NeuriteDetector2DAlgos (mitobo 2.0 API)

java.lang.Object
- de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos

public class NeuriteDetector2DAlgos
extends Object

 
 The class implements the basic algorithm for neurite detection based on a
 2D multichannel fluorescence image.
 
 The basic steps are:
  1. pre-segmentation step to get a coarse contour of the neurons, yielding a
     initialization for the active contour models (snake)
  2. refinement of the initial contours by the active contour models
  3. identification of structural neuron parts, like soma, neurites and
     growth cones via a wavelet based detection
  
 A lot of intermediate results are save to the special result directories.
 After detection of the neurites a result table with all measured morphology
 values is shown. An result image showing the detected neurites with their
 neurite traces and special points is saved to the output directory.

Author:: Danny Misiak
See Also:: NeuriteExtractor2D

Nested Class Summary

Nested Classes
Modifier and Type	Class and Description
`static class`	`NeuriteDetector2DAlgos.DetectorExternalEnergy` Label for different external energies of the snake which can be used by the detector.

Field Summary

Fields
Modifier and Type	Field and Description
`private double`	`alpha` Weighting factor for snake length term.
`private double`	`beta` Weighting factor for snake curvature term.
`private MTBNeurite2DSet`	`detectedNeuritesSet` Final set of detected neurites.
`private NeuriteDetector2DAlgos.DetectorExternalEnergy`	`energyLabel` Label of available external snake energies, which are usable by the detector.
`private String`	`file_name_noExtension` Current image name without file extension.
`private String`	`fileName` File name of the current multichannel fluorescence image.
`private int`	`height` Image size in y-direction, given in pixel.
`private MTBImage`	`inputImage` Multichannel fluorescence image of the labeled neuron.
`private int`	`maxFragmentDistance` Maximum distance to connect a fragment to a detected neuron, given in pixel.
`private int`	`maxIterations` Number of snake iterations.
`private int`	`maxSpineLength` Maximum length to define a branch of a neurite as spine (filopodia-like protrusion) in pixel.
`private double`	`motionFraction` Minimum fraction of points which should have stooped to move until the snake optimization stops.
`private Color`	`neuriteColor` Region color of detected neurites to view the neurites in the result image.
`private int`	`neuriteMaskSize` Mask size of average neurite with in pixel.
`private int[]`	`neuronChannels` Channel numbers, including the neuron stains for detection of the neurons in the current multichannel fluorescence image.
`private MTBImage`	`neuronMIP` Maximum intensity projection (MIP) image of the neuron.
`private double`	`niblackConstant` Application based constant for Niblack thresholding.
`private int`	`nucleiChannel` Channel number, including the nuclei, in the current multichannel fluorescence image.
`private MTBImage`	`nucleus` Fluorescence labeled nuclei image from the multichannel microscope image.
`private double`	`nucleusRatio` Ratio of nucleus pixels which should be included in a intact neuron region to specify the neuron region as active and use for detection.
`private int`	`nucleusSize` Minimum size of nucleus region to set region as intact nucleus.
`private org.rosuda.JRI.Rengine`	`rEngine` R engine to start R thread.
`private int`	`resampleConstant` Constant for resampling the snake control points.
`private String`	`result_energy` Result directory for snake energy results.
`private String`	`result_extraction` Result directory for neurite extraction results.
`private String`	`result_presegmentation` Result directory for pre-segmentation.
`private String`	`result_snakes` Result directory for snake results.
`private String`	`resultDir` Main directory for result output.
`private MTBTableModel`	`resultTable` Result table showing the the detection and morphology measurements.
`private int[]`	`snakeIterCount` Number of snake iterations used in current optimization process.
`private double`	`stepSize` Step size value for a snake step (gamma) during optimization.
`private Boolean`	`verbose` Verbose flag for standard console outputs.
`private int`	`width` Image size in x-direction, given in pixel.

