A B C D E F G H I J K L M N O P Q R S T U V W X Y Z _

O

objectify(VJMatrix) - Method in class VolumeJ.VJLight

Transform the position of this light into another coordinate system.

obsCompiledDirectory() - Static method in class stereodisc.Conventions

obsDirectory() - Static method in class stereodisc.Conventions

ObservationACDRs - Class in stereodisc

Determine the statistics of two observations (organized in stacks).

ObservationACDRs() - Constructor for class stereodisc.ObservationACDRs

Observations_Opener - Class in <Unnamed>

Loads a number of observations and creates an observations stack, with all images made OD (images with os in their name flipped).

Observations_Opener() - Constructor for class Observations_Opener

ObservationStatistics - Class in stereodisc

Determines the statistics for all observations (stacks) in a directory compared to a reference standard stack.

ObservationStatistics() - Constructor for class stereodisc.ObservationStatistics

ObserverAccuracy - Class in stereodisc

Analyzes performance of different observers / algorithms versus ground truth.

ObserverAccuracy() - Constructor for class stereodisc.ObserverAccuracy

occurences(float[], float[], int, int) - Static method in class bijnum.BIJmulticlass

Make a histogram of the occurence of n classes in gt corresponding to the feature value in v.

OCT_3D_analyzer - Class in <Unnamed>

Analyze a 3D OCT file.

OCT_3D_analyzer() - Constructor for class OCT_3D_analyzer

OCT_Reader - Class in <Unnamed>

OCT files are formatted as: 1.07847500000000 0.51040150000000 16 12 15 128 1024

OCT_Reader() - Constructor for class OCT_Reader

of3d - package of3d

OF3DClassifiers - Class in of3d

This class is a class whose only purpose is to contain all OFClassifier class definitions.

OF3DClassifiers() - Constructor for class of3d.OF3DClassifiers

OF3DDeformation - Class in of3d

OF3DDeformation() - Constructor for class of3d.OF3DDeformation

OF3DDeformation(double, double, double, double, double, double, double) - Constructor for class of3d.OF3DDeformation

OF3DDeformation(float[]) - Constructor for class of3d.OF3DDeformation

OF3DDeformer - Class in of3d

OF3DDeformer does a progressive deformation on a single volume, and creates a series of volumes that contain the progressively deformed volume.

OF3DDeformer() - Constructor for class of3d.OF3DDeformer

OF3DDisplay - Class in of3d

OF3DDisplay is an extension of OFDisplay to implement the 2D display of 3D flow fields.

OF3DDisplay() - Constructor for class of3d.OF3DDisplay

OF3DFlow - Class in of3d

This class implements a volume consisting of 3D optical flows and methods useful for volume rendering.

OF3DFlow() - Constructor for class of3d.OF3DFlow

OF3DFlow(int, int, int) - Constructor for class of3d.OF3DFlow

OF3DFlow(int, int, int, float, float, float) - Constructor for class of3d.OF3DFlow

OF3DFlow(String) - Constructor for class of3d.OF3DFlow

OF3DHalfSpot - Class in of3d

This class implements the creation of 3D half oriented spots from a 3D vector.

OF3DHalfSpot() - Constructor for class of3d.OF3DHalfSpot

OF3DLucas - Class in of3d

OF3DLucas(OF3DFlow, ImageStack, int, int, float, float, boolean) - Constructor for class of3d.OF3DLucas

OF3DSpot - Class in of3d

This class implements the creation of 3D spots from a 3D vector.

OF3DSpot() - Constructor for class of3d.OF3DSpot

OF3DSpot(float[], double, double) - Constructor for class of3d.OF3DSpot

OF3DUserInterface - Class in of3d

This class links the OF3D classes to the VJ classes and the ImageJ interface.
Copyright (c) 1999-2003, Michael Abramoff.

OF3DUserInterface() - Constructor for class of3d.OF3DUserInterface

OFClassifier - Class in of3d

This class is the superclass for all 3D optical flow visualization classifiers by extending VJClassifier.

OFClassifier() - Constructor for class of3d.OFClassifier

OFClassifierDCM2DNoGradient - Class in of3d

This class implements dynamic color mapping, a 2D classification function of 3D optical flows, displaying iso-shear surfaces.

