BIEN 1100

Final Exam

Definition of Biophotonics/Biomedical Optics

Interaction between light and biological systems, such as human cells and tissues

How does light modify tissue?

-Laser Surgery
-Laser Thermal Ablation
-Low Level Laser Therapy (LLLT)
-Photodynamic Therapy (PDT)

How does tissue modify light?

-Optical spectroscopy
-Imaging
-Biosensing

Polarization Imaging Definition

A light beam that is scattered by an object will contain a variety of information about the object's surface structure

What is Diffuse Optical Tomography (DOT)?

Non-invasive technique/proceudure that uses light (near the infrared spectral region) to measure optical properties of tissue and create a 3-D picture of the tissue.

What is diffuse optical tomography typically used to create an image of?

it works best on soft tissues such as breast and brain tissue

pixel definition

Pixels are a grid of dots or picture elements, each pixel contains a number (binary format=zeros and ones) representing the color (tone) of the pixel.

pixel size

When you zoom in you can't see any details smaller than the pixel size, the closer you zoom in the more likely you will start to see pixels

Bit depth

The greater the bit depth, the more tones in the image

File-Size Equation

Number of Pixels * bitdepth

Spatial Resolution defintion

The ability to depict small details; number of pixels used to comprise an image

Contrast definition

The difference in gray level value between the anatomy of interest and the background

Noise definition

The variance in gray level value; presence of artifacts in an image

Artifacts definition

Distortions and/or streaks; column of pixels darker than other

Higher spatial resolution

=may be more noise since there are a greater number of pixels

Lower spatial resolution

= less noise

Less noise

=higher contrast

More noise

=lower contrast

How can we measure image quality?

Phantoms

Anthropomorphic Phantoms

Model realistic anatomy

What do we need to image the body?

- Waves/material that can penetrate and exit the body
- Waves/material that interacts differently with different tissues to create contrast
- Safe
- Relatively fast

What imaging uses X-Rays from the electromagnetic spectrum?

X-rays

What imaging uses gamma rays from the electromagnetic spectrum?

Nuclear Medicine, PET (positron emission tomography)

What imaging uses infrared radiation (IR) from the electromagnetic spectrum?

Thermal imaging

What imaging uses radio waves from the electromagnetic spectrum?

MRI

Ionizing Radiation Modalities

-X-ray
-CT
-Nuclear Medicine/ Positron Emission Tomography (PET)

Nonionizing radiation modalities

-Ultrasound
-MRI

X-ray Radiography

* A beam of x-rays travels through the body
\-The amount of attenuation depends on tissue depth, atomic number, atomic weight, and density
\-Resulting image is a projection or shadow of the body

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* Application - used to diagnose fractures, scan bones, pneumonia, and cancers

Pros of X-ray radiography

- high spatial resolution (=0.1 mm)
- cheap
- fast (real time)

Cons of X-ray Radiography

-ionizing radiation
- 2D projection (shadow imaging)

The problem with X-ray

- projection (shadow) image
- 3D anatomy projected onto 2D image

X-ray Tomosynthesis

A digital X-ray advanced application that involves the acquisition of a series of low-dose projection images during a single sweep of the x-ray tube over a limited angle

Reconstructed image of x-ray tomosynthesis

the individual images are reconstructed into thin slices for viewing as a single image or in a cine mode

What is X-ray tomosynthesis?

Tomosynthesis acquires multiple projections, covers a range of projection angles, and provides multiple image plane reconstructions or "slices."

Tomosynthesis Pros

- Relatively fast
- Cheaper than CT
- Partial 3D info
- High spatial resolution (=0.5mm)

Tomosynthesis Cons

- More ionizing radiation than x-ray
- More expensive than x-ray
- Partial 3D info

Computed Tomography (CT)

X-ray projections acquired at multiple view angles. Cross-sectional images reconstructed.

