de.unihalle.informatik.MiToBo.apps.neurons2D

Class NeuronAnalyzer2D

java.lang.Object

de.unihalle.informatik.Alida.operator.ALDOperator

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

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,
              shortDescription="Analyzes 2D fluorescence microscope images of neurons.")
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, de.unihalle.informatik.Alida.operator.ALDOperator.HistoryConstructionMode

Field Summary

Fields

Modifier and Type	Field and Description
(package private) static de.unihalle.informatik.Alida.datatypes.ALDDirectoryString	currentInput Get initial directory from environment configuration.
private MTBTableModel	detectionResultTable
protected Boolean	extractParticles
protected Boolean	extractProfiles
private Integer[]	moleculeChannels
private String[]	molecules
private NeuriteDetector2D	neuriteDetector Define analyzer parameters.
private String	outpath Directory of output results.
private NeuriteParticleDetector2D	particleDetector
private org.rosuda.JRI.Rengine	rEngine JRI R engine to run R as a single thread.

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

completeDAG, name, operatorExecutionEventlistenerList, portHashAccess, verbose, versionProvider

Constructor Summary

Constructors

Constructor and Description
NeuronAnalyzer2D() Standard constructor.
NeuronAnalyzer2D(NeuriteDetector2D _neuriteDetector, Boolean _extractProfiles, String[] _molecules, Integer[] _moleculeChannels, Boolean _extractParticles, NeuriteParticleDetector2D _particleDetector, Boolean _verbose) Constructor.

Method Summary

Modifier and Type	Method and Description
private boolean	callNeuriteSrcipt(org.rosuda.JRI.Rengine re, String sourceFile, String[] scriptArgs) Call a specified R script for neurite calculations.
private void	extractMolProf(MTBImage moleculeImage, MTBNeurite2DSet neuriteSet, String imagePath, String outPath) Extraction of molecular profiles along the detected neurites.
private MTBRegion2DSet	extractParticles(MTBImage particleImage, MTBNeurite2DSet neuriteSet) Extraction of molecular particles along the detected neurites.
MTBTableModel	getDetectionResultTable() Get the result table of the detected neurites.
String	getDocumentation()
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.
private void	init() Initialization method.
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, addParameter, addParameter, addParameterUnconditioned, fieldContained, fireOperatorExecutionProgressEvent, getALDPortHashAccessKey, getConstructionMode, 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.

neuriteDetector

@Parameter(label="Neurite Detector",
           direction=IN,
           required=true,
           description="Detector to use for neurite detection.",
           mode=STANDARD,
           dataIOOrder=0)
private NeuriteDetector2D neuriteDetector

Define analyzer parameters.

extractProfiles

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

molecules

@Parameter(label="Define Molecules",
           direction=IN,
           required=true,
           description="Names of molecules stained in each image channel.",
           mode=STANDARD,
           dataIOOrder=2)
private String[] molecules

moleculeChannels

@Parameter(label="Profile Molecule Channels",
           direction=IN,
           required=true,
           description="Channels of molecules for profile extraction.",
           mode=STANDARD,
           dataIOOrder=3)
private Integer[] moleculeChannels

extractParticles

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

particleDetector

@Parameter(label="Particle Detector",
           direction=IN,
           required=true,
           description="Detector to use for  molecular particle detection.",
           mode=STANDARD,
           dataIOOrder=5)
private NeuriteParticleDetector2D particleDetector

detectionResultTable

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

rEngine

private transient org.rosuda.JRI.Rengine rEngine

JRI R engine to run R as a single thread.

outpath

private transient String outpath

Directory of output results.

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.

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

extractMolProf

private void extractMolProf(MTBImage moleculeImage,
                            MTBNeurite2DSet neuriteSet,
                            String imagePath,
                            String outPath)

Extraction of molecular profiles along the detected neurites.

extractParticles

private MTBRegion2DSet extractParticles(MTBImage particleImage,
                                        MTBNeurite2DSet neuriteSet)

Extraction of molecular particles along the detected neurites.

callNeuriteSrcipt

private boolean callNeuriteSrcipt(org.rosuda.JRI.Rengine re,
                                  String sourceFile,
                                  String[] scriptArgs)

Call a specified R script for neurite calculations.

Parameters:

re - current R engine (thread)

sourceFile - neurite calculation R script file

scriptArg - input directory path for the R script and other arguments

Returns:

True if R call is done successfully.

getDocumentation

public String getDocumentation()

Overrides:

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