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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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protected Boolean |
extractParticles
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protected Boolean |
extractProfiles
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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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NeuronAnalyzer2D()
Standard constructor. |
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NeuronAnalyzer2D(NeuriteDetector2D _neuriteDetector,
Boolean _extractProfiles,
String[] _molecules,
Integer[] _moleculeChannels,
Boolean _extractParticles,
NeuriteParticleDetector2D _particleDetector,
Boolean _verbose)
Constructor. |
Method Summary | |
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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()
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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="Extract Profiles", direction=IN, required=true, description="Flag to use molecular profile extraction.", mode=STANDARD, dataIOOrder=1) protected Boolean extractProfiles
@Parameter(label="Extract Particles", direction=IN, required=true, description="Flag to use molecular particle extraction.", mode=STANDARD, dataIOOrder=4) protected Boolean extractParticles
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, Boolean _extractProfiles, String[] _molecules, Integer[] _moleculeChannels, Boolean _extractParticles, NeuriteParticleDetector2D _particleDetector, 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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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 String[] getMolecules()
public Integer[] getMoleculeChannles()
public MTBTableModel getDetectionResultTable()
public NeuriteDetector2D getNeuriteDetector()
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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