1. CSE554IntroductionSlide 1 CSE 554: Geometric Computing for Biomedicine Fall 2013

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 Computing Algorithms and data structures for manipulating geometric forms

7. CSE554IntroductionSlide 7 Geometric Forms Continuous forms – Defined by mathematical functions – E.g.: parabolas, splines, subdivision surfaces Discrete forms – Disjoint elements with connectivity relations – E.g.: polylines, triangle surfaces, pixels and voxels Pixels Triangle surfaces (meshes) Polyline Voxels CurvesSurfaces

8. CSE554IntroductionSlide 8 Geometric Computing Algorithms and data structures for manipulating (discrete) geometric forms – 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

9. CSE554IntroductionSlide 9 Applications Industrial design Cultural heritage Movie CG Geology Engineering simulation

10. CSE554IntroductionSlide 10 Application: Biomedicine Modeling biological structures as geometric forms – A spectrum of scales: organs, tissues, cells, molecules, etc. Utility of geometric models – Visualization – Quantitative analysis – Simulation and interaction HumanVirus Surgical simulation Treatment planning

11. CSE554IntroductionSlide 11 This Course Classical algorithms for geometric computing – Those that have been useful for biomedical image analysis – Easy to understand, simple to implement

12. CSE554IntroductionSlide 12 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

13. CSE554IntroductionSlide 13 This Course Creating, processing, deforming, and analyzing geometry Segment Contour Fair & Simplify Align Shape analysis (Before)(After)

14. CSE554IntroductionSlide 14 Beyond This Course On-going research projects on biomedical modeling – Gorgon: protein modeling tool for density volumes (Gorgon.wustl.edu) Gorgon – Geneatlas: atlas-based gene expression pattern exploration (Geneatlas.org) Geneatlas – VolumeViewer: interactive 3D segmentation tool (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)

15. CSE554IntroductionSlide 15 Outline Introduction to course Mechanics Mathematica demo

16. CSE554IntroductionSlide 16 Staff Instructor: Tao Ju – Jolley 406 (taoju@cse.wustl.edu)taoju@cse.wustl.edu TA: – Ming Zou (mingzou.cn@gmail.com)mingzou.cn@gmail.com – Derek Burrows (derek.wayne.burrows@gmail.com)derek.wayne.burrows@gmail.com

17. CSE554IntroductionSlide 17 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

18. CSE554IntroductionSlide 18 Overview 2 meetings per week – Lectures on Tuesdays (Lopata 229) – Lab working (with instructor and TA) 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 – Start in October – Due end of semester Check out the calendar on course webpagecalendar No exams!

19. CSE554IntroductionSlide 19 Lectures Theory and algorithms – Power-point slides available before each lecture on the webpage – 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:

20. CSE554IntroductionSlide 20 Lab Modules Algorithm prototyping (in Mathematica) – Modules designed to help you implement the algorithm step-by-step – Emphasis on unit testing – Work individually Example:

21. CSE554IntroductionSlide 21 Course Project A working tool for bio-medical data analysis – Addressing problems in on-going bio-medical research – Meet the need of the specific research problem to a sufficient extent Measuring small bowel length (by Billy Bennett) Breast lesion segmentation (by Noa Ben-Zvi)

22. CSE554IntroductionSlide 22 Course Project Use your favorite programming language Work in team or individually Schedule: – October 8: Instructor presents candidate project ideas – October 24: Project proposals are due – December 3/5: In-class project demos

23. CSE554IntroductionSlide 23 Grading Lab modules: 75% (graded during Thursday lab time) 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.

24. CSE554IntroductionSlide 24 Outline Introduction to course Mechanics Mathematica demo

25. CSE554IntroductionSlide 25 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, and can be installed freely on campus – 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. 5) See you all on Thursday (Whitaker 130)!