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java.lang.Objectde.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
public class NeuriteDetector2DAlgos
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.
NeuriteExtractor2D
Nested Class Summary | |
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static class |
NeuriteDetector2DAlgos.DetectorExternalEnergy
Label for different external energies of the snake which can be used by the detector. |
Constructor Summary | |
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NeuriteDetector2DAlgos()
Standard constructor. |
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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 | |
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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. |
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. |
int[] |
getSnakeIterCount()
Get number snake iteration counts, used for optimization. |
double |
getStepSize()
Get step size of snake point movement. |
void |
neuriteDetection(MTBContour2DSet initContourSet)
Main method for 2D neurite detection. |
MTBContour2DSet |
preSegmentation()
Method for pre-segmentation. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public 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)
_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 fileresultDir
- 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 threadMethod Detail |
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public double getAlpha()
public double getBeta()
public int[] getSnakeIterCount()
public MTBImage getInputImage()
public int getNucleiChannel()
public int getNucleusSize()
public double getNucleusRatio()
public int[] getNeuronChannles()
public double getNiblackConstant()
public int getMaxFragmentDistance()
public NeuriteDetector2DAlgos.DetectorExternalEnergy getEnergyLabel()
public double getStepSize()
public double getMotionFraction()
public int getMaxIterations()
public int getResampleConstant()
public int getMaxSpineLength()
public int getNeuriteMaskSize()
public Color getNeuriteColor()
public String getResultDir()
public MTBTableModel getResultTable()
public MTBNeurite2DSet getDetectedNeuritesSet()
public void neuriteDetection(MTBContour2DSet initContourSet) throws NeuriteDetector2DException
initContourSet
- set of initial contours for snakes
NeuriteDetector2DException
public MTBContour2DSet preSegmentation() throws NeuriteDetector2DException
NeuriteDetector2DException
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