J. Cardinale, G. Paul, and I. F. Sbalzarini. Discrete region competition for unknown numbers of connected regions. IEEE Trans. Image Process., 21(8):35313545, 2012. (PDF)
Inputs 
Outputs 
Image source  Label output image 
Energy function  Intensity normalized image 
Energy function parameters  Animated iteration sequence 
Label image source (optional) 
Select an imagePress OpenImage button and choose the file, or drag and drop the file inside the rectangle. if the file is is already opened in ImageJ, choose it from the input selector. 
Select paramentersPress Parameters button in the main window, you can tune global parameters like the maxium number of iteration and the oscillation threshold that control the convergence of the algorithm. You can also tune global parameters related to the energy, like Lambda and Theta that we will explain below.Lambda E length: Lambda E length: Is a scaling factor for the Energy length, this term in general is sensitive to the shape of the region Theta E merge: Is a factor needed for the merging energy function, this term implements model that controls the merging of two regions Max Iteration: Is the maximum number of iteration Oscillation Threadshold: This parameter controls the convergence of the algorithm in this way, at each iteration the global energy is stored, the standard deviation is calculated along all history and starting from the last 10 iterations. Each time the event in fig A occurs the number of fixed particles needed to converge is reduced by a factor two 
PCNo Additional options are available 

PSRadius: Radius of the sphere where the mean of the intensity is calculated Beta Balloon force: Beta controls the strenght of the Balloon force 

DeconvolutionOpen PSF Image: Open an image and use it as Point Spread Function Generate:Generate a gaussian PSF Image, before starting the simulation 
From a practical point of view, this energy locally reduces concavity, tips , and globally the length of the countor region. The image show what happen when the segmentation is driven only by the Sphere Regularization energy term 
Sphere RegularizationRadius: Radius of the hypersphere in the curvature regularization 

ApproximativeCountor length regularization, no other parameters needed 
KullbackLeiblerThis parameter is controlled in the global region competition parameters (Theta E Merge) 
BubblesCreate a grid of bubbles with a specified radius and padding 

RectangleCreate a rectangle in the center of the image, the ratio is the division of the side of the rectangle with the side of the image on each dimension 

ROIBefore the simulation start, the normalized intensity image is shown, and it ask to user to draw a starting region using the selection tools of ImageJ, when done press shift to start the simulation 

Local Maximathe initial regions are created around the local maxima of the image, and the following three steps are performed1) Sigma:The first stage is to apply a gaussian blur filter to the image with sigma variance 2) Tolerance: Find out the locals maxima according to the tollerance parameter. The maxima are accepted only if protruding more than this value from the ridge to a higher maximum. High value of tollerance means that only high local maxima will be accepted, reducing the Tolerance, increases the group of possible maxima accepted (from left to right in the image) 3) Region Tol:Filter the regions found such that: If the region is smaller that "Region Tol", creates a bubble with radius (Radius) [1], otherwise leave the region unchanged [2] 
Show progress: Show the progress of the segmentation process during computation Keep frames: Save all frames produced by the algorithm Show normalized: Show the floating point normalized image Show statistics: Show statistics of the segmentation 
PCOscillation threshold: 0.001Theta E merge: 0.01 Lambda E length: 0.2 R_k: 8 Local Max Radius : 5 Local Max Sigma : 8 Local Max Tolarance: 0.002 

PCOscillation threshold: 0.00001Theta E merge: 0.2 Lambda E length: 0.04 R_k: 8 Bubble radius: 20 Bubble padding: 20 

PSOscillation threshold: 0.02Theta E merge: 0.2 Lambda E length: 0.07 R_k: 4 Rectangle fill ratio: 0.80 

PSOscillation threshold: 0.01Theta E merge: 0.4 Lambda E length: 0.08 R_k: 4 PS Radius: 4 Beta Ballon: 0.01 Rectangle fill ratio: 0.80 

DeconvolutionOscillation threshold: 0.8Theta E merge: 0.1 Lambda E length: 0.15 R_k: 2 Local Maxima 

DeconvolutionOscillation threshold: 0.18Theta E merge: 0.2 Lambda E length: 0.07 R_k: 4 Rectangle fill ratio: 0.80 