OFClassifierDCM2DNoGradient() - Constructor for class of3d.OFClassifierDCM2DNoGradient

OFClassifierDCM3DNoGradient - Class in of3d

This class implements a classification function of 3D optical flows that sets the color of a voxel to the 3D DCM color of the corresponding 3D flow vector.

OFClassifierDCM3DNoGradient() - Constructor for class of3d.OFClassifierDCM3DNoGradient

OFClassifierScintillans - Class in of3d

This class implements a classification function of 3D optical flows that sets a scintillation corresponding in size, color and direction to the flow vector.

OFClassifierScintillans() - Constructor for class of3d.OFClassifierScintillans

OFClassifierScintillansIx255 - Class in of3d

This class implements a classification function of 3D optical flows that sets a scintillation corresponding in size, color and direction to the flow vector.

OFClassifierScintillansIx255() - Constructor for class of3d.OFClassifierScintillansIx255

OFClassifierScintillansIxLT0 - Class in of3d

This class implements a classification function of 3D optical flows that sets a scintillation corresponding in size, color and direction to the flow vector.

OFClassifierScintillansIxLT0() - Constructor for class of3d.OFClassifierScintillansIxLT0

OFClassifierScintillansNoFlow - Class in of3d

This class implements a classification function of 3D optical flows that sets a scintillation corresponding in size, color and direction to the flow vector.

OFClassifierScintillansNoFlow() - Constructor for class of3d.OFClassifierScintillansNoFlow

OFClassifierScintillansNoStatic - Class in of3d

This class implements a classification function of 3D optical flows that sets a scintillation corresponding in size, color and direction to the flow vector.

OFClassifierScintillansNoStatic() - Constructor for class of3d.OFClassifierScintillansNoStatic

off() - Method in class stimulator.CCDcontrol

Turn off the CCD.

OFXYZ - Static variable in class of3d.OF3DUserInterface

OFXZY - Static variable in class of3d.OF3DUserInterface

OFYZX - Static variable in class of3d.OF3DUserInterface

OIDamplitudeAnalyzer - Class in retina

Analysis of the reflectance signal in terms of the amplitude at a certain moment.

OIDamplitudeAnalyzer(OIDScriptProcessor) - Constructor for class retina.OIDamplitudeAnalyzer

OIDAnalysisMethods - Class in retina

Optical Imaging frame sequence analysis.

OIDAnalysisMethods() - Constructor for class retina.OIDAnalysisMethods

OIDAnalyzer - Class in retina

Optical Imaging of the Retina first frame analyzer.

OIDAnalyzer() - Constructor for class retina.OIDAnalyzer

OIDAnalyzer(ScriptProcessor) - Constructor for class retina.OIDAnalyzer

OIDAverageAnalyzer - Class in retina

Optical Imaging of the Retina first frame analyzer.

OIDAverageAnalyzer() - Constructor for class retina.OIDAverageAnalyzer

OIDAverageAnalyzer(ScriptProcessor) - Constructor for class retina.OIDAverageAnalyzer

OIDBaseAnalyzer - Interface in retina

Is the abstract interface definition for all OID Analyzers.

OIDbaselineAnalyzer - Class in retina

Optical Imaging of the Retina baseline frame analyzer.

OIDbaselineAnalyzer() - Constructor for class retina.OIDbaselineAnalyzer

OIDbaselineAnalyzer(OIDScriptProcessor) - Constructor for class retina.OIDbaselineAnalyzer

OIDCanvas - Class in retina

User interface for optical imaging sequences.

OIDCanvas(ImagePlus) - Constructor for class retina.OIDCanvas

OIDDisplayMethods - Class in retina

OIDDisplayMethods() - Constructor for class retina.OIDDisplayMethods

OIDffAllAnalyzer - Class in retina

Optical Imaging of the Retina first frame analyzer for all frames (not only stimulus frames) but average across conditions.

OIDffAllAnalyzer() - Constructor for class retina.OIDffAllAnalyzer

OIDffAllAnalyzer(OIDScriptProcessor) - Constructor for class retina.OIDffAllAnalyzer

OIDHeader - Class in retina

Defines the header for KES/DAT files for OID devices.

