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Alternative Formats If You Require This Document in an Alternative Format, Please Contact: Openaccess@Bath.Ac.Uk University of Bath PHD The Application of X-RAY Computerised Tomography for the Advancement of Non- Invasive Imaging in Entomology Greco, Mark Award date: 2013 Awarding institution: University of Bath Link to publication Alternative formats If you require this document in an alternative format, please contact: [email protected] General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. • Users may download and print one copy of any publication from the public portal for the purpose of private study or research. • You may not further distribute the material or use it for any profit-making activity or commercial gain • You may freely distribute the URL identifying the publication in the public portal ? Take down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. Download date: 25. Sep. 2021 THE APPLICATION OF X-RAY COMPUTERISED TOMOGRAPHY FOR THE ADVANCEMENT OF NON-INVASIVE IMAGING IN ENTOMOLOGY Mark Kerry Greco A thesis submitted for the degree of Doctor of Philosophy University of Bath Department of Electronic and Electrical Engineering February 2013 COPYRIGHT Attention is drawn to the fact that copyright of this thesis rests with the author. A copy of this thesis has been supplied on condition that anyone who consults it is understood to recognise that its copyright rests with the author and that they must not copy it or use material from it except as permitted by law or with the consent of the author. This thesis may be made available for consultation within the University Library and may be photocopied or lent to other libraries for the purposes of consultation. ____________________ Mark K Greco TO MY WIFE AND DAUGHTERS… ii Table of Contents __________________________________________________________________ Dedication…………………….………...……………………………………………..…ii Table of Contents.....................…….……………………………………………………iii List of Figures………………………………………………………….………………viii List of Tables…………………………………………………………………………….xi Acknowledgements………………......…………………………………………………xii Thesis Summary………………………………………………………………………..xiii Chapter 1 Literature Review……………………………………….………..………1 1.1 Introduction…………………………………………………….….………..…....1 1.2 Non-invasive Imaging………………………………………………..…………..2 1.3 Techniques available for non-invasive imaging……………………..…..…….…2 1.4 Computed tomography (CT)…………….…………..…….….…………….........3 1.4.1 Tomography……………………………………….…………………….….……3 1.4.2 CT……………….……………………………………………………….…….…4 1.4.3 Back-Projection…………………………………………………….………….…5 1.4.4 Iterative methods………………………………………………………….…...…8 1.4.5 Analytic reconstruction……………….………………………………….…..…..9 1.4.6 Algebraic Reconstruction Technique (ART)………………………..……..…….9 1.4.7 Multiplicative Algebraic Reconstruction Technique (MART)………….…..….10 iii 1.4.8 Simultaneous Algebraic Reconstruction Technique (SART)…………………..11 1.5 Limitations of x-ray CT……………………………………………………..…..11 1.6 Types of scanners…………………………………………………………….…12 1.6.1 First-Generation Scanners………………………………………………...…….12 1.6.2 Second-Generation Scanners……………………………………………………12 1.6.3 Third-Generation Scanners…………………………………………….….…….12 1.6.4 Fourth-Generation Scanners……………………………………………….……12 1.6.5 Modern CT scanners………………………………………………………….…13 Chapter 2 Description of the methods…………………………………..….………14 2.1 Introduction……………………………..………………………………………14 2.2 Proof of concept for using X-ray Computer Tomography in insect biology studies…………………………………………………………………..……….15 2.3 Sample preparation……………………………………………..……….………16 2.4 Data capture………………………………………………………..……………18 2.5 X-ray beam energy……………………………………..…………………….…19 2.6 Scan field size………………………………………………….…..……………19 2.7 Slice thickness……………………………………………………………..……20 2.8 Detector number…………………………………………..…………….………20 2.9 Data storage…………………………………………………………………..…20 2.10 Post-processing………………………………………………………………….21 2.11 Data analyses……………………………………………………………………23 iv Chapter 3 Application of CT to morphology of locusts, ladybirds and butterflies………………………………………………………………..24 3.0 General Introduction…………………………………………………………….24 3.1 CT of locust…………………………………………………………..…………24 3.1.1 Introduction……………………………………………………………..………24 3.1.2 Methods…………………………………………………………………………27 3.1.2.1 The insects…………………………………………..…………………….…….27 3.1.2.2 Micro-CT scanning…………………………………………………….……..…27 3.1.2.3 Image reconstruction and viewing………………………………………………27 3.1.2.4 Masking and Segmenting………………………………………….……………27 3.1.2.5 Production of 3-D printed models………………………….…………….….….28 3.1.3 Results…………………………………………………………………………..29 3.1.3.1 Imaging………………………………………………………………………….29 3.1.3.2 The 3-D printed model………………………………………………….