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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

## A

ABOUT_MENU - Static variable in class ij.Menus
ABS - Static variable in interface ij.macro.MacroConstants
ACOS - Static variable in interface ij.macro.MacroConstants
ADD - Static variable in interface ij.process.Blitter
  dst=dst+src
ADD_TO_MANAGER - Static variable in class ij.plugin.filter.ParticleAnalyzer
  Add particles to ROI Manager.
ALL_KEYS - Static variable in class ij.IJ
AND - Static variable in interface ij.process.Blitter
  dst=dst AND src
ANGLE - Static variable in class ij.gui.Roi
ANGLE - Static variable in class ij.gui.Toolbar
ANGLE - Static variable in class ij.measure.ResultsTable
AREA - Static variable in interface ij.measure.Measurements
AREA - Static variable in class ij.measure.ResultsTable
AREA_FRACTION - Static variable in interface ij.measure.Measurements
AREA_FRACTION - Static variable in class ij.measure.ResultsTable
ARGB - Static variable in class ij.io.FileInfo
  32-bit interleaved ARGB.
ARRAY - Static variable in interface ij.macro.MacroConstants
ARRAY_FUNCTION - Static variable in interface ij.macro.MacroConstants
ASIN - Static variable in interface ij.macro.MacroConstants
ATAN - Static variable in interface ij.macro.MacroConstants
ATAN2 - Static variable in interface ij.macro.MacroConstants
AUTO_UPDATE - Static variable in interface ij.macro.MacroConstants
AVERAGE - Static variable in interface ij.process.Blitter
  dst=(dst+src)/2
AVG_METHOD - Static variable in class ij.plugin.ZProjector
AVIWriter - class ij.plugin.filter.AVIWriter.
  This plugin saves stacks in AVI format.
AVIWriter() - Constructor for class ij.plugin.filter.AVIWriter
AboutBox - class ij.plugin.AboutBox.
  This plugin implements the Help/About ImageJ command by opening the about.jpg in ij.jar, scaling it 400% and adding some text.
AboutBox() - Constructor for class ij.plugin.AboutBox
Analyzer - class ij.plugin.filter.Analyzer.
  This plugin implements ImageJ's Analyze/Measure and Analyze/Set Measurements commands.
Analyzer() - Constructor for class ij.plugin.filter.Analyzer
Analyzer(ImagePlus) - Constructor for class ij.plugin.filter.Analyzer
  Constructs a new Analyzer using the specified ImagePlus object and the system-wide measurement options and results table.
Analyzer(ImagePlus, int, ResultsTable) - Constructor for class ij.plugin.filter.Analyzer
  Construct a new Analyzer using an ImagePlus object and private measurement options and results table.
Animator - class ij.plugin.Animator.
  This plugin animates stacks.
Animator() - Constructor for class ij.plugin.Animator
abort() - Static method in class ij.Macro
  Aborts the currently running macro or any plugin using IJ.run().
abort() - Static method in class ij.macro.Interpreter
  Aborts currently running macro.
abortPaste() - Method in class ij.gui.Roi
abs() - Method in class ij.process.FloatProcessor
abs() - Method in class ij.process.ImageProcessor
  If this is a 32-bit or signed 16-bit image, performs an absolute value transform, otherwise does nothing.
abs() - Method in class ij.process.ShortProcessor
accept(File, String) - Method in class ij.plugin.Compiler
actionPerformed(ActionEvent) - Method in class ij.ImageJ
  Handle menu events.
actionPerformed(ActionEvent) - Method in class ij.gui.GenericDialog
actionPerformed(ActionEvent) - Method in class ij.gui.HTMLDialog
actionPerformed(ActionEvent) - Method in class ij.gui.HistogramWindow
actionPerformed(ActionEvent) - Method in class ij.gui.MessageDialog
actionPerformed(ActionEvent) - Method in class ij.gui.PlotWindow
actionPerformed(ActionEvent) - Method in class ij.gui.SaveChangesDialog
actionPerformed(ActionEvent) - Method in class ij.gui.StackWindow
actionPerformed(ActionEvent) - Method in class ij.gui.Toolbar
actionPerformed(ActionEvent) - Method in class ij.gui.YesNoCancelDialog
actionPerformed(ActionEvent) - Method in class ij.plugin.LUT_Editor
actionPerformed(ActionEvent) - Method in class ij.plugin.MacroInstaller
actionPerformed(ActionEvent) - Method in class ij.plugin.filter.Calibrator
actionPerformed(ActionEvent) - Method in class ij.plugin.filter.Convolver
actionPerformed(ActionEvent) - Method in class ij.plugin.frame.ContrastAdjuster
actionPerformed(ActionEvent) - Method in class ij.plugin.frame.Editor
actionPerformed(ActionEvent) - Method in class ij.plugin.frame.Fitter
actionPerformed(ActionEvent) - Method in class ij.plugin.frame.Recorder
actionPerformed(ActionEvent) - Method in class ij.plugin.frame.RoiManager
actionPerformed(ActionEvent) - Method in class ij.plugin.frame.ThresholdAdjuster
actionPerformed(ActionEvent) - Method in class ij.text.TextPanel
actionPerformed(ActionEvent) - Method in class ij.text.TextWindow
add(ImageProcessor, double) - Method in class ij.plugin.filter.SaltAndPepper
add(ImagePlus, Roi, int) - Method in class ij.plugin.frame.RoiManager
  Adds the specified ROI to the list.