Image contrast depends on DENSITY of tissue

Clinical applications of a CT scan

Primarily used to scan for diseases in soft tissue and organs

* Trauma
* Brain perfusions
* Oncology
* Abdominal
* Cardiac
* Lung

CT history

- Invented by Sir Godfrey Hounsfield and Alan Cormack (invented in 1972)
- Nobel Prize in Medicine 1979

CT pros

- Fast
- 3D
- High spatial resolution (=0.4mm)

CT cons

- Lots of ionizing radiation
- Only measures X-ray attenuation (density)

Nuclear Medicine/ PET

- Radioactive tracers injected into the body
- Tracers targeted to specific tissues
- Tracers emit radiation (gamma rays) that are imaged using a detector
- Functional imaging
- Can merge w/ CT to provide function and anatomical

Clinical applications of nuclear medicine/ PET

- Oncology
- Brain perfusion
- Cardiac

Nuclear Medicine/PET pros

- Functional imaging
- Limitless applications

Nuclear Medicine/PET cons

- Radiation that stays with patient (1/2 life < 4h)
- Noisy
-Low spatial resolution

Radiation Equivalence of 2 X-ray Exams

- 2 round-trip flight from NY to LA
- Moving from East coast to Denver for 2.5 months

Chest CT equivalence

100x chest x-ray

Radiation, risk of death (1 in 1 million) equivalent to:

- 10 mi on a bike
- 6 mins in a canoe
- Smoking 1.4 cigarettes
- Eating 100 charcoal broiled steaks

Radiation in chest x-ray

4 mRem

Radiation in X-ray coronary angiogram

460-1600 mRem

Radiation in head CT

200 mRem

Radiation in chest CT

800 mRem

Radiation in various PET FDG studies

1400 mRem

Radiation in Bone Nuclear Medicine

420 mRem

Radiation in heart stress test (nuclear medicine)

585 mRem

Ionizing Radiation modalities

- X-ray
- Computed Tomography (CT)
- Nuclear Medicine
- Positron Emission Tomography (PET)

Nonionizing Radiation Modalities

- Ultrasound
-MRI

Ultrasound Definition

High frequency sound waves are transmitted through the body. Echoes are recorded and converted to image

Ultrasound physics

A pulse (sound wave) is sent, the echoes from the sound waves reflecting occurs. The longer the echo the farther away the tissue.

3D Ultrasound

Created by moving transducer, many 2D images acquired. A computer reconstructs the 3D images

Ultrasound pros

* Safe
* 3D
* Inexpensive
* Real time
* Nonionizing

Ultrasound cons

- limited spatial resolution
- need acoustic window

Magnetic Resonance Imaging (MRI)

Uses magnetic field and radio waves to take images of your body's interior, and can diagnose/investigate conditions that affect soft tissue, such as tumors or brain disorders.

MRI physics (what our body contains)

Since our bodies are made mostly of water, and water contains hydrogen photons, those photons act as small magnets.

MRI physics (magnetic fields)

- Normally, magnetic fields point in all directions= no net magnetization
- Placed in a magnetic field, more protons align with field= net magnetization

MRI physics (Larmour Frequency)

- Net magnetization
- Protons precess about main magnetic field at Larmour frequency
-Larmour frequency depends on material and magnetic field strength

MRI physics (MRI image created)

* Radio frequency (RF) pulse applied to magnetized tissue, tuned to Larmour frequency
* Larmour frequency- specific range where the radio frequency does not disrupt living tissue (much lower than X-ray)


* Radio frequency pulse causes protons to RESONATE
* When RF pulse is turned off, protons return to equilibrium
\-Protons emit an RF pulse
* Image created by manipulating magnetic field and RF pulses
* Many different tissue contrasts possible

MRI Physics (2D image)

-Created by a proton spin frequency depends on the magnetic field
- Apply a varying magnetic field across the patient
- Frequency encodes location
- Fourier Transform used to decompose signal into frequencies

MRI applications

- Multiple Sclerosis
- Knee Imaging ACL
- MRI of the Spine

MRI pros

- Great soft tissue contrast
- Nonionizing radiation (safe)
- Limitless contrast possibilities

MRI cons

- Slow
- Can't image people with magnetic materials
- Claustrophobic
- Loud

mm to pixel

0.127 mm in one pixel

Ionizing radiation on electromagnetic spectrum

Uses more energy (more harmful)

Non-ionizing radiation on electromagnetic spectrum

uses less energy (less harmful)

Phantom definition

model used in the place of human anatomy

How are phantoms used?

used rather than testing a protoype on a human body

What are the 3 kinds of phantoms?

spatial resolution, contrast detail, anthropomorphic

Where are X-rays on electromagnetic spectrum

Towards the left end, high energy, decreasing wavelength

Where are Gammas (PET) on electromagnetic spectrum?

