3D+ Visualization: Tomography, VisIt, and Mathematica

Professor Les Butler Department of Chemistry

This is a class on visualization methods and 3D data acquisition for undergraduates students. This course builds on a grants to LSU, include a W.M. Keck Foundation grant to build a unique tomography instrument and an NSF MRI grant for high-performance computing supporting interactive visualization.

This course is intended for chemists, biologists, materials scientist, anthropologists, engineers, physicists, and computer scientists. In the 101 Frey Visualization Lab, we will use workstations, your laptops, and a high-performance computer cluster to visualize 3D+ data sets. The data sets are usually of tangible objects: rocks, polymers, microfabricated devices, human cadavers , or objects you image with a benchtop tomography instrument. The goal is to understand how tomography data are acquired, transformed into 3D data sets, visualized, and interpreted. You will make movies of your data sets.

Topics to be discussed include:
•Tomography: X-ray, Beer’s law, K-edge, sinogram, inverse Radon, interferometry
• Data sets: binary, HDF5, stacked TIFF, DICOM
• Software: ImageJ on your laptop, Mathematica and VisIt on HPC Melete 3
• Visualization: binarization, distance and watershed transformations, morphological
component analysis, affine transformations, machine learning
• Movie making: Mathematica and VisIt
• Computation: Run pre-written Mathematica on your laptop and HPC Melete. This is not a programming course, but some Mathematica and Python programming will happen.