1 / 27

CSE 554: Geometric Computing for Biomedicine

CSE 554: Geometric Computing for Biomedicine. Fall 2014. Outline. Introduction to course Mechanics Mathematica demo. Outline. Introduction to course Mechanics Mathematica demo. Geometry. Greek word: Earth-measuring One of the oldest sciences.

lilah
Download Presentation

CSE 554: Geometric Computing for Biomedicine

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript


  1. CSE 554: Geometric Computing for Biomedicine Fall 2014

  2. Outline • Introduction to course • Mechanics • Mathematica demo

  3. Outline • Introduction to course • Mechanics • Mathematica demo

  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 Cultural heritage Engineering simulation Geology 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 • Widely used for biomedical image analysis • Easy to understand, simple to implement

  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) • Machine learning (Kilian) • Human computer interaction (Caitlin)

  14. Outline • Introduction to course • Mechanics • Mathematica demo

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

  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. 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 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 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. Course Projects • Example projects (Fall 2013) (Ethan Green)

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

  23. Course Projects • Example projects (Fall 2013)

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

  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. Outline • Introduction to course • Mechanics • Mathematica demo

  27. Action Items – This Week • Make sure you have a SEAS account • Check with the 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 $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)!

More Related