CSE 554: Geometric Computing for Biomedicine

Fall 2015

CSE554 Introduction Slide 1

Outline

• • Introduction to course Mechanics CSE554 Introduction Slide 2

Outline

• • Introduction to course Mechanics CSE554 Introduction Slide 3

Geometry

• • Greek word: Earth-measuring One of the oldest sciences Chinese

Chou Pei Suan Ching

(500-200 BC) CSE554 Introduction Euclid’s

Element

(300 BC) Slide 4

Geometry

• • Greek word: Earth-measuring One of the oldest sciences Newton’s

Principia Mathematica (1687)

CSE554 Introduction Einstein’s General Relativity (1915) Slide 5

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 Curves

y



x

2 Polyline Pixels CSE554 Introduction Surfaces

z



Sin

[

x

]

Sin

[

y

] Triangle surfaces (meshes) Voxels Slide 6

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

Applications

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

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

CSE554

Treatment planning

Introduction

Surgical simulation

Slide 9

This Course

• Classical algorithms for geometric computing – Widely used for biomedical image analysis – Easy to understand, simple to implement CSE554 Introduction Slide 10

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 CSE554 Introduction Slide 11

This Course

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

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) CSE554 Introduction Slide 13

Outline

• • Introduction to course Mechanics CSE554 Introduction Slide 14

Staff

• Instructor: Tao Ju – Jolley 406 ( [email protected]

) • TA: – Yajie Yan ( [email protected]

) – Zhiyang Huang ( [email protected]

) CSE554 Introduction Slide 15

Prerequisites

• Programming – Experienced in at least one of the major programming languages • C/C++, Java, Matlab, Python, etc.

–

CSE332 is strongly recommended (required if you are a CS major)

• CS background – Basic data structures (e.g., queues, trees, hash tables) and algorithms –

CSE241 is strongly recommended (required if you are a CS major)

• Math – Linear algebra CSE554 Introduction Slide 16

Overview

• • • • 2 meetings per week – – Lectures on Mondays (Cupples II 200) Labs on Wednesdays (Whitaker 130) 6 lab modules – – 2 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!

CSE554 Introduction Slide 17

Lectures

• Theory and algorithms – Algorithms are explained in depth, pseudo-code given when possible Example:

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

CSE554 Introduction Slide 18

Lab Modules

• Algorithm prototyping (in

Mathematica

) – Step-by-step, easy to hard, 2D to 3D – Unit tests – Work individually Example: CSE554 Introduction Slide 19

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 CSE554 Introduction Slide 20

Course Project

• Example projects (Fall 2014) – Measuring length of sperm cells of fruit flyies CSE554 Introduction (Luis Velazquez-Irizarry) Slide 21

Course Project

• Example projects (Fall 2014) – Plotting concavity of bone surface CSE554 Introduction (Zhaonan Liu and Zhenyi Zhao) Slide 22

Course Project

• Example projects (Fall 2014) – Segmenting skull from MRI scan CSE554 Introduction (Hang Yan) Slide 23

Course Project

• Example projects (Fall 2014) – Measuring size of holes on skulls in CT scans CSE554 Introduction (Zhiyang Huang) Slide 24

Course Project

• Example projects (Fall 2014) – Matching and superimposing ancient prints CSE554 Introduction (Tom Wilkinson) Slide 25

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

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 already out – Due and graded two weeks from this Wednesday in lab (Sept. 9) – I will give a quick tutorial this Wednesday • See you all on Wednesday (Whitaker 130)!

CSE554 Introduction Slide 27