add(int) - Method in class ij.process.FloatProcessor
add(double) - Method in class ij.process.FloatProcessor
add(int) - Method in class ij.process.ImageProcessor
  Adds 'value' to each pixel in the image or ROI.
add(double) - Method in class ij.process.ImageProcessor
  Adds 'value' to each pixel in the image or ROI.
add(int) - Method in class ij.process.ShortProcessor
add(double) - Method in class ij.process.ShortProcessor
addBatchModeImage(ImagePlus) - Static method in class ij.macro.Interpreter
addChar(char) - Method in class ij.gui.TextRoi
  Adds the specified character to the end of the text string.
addCheckbox(String, boolean) - Method in class ij.gui.GenericDialog
  Adds a checkbox.
addCheckboxGroup(int, int, String[], boolean[]) - Method in class ij.gui.GenericDialog
  Adds a group of checkboxs using a grid layout.
addChoice(String, String[], String) - Method in class ij.gui.GenericDialog
  Adds a popup menu.
addCircle(String, String, String) - Static method in class ij.gui.ShapeRoi
addColumns() - Method in class ij.measure.ResultsTable
addDialogListener(DialogListener) - Method in class ij.gui.GenericDialog
  Add an Object implementing the DialogListener interface.
addErrorBars(float[]) - Method in class ij.gui.Plot
  Adds error bars to the plot.
addErrorBars(double[]) - Method in class ij.gui.Plot
  Adds error bars to the plot.
addErrorBars(float[]) - Method in class ij.gui.PlotWindow
  Adds error bars to the plot.
addImageListener(ImageListener) - Static method in class ij.ImagePlus
addKeyListener(KeyListener) - Method in class ij.text.TextPanel
  Unused keyPressed and keyTyped events will be passed to 'listener'.
addLabel(double, double, String) - Method in class ij.gui.Plot
  Draws text at the specified location, where (0,0) is the upper left corner of the the plot frame and (1,1) is the lower right corner.
addLabel(double, double, String) - Method in class ij.gui.PlotWindow
  Draws a label.
addLabel(String, String) - Method in class ij.measure.ResultsTable
  Adds a label to the beginning of the current row.
addLayoutComponent(String, Component) - Method in class ij.gui.ImageLayout
  Not used by this class.
addMacroTool(String, MacroInstaller, int) - Method in class ij.gui.Toolbar
  Used by the MacroInstaller class to install macro tools.
addMessage(String) - Method in class ij.gui.GenericDialog
  Adds a message consisting of one or more lines of text.
addNotify() - Method in class ij.gui.MultiLineLabel
addNumericField(String, double, int) - Method in class ij.gui.GenericDialog
  Adds a numeric field.
addNumericField(String, double, int, int, String) - Method in class ij.gui.GenericDialog
  Adds a numeric field.
addOffset() - Method in class ij.gui.PolygonRoi
addOpenRecentItem(String) - Static method in class ij.Menus
  Adds a file path to the beginning of the File/Open Recent submenu.
addPanel(Panel) - Method in class ij.gui.GenericDialog
  Adds a Panel to the dialog.
addPanel(Panel, int, Insets) - Method in class ij.gui.GenericDialog
  Adds a Panel to the dialog with custom contraint and insets.
addPoint(int, int) - Method in class ij.gui.PointRoi
  Adds a point to this selection and return the result.
addPoints(float[], float[], int) - Method in class ij.gui.Plot
  Adds a set of points to the plot or adds a curve if shape is set to LINE.
addPoints(double[], double[], int) - Method in class ij.gui.Plot
  Adds a set of points to the plot using double arrays.
addPoints(float[], float[], int) - Method in class ij.gui.PlotWindow
  Adds a set of points to the plot or adds a curve if shape is set to LINE.
addPoints(double[], double[], int) - Method in class ij.gui.PlotWindow
  Adds a set of points to the plot using double arrays.
addPreviewCheckbox(PlugInFilterRunner) - Method in class ij.gui.GenericDialog
  Adds a checkbox labelled "Preview" for "automatic" preview.
addPreviewCheckbox(PlugInFilterRunner, String) - Method in class ij.gui.GenericDialog
  Add the preview checkbox with user-defined label; for details see the addPreviewCheckbox method with standard "Preview" label Note that a GenericDialog can have only one PreviewCheckbox
addSlice(String, Object) - Method in class ij.ImageStack
  Adds an image in the forma of a pixel array to the end of the stack.
addSlice(String, ImageProcessor) - Method in class ij.ImageStack
  Adds the image in 'ip' to the end of the stack.
