Applications of CGAL in the Gel Analysis Software CAROL Klaus Kriegel Freie Universität Berlin...

45
Applications of CGAL in the Gel Analysis Software CAROL Klaus Kriegel Freie Universität Berlin Deutsches Herzzentrum Berlin DFG Projekt FL 165/4-2
  • date post

    22-Dec-2015
  • Category

    Documents

  • view

    214
  • download

    0

Transcript of Applications of CGAL in the Gel Analysis Software CAROL Klaus Kriegel Freie Universität Berlin...

Page 1: Applications of CGAL in the Gel Analysis Software CAROL Klaus Kriegel Freie Universität Berlin Deutsches Herzzentrum Berlin DFG Projekt FL 165/4-2.

Applications of CGAL in the Gel Analysis Software CAROL

Klaus KriegelFreie Universität Berlin

Deutsches Herzzentrum Berlin

DFG Projekt FL 165/4-2

Page 2: Applications of CGAL in the Gel Analysis Software CAROL Klaus Kriegel Freie Universität Berlin Deutsches Herzzentrum Berlin DFG Projekt FL 165/4-2.

CAROL (DFG 1997-2000)CAROL (DFG 1997-2000)

FU Berlin

H. Alt

F. Hoffmann

K. Kriegel

C. Schultz

C. Wenk

German Heart Center

E. Fleck

K.-P. Pleißner

I. Seefeldt

Page 3: Applications of CGAL in the Gel Analysis Software CAROL Klaus Kriegel Freie Universität Berlin Deutsches Herzzentrum Berlin DFG Projekt FL 165/4-2.

Outline of the talkOutline of the talk

Application Background (Electrophoresis)

Gel Matching with CAROL: . The Algorithmic Approach

Using CGAL in CAROL

Experience, Problems, and Further Perspectives

Page 4: Applications of CGAL in the Gel Analysis Software CAROL Klaus Kriegel Freie Universität Berlin Deutsches Herzzentrum Berlin DFG Projekt FL 165/4-2.

2D Gel Electrophoresis2D Gel Electrophoresis

Two-dimensional Gel Electrophoresis (2DE) is an important method in proteome research

It is a high resolution technique which is capable to separate thousands of protein spots from a tissue sample

Page 5: Applications of CGAL in the Gel Analysis Software CAROL Klaus Kriegel Freie Universität Berlin Deutsches Herzzentrum Berlin DFG Projekt FL 165/4-2.
Page 6: Applications of CGAL in the Gel Analysis Software CAROL Klaus Kriegel Freie Universität Berlin Deutsches Herzzentrum Berlin DFG Projekt FL 165/4-2.
Page 7: Applications of CGAL in the Gel Analysis Software CAROL Klaus Kriegel Freie Universität Berlin Deutsches Herzzentrum Berlin DFG Projekt FL 165/4-2.

2D Gel Electrophoresis2D Gel Electrophoresis

Proteins are concentrated in so called SPOTS of elliptic shape

Protein analysis by mass spectrometry (expensive)

Gel Matching : Protein identification by gel image comparison is faster and not expensive

Page 8: Applications of CGAL in the Gel Analysis Software CAROL Klaus Kriegel Freie Universität Berlin Deutsches Herzzentrum Berlin DFG Projekt FL 165/4-2.

Gel Matching: The Assumptions Gel Matching: The Assumptions

Images which have to be compared are similar, but, possibly there are:

Local and global geometric distortions

Corresponding spot pairs with (very) different intensities

Missing spots

Page 9: Applications of CGAL in the Gel Analysis Software CAROL Klaus Kriegel Freie Universität Berlin Deutsches Herzzentrum Berlin DFG Projekt FL 165/4-2.
Page 10: Applications of CGAL in the Gel Analysis Software CAROL Klaus Kriegel Freie Universität Berlin Deutsches Herzzentrum Berlin DFG Projekt FL 165/4-2.
Page 11: Applications of CGAL in the Gel Analysis Software CAROL Klaus Kriegel Freie Universität Berlin Deutsches Herzzentrum Berlin DFG Projekt FL 165/4-2.
Page 12: Applications of CGAL in the Gel Analysis Software CAROL Klaus Kriegel Freie Universität Berlin Deutsches Herzzentrum Berlin DFG Projekt FL 165/4-2.
Page 13: Applications of CGAL in the Gel Analysis Software CAROL Klaus Kriegel Freie Universität Berlin Deutsches Herzzentrum Berlin DFG Projekt FL 165/4-2.
Page 14: Applications of CGAL in the Gel Analysis Software CAROL Klaus Kriegel Freie Universität Berlin Deutsches Herzzentrum Berlin DFG Projekt FL 165/4-2.