Constructor Summary

Constructors
Constructor and Description
`NeuriteDetector2DAlgos()` Standard constructor.
NeuriteDetector2DAlgos(MTBImage _inputImage, int _nucleiChannel, int _nucleusSize, double _nucleusRation, int[] _neuronChannels, double _niblackConstant, int _maxFragmentDistance, String _pathToFile, String _resultDir, NeuriteDetector2DAlgos.DetectorExternalEnergy _energyLabel, double _alpha, double _beta, double _stepSize, double _motionFraction, int _maxIterations, int _resampleConstant, int _maxSpineLength, int _neuriteMaskSize, Color _neuriteColor, MTBTableModel _table, Boolean _verbose, org.rosuda.JRI.Rengine _re) Constructor.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`double`	`getAlpha()` Get weighting factor for snake length term.
`double`	`getBeta()` Get weighting factor for snake curvature term.
`MTBNeurite2DSet`	`getDetectedNeuritesSet()` Get set of detected neurites.
`NeuriteDetector2DAlgos.DetectorExternalEnergy`	`getEnergyLabel()` Get energy label for external energy, used for optimization.
`private MTBImage`	`getExtEnergyInit()` Calculate the initial image for the external energy of the snake.
`MTBImage`	`getInputImage()` Get multichannel fluorescence input image.
`int`	`getMaxFragmentDistance()` Get maximum fragment distance , in pixel.
`int`	`getMaxIterations()` Get maximum number of iterations to finish snake optimization,
`int`	`getMaxSpineLength()` Get maximum length of a spine, in pixel.
`double`	`getMotionFraction()` Get minimum motion fraction of snake control points, to finish snake optimization.
`Color`	`getNeuriteColor()` Get neurite region color (RGB) for result image.
`int`	`getNeuriteMaskSize()` Get maximum neurite mask size, in pixel.
`int[]`	`getNeuronChannles()` Get neuron channels, used for detection.
`double`	`getNiblackConstant()` Get Niblack thresholding constant.
`int`	`getNucleiChannel()` Get channel number, including the labeled nuclei.
`double`	`getNucleusRatio()` Get ratio of nucleus pixels which should be included in an intact neuron region
`int`	`getNucleusSize()` Get minimum nucleus size of nuclei regions
`int`	`getResampleConstant()` Get constant for snake point resampling.
`String`	`getResultDir()` Get directory of intermediate and final results.
`MTBTableModel`	`getResultTable()` Get final result table of morphology measurements.
`private Vector<MTBSnakePoint2D>`	`getSnakeControlPoints(MTBContour2D initContour)` Method to get each 7th point of the initial contour as snake control point.
`int[]`	`getSnakeIterCount()` Get number snake iteration counts, used for optimization.
`private MTBRegion2DSet`	`getSnakeRegion(MTBPolygon2DSet theSnakes)` Get the region which is included in the snake contour.
`double`	`getStepSize()` Get step size of snake point movement.
`private void`	`init()` Initialize detector.
`void`	`neuriteDetection(MTBContour2DSet initContourSet)` Main method for 2D neurite detection.
`private MTBPolygon2DSet`	`optimizeSnakes(MTBPolygon2DSet initSnakeSet)` Optimization of the snakes (main snake and inner snakes) with its specified parameters and energies.
`MTBContour2DSet`	`preSegmentation()` Method for pre-segmentation.
`private void`	`setResultDirs()` Create all output directories for the single detection steps.
`private boolean`	`testRegions(MTBRegion2D cell, MTBRegion2D core)` Test whether the number of pixels from a neuron region contains more than 90% of the pixels from a nucleus region.
`private boolean`	`testRegions2(MTBRegion2D cell, MTBRegion2D core)` Test whether a single pixel from a neuron region contains a pixel from a nucleus region.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - width
```
private int width
```
    Image size in x-direction, given in pixel.
  - height
```
private int height
```
    Image size in y-direction, given in pixel.
  - neuronMIP
```
private MTBImage neuronMIP
```
    Maximum intensity projection (MIP) image of the neuron. This image gives the basis for the automatic detection.
  - nucleus
```
private MTBImage nucleus
```
    Fluorescence labeled nuclei image from the multichannel microscope image.
  - snakeIterCount
```
private int[] snakeIterCount
```
    Number of snake iterations used in current optimization process.
  - detectedNeuritesSet
```
private MTBNeurite2DSet detectedNeuritesSet
```
    Final set of detected neurites.
  - result_presegmentation
```
private String result_presegmentation
```
    Result directory for pre-segmentation.
  - result_snakes
```
private String result_snakes
```