addSlice(String, ImageProcessor, int) - Method in class ij.ImageStack
  Adds the image in 'ip' to the stack following slice 'n'.
addSlice(String) - Method in class ij.VirtualStack
  Adds an image to the end of the stack.
addSlice(String, Object) - Method in class ij.VirtualStack
  Does nothing.
addSlice(String, ImageProcessor) - Method in class ij.VirtualStack
  Does nothing..
addSlice(String, ImageProcessor, int) - Method in class ij.VirtualStack
  Does noting.
addSlider(String, double, double, double) - Method in class ij.gui.GenericDialog
addStringField(String, String) - Method in class ij.gui.GenericDialog
  Adds an 8 column text field.
addStringField(String, String, int) - Method in class ij.gui.GenericDialog
  Adds a text field.
addTextAreas(String, String, int, int) - Method in class ij.gui.GenericDialog
  Adds one or two (side by side) text areas.
addToManager - Variable in class ij.plugin.filter.ParticleAnalyzer
addTool(String) - Method in class ij.gui.Toolbar
  Adds a tool to the toolbar.
addUnsignedShortSlice(String, Object) - Method in class ij.ImageStack
  Obsolete.
addValue(int, double) - Method in class ij.measure.ResultsTable
  Adds a value to the end of the given column.
addValue(String, double) - Method in class ij.measure.ResultsTable
  Adds a value to the end of the given column.
addWindow(Frame) - Static method in class ij.WindowManager
  Adds the specified window to the Window menu.
adjustmentValueChanged(AdjustmentEvent) - Method in class ij.gui.ColorChooser
adjustmentValueChanged(AdjustmentEvent) - Method in class ij.gui.GenericDialog
adjustmentValueChanged(AdjustmentEvent) - Method in class ij.gui.StackWindow
adjustmentValueChanged(AdjustmentEvent) - Method in class ij.plugin.frame.ContrastAdjuster
adjustmentValueChanged(AdjustmentEvent) - Method in class ij.plugin.frame.LineWidthAdjuster
adjustmentValueChanged(AdjustmentEvent) - Method in class ij.plugin.frame.ThresholdAdjuster
adjustmentValueChanged(AdjustmentEvent) - Method in class ij.text.TextPanel
altKeyDown() - Static method in class ij.IJ
  Returns true if the alt key is down.
analyze(ImagePlus) - Method in class ij.plugin.filter.LineGraphAnalyzer
  Uses ImageJ's particle analyzer to extract a set of coordinate pairs from a digitized line graph.
analyze(ImagePlus) - Method in class ij.plugin.filter.ParticleAnalyzer
  Performs particle analysis on the specified image.
analyze(ImagePlus, ImageProcessor) - Method in class ij.plugin.filter.ParticleAnalyzer
  Performs particle analysis on the specified ImagePlus and ImageProcessor.
analyzer - Variable in class ij.plugin.filter.ParticleAnalyzer
and(ShapeRoi) - Method in class ij.gui.ShapeRoi
  Unary intersection operator.
and(int) - Method in class ij.process.FloatProcessor
and(int) - Method in class ij.process.ImageProcessor
  Binary AND of each pixel in the image or ROI with 'value'.
and(int) - Method in class ij.process.ShortProcessor
angle - Variable in class ij.process.EllipseFitter
  Angle in degrees
angle - Variable in class ij.process.ImageStatistics
  Angle in degrees of fitted ellipse
angstromSymbol - Static variable in class ij.IJ
antialiasedText - Static variable in class ij.Prefs
  No longer used
antialiasedText - Variable in class ij.process.ImageProcessor
antialiasedTools - Static variable in class ij.Prefs
  Draw tool icons using antialiasing.
append(String) - Method in class ij.plugin.frame.Editor
append(String) - Method in class ij.text.TextPanel
  Adds one or more lines to the end of this TextPanel.
append(String) - Method in class ij.text.TextWindow
  Adds one or lines of text to the window.
appendLine(String) - Method in class ij.text.TextPanel
  Adds a single line to the end of this TextPanel.
applyLut() - Method in class ij.process.ByteProcessor
applyTable(int[]) - Method in class ij.process.ByteProcessor
applyTable(int[]) - Method in class ij.process.ColorProcessor
applyTable(int[], int) - Method in class ij.process.ColorProcessor
applyTable(int[]) - Method in class ij.process.FloatProcessor
applyTable(int[]) - Method in class ij.process.ImageProcessor
  Transforms the image or ROI using a lookup table.
applyTable(int[]) - Method in class ij.process.ShortProcessor
  Transforms the pixel data using a 65536 entry lookup table.
applyTable(int[]) - Method in class ij.process.StackProcessor
area - Variable in class ij.process.ImageStatistics
areaFraction - Variable in class ij.process.ImageStatistics
arrayFunctionIDs - Static variable in interface ij.macro.MacroConstants
arrayFunctions - Static variable in interface ij.macro.MacroConstants
autoClose - Static variable in class ij.gui.PlotWindow
  Automatically close window after saving values.
autoOutline(int, int) - Method in class ij.gui.Wand
  Traces the boundary of an area of uniform color, where 'startX' and 'startY' are somewhere inside the area.
autoOutline(int, int, double, double) - Method in class ij.gui.Wand
  Traces an object defined by lower and upper threshold values.
autoOutline(int, int, int, int) - Method in class ij.gui.Wand
  This is a variation of autoOutline that uses int threshold arguments.
autoThreshold() - Method in class ij.process.ColorProcessor
autoThreshold() - Method in class ij.process.FloatProcessor
  Not implemented.
autoThreshold() - Method in class ij.process.ImageProcessor
  Converts the image to binary using an automatically determined threshold.

