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java.lang.Objectde.unihalle.informatik.Alida.operator.ALDOperator
de.unihalle.informatik.MiToBo.core.operator.MTBOperator
de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
@ALDAOperator(genericExecutionMode=ALL, level=APPLICATION, allowBatchMode=false) public class NeuriteDetector2D
The Neurite Detector 2D application offers advanced functionality to detect neurites in 2D fluorescence microscope images of neurons. Neuron boundaries are coarsely detected and refined, using active contour models (snakes). Structural neuron parts, like soma, neurites and growth cones are identified, using an wavelet based detection. Morphology analysis of the detected neurites is performed and an collection of all measurements is visualized in the result table. Intermediate and final results are automatically saved and the results are stored in a result image and presented in a final result table. The specific algorithms can be found in the `NeuriteDetector2DAlgos` class.
NeuriteDetector2DAlgos
Nested Class Summary | |
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static class |
NeuriteDetector2D.NeuriteDetector2DMode
Different detection modes. |
Nested classes/interfaces inherited from class de.unihalle.informatik.Alida.operator.ALDOperator |
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de.unihalle.informatik.Alida.operator.ALDOperator.HidingMode |
Field Summary | |
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protected Color |
neuriteColor
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Fields inherited from class de.unihalle.informatik.Alida.operator.ALDOperator |
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completeDAG, name, operatorExecutionEventlistenerList, portHashAccess, verbose, versionProvider |
Constructor Summary | |
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NeuriteDetector2D()
Standard constructor. |
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NeuriteDetector2D(String _inputDir,
Integer _nucleiChannel,
int _nucleusSize,
double _nucleusRation,
Integer[] _neuronChannels,
double _niblackConstant,
int _maxFragmentDistance,
NeuriteDetector2D.NeuriteDetector2DMode _detectorMode,
NeuriteDetector2DAlgos.DetectorExternalEnergy _energy,
double _alpha,
double _beta,
double _stepSize,
double _motionFraction,
int _maxIterations,
int _resampleConstant,
int _maxSpineLength,
int _neuriteMaskSize,
Color _neuriteColor,
Boolean _verbose)
Constructor |
Method Summary | |
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double |
getAlpha()
Get snake length term weight alpha. |
Vector<String> |
getAnalyzedImages()
Get vector of analyzed images. |
double |
getBeta()
Get snake curvature term weight beta. |
Vector<MTBNeurite2DSet> |
getDetectedNeurites()
Get vector of detected neurite sets for each image. |
NeuriteDetector2D.NeuriteDetector2DMode |
getDetectorMode()
Get current detector mode. |
NeuriteDetector2DAlgos.DetectorExternalEnergy |
getEnergy()
Get external snake energy label. |
Vector<String> |
getImageFiles()
Get vector of all image files included in the experiment folder for detection. |
de.unihalle.informatik.Alida.datatypes.ALDDirectoryString |
getInputDir()
Get directory of input images. |
int |
getMaxFragmentDistance()
Get maximum neuron fragment distance in pixel. |
int |
getMaxIterations()
Get maximum number of iterations to stop detection. |
int |
getMaxSpineLength()
Get maximum length of a spine (filopodia-like protrusion) in pixel. |
double |
getMotionFraction()
Get minimum fraction of point motion to stop detection. |
Color |
getNeuriteColor()
Get neurite region color (RGB) for result image. |
int |
getNeuriteMaskSize()
Get neurite mask size in pixel. |
Integer[] |
getNeuronChannles()
Get neuron channels, used for detection. |
double |
getNiblackConstant()
Get niblack constant. |
Integer |
getNucleiChannel()
Get image channel of 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 |
String |
getOutputDir()
Get directory of output results. |
org.rosuda.JRI.Rengine |
getREngine()
Get JRI R engine to run R as a single thread. |
int |
getResampleConstant()
Get snake point resampling constant. |
MTBTableModel |
getResultTable()
Get the result table of the detected neurites. |
double |
getStepSize()
Get step size of snake movement. |
protected void |
operate()
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void |
validateCustom()
Custom validation of some input parameters. |
Methods inherited from class de.unihalle.informatik.MiToBo.core.operator.MTBOperator |
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readResolve |
Methods inherited from class de.unihalle.informatik.Alida.operator.ALDOperator |
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addOperatorExecutionProgressEventListener, fieldContained, fireOperatorExecutionProgressEvent, getALDPortHashAccessKey, getConstructionMode, getHidingMode, getInInoutNames, getInInoutNames, getInNames, getInOutNames, getMissingRequiredInputs, getName, getNumParameters, getOutInoutNames, getOutNames, getParameter, getParameterDescriptor, getParameterNames, getSupplementalNames, getVerbose, getVersion, handleOperatorExecutionProgressEvent, isConfigured, print, print, print, printInterface, printInterface, readHistory, reinitializeParameterDescriptors, removeOperatorExecutionProgressEventListener, runOp, runOp, runOp, setConstructionMode, setHidingMode, setName, setParameter, setVerbose, toStringVerbose, unconfiguredItems, validate, validateGeneric, writeHistory, writeHistory, writeHistory |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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@Parameter(label="Neurite Color", supplemental=true, direction=IN, description="Color of neurite regions in result image.") protected Color neuriteColor
Constructor Detail |
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public NeuriteDetector2D() throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
public NeuriteDetector2D(String _inputDir, Integer _nucleiChannel, int _nucleusSize, double _nucleusRation, Integer[] _neuronChannels, double _niblackConstant, int _maxFragmentDistance, NeuriteDetector2D.NeuriteDetector2DMode _detectorMode, NeuriteDetector2DAlgos.DetectorExternalEnergy _energy, double _alpha, double _beta, double _stepSize, double _motionFraction, int _maxIterations, int _resampleConstant, int _maxSpineLength, int _neuriteMaskSize, Color _neuriteColor, Boolean _verbose) throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException
_inputDir
- input directory with multichannel fluorescence images_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_detectorMode
- mode of neurite detection_energy
- 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_verbose
- flag for standard console outputs
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
Method Detail |
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public void validateCustom() throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException
validateCustom
in class de.unihalle.informatik.Alida.operator.ALDOperator
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
public de.unihalle.informatik.Alida.datatypes.ALDDirectoryString getInputDir()
public Integer getNucleiChannel()
public int getNucleusSize()
public double getNucleusRatio()
public Integer[] getNeuronChannles()
public int getMaxSpineLength()
public int getNeuriteMaskSize()
public int getMaxFragmentDistance()
public double getNiblackConstant()
public NeuriteDetector2D.NeuriteDetector2DMode getDetectorMode()
public NeuriteDetector2DAlgos.DetectorExternalEnergy getEnergy()
public double getAlpha()
public double getBeta()
public double getStepSize()
public int getResampleConstant()
public double getMotionFraction()
public int getMaxIterations()
public Color getNeuriteColor()
public Vector<MTBNeurite2DSet> getDetectedNeurites()
public MTBTableModel getResultTable()
public Vector<String> getImageFiles()
public Vector<String> getAnalyzedImages()
public org.rosuda.JRI.Rengine getREngine()
public String getOutputDir()
protected void operate() throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException, de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException
operate
in class de.unihalle.informatik.Alida.operator.ALDOperator
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException
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