Courses

NBCR Summer Training Program - "Data to Structural Models"

This week-long intensive program introduces students to principles, methods, and NBCR tools for generating high-quality three-dimensional meshes for numerical analysis in multi-scale modeling of subcellular, cell, tissue, and organ biophysics. Structural models will be derived from structural data obtained primarily from 3D imaging modalities, including electron tomography, multi-photon and confocal microscopy, and whole-body medical imaging modalities like CT and MRI.

  1. GAMer
  2. Kepler Workflow System

NBCR is pleased to present a Summer Training Program (STP) held on August 17th to 21st, 2015, on the theme of image-based meshing and structural modeling. This week-long intensive program introduces students to principles, methods, and NBCR tools for generating high-quality three-dimensional meshes for numerical analysis in multi-scale modeling of subcellular, cell, tissue, and organ biophysics. Structural models will be derived from structural data obtained primarily from 3D imaging modalities, including electron tomography, multi-photon and confocal microscopy, and whole-body medical imaging modalities like CT and MRI.

The course includes: (1) automated and manual image segmentation and annotation strategies; (2) improving the quality of surface meshes and generating volumetric meshes with GAMer; (3) using Hex-Blender to construct 3D models; (4) developing high-order finite-element meshes, including patient-specific organ models with Continuity; and (5) using Kepler workflows to streamline analysis. The resulting meshes are suitable for a range of biophysical modeling applications from stochastic Monte Carlo and Brownian Dynamics models to subcellular and whole-cell transport models to whole-organ biomechanics and electrophysiology that will be the topics of future NBCR training programs.

NBCR Summer Train Program: Data to Structural Models

August 17, 2015 to August 21, 2015

Day 1, Monday August 17

Topic: Introduction to NBCR image analysis and segmentation tools. Segmenting large electron microscopic image volumes.

Instructors: Alex Perez and Chris Churas

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

Day 2, Tuesday August 18

Topic: Modeling and Computing using Kepler Workflows

Instructors: Ilkay Altintas, Shweta Purawat, and Daniel Crawl

09:00 – 10:30 SESSION 1: Modeling and Computing using Kepler Workflows

10:30 – 10:45 Break

10:45 – 12:00 Hands-on 1: i) Introduction to Kepler ii) Searching and Moving Data


12:00 – 13:30 Lunch

14:30 – 17:00

SESSION 2: Computing Orchestration Using Workflows

Hands-on 2: i) Local BLAST ii) MPI BLAST iii) Demo Session on GPU workflow

SESSION 3: Reproducible Science Using Workflows

Demo Session: i) Provenance / Sharing ii) iPython

Day 3, Wednesday August 19

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

Instructors: Andrew McCulloch, Jeff Van Dorn, and Chris Villongco

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

Day 4, Thursday August 20

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

Instructors: Andrew McCulloch, Kevin Vincent and Eric Carruth

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

Day 5, Friday August 21

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

Instructors: Thomas M Bartol

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 – 16:30 Hands-On and Consultation Session 16:30 – 17:00 Closing Remarks