## B

BARG - Static variable in class ij.io.FileInfo
  32-bit interleaved BARG (MCID).
BCOLOR - Static variable in class ij.Prefs
BEEP - Static variable in interface ij.macro.MacroConstants
BGR - Static variable in class ij.io.FileInfo
  24-bit interleaved BGR.
BITMAP - Static variable in class ij.io.FileInfo
  1-bit black and white.
BITS_PER_SAMPLE - Static variable in class ij.io.TiffDecoder
BIT_DEPTH - Static variable in interface ij.macro.MacroConstants
BLACK - Static variable in class ij.process.ImageProcessor
  Value of pixels included in masks.
BLACK_AND_WHITE_LUT - Static variable in class ij.process.ImageProcessor
BMP - Static variable in class ij.io.FileInfo
BMP - Static variable in class ij.io.Opener
BMP_Reader - class ij.plugin.BMP_Reader.
  This plugin reads BMP files.
BMP_Reader() - Constructor for class ij.plugin.BMP_Reader
BMP_Writer - class ij.plugin.BMP_Writer.
  Implements the File/Save As/BMP command.
BMP_Writer() - Constructor for class ij.plugin.BMP_Writer
BOTTOM_MARGIN - Static variable in class ij.gui.Plot
  the margin width below the plot frame
BOX - Static variable in class ij.gui.Plot
  Display points using an box-shaped mark.
BOX - Static variable in class ij.gui.PlotWindow
  Display points using an box-shaped mark.
BackgroundSubtracter - class ij.plugin.filter.BackgroundSubtracter.
  Implements ImageJ's Subtract Background command.
BackgroundSubtracter() - Constructor for class ij.plugin.filter.BackgroundSubtracter
Benchmark - class ij.plugin.filter.Benchmark.
  Implements the Plugins/Utilities/Run Benchmark command.
Benchmark() - Constructor for class ij.plugin.filter.Benchmark
Binary - class ij.plugin.filter.Binary.
  Implements the commands in the Process/Binary submenu.
Binary() - Constructor for class ij.plugin.filter.Binary
BinaryFiller - class ij.plugin.filter.BinaryFiller.
  Binary Fill (Process/Binary/Fill) by Gabriel Landini, G.Landini at bham.ac.uk.
BinaryFiller() - Constructor for class ij.plugin.filter.BinaryFiller
BinaryProcessor - class ij.process.BinaryProcessor.
  This class processes binary images.
BinaryProcessor(ByteProcessor) - Constructor for class ij.process.BinaryProcessor
  Creates a BinaryProcessor from a ByteProcessor.
BitBuffer - class ij.io.BitBuffer.
  A class for reading arbitrary numbers of bits from a byte array.
BitBuffer(byte[]) - Constructor for class ij.io.BitBuffer
Blitter - interface ij.process.Blitter.
  ImageJ bit blitting classes must implement this interface.
BrowserLauncher - class ij.plugin.BrowserLauncher.
  This plugin implements the File/Import/URL command and the commands in the Help menu that open web pages.
BrowserLauncher() - Constructor for class ij.plugin.BrowserLauncher
ByteBlitter - class ij.process.ByteBlitter.
  This class does bit blitting of byte images.
ByteBlitter(ByteProcessor) - Constructor for class ij.process.ByteBlitter
  Constructs a ByteBlitter from a ByteProcessor.
ByteProcessor - class ij.process.ByteProcessor.
  This is an 8-bit image and methods that operate on that image.
ByteProcessor(Image) - Constructor for class ij.process.ByteProcessor
  Creates a ByteProcessor from an 8-bit, indexed color AWT Image.
ByteProcessor(int, int) - Constructor for class ij.process.ByteProcessor
  Creates a blank ByteProcessor of the specified dimensions.
ByteProcessor(int, int, byte[], ColorModel) - Constructor for class ij.process.ByteProcessor
  Creates a ByteProcessor from a pixel array and IndexColorModel.
ByteStatistics - class ij.process.ByteStatistics.
  8-bit image statistics, including histogram.
ByteStatistics(ImageProcessor) - Constructor for class ij.process.ByteStatistics
  Construct an ImageStatistics object from a ByteProcessor using the standard measurement options (area, mean, mode, min and max) and no calibration.
