de.unihalle.informatik.MiToBo.apps.neurons2D
Class NeuronAnalyzer2D

java.lang.Object
  extended by de.unihalle.informatik.Alida.operator.ALDOperator
      extended by de.unihalle.informatik.MiToBo.core.operator.MTBOperator
          extended by de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2D
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 NeuronAnalyzer2D
extends MTBOperator

 
 The Neuron Analyzer 2D application offers advanced functionality to analyze
 2D fluorescence microscope images of neurons.
  
 Features:
 - neuron boundary detection based on active contours
 - identification of structural neuron parts, like soma, neurites,
   growth cones
 - morphology analysis, e.g., neurite length, average neurite width, number
   of branch and end points, growth cone size and shape roundness, ...
 - extraction of molecular profiles from the given molecules, like labeled
   proteins, along the neurites from soma to growth cones
 - detection of molecular particles, for example FISH data,
   along the neurites from soma to growth cones
 - intermediate and final results are automatically saved
 - tabular presentation of result data
 
 

Author:
Danny Misiak
See Also:
NeuriteDetector2D, NeuriteMolProfExtractor2D, NeuriteParticleDetector2D

Nested Class Summary
 
Nested classes/interfaces inherited from class de.unihalle.informatik.Alida.operator.ALDOperator
de.unihalle.informatik.Alida.operator.ALDOperator.HidingMode
 
Field Summary
protected  Boolean extractParticles
           
protected  Boolean extractProfiles
           
 
Fields inherited from class de.unihalle.informatik.Alida.operator.ALDOperator
completeDAG, name, operatorExecutionEventlistenerList, portHashAccess, verbose, versionProvider
 
Constructor Summary
NeuronAnalyzer2D()
          Standard constructor.
NeuronAnalyzer2D(NeuriteDetector2D _neuriteDetector, Boolean _extractProfiles, String[] _molecules, Integer[] _moleculeChannels, Boolean _extractParticles, NeuriteParticleDetector2D _particleDetector, Boolean _verbose)
          Constructor.
 
Method Summary
 MTBTableModel getDetectionResultTable()
          Get the result table of the detected neurites.
 Integer[] getMoleculeChannles()
          Get molecule channels, used for molecular profile extraction.
 String[] getMolecules()
          Get names of molecules for each image channel.
 NeuriteDetector2D getNeuriteDetector()
          Get current neurite detector.
protected  void operate()
           
 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, 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
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

extractProfiles

@Parameter(label="Extract Profiles",
           direction=IN,
           required=true,
           description="Flag to use molecular profile extraction.",
           mode=STANDARD,
           dataIOOrder=1)
protected Boolean extractProfiles

extractParticles

@Parameter(label="Extract Particles",
           direction=IN,
           required=true,
           description="Flag to use molecular particle extraction.",
           mode=STANDARD,
           dataIOOrder=4)
protected Boolean extractParticles
Constructor Detail

NeuronAnalyzer2D

public NeuronAnalyzer2D()
                 throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException
Standard constructor.

Throws:
de.unihalle.informatik.Alida.exceptions.ALDOperatorException

NeuronAnalyzer2D

public NeuronAnalyzer2D(NeuriteDetector2D _neuriteDetector,
                        Boolean _extractProfiles,
                        String[] _molecules,
                        Integer[] _moleculeChannels,
                        Boolean _extractParticles,
                        NeuriteParticleDetector2D _particleDetector,
                        Boolean _verbose)
                 throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException
Constructor.

Parameters:
_detector - detector to use for neurite detection
_extractProfiles - flag to use molecular profile extraction
_molecules - names of molecules to analyze for each image channel
_moleculeChannels - channles including molecule stains
_extractParticles - flag to use molecular particle extraction
_particleDetector - detector for molecular particles
_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

getMolecules

public String[] getMolecules()
Get names of molecules for each image channel.


getMoleculeChannles

public Integer[] getMoleculeChannles()
Get molecule channels, used for molecular profile extraction.


getDetectionResultTable

public MTBTableModel getDetectionResultTable()
Get the result table of the detected neurites.


getNeuriteDetector

public NeuriteDetector2D getNeuriteDetector()
Get current neurite detector.


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


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