Medical Image Processing Lectures

Medical Image Segmentation

Prof. Leo Joskowicz
School of Engineering and Computer Science
The Hebrew University of Jerusalem, ISRAEL

MIS techniques: classification (1)

1. Manual methods
2. Thresholding and classification
– Shape-based histogram techniques
– Non-parametric optimal thresholding
– Parametric optimal thresholding
– Minimum distance / maximum likelihood methods
3. Edge-based techniques
– Border tracing
– Graph search
– Hough transforms
4. Morphological operators
– Opening, closing, erosion, dilation
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 MIS techniques: classification (2)
5. Region-based techniques
– region growing
– region splitting and merging
– connected components labeling
– watershed segmentation
6. Deformable models
– active contours
– snakes
– level-set
7. Graph-cut
8. Hybrid methods

MIS methods: user input

Manual: time consuming, error prone, subjective, not
reproducible, but may be the most accurate if an expert is
doing the work (non-fatigued + good interactive tools).
Automatic: segment and partition an image entirely
automatically, with no human intervention. Computer
intensive; may be error prone due to large variety of
image types and image characteristics.
Semi-automatic: Combination of computer processing and
human intervention. The expert initializes the process by
selecting initial boundaries or starting information. After
processing, the expert can correct erroneous results.
Nearly automatic: minimal interaction by end-user
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 MIS methods: prior knowledge
• Knowledge about the structures of interest can
greatly help in the segmentation process
• Prior knowledge comes in many forms:
• Intensity ranges, distributions
• Shape and morphology
• Adjacencies, texture, …
• Explicit  precoded
• Implicit  derived (learned) from a training set
• Prior knowledge is task and anatomy-dependent
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 Partial Volume Effect -- PVE

1. Manual MIS: cerebelum segmentation

Used to obtain ground truth since it is unbiased 8

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 2. Thresholding and classification
Basic idea:
a structure is uniquely characterized by
its intensity values in the image
valid for highly contrasted structures

Basic thresholding approach:

– thresholding between two grey-levels (windowing)
– representative value + range
– derived from histogram
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Intensity ranges variations in CT

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Example: simple global thresholding

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 Segmentation with histograms (1)
Object vs. background

background background
object object

Several objects

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Segmentation with histograms (2)

Region-based adaptive thresholding

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 MIS : simple thresholding

Copyright L. Joskowicz, 2010

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Example: head CT
Three peaks: background,
brain, skull.
Separating thresholds:
11 and 185.

Copyright L. Joskowicz, 2010

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 Three-class thresholding

background brain tissue skull

Copyright L. Joskowicz, 2010
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Morphology operations

brain mask largest connected

component
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 Morphology operations
final result

brain threshold dilation erosion

5×5 5×5
Copyright L. Joskowicz, 2010
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Morphology operations
original image dilation set dilation dilation
operation result

erosion erosion original vs

erosion set operation result result 10
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 Morphological operators
• Binarize image
• Dilation:
1 1 0 1 0
I = image; B =
1 1 1 1 1
0 1 0

• Erosion: dual of dilation

complement I; reflect B; dilate; complement result

Copyright L. Joskowicz, 2010

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MIS: thresholding example (1)

Abdominal CT Scan Thresholded Image

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 MIS: thresholding example (2)

After mathematical Surface model Marching Cubes

morphology operations + surface simplification

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MIS with thresholding: limitations (1)

• Works only for segmentation based on intensities
• Not specific to anatomy
• Robust only for images with global uniformity and
high contrast to noise
• Local variability caused by imaging inhomogeneities
and distortions
• Intrinsic assumption is made that the probability of
features is uniformly distributed
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 MIS with thresholding: limitations (2)
• Choice of threshold can be computed from grey-
level histogram.
• Does not assume any spatial correlation of voxel
intensity.
• Does not take into account the partial volume
effect (PVE)

motivates classification methods

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Limitations of thresholding

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 Intensity values of brain structures in MRI

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MIS challenges: intensities overlap

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 MIS challenges: intensities overlap

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Inhomogeneities in MRI images

original image inhomogeneity field corrected image

Image: Univ. of Utah 15

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 3. Edge-based segmentation
Ideal edge Ramp edge

Gray-level profile of a horizontal line through image

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Image edge derivatives

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 3. Edge-based segmentation techniques
• Edge = boundary One-dimensional edge profiles
between two
regions with distinct
gray-level
properties.
• Most edge detection
algorithms compute
a local derivative
operator.

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Edge detection with derivative operators

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 Derivatives
Derivative: instantaneous rate of change of a function f

Approximate partial derivatives


x f (i , j )  f (i , j )  f (i  1, j )

y f ( i , j )  f ( i , j )  f ( i , j  1)
• Approximate derivatives by convolution with (1,-1)

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Gradient operators (1)

• 2D first derivatives 
f (i, j)  f (i, j)  f (i 1, j)
x

• Magnitude of the gradient

• Direction of the gradient

• Numerical approximation: f  G x2  G y2  G x  G y
– Roberts Operator
– Sobel Operator  Gy 
 ( x, y )  tan 1  
– Prewitt Operator  Gx 
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 Image derivatives

Ix = * -1 1 =

-1
Iy = * 1
=

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Image gradient

Ix2 + Iy2 =
Gonzalez & Woods: Digital Image Processing, 2001.
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 Gradient operators (2)
Roberts Operator

G f  x, y  f i, j   f i 1, j 1  f i 1, j   f i, j 1 

 Gx  Gy

Gx  Gy 

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Gradient operators (3)

Prewitt operator

M  S x2  S y2 Sx  Sy 

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 Second derivative operators (1)
Laplacian operator: 2D equivalent of 2nd derivative

2 f 2 f
 f  2  2
2

x y

2 f x2 f xx  2 f x f y f xy  f y2 f yy

n 2
f x2  f y2

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Second derivative operators (2)

• Second directional derivative
• Laplacian of Gaussian
 x2  y2 
h  x , y   exp   
 2  2  "Mexican hat" operator
 
 2 h  x , y   f  x , y    2 h  x , y   f  x , y 

 x 2  y 2  2 2   x2  y2 
LoG   h  x , y   
2
 
 exp   2  2  
  4
  
 r 2  2    r2 
   exp  
2 
   2 
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 Cross section of intensity function

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 (a) Original image
(b) Convolving
image (a) with
(c) Binarization
(d) Zero crossing

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Example: lung CT slice

original image Laplacian derivative

Sobel derivative Closing

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 Edge detection: carpal bones

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Edge detection: vertebra results

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 MIS with edge detection: limitations
• Produces disconnected boundaries
• Over- of under-segmentation and spurious edges
• Connecting edges and filling in is challenging
• Problem is harder in 3D!

 boundary-based methods

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