Field Detail

• defaultBeadRegistration

  public static int defaultBeadRegistration

• defaultBeadDetectionType

  public static int defaultBeadDetectionType

• spimDataDirectory

  public static String spimDataDirectory

• timepoints

  public static String timepoints

• fileNamePattern

  public static String fileNamePattern

• angles

  public static String angles

• loadSegmentation

  public static boolean loadSegmentation

• relocalize

  public static int relocalize

• keepImagesOpen

  public static boolean keepImagesOpen

• iterativeRelocalization

  public static boolean iterativeRelocalization

• localization

  public static String[] localization

• beadBrightness

  public static String[] beadBrightness

• defaultBeadBrightness

  public static int defaultBeadBrightness

• overrideResolution

  public static boolean overrideResolution

• xyRes

  public static double xyRes

• zRes

  public static double zRes

• defaultModel

  public static int defaultModel

• loadRegistration

  public static boolean loadRegistration

• timeLapseRegistration

  public static boolean timeLapseRegistration

• defaultTimeLapseRegistration

  public static int defaultTimeLapseRegistration

• defaultTimePoint

  public static int defaultTimePoint

• fileNamePatternMC

  public static String fileNamePatternMC

• channelsBeadsMC

  public static String channelsBeadsMC

• defaultBeadBrightnessMC

  public static int[] defaultBeadBrightnessMC

Constructor Detail

• Bead_Registration

  public Bead_Registration()

Method Detail

• run

  public void run(String arg0)

  Specified by:

  run in interface ij.plugin.PlugIn

• singleChannel

  public SPIMConfiguration singleChannel(int choiceType)

• multiChannel

  public SPIMConfiguration multiChannel(int choiceType)

• getAdvancedDoGParameters

  public static double[][] getAdvancedDoGParameters(int[] channelIndices)

• getAdvancedIntegralImageParameters

  public static double[][] getAdvancedIntegralImageParameters(int[] channelIndices)

• getInteractiveDoGParameters

  public static void getInteractiveDoGParameters(String text,
                                                 double[] values)

  Can be called with values[ 3 ], i.e. [initialsigma, sigma2, threshold] or values[ 2 ], i.e. [initialsigma, threshold] The results are stored in the same array. If called with values[ 2 ], sigma2 changing will be disabled

  Parameters:

  text - - the text which is shown when asking for the file

  values - - the intial values and also contains the result

• getInteractiveIntegralParameters

  public static void getInteractiveIntegralParameters(String text,
                                                      double[] values)

  Can be called with values[ 3 ], i.e. [r1, r2, threshold] (r2 is only written as result) The results are stored in the same array.

  Parameters:

  text - - the text which is shown when asking for the file

  values - - the intial values and also contains the result

• init

  protected static boolean init(SPIMConfiguration conf)

• addHyperLinkListener

  public static final void addHyperLinkListener(MultiLineLabel text,
                                                String myURL)

• main

  public static void main(String[] args)