Final_Presentation

Document Sample
Final_Presentation Powered By Docstoc
					• David Avishai        027250463
• Eyal Cohen           025053414

• Supervisor: Nir Katzir - Applied Spectral Imaging

• Winter 2000/1
                  Chromosomes Segmentation Project    1
                    Final Presentation - June 2001
Human cell in Metaphase


          karyotyping




      Chromosomes Segmentation Project   2
        Final Presentation - June 2001
         Karyotyping Techniques




Manual G-bands   Computerized G-bands                Spectral
  karyotyping        karyotyping                    karyotyping




                 Chromosomes Segmentation Project             3
                   Final Presentation - June 2001
          Automatic Karyotyping
Requirement :
         Optimal segmentation of metaphase input photo

Task :

         Defining UI schemes and corresponding
         algorithms for segmenting a pair of touching or
         Overlapped chromosomes



                     Chromosomes Segmentation Project      4
                       Final Presentation - June 2001
         Segmentation Problems
1. Touching Chromosomes




2. Chromosomes Overlap




                  Chromosomes Segmentation Project   5
                    Final Presentation - June 2001
            Process Arguments
Input :

1. Binary array
2. Intensity array
3. Cut type and location

Output :

1. Number of resultant chromosomes
2. Chromosomes separation contour




                     Chromosomes Segmentation Project   6
                       Final Presentation - June 2001
 General Solution Algorithm
Input                          Operation
        UI
Array                           Mode



                     Automatic          Semi - Auto
                                                      User Input




                    Configuration
                       Check




                       Overlap / Touching / Single




                              Cut Contour

             Chromosomes Segmentation Project                7
               Final Presentation - June 2001
         Segmentation Criteria
1. Convex Hull ratio
2. Convex Hull labels
3. Curvature Extrema
4. User Input
                           Ch_Ratio                 If n > 1

 Image                       Labels                 X - shape
                                                    L - shape
                     Curvature Extrema              T - shape
                                                    I - shape
                          User Input
                 Chromosomes Segmentation Project          8
                   Final Presentation - June 2001
  Segmentation Criteria -
  Convex Hull ratio & labels
Ch_ratio = Blob area / Convex hull area

Labels = No. of holes



    Figure         Convex hull (filled)            Holes




                Chromosomes Segmentation Project           9
                  Final Presentation - June 2001
Segmentation Criteria -
  Curvature Extrema

 X shape overlap - 4 minima




 T shape touch - 2 minima




 L shape overlap - 1 minima
       Chromosomes Segmentation Project   10
         Final Presentation - June 2001
              Main Algorithm –
              Criteria Extraction
                 Noise                 BW Smoothing                  Contour
Image
                Filtering               (Opening)                    Detection




                Cut Type                            Convex Hull             Contour
                (Erosion)                            Detection              Filtering




                                                                            Curvature
                                                 Ch_ratio & Labels
                                                                             Analysis

    Decision Making
      Algorithm
                                                                         Min/Max Points


                       Chromosomes Segmentation Project                            11
                         Final Presentation - June 2001
              Main Algorithm –
             Choosing Mechanism
                                     Minima                          Ch_ratio
                                   Points Pairs                      & Labels




 Chosen          Distance           Minima
                                                     Configuration
                                                       Decision      Cut Type
Cut Points     Requirements       Points Fours
                                                        Table




                                  Min. & Max.                        Min/Max
                                  Points Pairs                        Points




                  Chromosomes Segmentation Project                    12
                    Final Presentation - June 2001
        Curvature Extrema
Curvature Min/Max Points Are Suspected
Cutting Points :

L( x, y ) = L(t)= Contour Line

                                = θ(t) = Line Gradient

C(t) = dθ /dt =Curvature
Min/Max Curvature  dC/dt =0


               Chromosomes Segmentation Project          13
                 Final Presentation - June 2001
Example 1




            14
Example 2




            15
                          R&D
Future Research:
• Multiple Chromosomes Criteria
• Spectral Analysis Criteria
• Overlap Precise Cut, Using:
       Color Intensity
       Banding Orientation
• Check Karyotyping after segmentation
• Multiple Chromosomes Segmentation


GUI & Algorithm Development :
• MATLAB Version 6.0

                    Chromosomes Segmentation Project   16
                      Final Presentation - June 2001
Chromosomes Segmentation Project   17
  Final Presentation - June 2001

				
DOCUMENT INFO