1. The University of SydneySlide 1 IMAGE PROCESSING Presented by Paul Wong AMME4981/9981 Semester 1, 2015 Lecture 2

2. The University of SydneySlide 2 Required Inputs Geometry What does it look like? Material properties What is it made of? Loads What forces is it subjected to? Boundary conditions What is happening at the system boundary?

3. The University of SydneySlide 3 Workflow for Biomedical Problems 1. Data acquisition Scan region of interest Obtain material properties for tissues and implants Estimate expected loads 2. Solid modelling Convert image stacks into a virtual replica Combine with CAD model of prosthesis 3. Finite element analysis Generate appropriate mesh Characterise interaction between anatomy and prosthesis Verify simulation results and prosthesis design

4. The University of SydneySlide 4 SEGMENTATION & RECONSTRUCTION

5. The University of SydneySlide 5 Objective –To replicate the geometry of the region of interest in silico –Prosthesis is typically modelled using CAD –Anatomy can also be made in CAD, but this is not ideal… REGION OF INTEREST Prosthesis Anatomy

6. The University of SydneySlide 6 Organic Shapes –Organic structures typically have a complex geometry – Irregular shape, non-uniform curves – No symmetry – Multiple parts and interfaces – Differences between individuals –Anatomy should be reconstructed from scans – Higher accuracy – Enables patient-specific studies

7. The University of SydneySlide 7 CT Scan of Proximal Femur

8. The University of SydneySlide 8 Typical Workflow Import image stack Separate into different tissue types or parts Apply smoothing filter and/or fit curves Create surface model Generate solid model

9. The University of SydneySlide 9 Commercial Software VSG Amira –User friendly interface –Easy to learn –Some very handy selection tools are unique to Amira –Excellent real-time visualisation options –Meshing often requires manual adjustment

10. The University of SydneySlide 10 Commercial Software Materialise Mimics –Market leader –Highest degree of user control –Very powerful tools –Not very user friendly –Extremely expensive

11. The University of SydneySlide 11 Commercial Software Simpleware ScanIP –Student licences are available in S322 and S345 –There are only 20 licences…first come, first served –How to learn the software: –“Basic segmentation from CT: Proximal femur” (Chapter 7, Simpleware Tutorial Guide) –“Import and positioning of CAD implant: Proximal femur” (Chapter 8, Simpleware Tutorial Guide) –Chapters 4-7, Simpleware Reference Guide –Just try something and see what happens

12. The University of SydneySlide 12 Typical Workflow Import image stack Separate into different tissue types or parts Apply smoothing filter and/or fit curves Create surface model Generate solid model

13. The University of SydneySlide 13 ScanIP User Interface

14. The University of SydneySlide 14 Segmentation

15. The University of SydneySlide 15 Selection Tools –Selection tools add voxels to masks NAMEFUNCTIONCOMMENTS BrushSelects voxels manuallyOnly use this if all others are insufficient, or for touch-ups ThresholdSelects voxels based on luminance Use if tissues have significantly different grey values in the image Flood fillSelects voxels based on connectivity There are a few variations: Left click, inside volume – Keeps connected voxels only Left click, outside volume – Fills gaps Right click, inside volume – Removes all connected voxels Right click, outside volume – Removes cavities

16. The University of SydneySlide 16 Smoothing –Usually required because: –Imaging rarely distinguishes tissues perfectly –Manual slice-by-slice processing is difficult to align –The dataset may have image artefacts –Organic structures are generally smooth –Misalignment creates jagged surfaces –Not ideal for meshing –Can result in stress concentrations and singularities at FEA stage that are not representative of real-world behaviour

17. The University of SydneySlide 17 Filters –Filters are used to manipulate a pre-existing mask TYPEFUNCTIONCOMMENTS SmoothingRemoves jagged edges and surfaces Small features tend to be lost, so test different amounts of smoothing (start small) to balance smoothness with geometric accuracy (i.e. to retain sufficient fine detail) MorphologicalManipulates size and shape There are a few variations: Dilate – Grows selected region Erode – Shrinks selected region Open – Removes small islands (i.e. erode then dilate) Close – Removes small cavities (i.e. dilate then erode)

18. The University of SydneySlide 18 Surface vs Volume Models Surface models –Only define the outside shell of an object –Most systems achieve this using non-uniform rational B-splines (NURBS) –Not fully-defined Volume models –Solid models define the entire volume of an object – e.g. Solidworks models –Representation is unambiguous

19. The University of SydneySlide 19 Dimensionality in Modelling DIMENSIONGEOMETRYMESH 0PointNode 1CurveLine element 2SurfaceShell element 3BodyVolume element

20. The University of SydneySlide 20 Visualisation –Fast preview –Renders approximate volume in 3D viewer (using voxels from masks) –May not represent segmentation accurately –Model preview –Creates and renders complete surface model (i.e. using triangles in 3D space) –Can be exported for volume meshing in other programs

21. The University of SydneySlide 21 Meshing –Full model –Generates and renders volume model and/or (non-conformal) NURBS surfaces –Requires masks to be added to a model object –Export options can be accessed through “Model setup” ATTRIBUTE+FE GRID+FE FREE RobustnessExcellent; can mesh virtually any geometry Good, but can fail with complex geometries Mesh sizeVery largeMedium; depends on refinement settings Mesh timeShortLonger FEA solution timeLongShorter

22. The University of SydneySlide 22 Tips & Tricks –Think in terms of layers (a la Photoshop) –Can perform Boolean operations –Can import multiple backgrounds –Learn the keyboard and mouse shortcuts –There is an undo button (5 actions by default) –Don’t forget to backup SIP files –If in doubt, check the help guides

23. The University of SydneySlide 23 COMING UP…

24. The University of SydneySlide 24 Next Week –Group project updates –Each group to give an informal short talk about their chosen topic –Expect up to 2 minutes with 1-2 slides

25. The University of SydneySlide 25 Week 4 –Guest lecture by Simon Richards from Simpleware Introduction and Live Demo: 3D Image Visualisation, Analysis and Model Generation with Simpleware –2-4pm in Electrical Engineering Lecture Theatre 2 (Room 450)

26. The University of SydneySlide 26 TO THE LABS!