1. CSE554IntroductionSlide 1 CSE 554: Geometric Computing for Biomedicine Fall 2014

2. CSE554IntroductionSlide 2 Outline Introduction to course Mechanics Mathematica demo

3. CSE554IntroductionSlide 3 Outline Introduction to course Mechanics Mathematica demo

4. CSE554IntroductionSlide 4 Geometry Greek word: Earth-measuring One of the oldest sciences Chinese Chou Pei Suan Ching (500-200 BC)Euclid’s Element (300 BC)

5. CSE554IntroductionSlide 5 Geometry Greek word: Earth-measuring One of the oldest sciences Newton’s Principia Mathematica (1687)Einstein’s General Relativity (1915)

6. CSE554IntroductionSlide 6 Geometric Forms Continuous geometry – Defined by mathematical functions – E.g.: parabolas, splines, subdivision surfaces Discrete geometry – Disjoint elements with connectivity relations – E.g.: polylines, triangle surfaces, pixels and voxels Pixels Triangle surfaces (meshes) Polyline Voxels CurvesSurfaces

7. CSE554IntroductionSlide 7 Geometric Computing Algorithms and data structures for (discrete) geometry – Creation From 2D/3D images, from point clouds, by hand, etc. – Processing De-noise, simplify, repair, transform, animate, etc. – Analysis Geometric, topological, shape and physical properties

8. CSE554IntroductionSlide 8 Applications Industrial design Cultural heritage Movie CG Geology Engineering simulation

9. CSE554IntroductionSlide 9 Application: Biomedicine Modeling biological structures as geometric forms – A spectrum of scales: organs, tissues, cells, molecules, etc. With geometric representation, we can do – Visualization – Quantitative analysis – Simulation and interaction HumanVirus Surgical simulation Treatment planning

10. CSE554IntroductionSlide 10 This Course Classical algorithms for geometric computing – Widely used for biomedical image analysis – Easy to understand, simple to implement

11. CSE554IntroductionSlide 11 This Course Working with biomedical imaging data – 2D: Light microscopy, slices of 3D images – 3D: Magnetic resonance imaging (MRI), Computed tomography (CT), Cryo-Electron Microscopy (Cryo-EM) CT Cryo-EM Microscopy

12. CSE554IntroductionSlide 12 This Course Creating, processing, deforming, and analyzing geometry Segment Extract boundary Fair & Simplify Align & Deform Shape analysis (Before)(After)

13. CSE554IntroductionSlide 13 Beyond This Course On-going research projects on biomedical modeling – Gorgon: shape analysis of proteins (Gorgon.wustl.edu) Gorgon – Geneatlas: image-based queries in mouse brains (Geneatlas.org) Geneatlas – VolumeViewer: interactive 3D segmentation (Volumeviewer.cse.wustl.edu) VolumeViewer Research opportunities in the M&M lab – Biomedical modeling (Tao) – Image analysis (Robert, Tao) – Computer vision (Robert, Yasu) – Machine learning (Kilian) – Human computer interaction (Caitlin)

14. CSE554IntroductionSlide 14 Outline Introduction to course Mechanics Mathematica demo

15. CSE554IntroductionSlide 15 Staff Instructor: Tao Ju – Jolley 406 (taoju@cse.wustl.edu)taoju@cse.wustl.edu TA: – Michelle Vaughan (mavaugha@wustl.edu)mavaugha@wustl.edu – Ming Zou (mingzou.cn@gmail.com)mingzou.cn@gmail.com

16. CSE554IntroductionSlide 16 Prerequisites Programming – Experienced in at least one of the major programming languages C/C++, Java, Matlab, Python, etc. – CSE332 is strongly recommended CS background – Basic data structures (e.g., queues, trees, hash tables) and algorithms – CSE241 is strongly recommended Math – Linear algebra, elementary geometry

17. CSE554IntroductionSlide 17 Overview 2 meetings per week – Lectures on Tuesdays (Cupples II 200) – Labs on Thursdays (Whitaker 130) 5+1 lab modules – 2 weeks for each module (1 week for Module 0) – Due and graded in lab on Thursdays. 1 course project – Proposal due in November – Final presentation in December Check out the calendar on course webpagecalendar No exams!

18. CSE554IntroductionSlide 18 Lectures Theory and algorithms – Algorithms are explained in depth, pseudo-code given when possible 1. … 2.Repeat until Q is empty: 1.Pop a pixel x from Q. 2.For each unvisited object pixel y connected to x, add y to S, set its flag to be visited, and push y to Q. 3.Output S 1. … 2.Repeat until Q is empty: 1.Pop a pixel x from Q. 2.For each unvisited object pixel y connected to x, add y to S, set its flag to be visited, and push y to Q. 3.Output S Example:

19. CSE554IntroductionSlide 19 Lab Modules Algorithm prototyping (in Mathematica) – Step-by-step, easy to hard, 2D to 3D – Unit tests – Work individually Example:

20. CSE554IntroductionSlide 20 Course Project A working tool that solves an existing problem in biomedical research – Topics provided by the instructor or identified by students Use your favorite programming language Work in team or individually

21. CSE554IntroductionSlide 21 Course Projects Example projects (Fall 2013) (Ethan Green)

22. CSE554IntroductionSlide 22 Course Projects Example projects (Fall 2013) (Qiushi Li)

23. CSE554IntroductionSlide 23 Course Projects Example projects (Fall 2013)

24. CSE554IntroductionSlide 24 Course Projects Example projects (Fall 2013) (Omer Turgeman and Matan Ronen)

25. CSE554IntroductionSlide 25 Grading Lab modules: 75% (graded during Thursday labs) Course project: 25% Late policy – Late modules and project will earn at most 50% credit for the late part – Modules submitted later than the Tuesday following the due date will not be accepted. – Extensions will be given only under exceptional conditions, by written requests ahead of time.

26. CSE554IntroductionSlide 26 Outline Introduction to course Mechanics Mathematica demo

27. CSE554IntroductionSlide 27 Action Items – This Week Make sure you have a SEAS account – Check with the help desk at EIT in Lopata 4 nd floor. Get access to Mathematica – Available on all SEAS machines; installed freely on campus computers – Purchase for personal use for $45 / semester Module 0 is out today – I will give a quick tutorial and help you with it this Thursday – Due and graded next Thursday in lab (Sept. 4) See you all on Thursday (Whitaker 130)!