de.unihalle.informatik.MiToBo.apps.neurites2D

Class NeuriteDetector2D

java.lang.Object

de.unihalle.informatik.Alida.operator.ALDOperator

de.unihalle.informatik.MiToBo.core.operator.MTBOperator

de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D

All Implemented Interfaces:

de.unihalle.informatik.Alida.datatypes.ALDConfigurationValidator, de.unihalle.informatik.Alida.operator.events.ALDOperatorExecutionProgressEventListener, EventListener

@ALDAOperator(genericExecutionMode=ALL,
              level=APPLICATION,
              allowBatchMode=false)
public class NeuriteDetector2D
extends MTBOperator

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.

Author:

Danny Misiak

See Also:

NeuriteDetector2DAlgos

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	NeuriteDetector2D.NeuriteDetector2DMode Different detection modes.

Nested classes/interfaces inherited from class de.unihalle.informatik.Alida.operator.ALDOperator

de.unihalle.informatik.Alida.operator.ALDOperator.HidingMode, de.unihalle.informatik.Alida.operator.ALDOperator.HistoryConstructionMode

Field Summary

Fields

Modifier and Type	Field and Description
private double	alpha
private Vector<String>	analyzedImages Vector with all analyzed image files.
private double	beta
(package private) static de.unihalle.informatik.Alida.datatypes.ALDDirectoryString	currentInput Get initial directory from environment configuration.
private Vector<MTBNeurite2DSet>	detectedNeurites Vector of detected neurite sets for each image.
private MTBTableModel	detectionResultTable
private NeuriteDetector2D.NeuriteDetector2DMode	detectorMode
private NeuriteDetector2DAlgos.DetectorExternalEnergy	energy
private Vector<String>	imageFiles Vector with all image files included in the experiment folder for detection.
private de.unihalle.informatik.Alida.datatypes.ALDDirectoryString	inputDir Define detector parameters.
private int	maxFragmentDistance
private int	maxIterations
private int	maxSpineLength
private double	motionFraction
protected Color	neuriteColor
private int	neuriteMaskSize
private Integer[]	neuronChannels
private double	niblackConstant
private Integer	nucleiChannel
private Double	nucleusRatio
private Integer	nucleusSize
private String	outputDir Directory of output results.
private org.rosuda.JRI.Rengine	rEngine JRI R engine to run R as a single thread.
private int	resampleConstant
private double	stepSize

Fields inherited from class de.unihalle.informatik.Alida.operator.ALDOperator

completeDAG, name, operatorExecutionEventlistenerList, portHashAccess, verbose, versionProvider

Constructor Summary

Constructors

Constructor and Description
NeuriteDetector2D() Standard constructor.
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

Modifier and Type	Method and Description
private org.rosuda.JRI.Rengine	createRengine() Method to generate a R thread inside the java application.
private void	createResultDir(String file) Create directory where all results will be stored.
double	getAlpha() Get snake length term weight alpha.
Vector<String>	getAnalyzedImages() Get vector of analyzed images.
double	getBeta() Get snake curvature term weight beta.
private String	getDate() Get current date for result dirs.
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.
private void	init() Initialization method.
private MTBTableModel	makeTable() Create the result table and include the specific table header.
protected void	operate()
private boolean	startDetectionMode() Method to start neurite detection mode with presegmentation, active contours and wavelet based neuron component detection.
void	validateCustom() Custom validation of some input parameters.

Methods inherited from class de.unihalle.informatik.MiToBo.core.operator.MTBOperator

readResolve

Methods inherited from class de.unihalle.informatik.Alida.operator.ALDOperator

addOperatorExecutionProgressEventListener, addParameter, addParameter, addParameterUnconditioned, fieldContained, fireOperatorExecutionProgressEvent, getALDPortHashAccessKey, getConstructionMode, getDocumentation, getHidingMode, getInactiveParameterNames, getInInoutNames, getInInoutNames, getInNames, getInOutNames, getMissingRequiredInputs, getName, getNumParameters, getOutInoutNames, getOutNames, getParameter, getParameterDescriptor, getParameterDescriptorUnconditioned, getParameterNames, getParameterUnconditioned, getSupplementalNames, getVerbose, getVersion, handleOperatorExecutionProgressEvent, hasInOutParameters, hasParameter, isAnnotatedParameter, isConfigured, print, print, print, printInterface, printInterface, readHistory, reinitializeParameterDescriptors, removeOperatorExecutionProgressEventListener, removeParameter, runOp, runOp, runOp, setConstructionMode, setConstructionMode, setConstructionMode, setHidingMode, setName, setParameter, setParameterUnconditioned, setVerbose, toStringVerbose, unconfiguredItems, validate, validateGeneric, writeHistory, writeHistory, writeHistory