    Result directory for snake results.
  - result_extraction
```
private String result_extraction
```
    Result directory for neurite extraction results.
  - result_energy
```
private String result_energy
```
    Result directory for snake energy results.
  - file_name_noExtension
```
private String file_name_noExtension
```
    Current image name without file extension.
  - inputImage
```
private MTBImage inputImage
```
    Multichannel fluorescence image of the labeled neuron.
  - nucleiChannel
```
private int nucleiChannel
```
    Channel number, including the nuclei, in the current multichannel fluorescence image.
  - nucleusSize
```
private int nucleusSize
```
    Minimum size of nucleus region to set region as intact nucleus.
  - nucleusRatio
```
private double nucleusRatio
```
    Ratio of nucleus pixels which should be included in a intact neuron region to specify the neuron region as active and use for detection.
  - neuronChannels
```
private int[] neuronChannels
```
    Channel numbers, including the neuron stains for detection of the neurons in the current multichannel fluorescence image.
  - niblackConstant
```
private double niblackConstant
```
    Application based constant for Niblack thresholding.
  - maxFragmentDistance
```
private int maxFragmentDistance
```
    Maximum distance to connect a fragment to a detected neuron, given in pixel.
  - fileName
```
private String fileName
```
    File name of the current multichannel fluorescence image.
  - resultDir
```
private String resultDir
```
    Main directory for result output.
  - energyLabel
```
private NeuriteDetector2DAlgos.DetectorExternalEnergy energyLabel
```
    Label of available external snake energies, which are usable by the detector.
  - alpha
```
private double alpha
```
    Weighting factor for snake length term.
  - beta
```
private double beta
```
    Weighting factor for snake curvature term.
  - stepSize
```
private double stepSize
```
    Step size value for a snake step (gamma) during optimization.
  - motionFraction
```
private double motionFraction
```
    Minimum fraction of points which should have stooped to move until the snake optimization stops.
  - maxIterations
```
private int maxIterations
```
    Number of snake iterations.
  - resampleConstant
```
private int resampleConstant
```
    Constant for resampling the snake control points.
  - maxSpineLength
```
private int maxSpineLength
```
    Maximum length to define a branch of a neurite as spine (filopodia-like protrusion) in pixel.
  - neuriteMaskSize
```
private int neuriteMaskSize
```
    Mask size of average neurite with in pixel. This mask size is used for the morphological opening to remove neurites from the soma in the neurite extraction step.
  - neuriteColor
```
private Color neuriteColor
```
    Region color of detected neurites to view the neurites in the result image.
  - resultTable
```
private MTBTableModel resultTable
```
    Result table showing the the detection and morphology measurements.
  - verbose
```
private Boolean verbose
```
    Verbose flag for standard console outputs.
  - rEngine
```
private org.rosuda.JRI.Rengine rEngine
```
    R engine to start R thread.
- Constructor Detail
  - NeuriteDetector2DAlgos
```
public NeuriteDetector2DAlgos()
```
    Standard constructor.
  - NeuriteDetector2DAlgos
```
public NeuriteDetector2DAlgos(MTBImage _inputImage,
                              int _nucleiChannel,
                              int _nucleusSize,
                              double _nucleusRation,
                              int[] _neuronChannels,
                              double _niblackConstant,
                              int _maxFragmentDistance,
                              String _pathToFile,
                              String _resultDir,
                              NeuriteDetector2DAlgos.DetectorExternalEnergy _energyLabel,
                              double _alpha,
                              double _beta,
                              double _stepSize,
                              double _motionFraction,
                              int _maxIterations,
                              int _resampleConstant,
                              int _maxSpineLength,
                              int _neuriteMaskSize,
                              Color _neuriteColor,
                              MTBTableModel _table,
                              Boolean _verbose,
                              org.rosuda.JRI.Rengine _re)
```
    Constructor.
    
