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CSE554 Introduction Slide 1
CSE 554: Geometric Computing for Biomedicine
CSE 554: Geometric Computing for Biomedicine
Fall 2015
CSE554 Introduction Slide 2
OutlineOutline
• Introduction to course
• Mechanics
CSE554 Introduction Slide 3
OutlineOutline
• Introduction to course
• Mechanics
CSE554 Introduction Slide 4
GeometryGeometry
• Greek word: Earth-measuring
• One of the oldest sciences
Chinese Chou Pei Suan Ching (500-200 BC) Euclid’s Element (300 BC)
CSE554 Introduction Slide 5
GeometryGeometry
• Greek word: Earth-measuring
• One of the oldest sciences
Newton’s Principia Mathematica (1687) Einstein’s General Relativity (1915)
CSE554 Introduction Slide 6
Geometric FormsGeometric 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
2xy ][][ ySinxSinz
Pixels
Triangle surfaces (meshes)
Polyline
Voxels
Curves Surfaces
CSE554 Introduction Slide 7
Geometric ComputingGeometric 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 8
ApplicationsApplications
Industrial design
Movie CGUrban design and evacuation planning
Engineering simulation3D printing
CSE554 Introduction Slide 9
Application: BiomedicineApplication: 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
Surgical simulation
Treatment planning
CSE554 Introduction Slide 10
This CourseThis Course
• Classical algorithms for geometric computing
– Widely used for biomedical image analysis
– Easy to understand, simple to implement
CSE554 Introduction Slide 11
This CourseThis 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)
CT Cryo-EMMicroscopy
CSE554 Introduction Slide 12
This CourseThis Course
• Creating, processing, deforming, and analyzing geometry
Segment Extract boundary Fair & Simplify
Align & DeformShape analysis
(Before) (After)
CSE554 Introduction Slide 13
Beyond This CourseBeyond 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 14
OutlineOutline
• Introduction to course
• Mechanics
CSE554 Introduction Slide 15
StaffStaff
• Instructor: Tao Ju
– Jolley 406 (taoju@cse.wustl.edu)
• TA:
– Yajie Yan (yajieyan@wustl.edu)
– Zhiyang Huang (zhiyang.huang@wustl.edu)
CSE554 Introduction Slide 16
PrerequisitesPrerequisites
• 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 17
OverviewOverview
• 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 18
LecturesLectures
• Theory and algorithms
– Algorithms are explained in depth, pseudo-code given when possible
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
Example:
CSE554 Introduction Slide 19
Lab ModulesLab Modules
• Algorithm prototyping (in Mathematica)
– Step-by-step, easy to hard, 2D to 3D
– Unit tests
– Work individually
Example:
CSE554 Introduction Slide 20
Course ProjectCourse 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 21
Course ProjectCourse Project
• Example projects (Fall 2014)
– Measuring length of sperm cells of fruit flyies
(Luis Velazquez-Irizarry)
CSE554 Introduction Slide 22
Course ProjectCourse Project
• Example projects (Fall 2014)
– Plotting concavity of bone surface
(Zhaonan Liu and Zhenyi Zhao)
CSE554 Introduction Slide 23
Course ProjectCourse Project
• Example projects (Fall 2014)
– Segmenting skull from MRI scan
(Hang Yan)
CSE554 Introduction Slide 24
Course ProjectCourse Project
• Example projects (Fall 2014)
– Measuring size of holes on skulls in CT scans
(Zhiyang Huang)
CSE554 Introduction Slide 25
Course ProjectCourse Project
• Example projects (Fall 2014)
– Matching and superimposing ancient prints
(Tom Wilkinson)
CSE554 Introduction Slide 26
GradingGrading
• 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 27
Action Items – This WeekAction 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 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)!