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The University of Sydney Slide 1

OVERVIEW / MEDICAL IMAGING

Presented by

Dr Paul Wong

AMME4981/9981

Semester 1, 2016

Lecture 1


Contact Details

Name Email Phone Room

Prof. Qing Li

(Unit of Study

Coordinator)

[email protected] 9351 8607 S509, Mechanical

Engineering

Building

Paul Wong

Andrian Sue

Phillip Tran

(Lecturers

and tutors)

[email protected]

[email protected]

[email protected]

9351 5674 Room 243,

Engineering Link

Building

mailto:[email protected]





UOS Websites

– All course documents and announcements will be posted on the AMME website

– Assessments need to be submitted via eLearning (Blackboard)

User name: applied

Password: biomed2014

http://web.aeromech.usyd.edu.au/AMME4981/

https://elearning.sydney.edu.au/


OPENING THOUGHTS


“As an educator, it’s my duty to empower you to think.So that you can go forth and think accurate thoughtsabout how the world is put together.”

~ Neil DeGrasse Tyson

My Motivation


Knowledge Acquisition

– In science (and engineering), we

use mathematics to understand

physical systems

– Different fields explore different

aspects of the universe, each with

their own sets of equations,

encapsulated in theories

– Computational research has

emerged to complement

experimental methods, particularly

in research, design and

optimisation

~ Victor Eijkhout

IN VIVO

IN VITRO

IN SILICO

NATURE

Abstraction

THEORY

https://bitbucket.org/VictorEijkhout/hpc-book-and-course/src


COURSE OVERVIEW


Driving Question

How does <implant> behavein the body?


Why Use Simulations?

1. In certain cases, computational simulations are the only possible approach for analysing a problem

2. When used correctly, they make complex or unintuitive systems easier to understand

3. Conceptual design and virtual prototyping can take place early in the development cycle to optimise performance and reduce costs


Workflow for Biomedical Problems

1. Data acquisition

• Scan region of interest

• Obtain material properties for tissues and implants

• Estimate expected loads

2. Solid modelling

• Convert image stacks into a virtual replica

• Combine with CAD model of prosthesis

3. Finite element analysis

• Generate appropriate mesh

• Characterise interaction between anatomy and prosthesis

• Verify simulation results and prosthesis design

3. Finite element analysis

• Generate appropriate mesh

• Characterise interaction between anatomy and prosthesis

• Verify simulation results and prosthesis design


Dealing with Uncertainties

“The art of finite element analysis is modelling

materials we do not wholly understand, in shapes we cannot precisely form so as to withstand forces we cannot properly assess,

in such a way that the analyst is confident in the design with the publichaving no reason to suspect the extent of one’s ignorance.”

~ David Beneke


STUFF I’VE BEEN WORKING ON


Driving Question

How can we improve the design of

cochlear implants?


› 6,092,537 DOFs

(quadratic)

› Solution time:

30 minutes<lots of code>

Model Development

ACQUIRE DATAIDENTIFY AND

SEGMENT TISSUES


Data Visualisation

Magnitude Direction Neural Response


MEDICAL IMAGING


Required Modelling Inputs

Geometry

• What does it look like?

Material Properties

• What is it made of?

Loads

• What forces is it being subjected to?

Boundary Conditions

• What is happening at the system boundary?


Imaging Requirements

Critical

– Imaging technique must clearly

show the region of interest

– Data must be volumetric

Desirable

– High resolution

– Strong contrast between tissues

– Free of artefacts

– Isotropic grid


Computed Tomography

Theory

– Developed by Sir Godfrey

Newbold Hounsfield and Allan

McLeod Cormack

– Structures with higher densities

absorb more x-rays than those

with lower densities

– Image brightness measures amount

of x-rays absorbed by an object

– Depends on duration and

strength of the x-ray beam,

other scan parameters

http://en.wikipedia.org/wiki/File:RIMG0277.JPG





Computed Tomography

Hounsfield Unit Scale

– Linear transformation of

attenuation coefficients (i.e. how

difficult it is for the x-rays to

penetrate a material)

– Calibration references:

– 0 HU: radiodensity of distilled

water at STP

– -1000 HU: radiodensity of air

at STP

– A 1 HU change represents a 0.1%

difference of the attenuation

coefficient of water (μair ≈ 0)

