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CSE 554: Geometric Computing for Biomedicine

Explore geometric computing in biomedicine through classical algorithms and practical applications in biomedical image analysis. No exams; focuses on theory, algorithms, and project work.

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CSE 554: Geometric Computing for Biomedicine

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  1. CSE 554: Geometric Computing for Biomedicine Fall 2016

  2. Outline • Introduction to course • Mechanics

  3. Outline • Introduction to course • Mechanics

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

  6. Geometric Forms Curves Surfaces • 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 Polyline Triangle surfaces (meshes) Pixels Voxels

  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. Applications Industrial design 3D printing Engineering simulation Urban design and evacuation planning Movie CG

  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 Human Virus Treatment planning Surgical simulation

  10. This Course • Classical algorithms for geometric computing • Easy to understand, simple to implement • Applicable to biomedical image analysis

  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) Microscopy Cryo-EM CT

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

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

  14. Outline • Introduction to course • Mechanics

  15. Staff • Instructor: Tao Ju • Jolley 406 (taoju@cse.wustl.edu) • TA: • Hang Dou (dou@wustl.edu)

  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 • CSE241/247 is strongly recommended (required for CS major/minor) • Math • Linear algebra

  17. Overview • 2 meetings per week • Lectures on Mondays (Lab Sciences 301) • Labs on Wednesdays (Urbauer 216) • 6 lab modules • 2-3 weeks for each module • Due and graded in Wednesdays labs • 1 course project • Proposal due in November • Final presentation in December • Check out the calendar on course webpage No exams!

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

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

  20. Course Project • A working tool that solves some problem using geometric computing • Preferably a problem in biomedical image analysis • Use your favorite programming language • Work individually

  21. Course Project • Example projects • Measuring length of sperm cells of fruit flyies (Luis Velazquez-Irizarry)

  22. Course Project • Example projects • Plotting concavity of bone surface (Zhaonan Liu and Zhenyi Zhao)

  23. Course Project • Example projects • Segmenting skull from MRI scan (Hang Yan)

  24. Course Project • Example projects • Measuring size of holes on skulls in CT scans (Zhiyang Huang)

  25. Course Project • Example projects • Matching and superimposing ancient prints (Tom Wilkinson)

  26. Grading • Lab modules: 75% (graded during Wednesday labs) • Course project: 25% • Late policy • Late modules are accepted till the Monday following the due date • The late part will earn at most 50% credit • Other extensions will be given only under exceptional conditions.

  27. Action Items – This Week • Make sure you can log into computers in Urbauer 216 • If not, see help desk at EIT in Lopata 4nd floor. • Get access to Mathematica • Available on all SEAS machines; installed freely on campus computers • Purchase for personal use for $38 / semester • Module 0 is already out • Due and graded next Wednesday in lab (Sept. 7) • I will give a quick tutorial this Wednesday • See you all on Wednesday (Urbauer 216)!

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