MICROCOMPUTEDTOMOGRAPHYMethodolOgV and Applications

Sluan R. Siock

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Library of Congress Cataloging-in-Publication Data

Stock, Stuart R.MicroComputed tomography: methodology and applications I Stuart R. Stock.

p.cm.Includes bibliographical references and index.ISBN 978-1-4200-5876-5 (hardcover: alk. paper)1. Tomography. I. Title.

RC78.7.T6S732009616.07'57--dc22

Visit the Taylor &: Francis Web site athttp://www.taylorandfrancis.com

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2008042180

Contents

Preface .Acknowledgments .Biography .

1 Introduction .References .

""xi. xiii

... xv

..... 1... 6

2 Fundamentals......................... ... 92.1 X-Radiation....................... . 9

2.1.1 Generation . 92.1.2 Interaction with Matter. 13

2.2 Imaging........................... . 152.3 X-Ray Contrast and Imaging.. . 17References 20

3 Reconstruction from Projections . 213.1 Basic Concepts............................. . 213.2 Algebraic Reconstruction.......... . 233.3 Back-Projection........................... . 243.4 Fourier-Based Reconstruction. . 293.5 Performance. . 313.6 Sinograms...................................................... . 33

3.6.1 Related Methods 33References . 36

4 MicroCT Systems and Their Components 394.1 Absorption MicroCT Methods.. . 394.2 X-Ray Sources....................................... . 444.3 Detectors............................................... . 464.4 Positioning Components . 514.5 Tube-Based Systems ... 524.6 Synchrotron Radiation Systems 574.7 NanoCT (FuU·Field, Microscopy-Based)................................ ... 614.8 MicroCT with Phase, Fluorescence, or Scattering Contrast 62

4.8.1 Phase Contrast MicroCT 624.8.2 Fluorescence MicroCT.. . 674.8.3 Scatter MicroCT .. . 69

4.9 System Specification 69References . 71

vii

viii Contents

5 MicroCT in Practice ... 855.1 Reconstruction Artifacts 85

5.1.1 Motion Artifacts . 855.1.2 Ring Artifacts................ . 865.1.3 Reconstruction Center Errors 875.1.4 Mechanical Imperfections Including Rotation Stage

Wobble................. . 875.1.5 Undersampling.. . 895.1.6 Beam Hardening 895.1.7 Streak Artifacts. . 915.1.8 Phase Contrast Artifacts ..... .91

5.2 Performance: Precision and Accuracy............. ...... 925.2.1 Correction for Nonidealities ..935.2.2 Partial Volume Effects ..935.2.3 Detection Limits for High-Contrast Features ..945.2.4 Geometry ..965.2.5 Linear Attenuation Coefficients........................... ... 99

5.3 Contrast Enhancement 1035.4 Data Acquisition Challenges 1045.5 Speculations 106References 108

6 Experimental Design, Data Analysis, Visualization . 1156.1 Experiment Design .1156.2 Data Analysis..................................... .117

6.2.1 Segmentation........................... .1196.2.2 Distance Transform Method ..1226.2.3 Watershed Segmentation. ..1226.2.4 Other Methods . 1226.2.5 Image Texture 1276.2.6 Interpretation of Voxel Values 1286.2.7 Tracking Evolving Structures 128

6.3 Data Representation 129References 138

7 Simple Metrology and Microstructure Quantification 1457.1 Distribution of Phases . 146

7.1.1 Pharmaceuticals 1467.1.2 Geological Materials 1467.1.3 Two or More Phase Metals, Ceramics, and Polymers 1487.1.4 Manufactured Composites 1487.1.5 Biological Tissues as Phases 151

7.2 Metrology and Phylogeny 1527.2.1 Industrial Metrology................ ..1537.2.2 Paleontology and Archeology................................. ..153

Contents ix

7.2.3 Invertebrates and Micro-Organisms 1547.2.4 Vertebrates . 159

References . 162

. 171171173

...176.181.182

8 Cellular or Trabecular Solids .8.1 Cellular Solids . .8.2 Static Cellular Structures .8.3 Temporally Evolving, Nonbiological Cellular Structures8.4 Mineralized Tissue .

8.4.1 Echinoderm Stereom .8.4.2 Cancellous Bone: Motivations for Study and the

Older Literature 1828.4.3 Cancellous Bone: Growth and Aging 1848.4.4 Cancellous Bone: Deformation, Damage, and Modeling 191

8.5 Implants and TIssue Scaffolds 1948.5.1 Implants 1948.5.2 Scaffold Structures and Processing 1958.5.3 Bone Growth into Scaffolds........................... . 196

References 198

9 Networks.9.1 Engineered Network Solids..9.2 Networks of Pores .9.3 Circulatory System .9.4 Respiratory SystemReferences .

