2015 Data to Structural Models Program

Monday, August 17, 2015

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

Instructors: Alex Perez and Chris Churas
Instruction type: L = Lecture, H= Hands on Tutorial

Time Track Type
08:30 - 08:50 Registration
08:50 - 09:00 Welcome: Profs. Amaro and McCulloch
09:00 - 10:30 Introduction to EM modalities for big data collection and segmentation L
10:30 - 10:45 Coffee Break
10:45 - 11:30 Manual Segmentaiton with IMOD H
11:30 - 12:00 Automated Segmentaiton with SLASH portal H
12:00 - 13:30 Lunch
13:30 - 14:30 Segmentation quality and building 3D models H

Tuesday, August 18, 2015

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

Instructor: Tom Bartol
Instruction type: L = Lecture, H= Hands on Tutorial

Time Track Type
09:00 - 10:30 Lecture - Part 1 L
10:30 - 10:45 Coffee Break
10:45 - 12:00 Lecture - Part 2 L
12:00 - 13:30 Lunch
13:30 - 17:00 Hands on, research projects, consultations H

Wednesday, August 19, 2015

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

Instructor: Andrew McCulloch, Jeff Van Dorn, and Chris Villongco
Instruction type: L = Lecture, H= Hands on Tutorial

Time Track Type
09:00 - 10:00 Introduction to image-based finite element meshing L
10:00 - 10:30 Verify Software Installation H
10:30 - 10:45 Coffee Break
10:45 - 11:30 Introduction to Blender and the HexBlender toolkit L
11:30 - 12:30 Creating cardiac anatomic model from segmented human CT images H
12:30 - 14:00 Lunch
14:00 - 15:30 Continuation of cardiac meshing from human CT images H
15:30 - 15:45 Coffee braek
15:45 - 17:00 Finalize mesh creation and prepare mesh for exporting to
Continuity: regularization and subdivision
H

Thursday, August 20, 2015

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

Instructor: Andrew McCulloch, Kevin Vincent and Eric Carruth
Instruction type: L = Lecture, H= Hands on Tutorial

Time Track Type
09:00 - 10:00 Introduction to cardiac fiber architecture and diffusion tensor MRI imaging L
10:00 - 10:45 Introduction to continuity L
10:45 - 11:00 Coffee Break
11:00 - 12:00 Exporting with cardiac model from Blender to Continuity H
12:00 - 13:30 Lunch
13:30 - 14:30 Using Continuity to fit a high-order cardiac anatomic model H
14:30 - 15:00 Group photo
15:00 - 17:00 Fitting fiber architecture model to Diffusion Tensor MRI data with Continuity H

Friday, August 21, 2015

Kepler Workflows for 3-D image-based model dev-elopment.

Instructor: Ilkay Altintas and Shweta Purawat
Instruction type: L = Lecture, H= Hands on Tutorial

Time Track Type
09:00 - 10:30 Lecture - Part 1 L
10:30 - 10:45 Coffee Break
10:45 - 12:00 Lecture - Part 2 L
12:00 - 13:30 Lunch
13:30 - 16:30 Hands on and Consultation Session L
16:30 - 17:00 Closing Remarks

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.