OIDHeader() - Constructor for class retina.OIDHeader

OIDHeader(byte[], String) - Constructor for class retina.OIDHeader

Instantiates an OIDHeader from known header bytes (in .kes file) and String from .dat file.

OIDHeader(String, String) - Constructor for class retina.OIDHeader

Instantiates an OIDHeader from both .kes and .dat files.

OIDHeader(File) - Constructor for class retina.OIDHeader

Instantiates an OIDHeader from a .dat File.

OIDHeader(int, int, int, String) - Constructor for class retina.OIDHeader

Instantiates an OIDHeader from image file parameters and properly formatted String headerInfo.

OIDMapsFitter - Class in retina

Fits stimulus map stacks into retinal reflectance images.

OIDMapsFitter() - Constructor for class retina.OIDMapsFitter

OIDMapsFitter(OIDScriptProcessor) - Constructor for class retina.OIDMapsFitter

OIDOpener_URL - Class in <Unnamed>

Plugin to open Plugin to decode and open KESTREL OID .dat and _Data.kes files.

OIDOpener_URL() - Constructor for class OIDOpener_URL

OIDPCAAnalyzer - Class in retina

Does PCA analysis on OID files.

OIDPCAAnalyzer() - Constructor for class retina.OIDPCAAnalyzer

OIDPCAAnalyzer(ScriptProcessor) - Constructor for class retina.OIDPCAAnalyzer

OIDProcessor - Class in retina

Optical Imaging frame sequence analysis.

OIDProcessor() - Constructor for class retina.OIDProcessor

Start an OIDProcessor.

OIDProcessor(FileInfo, String[]) - Constructor for class retina.OIDProcessor

Start an OIDProcessor for the FileInfo fi and epochNames, an array of file names.

OIDReader_ - Class in <Unnamed>

Plugin to decode and open KESTREL OID .dat and _Data.kes files.

OIDReader_() - Constructor for class OIDReader_

OIDReconstructor - Class in retina

OID reconstructor with directory navigation.

OIDReconstructor(String, Object, String) - Constructor for class retina.OIDReconstructor

Open a preview open dialog, a dialog that shows a list of files in the directory, and shows a text (currently header text) related to that file, to ease selection.

OIDroiAnalyzer - Class in retina

Does ROI analysis of OID files.

OIDroiAnalyzer() - Constructor for class retina.OIDroiAnalyzer

OIDroiAnalyzer(ScriptProcessor) - Constructor for class retina.OIDroiAnalyzer

OIDroiTCAnalyzer - Class in retina

Does ROI analysis of OID files and looks for timecourse of all different possible stimuli.

OIDroiTCAnalyzer() - Constructor for class retina.OIDroiTCAnalyzer

OIDroiTCAnalyzer(OIDScriptProcessor) - Constructor for class retina.OIDroiTCAnalyzer

OIDROItimecourseAnalyzer - Class in retina

Optical Imaging of the Retina timecourse analyzer.

OIDROItimecourseAnalyzer() - Constructor for class retina.OIDROItimecourseAnalyzer

OIDScriptProcessor - Class in retina

Class to process / analyze OID files and directories of OID using an XML script file.

OIDScriptProcessor(String, String, OIDBaseAnalyzer) - Constructor for class retina.OIDScriptProcessor

Create a new ScriptProcessor that can call back to an analyzer.

OIDScriptProcessor(String, String) - Constructor for class retina.OIDScriptProcessor

Create a new OIDFileProcessor to process the control file.

OIDStackWindow - Class in retina

Optical Imaging frame sequence analysis.

OIDStackWindow(ImagePlus, ImageCanvas, FileInfo, String[]) - Constructor for class retina.OIDStackWindow

Start an OIDProcessor for imp.

OIDStackWindow(ImagePlus) - Constructor for class retina.OIDStackWindow

Start an OIDProcessor for imp.

OIDtc - Class in retina

Does truncated differencing on existing PCA files.

