CSE 554: Geometric Computing for Biomedicine

Transcription

1 CSE 554: Geometric Computing for Biomedicine Fall 2016 CSE554 Introduction Slide 1

2 Outline Introduction to course Mechanics CSE554 Introduction Slide 2

3 Outline Introduction to course Mechanics CSE554 Introduction Slide 3

4 Geometry Greek word: Earth-measuring One of the oldest sciences Chinese Chou Pei Suan Ching ( BC) Euclid s Element (300 BC) CSE554 Introduction Slide 4

5 Geometry Greek word: Earth-measuring One of the oldest sciences Newton s Principia Mathematica (1687) Einstein s General Relativity (1915) CSE554 Introduction Slide 5

6 Geometric Forms Continuous geometry Defined by mathematical functions Curves Surfaces E.g.: parabolas, splines, subdivision surfaces 2 y x z Sin[ x] Sin[ y] Discrete geometry Disjoint elements with connectivity relations E.g.: polylines, triangle surfaces, pixels and voxels Polyline Triangle surfaces (meshes) CSE554 Introduction Slide 6 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 CSE554 Introduction Slide 7

8 Applications Industrial design 3D printing Engineering simulation Urban design and evacuation planning Movie CG CSE554 Introduction Slide 8

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 CSE554 Introduction Slide 9

10 This Course Classical algorithms for geometric computing Easy to understand, simple to implement Applicable to biomedical image analysis CSE554 Introduction Slide 10

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 CT Cryo-EM CSE554 Introduction Slide 11

12 This Course Creating, processing, deforming, and analyzing geometry Segment Extract boundary Fair & Simplify Shape analysis Align & Deform (Before) (After) CSE554 Introduction Slide 12

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) CSE554 Introduction Slide 13

14 Outline Introduction to course Mechanics CSE554 Introduction Slide 14

15 Staff Instructor: Tao Ju TA: Jolley 406 Hang Dou CSE554 Introduction Slide 15

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 CSE554 Introduction Slide 16

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 No exams! Proposal due in November Final presentation in December Check out the calendar on course webpage CSE554 Introduction Slide 17

18 Lectures Theory and algorithms Algorithms are explained in depth, pseudo-code given when possible Example: 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 CSE554 Introduction Slide 18

19 Lab Modules Algorithm prototyping (in Mathematica) Step-by-step, easy to hard, 2D to 3D Unit tests Work individually Example: CSE554 Introduction Slide 19

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 CSE554 Introduction Slide 20

21 Course Project Example projects Measuring length of sperm cells of fruit flyies (Luis Velazquez-Irizarry) CSE554 Introduction Slide 21

22 Course Project Example projects Plotting concavity of bone surface (Zhaonan Liu and Zhenyi Zhao) CSE554 Introduction Slide 22

23 Course Project Example projects Segmenting skull from MRI scan (Hang Yan) CSE554 Introduction Slide 23

24 Course Project Example projects Measuring size of holes on skulls in CT scans (Zhiyang Huang) CSE554 Introduction Slide 24

25 Course Project Example projects Matching and superimposing ancient prints (Tom Wilkinson) CSE554 Introduction Slide 25

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. CSE554 Introduction Slide 26

27 Action Items This Week Make sure you can log into computers in Urbauer 216 If not, see 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 $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)! CSE554 Introduction Slide 27