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


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

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Source proteomics 2003 vol 3 pp 392 401 authors paul cutler geoffrey heald ian r

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), …


Experimental results

Experimental results


Experimental results1

Experimental results


Experimental results2

Experimental results


Experimental results3

Experimental results


Experimental results4

Experimental results


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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