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

currentInput

static de.unihalle.informatik.Alida.datatypes.ALDDirectoryString currentInput

Get initial directory from environment configuration.

inputDir

@Parameter(label="Input Directory",
           direction=IN,
           required=true,
           description="Directory of input images.",
           mode=STANDARD,
           dataIOOrder=0)
private de.unihalle.informatik.Alida.datatypes.ALDDirectoryString inputDir

Define detector parameters.

nucleiChannel

@Parameter(label="Nuclei Channel",
           direction=IN,
           required=true,
           description="Image channel including nuclei (1 labels first channel).",
           mode=STANDARD,
           dataIOOrder=1)
private Integer nucleiChannel

nucleusSize

@Parameter(label="Nucleus Size",
           direction=IN,
           required=true,
           description="Minimum size of nuclei regions in pixel.",
           mode=ADVANCED,
           dataIOOrder=2)
private Integer nucleusSize

nucleusRatio

@Parameter(label="Nucleus Ratio",
           direction=IN,
           required=true,
           description="Ratio of nucleus pixels which should be included in an intact neuron region in percent.",
           mode=ADVANCED,
           dataIOOrder=3)
private Double nucleusRatio

neuronChannels

@Parameter(label="Neuron Channels",
           direction=IN,
           required=true,
           description="Channels which stain the neurons for detection.",
           mode=STANDARD,
           dataIOOrder=4)
private Integer[] neuronChannels

maxSpineLength

@Parameter(label="Maximum Spine Length",
           required=true,
           direction=IN,
           description="Maximum length of a spine in pixel.",
           mode=STANDARD,
           dataIOOrder=5)
private int maxSpineLength

neuriteMaskSize

@Parameter(label="Neurite Mask Size",
           required=true,
           direction=IN,
           description="Neurite mask size in pixel.",
           mode=ADVANCED,
           dataIOOrder=6)
private int neuriteMaskSize

maxFragmentDistance

@Parameter(label="Maximum Fragment Distance",
           required=true,
           direction=IN,
           description="Maximum distance of neuron frgaments in pixel.",
           mode=ADVANCED,
           dataIOOrder=7)
private int maxFragmentDistance

niblackConstant

@Parameter(label="Niblack Constant",
           required=true,
           direction=IN,
           description="Niblack threshold constant.",
           mode=ADVANCED,
           dataIOOrder=8)
private double niblackConstant

detectorMode

@Parameter(label="Detector Mode",
           required=true,
           direction=IN,
           description="Mode of neurite detector.",
           mode=ADVANCED,
           dataIOOrder=9)
private NeuriteDetector2D.NeuriteDetector2DMode detectorMode

energy

@Parameter(label="External Energy",
           direction=IN,
           required=true,
           description="External energy label for detection.",
           mode=ADVANCED,
           dataIOOrder=10)
private NeuriteDetector2DAlgos.DetectorExternalEnergy energy

alpha

@Parameter(label="Alpha",
           required=true,
           direction=IN,
           description="Weighting factor for snake length term.",
           mode=ADVANCED,
           dataIOOrder=11)
private double alpha

beta

@Parameter(label="Beta",
           required=true,
           direction=IN,
           description="Weighting factor for snake curvature term.",
           mode=ADVANCED,
           dataIOOrder=12)
private double beta

stepSize

@Parameter(label="Step Size",
           required=true,
           direction=IN,
           description="Step size of snake movement.",
           mode=ADVANCED,
           dataIOOrder=13)
private double stepSize

resampleConstant

@Parameter(label="Resample Constant",
           required=true,
           direction=IN,
           description="Snake point resampling constant.",
           mode=ADVANCED,
           dataIOOrder=14)
private int resampleConstant

motionFraction

@Parameter(label="Motion Fraction",
           required=true,
           direction=IN,
           description="Fraction of minimum point motion to stop detection in percent.",
           mode=ADVANCED,
           dataIOOrder=15)
private double motionFraction

maxIterations

@Parameter(label="Maximum Iterations",
           required=true,
           direction=IN,
           description="Maximum iteration count to stop optimization.",
           mode=ADVANCED,
           dataIOOrder=16)
private int maxIterations

neuriteColor

@Parameter(label="Neurite Color",
           supplemental=true,
           direction=IN,
           description="Color of neurite regions in result image.")
protected Color neuriteColor

detectionResultTable

@Parameter(label="Detection Result Table",
           direction=OUT,
           required=true,
           description="Table of detection results.")
private transient MTBTableModel detectionResultTable

imageFiles

private transient Vector<String> imageFiles

Vector with all image files included in the experiment folder for detection.