ByteStatistics(ImageProcessor, int, Calibration) - Constructor for class ij.process.ByteStatistics
  Constructs a ByteStatistics object from a ByteProcessor using the specified measurement and calibration.
bLUT1 - Variable in class ij.process.ImageProcessor
bLUT2 - Variable in class ij.process.ImageProcessor
backgroundColor - Static variable in class ij.ImageJ
backgroundIsZero - Variable in class ij.plugin.filter.BinaryFiller
baseCM - Variable in class ij.process.ImageProcessor
beep() - Static method in class ij.IJ
  Emits an audio beep.
binSize - Variable in class ij.process.ImageStatistics
blackBackground - Static variable in class ij.Prefs
  Backgound is black in binary images
blackCanvas - Static variable in class ij.Prefs
  Use black image border.
blue - Variable in class ij.plugin.filter.RGBStackSplitter
  These are the three stacks created by the split(ImageStack) method.
blues - Variable in class ij.io.FileInfo
blur(ImageProcessor, double) - Method in class ij.plugin.filter.GaussianBlur
  Gaussian Filtering of an ImageProcessor.
blur1Direction(FloatProcessor, double, double, boolean, int) - Method in class ij.plugin.filter.GaussianBlur
  Blur an image in one direction (x or y) by a Gaussian.
blurFloat(FloatProcessor, double, double, double) - Method in class ij.plugin.filter.GaussianBlur
  Gaussian Filtering of a FloatProcessor.
blurGaussian(ImageProcessor, double, double, double) - Method in class ij.plugin.filter.GaussianBlur
  Gaussian Filtering of an ImageProcessor.
boldFont - Variable in class ij.process.ImageProcessor
buildControlDialog(int, int) - Method in class ij.plugin.ZProjector
  Builds dialog to query users for projection parameters.
button - Variable in class ij.gui.MessageDialog

## C

CALCULATOR - Static variable in interface ij.macro.MacroConstants
CALIBRATE - Static variable in interface ij.macro.MacroConstants
CALL - Static variable in interface ij.macro.MacroConstants
CANCELED - Static variable in class ij.IJ
CENTER_JUSTIFY - Static variable in class ij.process.ImageProcessor
  Center justify text.
CENTER_OF_MASS - Static variable in interface ij.measure.Measurements
CENTROID - Static variable in interface ij.measure.Measurements
CHANGE_VALUES - Static variable in interface ij.macro.MacroConstants
CHAR_CODE_AT - Static variable in interface ij.macro.MacroConstants
CHECK_AVAILABLE_MEMORY - Static variable in class ij.gui.NewImage
CIRCLE - Static variable in class ij.gui.Plot
  Display points using a circle 5 pixels in diameter.
CIRCLE - Static variable in class ij.gui.PlotWindow
  Display points using a circle 5 pixels in diameter.
CIRCULARITY - Static variable in interface ij.measure.Measurements
CIRCULARITY - Static variable in class ij.measure.ResultsTable
CLEAR_WORKSHEET - Static variable in class ij.plugin.filter.ParticleAnalyzer
  Clear ImageJ console before starting.
CLOSE - Static variable in interface ij.macro.MacroConstants
CLOSED - Static variable in class ij.ImagePlus
COLOR8 - Static variable in class ij.io.FileInfo
  8-bit unsigned integer with color lookup table.
COLOR_256 - Static variable in class ij.ImagePlus
  8-bit indexed color
COLOR_MAP - Static variable in class ij.io.TiffDecoder
COLOR_RGB - Static variable in class ij.ImagePlus
  32-bit RGB color
COLUMN_IN_USE - Static variable in class ij.measure.ResultsTable
COLUMN_NOT_FOUND - Static variable in class ij.measure.ResultsTable
COMMAND_IN_USE - Static variable in class ij.Menus
COMMAND_NOT_FOUND - Static variable in class ij.Menus
COMPOSITE - Static variable in class ij.gui.Roi
COMPOUND_FILTER - Static variable in class ij.Undo
COMPOUND_FILTER_DONE - Static variable in class ij.Undo
COMPRESSION - Static variable in class ij.io.TiffDecoder
COMPRESSION_NONE - Static variable in class ij.io.FileInfo
COMPRESSION_UNKNOWN - Static variable in class ij.io.FileInfo
CONSTRUCTING - Static variable in class ij.gui.Roi
CONVERT_TO_FLOAT - Static variable in interface ij.plugin.filter.PlugInFilter
  Set this flag to have the ImageProcessor that is passed to the run() method converted to a FloatProcessor.
COPY - Static variable in interface ij.process.Blitter
  dst=src
COPY_INVERTED - Static variable in interface ij.process.Blitter
  dst=255-src (8-bits and RGB)
COPY_TRANSPARENT - Static variable in interface ij.process.Blitter
  Copies with white pixels transparent.
COS - Static variable in interface ij.macro.MacroConstants
COUNT - Static variable in class ij.plugin.filter.MaximumFinder
  Do not create an image, just count maxima and add count to Results table
CROSS - Static variable in class ij.gui.Plot
  Display points using an cross-shaped mark.
