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Up Directory CCL 15.08.18 NBCR Summer Training Program: Data to Structural Models, UC-San Diego, La Jolla, CA
From: chemistry-request at
To: chemistry-request at
Date: Wed Jun 24 16:46:36 2015
Subject: 15.08.18 NBCR Summer Training Program: Data to Structural Models, UC-San Diego, La Jolla, CA
NBCR is pleased to offer a Summer Training Program (STP) August 17th to 21st, 2015, 
on the theme of image-based meshing and structural modeling. This week-long
intensive program will introduce  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 will include: 
(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 will be 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.
In consultation with the course organizers, those accepted into the program 
will be encouraged to bring and work with their own data sets.

The schedule is:

Day 1, Monday August 17th: 
           Introduction to NBCR image analysis and segmentation tools.
           Segmenting large electron tomographic image volumes.

Day 2, Tuesday August 18th:
           Creating high-quality triangular and tetrahedral meshes for numerical
           analysis from segmented image volumes with GAMer and Blamer.

Day 3, Wednesday August 19th:
           Using HexBlender to generate, refine and visualizes high-quality
           hexahedral Lagrange and cubic Hermite meshes from segmented
           tomographic image volumes.

Day 4, Thursday August 20th:
           Least squares fitting of three-dimensional anatomic models of geometry
           and structure using Continuity.

Day 5, Friday August 21st: 
          Kepler Workflows for 3-D image-based model development.

To register for this workshop please visit
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