Fall 2013
CSE554 Introduction Slide 1

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Introduction to course
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Mechanics
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Mathematica demo
CSE554 Introduction Slide 2

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Introduction to course
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Mechanics
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Mathematica demo
CSE554 Introduction Slide 3

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Greek word: Earth-measuring
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One of the oldest sciences
Chinese Chou Pei Suan Ching (500-200 BC)
CSE554 Introduction
Euclid’s
Element (300 BC)
Slide 4

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

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Algorithms and data structures for manipulating geometric forms
CSE554 Introduction Slide 6

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Continuous forms
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Defined by mathematical functions
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E.g.: parabolas, splines, subdivision surfaces
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Discrete forms
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Disjoint elements with connectivity relations
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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 7

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Algorithms and data structures for manipulating (discrete) geometric forms
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Creation
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From 2D/3D images, from point clouds, by hand, etc.
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Processing
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De-noise, simplify, repair, transform, animate, etc.
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Analysis
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Geometric, topological, shape and physical properties
CSE554 Introduction Slide 8

Industrial design
Engineering simulation Cultural heritage
CSE554
Geology
Introduction
Movie CG
Slide 9

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Modeling biological structures as geometric forms
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A spectrum of scales: organs, tissues, cells, molecules, etc.
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Utility of geometric models
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Visualization
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Quantitative analysis
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Simulation and interaction
Human Virus
CSE554
Treatment planning
Introduction
Surgical simulation
Slide 10

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Classical algorithms for geometric computing
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Those that have been useful for biomedical image analysis
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Easy to understand, simple to implement
CSE554 Introduction Slide 11

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Working with biomedical imaging data
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2D: Light microscopy, slices of 3D images
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3D: Magnetic resonance imaging (MRI), Computed tomography (CT),
Cryo-Electron Microscopy (Cryo-EM)
Microscopy Cryo-EM
CT
CSE554 Introduction Slide 12

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Creating, processing, deforming, and analyzing geometry
Fair & Simplify Segment Contour
Shape analysis Align
CSE554 Introduction
(Before) (After)
Slide 13

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On-going research projects on biomedical modeling
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Gorgon : protein modeling tool for density volumes (Gorgon.wustl.edu)
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Geneatlas : atlas-based gene expression pattern exploration (Geneatlas.org)
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VolumeViewer : interactive 3D segmentation tool (Volumeviewer.cse.wustl.edu)
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Research opportunities in the M&M lab
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Biomedical modeling (Tao)
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Image analysis (Robert, Tao)
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Computer vision (Robert, Yasu)
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Machine learning (Kilian)
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Human computer interaction (Caitlin)
CSE554 Introduction Slide 14

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Introduction to course
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Mechanics
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Mathematica demo
CSE554 Introduction Slide 15

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Instructor: Tao Ju
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Jolley 406 ( taoju@cse.wustl.edu
)
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TA:
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Ming Zou ( mingzou.cn@gmail.com
)
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Derek Burrows ( derek.wayne.burrows@gmail.com
)
CSE554 Introduction Slide 16

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Programming
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Experienced in at least one of the major programming languages
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C/C++, Java, Matlab, Python, etc.
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CSE332 is strongly recommended
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CS background
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Basic data structures (e.g., queues, trees, hash tables) and algorithms
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CSE241 is strongly recommended
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Math
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Linear algebra, elementary geometry
CSE554 Introduction Slide 17

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2 meetings per week
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Lectures on Tuesdays (Lopata 229)
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Lab working (with instructor and TA) on Thursdays (Whitaker 130)
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5+1 lab modules
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2 weeks for each module (1 week for Module 0)
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Due and graded in lab on Thursdays.
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1 course project
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Start in October
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Due end of semester
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Check out the calendar on course webpage
CSE554 Introduction Slide 18

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Theory and algorithms
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Power-point slides available before each lecture on the webpage
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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 19

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Algorithm prototyping (in Mathematica )
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Modules designed to help you implement the algorithm step-by-step
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Emphasis on unit testing
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Work individually
Example:
CSE554 Introduction Slide 20

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A working tool for bio-medical data analysis
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Addressing problems in on-going bio-medical research
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Meet the need of the specific research problem to a sufficient extent
Measuring small bowel length
(by Billy Bennett)
CSE554
Breast lesion segmentation
(by Noa Ben-Zvi)
Introduction Slide 21

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Use your favorite programming language
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Work in team or individually
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Schedule:
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October 8: Instructor presents candidate project ideas
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October 24: Project proposals are due
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December 3/5: In-class project demos
CSE554 Introduction Slide 22

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Lab modules: 75% (graded during Thursday lab time)
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Course project: 25%
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Late policy
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Late modules and project will earn at most 50% credit for the late part
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Modules submitted later than the Tuesday following the due date will not be accepted.
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Extensions will be given only under exceptional conditions, by written requests ahead of time.
CSE554 Introduction Slide 23

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Introduction to course
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Mechanics
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Mathematica demo
CSE554 Introduction Slide 24

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Make sure you have a SEAS account
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Check with the help desk at EIT in Lopata 4 nd floor.
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Get access to Mathematica
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Available on all SEAS machines, and can be installed freely on campus
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Purchase for personal use for $45 / semester
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Module 0 is out today
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I will give a quick tutorial and help you with it this Thursday
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Due and graded next Thursday in lab (Sept. 5)
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See you all on Thursday (Whitaker 130)!
CSE554 Introduction Slide 25