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java.lang.Objectde.unihalle.informatik.Alida.operator.ALDOperator
de.unihalle.informatik.MiToBo.core.operator.MTBOperator
de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2D
@ALDAOperator(genericExecutionMode=ALL, level=APPLICATION, allowBatchMode=false) public class NeuronAnalyzer2D
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
NeuriteDetector2D
,
NeuriteMolProfExtractor2D
,
NeuriteParticleDetector2D
Nested Class Summary |
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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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(package private) static de.unihalle.informatik.Alida.datatypes.ALDDirectoryString |
currentInput
Get initial directory from environment configuration. |
private MTBTableModel |
detectionResultTable
|
protected java.lang.Boolean |
extractParticles
|
protected java.lang.Boolean |
extractProfiles
|
private java.lang.Integer[] |
moleculeChannels
|
private java.lang.String[] |
molecules
|
private NeuriteDetector2D |
neuriteDetector
Define analyzer parameters. |
private java.lang.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 |
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completeDAG, name, portHashAccess, verbose, versionProvider |
Constructor Summary | |
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NeuronAnalyzer2D()
Standard constructor. |
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NeuronAnalyzer2D(NeuriteDetector2D _neuriteDetector,
java.lang.Boolean _extractProfiles,
java.lang.String[] _molecules,
java.lang.Integer[] _moleculeChannels,
java.lang.Boolean _extractParticles,
NeuriteParticleDetector2D _particleDetector,
java.lang.Boolean _verbose)
Constructor. |
Method Summary | |
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private boolean |
callNeuriteSrcipt(org.rosuda.JRI.Rengine re,
java.lang.String sourceFile,
java.lang.String[] scriptArgs)
Call a specified R script for neurite calculations. |
private void |
extractMolProf(MTBImage moleculeImage,
MTBNeurite2DSet neuriteSet,
java.lang.String imagePath,
java.lang.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. |
java.lang.Integer[] |
getMoleculeChannles()
Get molecule channels, used for molecular profile extraction. |
java.lang.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 |
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readResolve |
Methods inherited from class de.unihalle.informatik.Alida.operator.ALDOperator |
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deserializeFromXmlFile, fieldContained, getALDPortHashAccessKey, getConstructionMode, getInInoutNames, getInInoutNames, getInNames, getInOutNames, getMissingRequiredInputs, getName, getNumParameters, getOutInoutNames, getOutNames, getParameter, getParameterDescriptor, getParameterNames, getSupplementalNames, getVerbose, getVersion, isConfigured, parametersToXmlObject, print, print, print, printInterface, printInterface, readHistory, reinitializeParameterDescriptors, runOp, runOp, runOp, serializeToXmlFile, setConstructionMode, setName, setParameter, setParametersFromXml, setParametersFromXml, setVerbose, toStringVerbose, unconfiguredItems, validate, validateGeneric, writeHistory, writeHistory, writeHistory, writeParametersToXml |
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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static de.unihalle.informatik.Alida.datatypes.ALDDirectoryString currentInput
@Parameter(label="Detection Result Table", direction=OUT, required=true, description="Table of detection results.") private transient MTBTableModel detectionResultTable
@Parameter(label="Extract Particles", direction=IN, required=true, description="Flag to use molecular particle extraction.", mode=STANDARD, dataIOOrder=4) protected java.lang.Boolean extractParticles
@Parameter(label="Extract Profiles", direction=IN, required=true, description="Flag to use molecular profile extraction.", mode=STANDARD, dataIOOrder=1) protected java.lang.Boolean extractProfiles
@Parameter(label="Profile Molecule Channels", direction=IN, required=true, description="Channels of molecules for profile extraction.", mode=STANDARD, dataIOOrder=3) private java.lang.Integer[] moleculeChannels
@Parameter(label="Define Molecules", direction=IN, required=true, description="Names of molecules stained in each image channel.", mode=STANDARD, dataIOOrder=2) private java.lang.String[] molecules
@Parameter(label="Neurite Detector", direction=IN, required=true, description="Detector to use for neurite detection.", mode=STANDARD, dataIOOrder=0) private NeuriteDetector2D neuriteDetector
private transient java.lang.String outpath
@Parameter(label="Particle Detector", direction=IN, required=true, description="Detector to use for molecular particle detection.", mode=STANDARD, dataIOOrder=5) private NeuriteParticleDetector2D particleDetector
private transient org.rosuda.JRI.Rengine rEngine
Constructor Detail |
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public NeuronAnalyzer2D() throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
public NeuronAnalyzer2D(NeuriteDetector2D _neuriteDetector, java.lang.Boolean _extractProfiles, java.lang.String[] _molecules, java.lang.Integer[] _moleculeChannels, java.lang.Boolean _extractParticles, NeuriteParticleDetector2D _particleDetector, java.lang.Boolean _verbose) throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException
_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
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
Method Detail |
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private boolean callNeuriteSrcipt(org.rosuda.JRI.Rengine re, java.lang.String sourceFile, java.lang.String[] scriptArgs)
re
- current R engine (thread)sourceFile
- neurite calculation R script filescriptArg
- input directory path for the R script and other arguments
private void extractMolProf(MTBImage moleculeImage, MTBNeurite2DSet neuriteSet, java.lang.String imagePath, java.lang.String outPath)
private MTBRegion2DSet extractParticles(MTBImage particleImage, MTBNeurite2DSet neuriteSet)
public MTBTableModel getDetectionResultTable()
public java.lang.Integer[] getMoleculeChannles()
public java.lang.String[] getMolecules()
public NeuriteDetector2D getNeuriteDetector()
private void init()
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
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
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