All the way to the left

Where is the MRI on the electromagnetic spectrum?

towards the right side (radio waves)

Compare and Contrast X-ray and CT

X-ray (ONLY)- 2d, inexpensive, used primarily to see bones and scan for pneumonia and cancers.

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CT (ONLY)- full 3d projection, more radiation, used primarily to diagnose diseases in soft tissues and organs

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BOTH- ionizing radiation \[X-rays\], high spatial resolution, fast scans

Why is it important for MRI systems that our bodies are mostly made of water?

Each water molecule contains two hydrogen protons that act as magnets. MRI generates a magnetic field that aligns the protons in water. The protons resonate when radiofrequency pulse is applied. The MRI manipulates magnetic field and RD pulse to create images.

During which phase of the design process do you identify the scope of the problem?

Problem identification

What are other stages of the design process?

- identification of customer needs
- establishment of target specifications
-generation of concepts
-construction of protoype
-design validation and verification

What is the term for a method for adding contrast to images by only allowing grayscale values within a certain range in?

__Windowing__

* grayscale pixel values outside the window are displayed as black or white
* narrower windows= starker contrasts

2D Fourier transform: image to frequency

- If the dots are closer together, then the lines are in bigger chunks (there are less lines)
- If the dots are farther apart, then the lines are in smaller chunks and there are more lines.
-The lines are perpendicular to the dots

Filtering images- salt and pepper noise

Equation: sum of pixels/number of pixels

What are the four required sections of a student resume?

1)personal/contact information
2)education
3)experience
4)activities/interests

Median Filtering

Removes outlier values - artifacts

How to filter using the median

- Sort the pixels in the neighborhood from lowest to highest
- The value at the pixel of interest is REPLACED by the MEDIAN value in the neighborhood
-This removes the artifacts

Filtering

\- Way to remove unwanted info

\- Preserves integrity of underlying image

\- Works differently for different types of noise

\- Has many forms

Difference in filter design. Can one remove all types of noise?

In image processing lab the filter only worked on salt and pepper noise and did not work for right-left streak noise.

Pseudocode

Artificial and informal language that helps programmers develop algorithms (fake code, text-based)

Customer needs

1. phantom models knee joint anatomy (femur and tibia) and soft tissue
2. Materials used resemble bone and tissue
3. Max JSW will model a healthy person, min JSW will model a person with cartilage degradation
4. JSW must be adjustable
5. Represents bone and tissue size of average to large middle ages male
6. Comprised of affordable and available products
7. Must stand unassisted

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Specifications for Phantom

Target specifications - converts customer needs into quantitative and measurable specification


1. minimum joint space width - 0mm
2. maximum joint space width - 1cm.
3. diameter of femur and tibia bone at joint - 5-10cm
4. material density is equivalent to bone - 2 g/cm^3
5. material density is equivalent to soft tissue - 1.2 g/cm^3
6. total phantom height- 15-30cm
7. Width or diameter of soft tissue - 12-18cm
8. Free standing
9. Common/non-toxic materials
10. Max budget - $25

window width/level settings for phantom

* increase/decrease brightness
* Create contrast for bone and soft tissue

Concept generation of the phantom

* Each person generated their own ideas (no comparison)
* Share with group and come up with new ideas
* Choose three ideas
* compare and contrast the candidates to determine the final design concept (technical feasibility, economic feasibility, usability constraints)

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X-ray images reconstruction

The x-ray will not pass through dense materials (bone) = shows up white

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The x-ray will pass through less dense material (tissue)= shows up darker

2D space patterns

* frequency space is symmetric
* spatial frequency increases the further from the center of 2D Fourier space
* vertical axis results in streaks that appear in the “up-down” direction
* horizontal axis results in “left-right” streaks
* changing the angle in frequency space changes the orientation