. 215. 215. 217

. 223............................................ .227

. 229

10 Evolution of Structures.... . 23710.1 Materials Processing. . 237

10.1.1 Solidification... . 23810.1.2 Vapor Phase Processing . 24010.1.3 Plastic Forming . 24310.1.4 Particle Packing and Sintering 247

10.2 Environmental Interactions . 24810.2.1 Geological Applications........... . 24910.2.2 Construction Materials . 25110.2.3 Degradation of Biological Structures................... . 25310.2.4 Corrosion of Metals .257

10.3 Bone and Soft Tissue Adaptation.................. . 26010.3.1 Mineralized Tlssue: Implants, Healing, Mineral

Levels, and Remodeling 26010.3.2 Soft TIssue and Soft TIssue Interfaces 264

References . 266

x Contents

11 Mechanically Induced Damage, Deformation, and Cracking 28111.1 Deformation Studies 28111.2 Monolithic Materials: Crack Face Interactions and Crack

Closure . 28311.3 Composite Systems.................................. . 289

11.3.1 Particle-Reinforced Composites.. . 28911.3.2 Fiber-Reinforced Composites....... . 294

References . 300

. 310

. 312

. 315

. 316

............................................................... 319Index .

12 Multimode Studies....... . 30712.1 Sea Urchin Teeth............. . 30712.2 SuJ1ate Ion Attack of Portland Cement 30812.3 Fatigue Crack Path and Mesotexture.. . 30912.4 Creep Damage . 30912.5 Load Redistribution in Damaged Monofilament

Composites... . .12.6 Bone .12.7 Netvvorks .References . ..

Preface

MicroComputed Tomography (microCT) systems are high-resolutionsiblings of the medical CT scanners and are a bit more than one decadeyounger than the clinical CT scanners of the mid-1970s. MicroCT hasdeveloped at a slower rate than clinical CT for the obvious economic rea­son: much more expensive systems were and are more viable in hospitalsthan in the research realm where microCT finds its principal home. Thenumber of microCT systems began to climb about the time that biomedi­cal researchers began to emphasize use of small animal knockout modelsfor the study of human diseases and that commercial microCT systemscould be obtained at costs lower than many electron microscopes. inbroad brush strokes, this corresponded to the mid- to late 1990s.

The increase in the number of x-ray microCT papers since the turn ofthe century amounts to an explosion (discussed in Chapter 1), and sum­marizing the literature to date was one motivation for the author to writethis book. There have been any number of reviews covering microCT or,more recently, nanoCT, including two by the author (Stock, 1999, 2008),but, to the best of the author's knowledge, only one book has had x-raymicroCT as its central focus (Baruchel et al., 2(00), and this book was acollection of chapters by different authors on different materials sciencetopics. There has been no detailed synthesis of biological and physical sci­ences and engineering approaches to microCT and analysis of its data, alack this book was designed to address.

It is difficult for readers new to microCT to learn enough about theexperimental side of microCT without a text starting at the beginning.Therefore, a second motivation for the author was filling this gap.

The author continues to be amazed by the many m icroCT papers he hasreviewed that inadequately cite prior work. Whether this is at all uniqueto microCT (the author suspects not), it is certainly worth assembling acomprehensive report of the field to help improve the citation situation.The 1Q3 references in this book certainly do not cover all of the literature,but these are a significant fraction of the papers, or at least a significantsampling of those employing microCT for diverse purposes. The citationsin this book are biased toward those the author was able to obtain elec­tronically through Northwestern University's libraries.

The nature of microCT as a subspecialty is responsible, in part, for someindividuals' poor appreciation for prior work. Some authors of microCTstudies use synonyms (including micro-CT, x~ray tomographic micros­copy, computerized microtomography, the recent nanoCT, and even justtomography) in describing their studies, and this complicates the searchfor relevant papers. Furthermore, the same class of structure requiring

xi

xii Preface

similar analysis tools can occur in disciplines spanning the life sciencesto art conservation to the physical sciences and engineering, and reportsappear in a wide dispersion of journals and conference proceedings.One example is cellular solids with trabecular or spongy bone and bonegrowth scaffolds found in the biomedical literature and with metal foamsin engineering publications. These two factors combine to hinder new­comers finding prior paradigms on which to base their analyses and toproduce examples of unneeded (except perhaps in an existential sense)sweat expenditure via wheel reinvention.

