PAST MEETINGS
Meeting on Nov 18, 2013
Introduction to Electron Tomography and Reconstruction Techniques
Charudatta Phatak
Assistant Material Scientist, Argonne National Lab
Abstract
In this talk, I will highlight the major principles of electron tomography. I will talk about the different modalities in a TEM such as Bright field tomography, electron energy-loss spectroscopy, STEM etc. and what type of information can be obtained from performing such tomography experiments. I will also present a brief introduction to various methods of reconstruction which can be used to getting the 3D data as well as various softwares/programs which are available for performing the reconstruction and analysis.
This meeting was sponsored by Materials Science Umbrella Society
Meeting on Sep 9, 2013
An Express Introduction to Focused Ion Beam Tomography : Basic Principles
Kyle Yakal-Kremski
This meeting was sponsored by Materials Science Umbrella Society
Meeting on Jul 15, 2013
An Express Introduction to X-Ray Tomography : Basic Principles
Stuart Stock
This meeting was sponsored by Materials Science Umbrella Society
Meeting on Jun 17, 2013
High-energy X-ray Tomography and Diffraction Measurements at the APS 1-ID
Peter Kenesei
Advanced Photon Source, Argonne National Lab
Abstract
In this talk I would like to present some recent developments at 1-ID of the Advanced Photon Source (APS), which is originally a high-energy diffraction beamline. High-energy diffraction microscopy (HEDM) has been demonstrated to be a powerful tool for the structural characterization of polycrystalline bulk materials: crystallographic orientation and stress states have been measured on the grain and sub-grain scales. Tomography provides fast three-dimensional maps of electron density with spatial resolution down to one micrometer. Combination of these two complementary contrast mechanisms is highly beneficial for the characterization of inhomogeneities such as cracks or voids. The examples include wide field-of-view reconstructions of thick (few millimeters) specimens by “stitching” data sets. Furthermore, the combination of tomographic reconstruction and crystallographic orientation mapping from the same data set will be demonstrated. These new techniques provided by 3rd generation synchrotrons enable in situ investigations of complex problems including but not limited to materials physics and engineering by registration and evaluation of differently collected data sets.
This meeting was sponsored by Materials Research Science & Engineering Center (MRSEC)
Meeting on Mar 18, 2013 / Apr 15, 2013 / May 20, 2013
Comparison of Segmentation Methods I-II-III
This series was sponsored by Materials Science Umbrella Society
This series aims to present various conventional and novel segmentation techniques and to explore them using real experimental images submitted the tomography community at Northwestern University. At each meeting we will improve our understanding of using various segmentation techniques given a wide range of data collection methods as well as structural differences. At the end of the series we will revisit each individual image submitted and have the submitter compare the different segmentations. We hope that this exercise will not only broaden the segmentation knowledge and understanding of our community but also facilitate solving future image processing problems.
Introductions to Images to be used at the Segmentation Series
John Gibbs - AlSi and AlCu Alloys / X-Ray Computed Tomography
Chad Haney - Identifying Blood Vessels on Mouse Leg / Histology
Sarah Miller - Porous Alumina Ceramic / X-Ray Computed Tomography
Jerry Rhee - Mouse Cornea / Confocal Microscopy
Stuart Stock - Sea Urchin Tooth / Synchrotron MicroCT
John Thompson - PbSn Alloy / Optical Microscopy
Kyle Yakal-Kremski - Solid Oxide Fuel Cell Composite Cathode / FIB Microscopy
Histogram Thresholding
Kyle Yakal-Kremski
Expectation Maximization / Maximization of Posterior Marginals (EM/MPM)
Begum Gulsoy
Level Set Method
John Gibbs
Graph-cut Based Segmentation
Jin Qi
Fuzzy C-Means Method
Chad Haney
Comparison of Results
All Image Submitters
Meeting on Feb 18, 2013
Brainstorming session on 'Comparison of Segmentation Series'
Meeting on Jan 28, 2013
So, About That 4th Dimension
Begum Gulsoy
Meeting on Dec 10, 2012
TOMOGRAPHERS ANONYMOUS POSTER SESSION
This poster session was sponsored by Materials Science Umbrella Society
On the Usefulness of the Golden Spiral on Mouse Corneas
Jerry Rhee
4D Grain Growth via X-Ray Diffraction Contrast Tomography
Anthony Johnson (Second Place Winner)
Practical Aspects of Working with a Lot of CT Data
John Gibbs
Effect Of Current Switching On LSM-YSZ Composite Electrode Durability
Kyle Yakal-Kremski
Tomographic Analysis of the Microstructure of Metallic Alloys Using Mechanical Serial Sectioning
John Thompson
Effect of Freezing Gradients on Pore Network Characteristics for Freeze-Cast Alumina
Sarah Miller
Using Three-Dimensional MRI to Study the Effects of Spinal Manipulation on Cervical Kinematics In Vivo: Discussion and Study Protocol
Kenneth Weber
Three Dimensional Nanoscale Characterization of the Dopant Distribution in the PbTe - PbS - Na System for Thermoelectric Applications
Ivan Blum (Best Poster Award Winner)
Atom-probe Tomography of Biological Minerals
Lyle Gordon
Fatigue Resistant Shape Memory Alloys for Medical Applications
Dana Frenkel
Microscopical Fly Eye Nuclei Segmentation and Reconstruction Using Graph Cut and Sparse Coding
Jin Qi
Meeting on Nov 12, 2012
Chalking It Up to Adhesion:
The Mineralized Adhesive Structure of the Mermaid's Toenail (Anomia Simplex)
Hanna Leemreize
Aarhus University, Denmark
Meeting on Oct 15, 2012
Graph Cut Based Segmentation: Touching Nuclei in Fluorescent Microscopic Images of Fruit Fly Eye
Jin Qi
Meeting on Sep 17, 2012
Validating CT Data Routines
John Gibbs
Defining Interfaces and Interphases
Lyle Gordon
Meeting on Aug 20, 2012
In Quest of the Golden Spiral in Mouse Cornea
Jerry Rhee
A Three-Phase Segmentation Challenge
Scott Cronin
Meeting on Jul 23, 2012
3D Segmentation of Nuclei From Developing Fly Eyes
Nicolas Pelaez & Bao Wang
Meeting on Jun 11, 2012
Investigating Ni-Based Superalloys using Atom Probe Tomography
Lisa Plotnikov
Meeting on Apr 30, 2012
Getting to Know Your Local Supercomputer:
Local (and free) Resources For Tomographic 3D Data sets That You Can Use Today
Kyle Yakal-Kremski
Tomographers, it's been a year. How was it?
