LECTURE 7: Medical Image Segmentation (I) (Radiology ...bagci/teaching/mic16/lec7.pdf · LECTURE 7: Medical Image Segmentation (I) (Radiology Applications of Segmentation, and Thresholding)

MEDICAL IMAGE COMPUTING (CAP 5937)

LECTURE 7: Medical Image Segmentation (I)(Radiology Applications of Segmentation, and Thresholding)

Dr. Ulas BagciHEC 221, Center for Research in Computer Vision (CRCV), University of Central Florida (UCF), Orlando, FL [email protected] or [email protected]

1SPRING 2016

Outline• Introduction to Medical Image Segmentation, type of

segmentation methods, and definitions– Recognition & Delineation

• Simplest Segmentation Method(s): Thresholding– Otsu Thresholding– Parametric Method– PET Image Thresholding Methods

• ITM (Iterative Thresholding Method)

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Motivation for Image SegmentationIn the last 20 years the computer vision and medical imaging communities have produced a number of useful algorithms for localizing object boundaries in images.

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Motivation for Image Segmentation• Content based image retrieval• Machine Vision• Medical Imaging applications (tumor delineation,..)• Object detection (face detection,…)• 3D Reconstruction• Object/Motion Tracking• Object-based measurements such as size and shape• Object recognition (face recognition,…)• Fingerprint recognition,• Video surveillance• …

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Segmentation Tools in Radiology Applications

• 3D views to visualize structural information and spatial anatomic relationships is a difficult task, which is usually carried out in the clinician’s mind.

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• 3D views to visualize structural information and spatial anatomic relationships is a difficult task, which is usually carried out in the clinician’s mind.

• Image-processing tools provide the surgeon with interactively displayed 3D visual information.

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Credit: Kaus, et al. Radiology 2001.

• Determination of the volumes of abdominal solid organs and focal lesions has great potential importance (liver, spleen, …).

• Monitoring the response to therapy and the progression of neoplastic disease and preoperative examination of living liver donors are the most common clinical applications of volume determination.

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(credit: Farraher, et al.Radiology 2005)


• Gross Tumor Volume in CT/MRI• Metabolic Tumor Volume in PET/SPECT/

– Surgery/Therapy Planning• Planning Tumor Volume (PTV)

– Tumor characterization• Texture Extraction requires

segmentation to be done• Shape analysis

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• There is a strong interest in automatic and reproducible techniques for detection and quantification of vascular disease

• A first step toward an effective vessel analysis tool is segmentation of the vasculature.

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axial coronal sagittal

Credit: Manniesing, et al, Radiology 2008

MIP: maximum intensityProjection image of cerebral vessels (in CTA)


• MR volumetry of the hippocampus can help distinguish patients with AD (Alzheimer’s Disease) from elderly controls with a high degree of accuracy (80%–90%).

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• MR volumetry of the hippocampus can help distinguish patients with AD (Alzheimer’s Disease) from elderly controls with a high degree of accuracy (80%–90%).

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hippocampusamygdala

Credit: Colliot et al, Radiology 2008.

Image SegmentationDefinition: Partitioning a picture/image into distinctive subsets is called segmentation.

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Segmentation of an image entails the division or separation of the image

into regions of similar attribute.


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Segmentation of an image entails the division or separation of the image

into regions of similar attribute.

The most basic attributes:-intensity

-edges-texture

-other features…


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Purpose: To extract object information and represent this as a hard/fuzzy geometricstructure.

Recognition: Determining the object’swhereabouts in the scene.(humans > computer)

Delineation: Determining the object’sspatial extent andcomposition in the scene.(computers > humans)

Recognition - Example

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(slice credit: J. Kim et al,Signal Processing 2007)

Model is induced No Model is induced

Approaches to Recognition

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• Model-based• Knowledge-based - Non-interactive• Atlas-based

• Human-assisted - Interactive

Approaches to Recognition

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• Model-based• Knowledge-based - Non-interactive• Atlas-based

• Human-assisted - Interactive

- They all originate from human knowledge.- Their relative efficacy is unknown.