Substance HU

Air -1000

Fat -120

Water 0

Blood 30–45

Muscle 40

Contrast medium 130

Bone 400+


Computed Tomography

Practice

– A series of x-ray images is taken

around an axis of rotation

– Computers process the raw 2D

slices to give a 3D representation

of the structures inside the scanned

body

– The 3D structures are then

converted back into a stack of

orthogonal 2D images

– Clinical, micro, and nano variants

GP_coch_microfil_6EDTA_120520_3D_3.avi




Computed Tomography

Usage Considerations

– Ideal for objects that can be distinguished by density

– Simple threshold-based tools can then be used to identify and separate them

– Not great for separating different types of soft tissue

– Metal artefacts

– High density objects tend to obscure those with lower densities

– Geometric information becomes hidden (but not distorted)

– Best to avoid scanning low and high density objects together

– Stronger radiation levels can overcome this, but must not exceed safety limits

– Due to the use of ionising radiation, extended exposure should be avoided for live subjects


Computed Tomography

Examination Type Typical Effective Dose (mSv)

Personnel security screening 0.00025

Chest x-ray 0.1

Head CT 1.5

Screening mammography 3

Abdomen CT 5.3

Chest CT 5.8

Virtual (CT) colonoscopy 3.6-8.8

Chest, abdomen and pelvis CT 9.9

Cardiac CT angiogram 6.7-13

Barium enema 15

Neonatal abdominal CT 20


Magnetic Resonance Imaging

Theory

– An electromagnetic field is

applied at the resonant frequency

of hydrogen protons, changing

their orientation

– When the field is removed, they

realign with the static magnetic

field, emitting a radio frequency

signal that is detected

– Image brightness corresponds to

density of hydrogen in a region



Variants

– Targeting different relaxation times emphasises different structures:

– T1: Fat and large molecules

– T2: Fluids and diseased tissues

– Proton density: Urine, CSF

– Diffusion MRI: Maps diffusion of water through tissues (anisotropy)



Usage Considerations

– Ideal for distinguishing between soft tissues due to texture

– Threshold based segmentation may not work well due to similar grey levels

– Often exhibit signal attenuation and/or noise near borders of image

– No known significant impact on health

– More expensive than CT

– Metallic objects will not influence the image, but magnetic objects will cause distortions

– Electronic components (e.g. pacemakers) may be damaged


Image Comparison

CT MRI


Histology

– Slides prepared from tissue

sample and imaged using a

microscope

– High resolution provides plenty of

detail

– Tissues can be distinguished using

cell staining techniques

– Destructive since specimen must be

divided into thin slices

– Artefacts from slicing process


Serial Photography

– Sample embedded in gel, frozen

and photographs taken at set

intervals

– Good for larger samples

– Extra information encoded in

colour

– Loss of contrast when

converted to greyscale

– Destructive since specimen must be

divided into thin slices

– Artefacts from grinding process


Thin-Sheet Laser Imaging Microscopy

– Specimen is chemically treated to

make it translucent

– A laser light sheet is passed

through the sample and an image

taken perpendicular to the plane

– Very high resolution

– Non-destructive

– Long treatment time

– Shadow artefacts

santi_data.avi

santi_data.avi


Summary

– Different imaging techniques capture different types of information

– Each has its relative strengths and weaknesses, so choose one that is suitable for your purposes

– It is possible to combine multiple datasets, but requires additional planning, effort, and cost


GROUP PROJECTS


Project Overview

People Timeframe

1-2 Week 3

3-5 Week 7

3-4 Week 12

Image

Processing

Modelling

and Design

Experimental

Validation


Teams and Topics

Transarticular screw fixation Dental bridges

Dental implantsSkull plate fixation


Tips for a Successful Project

– Exercise in project planning

– Establish your aims and scope early on

– Distribute the workload according to strengths

– Pull your weight (i.e. don’t be “that guy”)

– Have redundancies in case of “missing” group members

– Plan ahead to validate the model

“If you reach for the stars, you might not quite get one, but you

won’t end up with a handful of mud, either.”

~ Leo Burnett


DISCUSSION TIME

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