Scott Cronin & Begum Gulsoy
Quick Research Questions
Stuart Stock
Here's a link to the meeting flyer.
Meeting on Mar 26, 2012
Synchrotron-based Hard X-ray Microtomography: Exploiting Contrast to Answer Questions From Materials Research
Alexander Rack
European Synchrotron Radiation Facility
Microtomography (microCT) is a well-established and mature technique in use at synchrotron light sources around the globe. In this presentation the instrumentation as well as the advantages of synchrotron-based microCT will be outlined in a brief manner [1]. By exploiting the specific contrast modes available at a synchrotron light source, namely due to the available photon flux density and quality of the wave front (i.e. coherence) microCT provides a powerful analytical tool to answer questions arising from applied materials research: the excellent signal-to-noise ratio in the images allows for the application of volume image analysis techniqes. Spatial cross-correlations can be investigated which depict, e.g. the nature of pore formation control mechanisms in an evolving metal foam [2]. Besides the excellent statistics in the image reachable, refraction at interfaces within the sample reveals details about hidden structures with physical dimensions well below the resolution limit of the imaging system. Microgaps in industrial produced dental implants can be probed: most risk failure of an implant nowadays is associated to microbacterial leakage due to gaps in the implant body [3]. Furthermore, complementary contrast modes are accessible by, e.g. scanning the sample in the focal spot of an X-ray optical system: collecting diffraction patterns downstream of the sample allows for depicting spatial distributions of crystalline phases within the specimen such as ZrO in use for medical prostheses [4].
References
[1] A. Rack, S. Zabler, B. R. Müller, H. Riesemeier, G. Weidemann, A. Lange, J. Goebbels, M. Hentschel, W. Görner High resolution synchrotron-based radiography and tomography using hard X-rays at the BAMline (BESSY II) Nuclear Instruments and Methods in Physics Research A vol. 586 (2), pp. 327–344 (2008)
[2] A. Rack, H.-M. Helwig, A. Bütow, A. Rueda, B. Matijasevic-Lux, L. Helfen, J. Goebbels, J. Banhart Early pore formation in aluminium foams studied by synchrotron-based microtomography and 3-D image analysis Acta Materialia vol 57 (16), p. 4809–4821 (2009)
[3] S. Zabler, T. Rack, A. Rack, K. Nelson Fatigue induced deformation of taper connections in dental Titanium implants International Journal of Materials Research, vol. 103, no. 2, 207–216 (2012)
[4] C. Mochales, A. Maerten, A. Rack, P. Cloetens, W. D. Mueller, P. Zaslansky, C. Fleck Monoclinic phase transformations of zirconia-based dental prostheses, induced by clinically practised surface manipulations Acta Biomaterialia, vol. 7, issue 7, 2994–3002 (2011)
Here's the link to the meeting flyer.
Meeting on Feb 27, 2012
I've CT Scanned a Dinosaur
Rudyard Sadleir
FIB-SEM Tomography Study on Lithium-Ion Battery Cathode
Zhao Liu
Here's a link to the meeting flyer.
Meeting on Jan 16, 2012
Forward Simulation Techniques for Reconstructing Diffraction Contrast Tomography Data
Anthony Johnson
How Can We Best Utilize Imaging Science to Investigate Morphological Transformations?
Jerry Rhee
Here's a link to the meeting flyer.
Meeting on Dec 5, 2011
Visualizing Scientific Data in Blender- An Introduction: also, my research involves molecular simulations
Chris Wilmer
A Discussion on Automated Image Processing: Registration
Begum Gulsoy
Here's a link to the meeting flyer.
Meeting on Oct 24, 2011
Scaffolds for Tissue Regeneration
Adam Jakus
Serial Sectioning via Micro-Miller
John Thompson
Here's a link to the meeting flyer.
Meeting on Oct 3, 2011
Implicit Surfaces and Level Set Methods
John Gibbs
XCT Reconstructions of Graphite/Copper
Matthew Johnson
Meeting on Aug 22, 2011
Calculating Particle Size Distributions in Continuous 3D Structures
Scott Cronin
Investigating Errors in TPB Length from Segmentation and Calculation Methods
Kyle Yakal-Kremski
Meeting on Jul 18, 2011
Use of XCT for Needle-like Microstructures
Harold Hsiung
A Discussion on Utilizing SEM for Pore Size Measurements
Sarah Miller
Meeting on May 16, 2011
Image Processing 102 - Part 2
Begum Gulsoy
Validation of Curvature Calculation Using a Known Shape
John Gibbs
Meeting on Apr 11, 2011
Image Processing 101 - Part 1
Begum Gulsoy
Meeting on Mar 14, 2011
Welcome
Harold Hsiung
Introduction to Individual Interests & Projects
Everyone