CROSS - Static variable in class ij.gui.PlotWindow
  Display points using an cross-shaped mark.
CROSSHAIR - Static variable in class ij.gui.Toolbar
CUSTOM - Static variable in class ij.io.Opener
CUSTOM - Static variable in class ij.measure.Calibration
Calibration - class ij.measure.Calibration.
  Calibration objects contain an image's spatial and density calibration data.
Calibration(ImagePlus) - Constructor for class ij.measure.Calibration
  Constructs a new Calibration object using the default values.
Calibration() - Constructor for class ij.measure.Calibration
  Constructs a new Calibration object using the default values.
CalibrationBar - class ij.plugin.filter.CalibrationBar.
  This plugin displays a calibration bar on the active image.
CalibrationBar() - Constructor for class ij.plugin.filter.CalibrationBar
Calibrator - class ij.plugin.filter.Calibrator.
  Implements the Analyze/Calibrate command.
Calibrator() - Constructor for class ij.plugin.filter.Calibrator
CanvasResizer - class ij.plugin.CanvasResizer.
  This plugin implements the Image/Adjust/Canvas Size command.
CanvasResizer() - Constructor for class ij.plugin.CanvasResizer
ClassChecker - class ij.plugin.ClassChecker.
  Checks for duplicate class files in the plugins directory and deletes older duplicates.
ClassChecker() - Constructor for class ij.plugin.ClassChecker
Clipboard - class ij.plugin.Clipboard.
  Copies and pastes images to the clipboard.
Clipboard() - Constructor for class ij.plugin.Clipboard
ColorBlitter - class ij.process.ColorBlitter.
  This class does bit blitting of RGB images.
ColorBlitter(ColorProcessor) - Constructor for class ij.process.ColorBlitter
  Constructs a ColorBlitter from a ColorProcessor.
ColorChooser - class ij.gui.ColorChooser.
  Displays a dialog that allows the user to select a color using three sliders.
ColorChooser(String, Color, boolean) - Constructor for class ij.gui.ColorChooser
  Constructs a ColorChooser using the specified title and initial color.
ColorPicker - class ij.plugin.ColorPicker.
  Implements the Image/Color/Color Picker command.
ColorPicker() - Constructor for class ij.plugin.ColorPicker
ColorProcessor - class ij.process.ColorProcessor.
  This is an 32-bit RGB image and methods that operate on that image..
ColorProcessor(Image) - Constructor for class ij.process.ColorProcessor
  Creates a ColorProcessor from an AWT Image.
ColorProcessor(int, int) - Constructor for class ij.process.ColorProcessor
  Creates a blank ColorProcessor of the specified dimensions.
ColorProcessor(int, int, int[]) - Constructor for class ij.process.ColorProcessor
  Creates a ColorProcessor from a pixel array.
ColorStatistics - class ij.process.ColorStatistics.
  RGB image statistics, including histogram.
ColorStatistics(ImageProcessor) - Constructor for class ij.process.ColorStatistics
  Construct an ImageStatistics object from a ColorProcessor using the standard measurement options (area, mean, mode, min and max).
ColorStatistics(ImageProcessor, int, Calibration) - Constructor for class ij.process.ColorStatistics
  Constructs a ColorStatistics object from a ColorProcessor using the specified measurement options.
Colors - class ij.plugin.Colors.
  This plugin implements most of the Edit/Options/Colors command.
Colors() - Constructor for class ij.plugin.Colors
CommandLister - class ij.plugin.CommandLister.
  Lists ImageJ commands or keyboard shortcuts in a text window.
CommandLister() - Constructor for class ij.plugin.CommandLister
Commands - class ij.plugin.Commands.
  Runs File and Window menu commands.
Commands() - Constructor for class ij.plugin.Commands
Compiler - class ij.plugin.Compiler.
  Compiles and runs plugins using the javac compiler.
Compiler() - Constructor for class ij.plugin.Compiler
CompositeImage - class ij.CompositeImage.
CompositeImage(ImagePlus, int) - Constructor for class ij.CompositeImage
Composite_Image - class ij.plugin.Composite_Image.
Composite_Image() - Constructor for class ij.plugin.Composite_Image
ContrastAdjuster - class ij.plugin.frame.ContrastAdjuster.
  This plugin implements the Brightness/Contrast, Window/level and Color Balance commands, all in the Image/Adjust sub-menu.
ContrastAdjuster() - Constructor for class ij.plugin.frame.ContrastAdjuster
ContrastEnhancer - class ij.plugin.ContrastEnhancer.
  Implements ImageJ's Process/Enhance Contrast command.
ContrastEnhancer() - Constructor for class ij.plugin.ContrastEnhancer
ControlPanel - class ij.plugin.ControlPanel.
  ControlPanel.
ControlPanel() - Constructor for class ij.plugin.ControlPanel
Converter - class ij.plugin.Converter.
  Implements the conversion commands in the Image/Type submenu.