Consider the following experiment (done at the end of 2006) in locatingmicroCT papers relating to foams, a class of cellular solids described inChapter 8. Over the preceding several years, the author desultorily col­lected nine papers on microCT of cellular solids (excluding those on tra­becular bone) without any particular purpose beyond perhaps preparinga review. A literature search in Compendex, a database for engineeringpapers, on "microCT and foam" revealed one paper (one of the nine), asearch on "microtomography and foam" produced 30 hits (three more ofthe nine), and a search on "tomography and foam" resulted in 139 hits(six of the nine). Separate searches on "cellular solid and tomography"or "wood and tomography" or "scaffolds and tomography" would berequired to reveal the other three papers of the nine; note that the middlesearch yields 204 hits, most of which are irrelevant to microCT.

In summary, this book, covering the literature through the end of 200?;with only a very few exceptions, follows two principles. First, it gatherstogether fundamentals and applications into as integrated a treatment aspossible without descending too deeply into details. The author hopesthat presenting a few fundamentals (x-ray generation, instrumentation,etc.) will allow those with no background in x-ray imaging to achieve,relatively quickly, an appreciation for the literature and for how to designtheir own microCT studies. Second, given that different subdisciplinesrequire similar analyses, the book gathers like structures together insteadof grouping applications by subdiscipline. Learning from other fieldsseems only sensible. Although the mental exercise of reinventing thewheel has its own existential benefits, the author thinks it would be betterto spend the effort on science rather than algorithm.

References

Baruchel, J., J.Y. Buffiere, et a!. (Eds.) (2000). X-Ray Tomography ill Materials Sciellce.Paris, Hermes Science.

Stock, S.R. (1999). Microtomography of materials. lilt Mater Rev 44: 141-164.Stock, S.R. (2008). Recent advances in x-ray microtomography applied to materi­

als. lilt Mater Rev 58: 129-181.

Acknowledgments

Over the years, many people helped the author reach the point where hecould put this book in your hands. Here mention is restricted to thosedirectly involved with the subject and topics of this book, lest the authorgo on for too long. The author feels extraordinarily lucky to have benefitedfrom these individuals' expertise, advice, and guidance.

John Hilliard introduced the author to numerical analysis of micro­structure, Mike Meshii to incorporation of microstructural data intonumerical models, and Morris Fine to the notion of microstructure map­ping of numerical quantities derived from different modalities. HowardBirnbaum and Hadyn Chen guided the author in his first foray into x-rayimaging of materials, and Keith Bowen introduced him to synchrotronradiation imaging. Jerry Cohen taught the author much about represent­ing spatial structure by its periodicities. Ray Young helped the authorrefine his thinking about this subject.

During his Georgia Tech years, the author's graduate and undergraduatestudents taught him much about x-ray imagingand microstructurecharacter­ization' more than anyone else will appreciate. These students' work, amongthe very earliest in microCT, dictated, toa large extent, the future direction ofthis field. They should have gotten more credit as true innovators.

For many years, Zofia Rek collaborated with the author on synchrotronx-ray imaging studies. John Kinney collaborated with the author for someyears, producing some wonderful microCT papers. Jim Elliott and hisco\\'orkers, Paul Anderson, Graham Davis, and Stephanie Dowker, have col­laborated with the author for more than twenty years in a wide variety ofmicroCT studies and have helped him enter the area of mineralized tissueresearch. Wah-Keat Lee and Kamel Fezzaa introduced the author to x-rayphase imaging. Since moving to the Chicago area, the author has collabo­rated with Francesco De Carlo in a large number of very productive syn­chrotron microCT studies of all manner of subjects biological and material.

The editors of this book, Marsha Pronin and Nora Konopka, were verypatient, and the author thanks them for their help.

Finally, the author's wife, Chris, and children, Michala, Sebastian, andMeredith, need to be thanked for their support and patience during manyperiods of synchrotron beam time and during inconveniences during theseveral periods in which this material was compiled.

xiii

Biography

Stuart R. Stock

Dr. Stock completed his undergraduate and master's degrees in materialsscience and engineering at Northwestern University, where he later wasa post·doc in the same fields. His PhD was in metallurgical engineeringat the University of Illinois Urbana-Champaign. He was on the materialsscience faculty at Georgia Tech for more than sixteen years, rising to therank of professor. In 2001, he returned to Northwestern University, thistime to the medical school.

Dr. Stock has used x-ray diffraction for materials characterization formore than thirty years and revised Cullity's classic text Elements of X-rayDiffraction. He has employed x-ray imaging for the same length of time.His first synchrotron radiation experiments were twenty-five years ago,and he currently travels to the Advanced Photon Source six or more timesa year to collect data. He has published results of microCT studies of inor­ganic materials and composites and of mineralized tissue throughout thelast twenty years.

xv