    Parameters:
    
    _inputImage - multichannel fluorescence image
    
    _nucleiChannel - channel number including nuclei image
    
    _nucleusSize - minimum size of nucleus region
    
    _nucleusRation - ratio of nucleus pixels which should be included in an intact neuron region
    
    _neuronChannels - channel numbers including neuron stains for detection
    
    _niblackConstant - constant for niblack thresholding
    
    _maxFragmentDistance - maximum distance to connect a fragment to the neuron, in pixel
    
    _pathToFile - path to current image file
    
    resultDir - directory of output results
    
    _energyLabel - label of available external energies for detection using snakes
    
    _alpha - weighting factor for snake length term
    
    _beta - weighting factor for snake curvature term
    
    _stepSize - step size gamma to move snake in a optimization step
    
    _motionFraction - minimum fraction of not moving points to stop optimization
    
    _maxIterations - maximum iteration to stop optimization
    
    _resampleConstant - constant for resampling snake control points
    
    _maxSpineLength - maximum length of a branch to define it as spine, in pixel
    
    _neuriteMaskSize - mask size of average neurite width, in pixel
    
    _neuriteColor - color for neurite regions in result image
    
    _table - result table
    
    _verbose - flag for standard console outputs
    
    _re - R engine to call R scripts from a Java thread
- Method Detail
  - getAlpha
```
public double getAlpha()
```
    Get weighting factor for snake length term.
  - getBeta
```
public double getBeta()
```
    Get weighting factor for snake curvature term.
  - getSnakeIterCount
```
public int[] getSnakeIterCount()
```
    Get number snake iteration counts, used for optimization.
  - getInputImage
```
public MTBImage getInputImage()
```
    Get multichannel fluorescence input image.
  - getNucleiChannel
```
public int getNucleiChannel()
```
    Get channel number, including the labeled nuclei.
  - getNucleusSize
```
public int getNucleusSize()
```
    Get minimum nucleus size of nuclei regions
  - getNucleusRatio
```
public double getNucleusRatio()
```
    Get ratio of nucleus pixels which should be included in an intact neuron region
  - getNeuronChannles
```
public int[] getNeuronChannles()
```
    Get neuron channels, used for detection.
  - getNiblackConstant
```
public double getNiblackConstant()
```
    Get Niblack thresholding constant.
  - getMaxFragmentDistance
```
public int getMaxFragmentDistance()
```
    Get maximum fragment distance , in pixel.
  - getEnergyLabel
```
public NeuriteDetector2DAlgos.DetectorExternalEnergy getEnergyLabel()
```
    Get energy label for external energy, used for optimization.
  - getStepSize
```
public double getStepSize()
```
    Get step size of snake point movement.
  - getMotionFraction
```
public double getMotionFraction()
```
    Get minimum motion fraction of snake control points, to finish snake optimization.
  - getMaxIterations
```
public int getMaxIterations()
```
    Get maximum number of iterations to finish snake optimization,
  - getResampleConstant
```
public int getResampleConstant()
```
    Get constant for snake point resampling.
  - getMaxSpineLength
```
public int getMaxSpineLength()
```
    Get maximum length of a spine, in pixel.
  - getNeuriteMaskSize
```
public int getNeuriteMaskSize()
```
    Get maximum neurite mask size, in pixel. Defines the average width of a neurite.
  - getNeuriteColor
```
public Color getNeuriteColor()
```
    Get neurite region color (RGB) for result image.
  - getResultDir
```
public String getResultDir()
```
    Get directory of intermediate and final results.
  - getResultTable
```
public MTBTableModel getResultTable()
```
    Get final result table of morphology measurements.
  - getDetectedNeuritesSet
```
public MTBNeurite2DSet getDetectedNeuritesSet()
```
    Get set of detected neurites.
  - init
```
private void init()
```
    Initialize detector.
  - setResultDirs
```
private void setResultDirs()
```
    Create all output directories for the single detection steps.
  - neuriteDetection
```
public void neuriteDetection(MTBContour2DSet initContourSet)
                      throws NeuriteDetector2DException
```
    Main method for 2D neurite detection. Using the initial contours of the pre-segmented neurons as input for the active contour models to calculate an exact contour of each neuron.
    
