2016 Data to Structural Models Program

Monday, August 1, 2016

Title:Image Analysis and Segmentation

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

Instructors: Alex Perez 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 form 2D segmentation

Tuesday, August 2, 2016
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
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 3, 2016

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 4, 2016

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

Instructors: Andrew McCulloch, Kevin Vincent 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 5, 2016

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

  • 09:00 – 10:30 Work Session 1
  • 10:30 – 10:45 Break
  • 10:45 – 12:00 Work Session 2
  • 12:00 – 13:30 Lunch and Closing Remarks
  • 13:30 – 17:00 Work Session 3

The materials for this workshop, including videos of the lectures and tutorials, will available during and after the course through the Biomedical Big Data Training Collaborative.

The materials for this workshop, including videos of the lectures and tutorials, are available through the Biomedical Big Data Training Collaborative.

Those with accounts on the site can directly access the course via this link.