The Algorithmic Problem The Algorithmic Problem

Partial Approximate Point Pattern Matching

The CAROL Approach:

Design first an efficient algorithm finding all occurrencies of a small local pattern in a target image (Local Matching)

Global Matching via Local Matching

Page 15: Applications of CGAL in the Gel Analysis Software CAROL Klaus Kriegel Freie Universität Berlin Deutsches Herzzentrum Berlin DFG Projekt FL 165/4-2.
Page 16: Applications of CGAL in the Gel Analysis Software CAROL Klaus Kriegel Freie Universität Berlin Deutsches Herzzentrum Berlin DFG Projekt FL 165/4-2.
Page 17: Applications of CGAL in the Gel Analysis Software CAROL Klaus Kriegel Freie Universität Berlin Deutsches Herzzentrum Berlin DFG Projekt FL 165/4-2.
Page 18: Applications of CGAL in the Gel Analysis Software CAROL Klaus Kriegel Freie Universität Berlin Deutsches Herzzentrum Berlin DFG Projekt FL 165/4-2.
Page 19: Applications of CGAL in the Gel Analysis Software CAROL Klaus Kriegel Freie Universität Berlin Deutsches Herzzentrum Berlin DFG Projekt FL 165/4-2.
Page 20: Applications of CGAL in the Gel Analysis Software CAROL Klaus Kriegel Freie Universität Berlin Deutsches Herzzentrum Berlin DFG Projekt FL 165/4-2.

The Local Matching Approach The Local Matching Approach

Find a k-pattern in a set of n points

Naive Alignment Approach: O(k³n²log n)

Alignment with Delaunay Edges: O(k²n log n)

Scoring Scheme (Geometric Hashing): O(kn)

(+O(G) where G = size of the scheme)

Page 21: Applications of CGAL in the Gel Analysis Software CAROL Klaus Kriegel Freie Universität Berlin Deutsches Herzzentrum Berlin DFG Projekt FL 165/4-2.
Page 22: Applications of CGAL in the Gel Analysis Software CAROL Klaus Kriegel Freie Universität Berlin Deutsches Herzzentrum Berlin DFG Projekt FL 165/4-2.
Page 23: Applications of CGAL in the Gel Analysis Software CAROL Klaus Kriegel Freie Universität Berlin Deutsches Herzzentrum Berlin DFG Projekt FL 165/4-2.
Page 24: Applications of CGAL in the Gel Analysis Software CAROL Klaus Kriegel Freie Universität Berlin Deutsches Herzzentrum Berlin DFG Projekt FL 165/4-2.

Incremental Delaunay TriangulationIncremental Delaunay Triangulation

Alt et al.: If the intensity orderings are consistent with the matching then it is sufficient to use the history edges of the incremental Delaunay Triangulation where points are inserted by decreasing intensity.

Seidel: The expected number of edges in the history of the incremental Delaunay Triangulation is O(n).

To cope with differences in the intensity orderings we add all flip edges to the history!

Page 25: Applications of CGAL in the Gel Analysis Software CAROL Klaus Kriegel Freie Universität Berlin Deutsches Herzzentrum Berlin DFG Projekt FL 165/4-2.
Page 26: Applications of CGAL in the Gel Analysis Software CAROL Klaus Kriegel Freie Universität Berlin Deutsches Herzzentrum Berlin DFG Projekt FL 165/4-2.
Page 27: Applications of CGAL in the Gel Analysis Software CAROL Klaus Kriegel Freie Universität Berlin Deutsches Herzzentrum Berlin DFG Projekt FL 165/4-2.
Page 28: Applications of CGAL in the Gel Analysis Software CAROL Klaus Kriegel Freie Universität Berlin Deutsches Herzzentrum Berlin DFG Projekt FL 165/4-2.
Page 29: Applications of CGAL in the Gel Analysis Software CAROL Klaus Kriegel Freie Universität Berlin Deutsches Herzzentrum Berlin DFG Projekt FL 165/4-2.
Page 30: Applications of CGAL in the Gel Analysis Software CAROL Klaus Kriegel Freie Universität Berlin Deutsches Herzzentrum Berlin DFG Projekt FL 165/4-2.
Page 31: Applications of CGAL in the Gel Analysis Software CAROL Klaus Kriegel Freie Universität Berlin Deutsches Herzzentrum Berlin DFG Projekt FL 165/4-2.
Page 32: Applications of CGAL in the Gel Analysis Software CAROL Klaus Kriegel Freie Universität Berlin Deutsches Herzzentrum Berlin DFG Projekt FL 165/4-2.

