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Source: Proteomics, 2003, vol.3, pp.392-401 Authors: Paul Cutler, Geoffrey Heald, Ian R.

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A novel approach to spot detection for two-dimensional gel electrophoresis images using pixel value collection. Source: Proteomics, 2003, vol.3, pp.392-401 Authors: Paul Cutler, Geoffrey Heald, Ian R. White and Jason Ruan Speaker: Shu-Fen Chiou ( 邱淑芬 ) Date: 2005/03/18.

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slide1

A novel approach to spot detection for two-dimensional gel electrophoresis images using pixel value collection

Source: Proteomics, 2003, vol.3, pp.392-401

Authors: Paul Cutler, Geoffrey Heald, Ian R.

White and Jason Ruan

Speaker: Shu-Fen Chiou (邱淑芬)

Date: 2005/03/18

outline
Outline
  • Introduction
  • Proposed Method
  • Experimental results
  • Conclusions
  • Comment
introduction
Introduction
  • A common goal of proteomic analysis:

Quantitation and identification of proteins which are

differentially expressed under defined physiological

conditions.

  • 2D-gel is a proteomic technology.
introduction1
Introduction
  • Drawbacks of the available methods:
    • Noise and artefacts
    • Need extensive parameter setting
    • Take much time
    • Operator subjectivity
  • A new method using a segmentation method involving pixel value collection via serial analysis of the image through its range of density levels.
proposed method

1616 2d gel image

Proposed method
  • Smallest pixel value:246
  • Highest pixel value:56
  • Limits:
    • Size (maxSize, minSize)
    • Shape (ellipse or circle)
proposed method1
Proposed method

High

The first range:56~76

Threshold 1: (56+61+67)/3=61

56

61

67

The second range:105~125

Threshold 2: (105+109)/2=107

Range:20

105

109

Low

proposed method2
Proposed method

Threshold 1:61

Find the pixel <= threshold 1

minSize:12

maxSize:28

Spot 1: (10,9), (10,10), (11,10)

proposed method3
Proposed method

Threshold 2:107

Find the pixel <= threshold 2

minSize:12

maxSize:28

Spot 1: (10,9), (10,10), (11,10), (9,9), …

compare with edge detection
Compare with edge detection

Edge detection

Proposed method

conclusions
Conclusions
  • The method can be automated and hence reduce operator subjectivity.
  • The method can detect a large dynamic range of spot intensities and areas, and has the potential to detect and resolve merged spots.
comment
Comment

Find the spots using the pixel value collection

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