    Parameters:
    
    initContourSet - set of initial contours for snakes
    
    Throws:
    
    NeuriteDetector2DException
  - preSegmentation
```
public MTBContour2DSet preSegmentation()
                                throws NeuriteDetector2DException
```
    Method for pre-segmentation. Binarization, regions- and contour labeling take place. As result the rough contours of the neurons are returned to be used as initial contours for active contour models in the `neuriteDetection` method.
    
    Returns:
    
    Set of 2D neuron contours.
    
    Throws:
    
    NeuriteDetector2DException
  - getSnakeControlPoints
```
private Vector<MTBSnakePoint2D> getSnakeControlPoints(MTBContour2D initContour)
```
    Method to get each 7th point of the initial contour as snake control point.
    
    Parameters:
    
    initContour - initial contour to extract snake control points
    
    Returns:
    
    List of control points of the snake.
  - getSnakeRegion
```
private MTBRegion2DSet getSnakeRegion(MTBPolygon2DSet theSnakes)
```
    Get the region which is included in the snake contour.
    
    Parameters:
    
    snake - current snake
    
    Returns:
    
    2D region with all pixels included in the snake, including the snake points.
  - getExtEnergyInit
```
private MTBImage getExtEnergyInit()
```
    Calculate the initial image for the external energy of the snake. This image is used to generate the final external energy in the snake optimization method below.
  - optimizeSnakes
```
private MTBPolygon2DSet optimizeSnakes(MTBPolygon2DSet initSnakeSet)
```
    Optimization of the snakes (main snake and inner snakes) with its specified parameters and energies.
    
    Parameters:
    
    initSnakes - initial snakes for optimization start
    
    Returns:
    
    optimized set of snakes
  - testRegions
```
private boolean testRegions(MTBRegion2D cell,
                            MTBRegion2D core)
```
    Test whether the number of pixels from a neuron region contains more than 90% of the pixels from a nucleus region. The nucleus region must be smaller than the neuron region! If yes, the neuron region contains the nucleus region and is a potential living cell to detect a new neuron region.
    
    Parameters:
    
    cell - region of the neuron cell
    
    core - region of the nucleus
    
    Returns:
    
    True if core region is included with at least 90% of its pixel in the neuron region.
  - testRegions2
```
private boolean testRegions2(MTBRegion2D cell,
                             MTBRegion2D core)
```
    Test whether a single pixel from a neuron region contains a pixel from a nucleus region. If yes, the neuron region contains parts of the nucleus region.
    
    Parameters:
    
    cell - region of the neuron cell
    
    core - region of the nucleus
    
    Returns:
    
    Is core included in neuron region false or true.

Class NeuriteDetector2DAlgos

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

width

height

neuronMIP

nucleus

snakeIterCount

detectedNeuritesSet

result_presegmentation

result_snakes

result_extraction

result_energy

file_name_noExtension

inputImage

nucleiChannel

nucleusSize

nucleusRatio

neuronChannels

niblackConstant

maxFragmentDistance

fileName

resultDir

energyLabel

alpha

beta

stepSize

motionFraction

maxIterations

resampleConstant

maxSpineLength

neuriteMaskSize

neuriteColor

resultTable

verbose

rEngine

Constructor Detail

NeuriteDetector2DAlgos

NeuriteDetector2DAlgos

Method Detail

getAlpha

getBeta

getSnakeIterCount

getInputImage

getNucleiChannel

getNucleusSize

getNucleusRatio

getNeuronChannles

getNiblackConstant

getMaxFragmentDistance

getEnergyLabel

getStepSize

getMotionFraction

getMaxIterations

getResampleConstant

getMaxSpineLength

getNeuriteMaskSize

getNeuriteColor

getResultDir

getResultTable

getDetectedNeuritesSet

init

setResultDirs

neuriteDetection

preSegmentation

getSnakeControlPoints

getSnakeRegion

getExtEnergyInit

optimizeSnakes

testRegions

testRegions2