Approaches to Delineations

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pI (purely image-based) approaches• Rely mostly on information available in the given image

only. • Recognition: manual


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SM (shape model-based) approaches• Employ models to codify object family shape info.• Recognition: model-based/manual


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SM (shape model-based) approaches• Employ models to codify object family shape info.• Recognition: model-based/manual

Hybrid approaches• Combine among pI and SM approaches.• Recognition: model-based, automatic.

Classification of Methods

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Boundary-based (BpI):• optimum boundary• active boundary• live wire• level sets


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Region-based (RpI):• clustering – kNN, CM, FCM• graph cut• fuzzy connectedness• MRF• watershed• optimum partitioning• (Mumford-Shah)


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SM Approaches• manual tracing• live wire• active shape/appearance• M-reps• atlas-based


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SM Approaches• manual tracing• live wire• active shape/appearance• M-reps• atlas-based

Hybrid Approaches

• BpI + BpI• RpI + RpI• BpI + RpI• BpI + SM• RpI + SM• SM + SM


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pI Approaches

+ Where image info is good,accuracy is good;

- Bad where it is poor/absent;

- Need recognition help;

+ Can determine degree of match of model to image well;

- Lack obj shape &geographic info;


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SM Approaches

- Even where image info isgood, accuracy suffers;

+ Where bad, model helps;

+ Can help in recognition;

- Need best match info;

+ Good models embody objshape & geographic info;

Purely Image Based Segmentation Methods

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Thresholding – Simple Segmentation• Image binarization

– mapping a scalar image I into a binary image J

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J(x, y) =

(0 if I(x, y) < T

1 otherwise.

Thresholding – Simple Segmentation• Image binarization

– mapping a scalar image I into a binary image J

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J(x, y) =

(0 if I(x, y) < T

1 otherwise.

Thresholding – Simple Segmentation

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Brighter objects

Darker objects

Thresholding – Simple Segmentation

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Brighter objects

Darker objects

DIFFICULTIES1. The valley may be so broad that

it is difficult to locate a significant minimum

2. Number of minima due to type of details in the image

3. Noise4. No visible valley5. Histogram may be multi-modal

Example: CT Scan

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Example: CT Scan

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Example: CT Scan

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Example: CT Scan

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Example: CT Scan

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Thresholding Methods• Huang• Intermode• Isodata• Li• MaxEntropy• Mean• MinError• Otsu• Percentile• RenyiEntropy• Moments

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Thresholding Methods• Huang• Intermode• Isodata• Li• MaxEntropy• Mean• MinError• Otsu• Percentile• RenyiEntropy• Moments

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Thresholding MethodsPET Imaging

Fixed ThresholdingAdaptive ThresholdingIterative Thresholding

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• Huang• Intermode• Isodata• Li• MaxEntropy• Mean• MinError• Otsu (non-parametric)• Percentile• RenyiEntropy• Moments

Otsu Thresholding• Definition: The method uses the grey-value histogram of the

given image I as input and aims at providing the best threshold in the sense that the “overlap” between two classes, set of object and background pixels, is minimized (i.e., by finding the best balance).

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• Otsu’s algorithm selects a threshold that maximizes the between-class variance . In the case of two classes,

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�2b

�2b = P1(µ1 � µ)2 + P2(µ2 � µ)2 = P1P2(µ1 � µ2)

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• Otsu’s algorithm selects a threshold that maximizes the between-class variance . In the case of two classes,

• where P1 and P2 denote class probabilities, and μi the means of object and background classes.

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�2b

�2b = P1(µ1 � µ)2 + P2(µ2 � µ)2 = P1P2(µ1 � µ2)

2



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P1 =uX

ı=0

p(i)

P2 =G

maxX

ı=u+1

p(i)

u

u



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P1 =uX

ı=0

p(i)

P2 =G

maxX

ı=u+1

p(i)

µ1 =uX

ı=0

ip(i)/P1

µ2 =G

maxX

ı=u+1

ip(i)/P2

CLASS MEANS

Otsu Thresholding-Algorithm

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cI(u) 1� cI(u)

P1 P2

c indicates cumulative histogram, and P1 and P2can be approximated well with cumulative density function.