………36 3.2 CT of Ladybird………………………………………………………….………38 3.2.1 Introduction…………………………………………………………….……….38 3.2.2 Methods…………………………………………………………………………38 3.2.3 Results…………………………………………………………………………..39 3.3 CT of the Butterfly………………………………………………………….…..48 3.3.1 Introduction……………………………………………………………………..48 3.3.2 Methods…………………………………………………………………………49 v 3.3.3 Results…………………………………………………………………………..51 3.4 Discussion………………………………………………………………….……52 3.4.1 The locust……………………………………………………………………….52 3.4.2 The ladybird……………………………………………………….…………….53 3.4.3 The butterfly…………………………………………………………….………54 3.5 Future Directions………………………………………………………………..54 Chapter 4 A specific case for non-invasive CT “The Honeybee Bee Brain”.…..…56 4.1 Introduction……………………………………………………………….…….56 4.2 Methods…………………………………………………………………………57 4.3 Results…………………………………………………………………………..60 4.4 Discussion………………………………………………………………………61 4.5 Future Directions………………………………………………………………..62 Chapter 5 Application of CT to Insect Behaviour…………………………………63 5.1 Introduction……………………………………………………………………..63 5.2 Methods…………………………………………………………………………66 5.2.1 Hive preparation…………………………………………………………….…..66 5.2.2 Diagnostic Radioentomology (CT)……………………………………………..68 5.2.3 Statistics…………………………………………………………………………68 5.2.4 Distribution of storage cells on combs…………………………………….……70 vi 5.2.5 Sugar concentration versus distance from brood centre……………………..…70 5.3 Results…………………………………………………………………….….…71 5.3.1 Honey storage frequency ratios…………………………………………..……..71 5.3.2 Distribution of storage cells on combs………………………………..….…..…71 5.3.3 Sugar concentration versus distance from brood centre……………..….…....…71 5.4 Discussion……………………………………………………………..…..….…73 5.5 Future Directions………………………………………………………………..76 Chapter 6 Conclusion and Future Research……………………………..…..…..…77 Literature Cited………………………………………………………………..…..….…81 Appendices………………………………………………………………………..…...103 vii List of Figures Figure 1 A schematic of focal plane tomography……..…………………………...4 Figure 2 An object of random shape, f(x,y) and its projection are shown for an angle of….………………………………………………………………………………..7 Figure 3 A schematic diagram of how CT values are calculated using the Sum along ray method……………………………………………..........……………….…….8 Figure 4 Sample preparation for MacroCT .…………………………...…………17 Figure 5 A schematic diagram of sample positioning for MicroCT.……….…….18 Figure 6 A BeeView post-processing table representing quantitative measurements of wax volume in a managed A. mellifera hive…………………………………………22 Figure 7 Four 3-D views of the desert locust (S. gregaria)………………………29 Figure 8 Four 3-D views of the head and thorax…………………………………31 Figure 9 Three views of the head and thorax..……………………………………32 Figure 10 Two 3-D views of the segmented tracheal system.……………………..33 Figure 11 Three MIP volume rendered images of the thorax including details of legs, HAS and tracheae……………………………………………………………...…..34 Figure 12 Two 3-D views of the metathorax and anterior abdomen……….……...35 Figure 13 STL file of the segmented tracheal system of the locust’s abdominal tracheal system………………………………………………………..………….……..36 Figure 14 The STL image of a section of the segmented tracheal system of the locust’s abdominal tracheae……………………………………………………..….…..37 Figure 15 Photomicrograph of “stage 1” dissection of C. septempunctata with elytra and tergites removed………………………………………………………………..…..40 viii Figure 16 Photomicrograph of “stage 2” dissection of C. septempunctata detailing the abdominal portion of the alimentary tract…………………………………………..41 Figure 17 Photomicrograph of the resected thoracic and abdominal sections of the alimentary tract of C. septempunctata…………………………………………………..42 Figure 18 Schematic diagram of thoracic and abdominal sections of the alimentary tract of C. septempunctata…...………………………………………………………….43 Figure 19 A 3D, volume rendered, micro-CT image of a male C. septempunctata using Maximum Intensity Projection………………………………………….………..44 Figure 20 A 2D micro-CT image showing a transverse section through a C. septempunctata abdomen…………………………………………….………..………..45 Figure 21 A 2D micro-CT image showing a transverse section through a C. septempunctata abdomen………………………………………………………..….…..46 Figure 22 A 3D, volume-rendered and segmented image of the radio-opaque malpighian tubules in C. septempunctata………………………………………..……..47 Figure 23 Three individuals of M. menelaus, a late-stage caterpillar (larva), a mid- stage chrysalis (pupa) and a late-stage chrysalis (adult)………………………………..49 Figure 24 Four 3-D images of M. menelaus……………..………….….…..….…..51 Figure 25 The 3D rendered brain……………………….……………..…..……….58 Figure 26 A 3D volume rendered image of a live honey bee’s head
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