CSE 554: Geometric Computing for Biomedicine CSE 554 ...

CSE 554: Geometric Computing for Biomedicine Fall 2016

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Outline • Introduction to course • Mechanics

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

Chinese Chou Pei Suan Ching (500-200 BC) CSE554

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Euclid’s Element (300 BC) Slide 4

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

Newton’s Principia Mathematica (1687) CSE554

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Einstein’s General Relativity (1915) Slide 5

Geometric Forms Curves

• Continuous geometry

Surfaces

– Defined by mathematical functions – E.g.: parabolas, splines, subdivision y  x2

surfaces

z  Sin[ x]Sin[ y]

• Discrete geometry – Disjoint elements with connectivity

Polyline

relations

Triangle surfaces (meshes)

– E.g.: polylines, triangle surfaces, pixels and voxels

Pixels

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Voxels

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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

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Applications

Industrial design

3D printing

Urban design and evacuation planning

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Engineering simulation

Movie CG

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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

Treatment planning

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Virus

Surgical simulation

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This Course • Classical algorithms for geometric computing – Easy to understand, simple to implement – Applicable to biomedical image analysis

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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

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Cryo-EM

CT

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This Course • Creating, processing, deforming, and analyzing geometry

Segment

Extract boundary

Fair & Simplify

Shape analysis

Align & Deform

(Before)

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(After)

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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

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

• TA: – Hang Dou ([email protected])

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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

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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

No exams!

– Due and graded in Wednesdays labs

• 1 course project – Proposal due in November – Final presentation in December

• Check out the calendar on course webpage

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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

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Lab Modules • Algorithm prototyping (in Mathematica) – Step-by-step, easy to hard, 2D to 3D

– Unit tests – Work individually

Example:

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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

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Course Project • Example projects – Measuring length of sperm cells of fruit flyies

(Luis Velazquez-Irizarry)

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Course Project • Example projects – Plotting concavity of bone surface

(Zhaonan Liu and Zhenyi Zhao)

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Course Project • Example projects – Segmenting skull from MRI scan

(Hang Yan)

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Course Project • Example projects – Measuring size of holes on skulls in CT scans

(Zhiyang Huang)

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Course Project • Example projects – Matching and superimposing ancient prints

(Tom Wilkinson)

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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.

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Action Items – This Week • Make sure you can log into computers in Urbauer 216 – If not, see 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 $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

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