OIDtc() - Constructor for class retina.OIDtc

OIDTimecourseAnalyzer - Class in retina

Optical Imaging of the Retina timecourse analyzer for all frames (not only stimulus frames).

OIDTimecourseAnalyzer() - Constructor for class retina.OIDTimecourseAnalyzer

OIDTimecourseAnalyzer(OIDScriptProcessor) - Constructor for class retina.OIDTimecourseAnalyzer

OIDTimecourseStimulatedAnalyzer - Class in retina

Optical Imaging of the Retina timecourse analyzer.

OIDTimecourseStimulatedAnalyzer() - Constructor for class retina.OIDTimecourseStimulatedAnalyzer

OIDTimecourseStimulatedAnalyzer(OIDScriptProcessor) - Constructor for class retina.OIDTimecourseStimulatedAnalyzer

OIDWindow - Class in retina

Optical Imaging frame sequence analysis.

OIDWindow(ImagePlus, ImageCanvas, FileInfo, String[]) - Constructor for class retina.OIDWindow

Start an OIDWindow for imp.

OIDXMLAnalyzer - Class in retina

Class to process / analyze OID files and directories of OID using a script file.

OIDXMLAnalyzer() - Constructor for class retina.OIDXMLAnalyzer

OLD - Static variable in class bd.BlobDetector

on() - Method in class stimulator.CCDcontrol

Trigger the CCD.

open(String) - Method in class retina.RTA_Reader

Opens the specified text file as a float image.

open(String) - Method in class retina.RTA_Thickness_Reader

Opens the specified RTA map and process thickness array.

OPEN_NEVER - Static variable in class va.PVCAM

Class 2: Shutter mode flags

OPEN_NO_CHANGE - Static variable in class va.PVCAM

OPEN_PRE_EXPOSURE - Static variable in class va.PVCAM

OPEN_PRE_SEQUENCE - Static variable in class va.PVCAM

OPEN_PRE_TRIGGER - Static variable in class va.PVCAM

OPPONENCIES - Static variable in class features.filterBanks.FilterBank

Opponency - Class in features.color

Opponency() - Constructor for class features.color.Opponency

Opponency.Channel - Enum in features.color

Optic_Flow_3D - Class in <Unnamed>

This class makes OF3D available as a plugin to ImageJ.
Copyright (c) 1999-2002, Michael Abramoff.

Optic_Flow_3D() - Constructor for class Optic_Flow_3D

OptimalAdmissibleRegion - Class in segmentation

OptimalAdmissibleRegion finds the region of MAXIMUM gain in an image.

OptimalAdmissibleRegion() - Constructor for class segmentation.OptimalAdmissibleRegion

OptimalClosedDualPath - Class in segmentation

OptimalClosedDualPath() - Constructor for class segmentation.OptimalClosedDualPath

OptimalClosedDualPath.Bounds - Class in segmentation

OptimalClosedDualPath.Bounds(int, int, int) - Constructor for class segmentation.OptimalClosedDualPath.Bounds

OptimalClosedDualPath.Bounds(int[], int[]) - Constructor for class segmentation.OptimalClosedDualPath.Bounds

OptimalClosedPath - Class in segmentation

OptimalClosedPath() - Constructor for class segmentation.OptimalClosedPath

OptimalClosedPath.Bounds - Class in segmentation

OptimalClosedPath.Bounds(int, int, int) - Constructor for class segmentation.OptimalClosedPath.Bounds

OptimalClosedPath.Bounds(int[], int[]) - Constructor for class segmentation.OptimalClosedPath.Bounds

OptimalConvexRegion - Class in segmentation

OptimalConvexRegion finds the region of MAXIMUM gain in an image.

OptimalConvexRegion() - Constructor for class segmentation.OptimalConvexRegion

orientationxy(float[]) - Static method in class FlowJ.FlowJFlow

orientationxy(float, float) - Static method in class FlowJ.FlowJFlow

return the orientation (in radians) in the xy plane of a rectangular motion vector r

orientationz(float[]) - Static method in class FlowJ.FlowJFlow

OUTPUTTAG - Static variable in class scripts.ScriptProcessor

overThreshold(float) - Method in class VolumeJ.VJClassifierIsosurface