Scoring SchemesScoring Schemes

It is also possible to take into account image scalings:

simple scaling --> 3-dimensional scheme

independend scalings of x-axis and y-axis

--> 4-dimensional scheme

Page 33: Applications of CGAL in the Gel Analysis Software CAROL Klaus Kriegel Freie Universität Berlin Deutsches Herzzentrum Berlin DFG Projekt FL 165/4-2.

Global MatchingGlobal Matching

........via local matching

1) Cover the source image by small patterns (5x5)

2) Compute all local matchings of the patterns

3) For many of the patterns the correct local

matching will be included (within a lot of proposals)

4) Find out the correct local matchings by a

consistency test

Page 34: Applications of CGAL in the Gel Analysis Software CAROL Klaus Kriegel Freie Universität Berlin Deutsches Herzzentrum Berlin DFG Projekt FL 165/4-2.
Page 35: Applications of CGAL in the Gel Analysis Software CAROL Klaus Kriegel Freie Universität Berlin Deutsches Herzzentrum Berlin DFG Projekt FL 165/4-2.

CGAL Components in CAROLCGAL Components in CAROL

Geometric primitives from the CGAL kernel:

CGAL_Point_2

CGAL_Bbox_2

CGAL_squared _distance

Page 36: Applications of CGAL in the Gel Analysis Software CAROL Klaus Kriegel Freie Universität Berlin Deutsches Herzzentrum Berlin DFG Projekt FL 165/4-2.

CGAL Components in CAROLCGAL Components in CAROL

The Delaunay Triangulation

from the CGAL basic library

Delaunay Traits

Vertex Circulators

Page 37: Applications of CGAL in the Gel Analysis Software CAROL Klaus Kriegel Freie Universität Berlin Deutsches Herzzentrum Berlin DFG Projekt FL 165/4-2.

Delaunay TraitsDelaunay Traits

class CAROL_Point : CGAL_Point_2

{ private:

double intensity;

..................

}

Defining special Traits classes triangulation vertices can be represented by CAROL_Points

Page 38: Applications of CGAL in the Gel Analysis Software CAROL Klaus Kriegel Freie Universität Berlin Deutsches Herzzentrum Berlin DFG Projekt FL 165/4-2.

Vertex CirculatorsVertex Circulators

Vertex circulators are used to get a list of the neighbors of an inserted vetex

Vertex circulators are used to construct flip edges

Page 39: Applications of CGAL in the Gel Analysis Software CAROL Klaus Kriegel Freie Universität Berlin Deutsches Herzzentrum Berlin DFG Projekt FL 165/4-2.
Page 40: Applications of CGAL in the Gel Analysis Software CAROL Klaus Kriegel Freie Universität Berlin Deutsches Herzzentrum Berlin DFG Projekt FL 165/4-2.
Page 41: Applications of CGAL in the Gel Analysis Software CAROL Klaus Kriegel Freie Universität Berlin Deutsches Herzzentrum Berlin DFG Projekt FL 165/4-2.
Page 42: Applications of CGAL in the Gel Analysis Software CAROL Klaus Kriegel Freie Universität Berlin Deutsches Herzzentrum Berlin DFG Projekt FL 165/4-2.

The Use of CGALThe Use of CGAL CGAL supplies various useful data structures and basic algorithms.

The concept is very flexible according to the user’s needs.

The user can be sure to get efficient implementations.

Several compilers are supported ( gnu, sun, virtual c++ )

Page 43: Applications of CGAL in the Gel Analysis Software CAROL Klaus Kriegel Freie Universität Berlin Deutsches Herzzentrum Berlin DFG Projekt FL 165/4-2.

CGAL with Visual C++CGAL with Visual C++

PDQUEST

CAROL library with CGAL components

Interface

Page 44: Applications of CGAL in the Gel Analysis Software CAROL Klaus Kriegel Freie Universität Berlin Deutsches Herzzentrum Berlin DFG Projekt FL 165/4-2.

CGAL with Visual C++CGAL with Visual C++

PDQUEST

virtual c++ stl

CAROL library with CGAL components

stl_port

Interface_1

Points

Interface_2

Page 45: Applications of CGAL in the Gel Analysis Software CAROL Klaus Kriegel Freie Universität Berlin Deutsches Herzzentrum Berlin DFG Projekt FL 165/4-2.

The End

http://gelmatching.inf.fu-berlin.de