1 / 45

Applications of CGAL in the Gel Analysis Software CAROL

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). FU Berlin H. Alt F. Hoffmann K. Kriegel C. Schultz C. Wenk. German Heart Center E. Fleck K.-P. Pleißner

suzuki
Télécharger la présentation

Applications of CGAL in the Gel Analysis Software CAROL

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

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

  2. 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

  3. Outline of the talk Application Background (Electrophoresis) Gel Matching with CAROL: . The Algorithmic Approach Using CGAL in CAROL Experience, Problems, and Further Perspectives

  4. 2D 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

  5. 2D 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

  6. 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

  7. 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

  8. 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)

  9. Incremental 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!

  10. Scoring 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

  11. Global 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

  12. CGAL Components in CAROL Geometric primitives from the CGAL kernel: CGAL_Point_2 CGAL_Bbox_2 CGAL_squared _distance

  13. CGAL Components in CAROL The Delaunay Triangulation from the CGAL basic library Delaunay Traits Vertex Circulators

  14. Delaunay Traits class CAROL_Point : CGAL_Point_2 { private: double intensity; .................. } Defining special Traits classes triangulation vertices can be represented by CAROL_Points

  15. Vertex Circulators Vertex circulators are used to get a list of the neighbors of an inserted vetex Vertex circulators are used to construct flip edges

  16. The 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++ )

  17. CGAL with Visual C++ PDQUEST Interface CAROL library with CGAL components

  18. CGAL with Visual C++ PDQUEST virtual c++ stl Interface_1 Points Interface_2 CAROL library with CGAL components stl_port

  19. The End http://gelmatching.inf.fu-berlin.de

More Related