Field Detail

• debugBeads

  public static final boolean debugBeads

  See Also:

  Constant Field Values

• viewStructure

  public ViewStructure viewStructure

• benchmark

  public SegmentationBenchmark benchmark

• subpixel

  public static boolean subpixel

Constructor Detail

• BeadSegmentation

  public BeadSegmentation(ViewStructure viewStructure)

Method Detail

• segment

  public void segment()

• segment

  public void segment(SPIMConfiguration conf,
                      ArrayList<ViewDataBeads> views)

• reLocalizeTrueCorrespondences

  public int reLocalizeTrueCorrespondences(boolean run)

• gaussFit

  public static void gaussFit(Image<FloatType> image,
                              ArrayList<Bead> beadList,
                              double[] typicalSigma)

• getFoundBeads

  public Image<FloatType> getFoundBeads(ViewDataBeads view)

• extractBeadsDOM

  protected BeadStructure extractBeadsDOM(ViewDataBeads view,
                                          SPIMConfiguration conf)

  Computes potential beads based on the difference-of-mean (DOM). The computation of the DOM is based on integral images for high performance

  Parameters:

  view -

  conf -

  Returns:

• extractBeadsLaPlaceImgLib

  protected BeadStructure extractBeadsLaPlaceImgLib(ViewDataBeads view,
                                                    SPIMConfiguration conf)

• extractBeadsThresholdSegmentation

  protected BeadStructure extractBeadsThresholdSegmentation(ViewDataBeads view,
                                                            float thresholdI,
                                                            int minSize,
                                                            int maxSize,
                                                            int minBlackBorder)

• getNeighboringLabels

  protected ArrayList<Integer> getNeighboringLabels(Image<IntType> connectedComponents,
                                                    ArrayList<Point3i> neighbors,
                                                    int x,
                                                    int y,
                                                    int z)

• getVisitedNeighbors

  protected ArrayList<Point3i> getVisitedNeighbors()