
  • 10:45 – 11:30 Hands-On – Manual segmentation with IMOD
  • 11:30 – 12:00 Hands-On – Automated segmentation with the SLASH Portal
  • 12:00 – 13:30 Lunch
  • 13:30 – 14:30 Lecture – Segmentation quality and building 3D models
  • 14:30 – 17:00 Hands-On – Building 3D models from 2D segmentation

Tuesday, August 8, 2017 - Atkinson Hall 5302

Title: Meshing with GAMer and Blamer

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

Instructors: Thomas M Bartol and Chris Churas
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 9, 2017 - PFBH 161

Title: HexBlender

Using HexBlender to generate, refine and visualize high-quality hexahedral Lagrange and cubic Hermite meshes from segmented tomographic image volumes.

Instructors: Andrew McCulloch and Chris Villongco
Schedule

  • 09:00 – 10:00 Lecture – Introduction to image-based finite element meshing
  • 10:00 – 10:30 Hands-On – Verify software installation
  • 10:30 – 10:45 Break
  • 10:45 – 11:30 Lecture – Introduction to Blender and the HexBlender toolkit
  • 11:30 – 12:30 Hands-On – Creating a cardiac anatomic model from segmented human CT images
  • 12:30 – 14:00 Lunch
  • 14:00 – 15:30 Hands-On – Continuation of cardiac meshing from human CT images
  • 15:30 – 15:45 Break
  • 15:45 – 17:00 Hands-On – Finalize mesh creation and prepare mesh for exporting to Continuity: regularization and subdivision

Thursday, August 10, 2017 - PFBH 161

Title: Continuity

Least squares fitting of three-dimensional anatomic models of geometry and structure using Continuity.

Instructors: Andrew McCulloch, Kevin Vincent, Frank Spitulski and Eric Carruth
Schedule

  • 09:00 – 10:00 Lecture – Introduction to cardiac fiber architecture and diffusion tensor MR imaging
  • 10:00 – 10:45 Lecture – Introduction to Continuity
  • 10:45 – 11:00 Break
  • 11:00 – 12:00 Hands-On – Exporting with cardiac model from Blender to Continuity
  • 12:00 – 13:30 Lunch
  • 13:30 – 14:30 Hands-On – Using Continuity to fit a high-order cardiac anatomic model
  • 14:30 – 15:00 Group Photo
  • 15:00 – 17:00 Hands-On – Fitting fiber architecture model to Diffusion Tensor MRI data with Continuity

Friday, August 11, 2017 - Atkinson Hall 5302

Title: Open Consultation

Open consultation on attendees’ project by instructors and NBCR scientist. Please bring your projects and questions so that you can get help from our experts.

Instructors: NBCR PIs and Researchers
Schedule

  • 13:30 – 17:00 Work Session