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cI(u) 1� cI(u)

P1 P2


�2b = P1(µ1 � µ)2 + P2(µ2 � µ)2 = P1P2(µ1 � µ2)

2


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cI(u) 1� cI(u)

P1 P2



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cI(u) 1� cI(u)

P1 P2



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cI(u) 1� cI(u)

P1 P2



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cI(u) 1� cI(u)

P1 P2



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cI(u) 1� cI(u)

P1 P2


optimal

Parametric Method for Optimal Thresholding

• Assuming again a two-class problem and assuming that the distribution of gray levels for each class can be modeled by a normal distribution with mean and variance

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• the overall normalized intensity histogram can be written as the following mixture probability density function:

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• the overall normalized intensity histogram can be written as the following mixture probability density function:

where P1 and P2 are class probabilities. The optimal threshold (T) can be found as solving the quadratic equation à

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In case, variances of both classes are equal, then->


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In case, variances of both classes are equal, then->

Thresholding methods for PET Image Segmentation

• Due to the nature of PET images (i.e., low resolution with high contrast), thresholding-based methods are suitable – because the local or global intensity histogram usually provides a

sufficient level of information for separating the foreground (object of interest) from the background. (Foster, Bagci, et al., CBM 2014)

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Fixed Thresholding

Adaptive Thresholding

Iterative Thresholding

Fixed Thresholding Methods



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Fixed Thresholding



Phantom Based

Image Quality metrics based

Adaptive Thresholding 64




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Fixed Thresholding



Phantom Based

Image Quality metrics based

Iterative Thresholding Method (ITM)

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S/B: Source to background ratio.

The method is based on calibrated threshold-volume curves at varying S/B ratio acquired by phantom measurements using spheres of known volumes.


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The measured S/B ratios of the lesions are then estimated from PET images, and their volumes are iteratively calculated using the calibrated S/B-threshold-volume curves


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The measured S/B ratios of the lesions are then estimated from PET images, and their volumes are iteratively calculated using the calibrated S/B-threshold-volume curves

The resulting PET volumes are then compared with the known sphere volume and CT volumes of tumors that served as gold standards.

ITM Example Result on PET Images/Lung

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Another Example for PET Thresholding

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ITM for tumor segmentation/FDG PET

Another Example for PET Thresholding

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Further Thresholding Example – CT Bones

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Further Thresholding Example – CT Bones

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Head-Neck CT – Thresholding for Skull Modeling

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(Slice Credit: P.Seutens)

Segmentation of the skull and the mandibula in CT images using thresholding. (a) Original CT image of the head. (b) Result with a threshold value of 276 Hounsfield units. The segmented bony structures are represented in color. (c) 3D rendering of the skull shows a congenital growth deficiency of the mandibula in this 8-year-old patient. This information was used preoperatively to plan a repositioning of the mandibula.

Multiple Thresholds – MRI Thresholding

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Thresholding can be done interactively and separates the image into different regions. Valleys in the histogram indicate potentially useful threshold values

Credit: Toeonies, K.

Summary of today’s lecture• Introduction into the Medical Image Segmentation• Recognition and Delineation concepts in Segmentation• Simplest Segmentation method: Thresholding

– Otsu– Parametric method for optimal thresholding– PET Image thresholding

• ITM, fixed thresholding, etc.

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Slide Credits and References• Jayaram K. Udupa, MIPG of University of Pennsylvania, PA.• P. Suetens, Fundamentals of Medical Imaging, Cambridge

Univ. Press.

• Foster, B., et al. CBM, Review paper, 2014.• Kaus, et al. Radiology 2001.• Toeonies, K., Medical Image Analysis.• Farraher, et al., Radiology 2005• Zaidi, H., Quantitative Analysis in Nuclear Medicine Imaging.• Bailey et al. Positron Emission Tomography, Springer.• Dawood, M., et al. Correction Techniques in Emission

Tomography

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LECTURE 7: Medical Image Segmentation (I) (Radiology ...bagci/teaching/mic16/lec7.pdf · LECTURE 7: Medical Image Segmentation (I) (Radiology Applications of Segmentation, and Thresholding)