Converter() - Constructor for class ij.plugin.Converter
Convolver - class ij.plugin.filter.Convolver.
  This plugin convolves images using user user defined kernels.
Convolver() - Constructor for class ij.plugin.filter.Convolver
CurveFitter - class ij.measure.CurveFitter.
  Curve fitting class based on the Simplex method described in the article "Fitting Curves to Data" in the May 1984 issue of Byte magazine, pages 340-362.
CurveFitter(double[], double[]) - Constructor for class ij.measure.CurveFitter
  Construct a new CurveFitter.
c2hex(Color) - Static method in class ij.util.Tools
  Converts a Color to an 7 byte hex string starting with '#'.
cTable - Variable in class ij.process.ImageProcessor
cache - Variable in class ij.io.PluginClassLoader
cachedMask - Variable in class ij.gui.Roi
cal - Variable in class ij.gui.HistogramWindow
cal - Variable in class ij.process.ImageStatistics
calculate(String, ImagePlus, ImagePlus) - Method in class ij.plugin.ImageCalculator
calibrate(ImagePlus) - Method in class ij.plugin.filter.Calibrator
calibrated() - Method in class ij.measure.Calibration
  Returns true if this image is density calibrated.
calibrationFunction - Variable in class ij.io.FileInfo
canEnlarge(int, int) - Method in class ij.gui.ImageCanvas
cancelPressed() - Method in class ij.gui.SaveChangesDialog
  Returns true if the user dismissed dialog by pressing "Cancel".
cancelPressed() - Method in class ij.gui.YesNoCancelDialog
  Returns true if the user dismissed dialog by pressing "Cancel".
center(Window) - Static method in class ij.gui.GUI
  Positions the specified window in the center of the screen.
center - Variable in class ij.gui.Roi
centerNextImage() - Static method in class ij.gui.ImageWindow
  Causes the next image to be opened to be centered on the screen and displayed without informational text above the image.
changeFont(Font) - Method in class ij.gui.Plot
  Changes the font.
changeFont(Font) - Method in class ij.gui.PlotWindow
  Changes the font.
changes - Variable in class ij.ImagePlus
  True if any changes have been made to this image.
checkForDuplicateName - Static variable in class ij.WindowManager
checkbox - Variable in class ij.gui.GenericDialog
choice - Variable in class ij.gui.GenericDialog
clear(ImageProcessor) - Method in class ij.plugin.filter.Filler
clear() - Method in class ij.text.TextPanel
  Deletes all the lines.
clearOutside(ImageProcessor) - Method in class ij.plugin.filter.Filler
clearSelection() - Method in class ij.text.TextPanel
  Deletes the selected lines.
clipHeight - Variable in class ij.gui.Roi
clipWidth - Variable in class ij.gui.Roi
clipX - Variable in class ij.gui.Roi
clipXMax - Variable in class ij.process.ImageProcessor
clipXMin - Variable in class ij.process.ImageProcessor
clipY - Variable in class ij.gui.Roi
clipYMax - Variable in class ij.process.ImageProcessor
clipYMin - Variable in class ij.process.ImageProcessor
clipboard - Variable in class ij.gui.Roi
clone() - Method in class ij.gui.PolygonRoi
  Returns a copy of this PolygonRoi.
clone() - Method in class ij.gui.Roi
  Returns a copy of this roi.
clone() - Method in class ij.gui.ShapeRoi
  Returns a deep copy of this.
clone() - Method in class ij.measure.Calibration
clone() - Method in class ij.measure.ResultsTable
  Creates a copy of this ResultsTable.
close() - Method in class ij.ImagePlus
  Closes this image and sets the pixel arrays to null.
close() - Method in class ij.gui.ImageWindow
  Removes this window from the window list and disposes of it.
close() - Method in class ij.gui.StackWindow
close() - Method in class ij.io.RandomAccessStream
close() - Method in class ij.plugin.frame.ContrastAdjuster
  Overrides close() in PlugInFrame.
close() - Method in class ij.plugin.frame.Editor
  Overrides close() in PlugInFrame.
close() - Method in class ij.plugin.frame.LineWidthAdjuster
  Overrides close() in PlugInFrame.
close() - Method in class ij.plugin.frame.PasteController
close() - Method in class ij.plugin.frame.PlugInFrame
  Closes this window.
close() - Method in class ij.plugin.frame.Recorder
close() - Method in class ij.plugin.frame.RoiManager
  Overrides PlugInFrame.close().
close() - Method in class ij.plugin.frame.ThresholdAdjuster
  Overrides close() in PlugInFrame.
close() - Method in class ij.text.TextWindow
closeAllWindows() - Static method in class ij.WindowManager
  Closes all windows.
closed - Variable in class ij.gui.ImageWindow
cm - Variable in class ij.process.ImageProcessor
cm2 - Variable in class ij.process.ImageProcessor
coefficients - Variable in class ij.io.FileInfo
columnExists(int) - Method in class ij.measure.ResultsTable
  Returns true if the specified column exists and is not empty.