analyzedImages

private transient Vector<String> analyzedImages

Vector with all analyzed image files.

outputDir

private transient String outputDir

Directory of output results.

detectedNeurites

private transient Vector<MTBNeurite2DSet> detectedNeurites

Vector of detected neurite sets for each image.

rEngine

private transient org.rosuda.JRI.Rengine rEngine

JRI R engine to run R as a single thread.

Constructor Detail

NeuriteDetector2D

public NeuriteDetector2D()
                  throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Standard constructor.

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

NeuriteDetector2D

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

Constructor

Parameters:

_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

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Method Detail

validateCustom

public void validateCustom()
                    throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Custom validation of some input parameters.

Overrides:

validateCustom in class de.unihalle.informatik.Alida.operator.ALDOperator

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

getInputDir

public de.unihalle.informatik.Alida.datatypes.ALDDirectoryString getInputDir()

Get directory of input images.

getNucleiChannel

public Integer getNucleiChannel()

Get image channel of 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 Integer[] getNeuronChannles()

Get neuron channels, used for detection.

getMaxSpineLength

public int getMaxSpineLength()

Get maximum length of a spine (filopodia-like protrusion) in pixel.

getNeuriteMaskSize

public int getNeuriteMaskSize()

Get neurite mask size in pixel. This value defines the maximum average width of a neurite.

getMaxFragmentDistance

public int getMaxFragmentDistance()

Get maximum neuron fragment distance in pixel.

getNiblackConstant

public double getNiblackConstant()

Get niblack constant.

getDetectorMode

public NeuriteDetector2D.NeuriteDetector2DMode getDetectorMode()

Get current detector mode.

getEnergy

public NeuriteDetector2DAlgos.DetectorExternalEnergy getEnergy()

Get external snake energy label.

getAlpha

public double getAlpha()

Get snake length term weight alpha.

getBeta

public double getBeta()

Get snake curvature term weight beta.

getStepSize

public double getStepSize()

Get step size of snake movement.

getResampleConstant

public int getResampleConstant()

Get snake point resampling constant.

getMotionFraction

public double getMotionFraction()

Get minimum fraction of point motion to stop detection.

getMaxIterations

public int getMaxIterations()

Get maximum number of iterations to stop detection.

getNeuriteColor

public Color getNeuriteColor()

Get neurite region color (RGB) for result image.

getDetectedNeurites

public Vector<MTBNeurite2DSet> getDetectedNeurites()

Get vector of detected neurite sets for each image.

Returns:

Vector of neurite sets.

getResultTable

public MTBTableModel getResultTable()

Get the result table of the detected neurites.

Returns:

Result table.

getImageFiles

public Vector<String> getImageFiles()

Get vector of all image files included in the experiment folder for detection.

Returns:

Input images.

getAnalyzedImages

public Vector<String> getAnalyzedImages()

Get vector of analyzed images.

Returns:

Analyzed images.

getREngine

public org.rosuda.JRI.Rengine getREngine()

Get JRI R engine to run R as a single thread.

getOutputDir

public String getOutputDir()

Get directory of output results.

init

private void init()

Initialization method.

operate

protected void operate()
                throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                       de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

Specified by:

operate in class de.unihalle.informatik.Alida.operator.ALDOperator

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

startDetectionMode

private boolean startDetectionMode()

Method to start neurite detection mode with presegmentation, active contours and wavelet based neuron component detection.

createResultDir

private void createResultDir(String file)

Create directory where all results will be stored. The directory is created in the directory where the image files are stored.

Parameters:

file - name of the current experiment (directory name where input images are stored)

getDate

private String getDate()

Get current date for result dirs.

Returns:

Current date.

createRengine

private org.rosuda.JRI.Rengine createRengine()

Method to generate a R thread inside the java application.

Returns:

Generated R engine.

makeTable

private MTBTableModel makeTable()

Create the result table and include the specific table header.