commandInUse(String) - Static method in class ij.Menus
commandPrefix - Static variable in class ij.plugin.MacroInstaller
compositeImage - Variable in class ij.ImagePlus
compression - Variable in class ij.io.FileInfo
conjugateMultiply(FHT) - Method in class ij.process.FHT
  Returns the image resulting from the point by point Hartley conjugate multiplication of this image and the specified image.
constrain - Variable in class ij.gui.Roi
contains(int, int) - Method in class ij.gui.Line
contains(int, int) - Method in class ij.gui.OvalRoi
  Tests if the specified point is inside the boundary of this OvalRoi.
contains(int, int) - Method in class ij.gui.PointRoi
  Returns true if (x,y) is one of the points in this collection.
contains(int, int) - Method in class ij.gui.PolygonRoi
contains(int, int) - Method in class ij.gui.Roi
contains(int, int) - Method in class ij.gui.ShapeRoi
  Checks whether the specified coordinates are inside a on this ROI's shape boundaries.
convert(String) - Method in class ij.plugin.Converter
  Converts the ImagePlus to the specified image type.
convert(int) - Method in class ij.process.MedianCut
  Uses Heckbert's median-cut algorithm to divide the color space defined by "hist" into "maxcubes" cubes.
convertGrayJpegTo8Bits(ImagePlus) - Static method in class ij.io.Opener
  If this image is grayscale, convert it to 8-bits.
convertHSBToRGB() - Method in class ij.process.ImageConverter
  Converts a 3-slice (hue, saturation, brightness) 8-bit stack to RGB.
convertImagesToStack() - Method in class ij.plugin.StackEditor
convertRGBStackToRGB() - Method in class ij.process.ImageConverter
  Converts a 2 or 3 slice 8-bit stack to RGB.
convertRGBtoIndexedColor(int) - Method in class ij.process.ImageConverter
  Converts an RGB image to 8-bits indexed color.
convertShortcutToCode(String) - Static method in class ij.Menus
convertStackToImages(ImagePlus) - Method in class ij.plugin.StackEditor
convertToByte(boolean) - Method in class ij.process.ImageProcessor
  Returns an 8-bit version of this image as a ByteProcessor.
convertToByte(int) - Method in class ij.process.MedianCut
  This is a version of convert that returns a ByteProcessor.
convertToByte() - Method in class ij.process.TypeConverter
  Converts processor to a ByteProcessor.
convertToFloat() - Method in class ij.process.ImageProcessor
  Returns a 32-bit float version of this image as a FloatProcessor.
convertToFloat(float[]) - Method in class ij.process.TypeConverter
  Converts processor to a FloatProcessor.
convertToGray16() - Method in class ij.process.ImageConverter
  Converts this ImagePlus to 16-bit grayscale.
convertToGray16() - Method in class ij.process.StackConverter
  Converts this Stack to 16-bit grayscale.
convertToGray32() - Method in class ij.process.ImageConverter
  Converts this ImagePlus to 32-bit grayscale.
convertToGray32() - Method in class ij.process.StackConverter
  Converts this Stack to 32-bit (float) grayscale.
convertToGray8() - Method in class ij.process.ImageConverter
  Converts this ImagePlus to 8-bit grayscale.
convertToGray8() - Method in class ij.process.StackConverter
  Converts this Stack to 8-bit grayscale.
convertToHSB() - Method in class ij.process.ImageConverter
  Converts an RGB image to a HSB (hue, saturation and brightness) stack.
convertToIndexedColor(int) - Method in class ij.process.StackConverter
  Converts the stack to 8-bits indexed color.
convertToRGB() - Method in class ij.process.ImageConverter
  Converts this ImagePlus to RGB.
convertToRGB() - Method in class ij.process.ImageProcessor
  Returns an RGB version of this image as a ColorProcessor.
convertToRGB() - Method in class ij.process.StackConverter
  Converts the Stack to RGB.
convertToRGB() - Method in class ij.process.TypeConverter
  Converts processor to a ColorProcessor.
convertToRGBStack() - Method in class ij.process.ImageConverter
  Converts an RGB image to an RGB (red, green and blue) stack.
convertToShort(boolean) - Method in class ij.process.ImageProcessor
  Returns a 16-bit version of this image as a ShortProcessor.
convertToShort() - Method in class ij.process.TypeConverter
  Converts processor to a ShortProcessor.
convolve(ImageProcessor, float[], int, int) - Method in class ij.plugin.filter.Convolver
convolve(float[], int, int) - Method in class ij.process.ByteProcessor
  Performs a convolution operation using the specified kernel.
convolve(float[], int, int) - Method in class ij.process.ColorProcessor
  Performs a convolution operation using the specified kernel.
convolve(float[], int, int) - Method in class ij.process.FloatProcessor
  Performs a convolution operation using the specified kernel.
convolve(float[], int, int) - Method in class ij.process.ImageProcessor
  Performs a convolution operation using the specified kernel.
convolve(float[], int, int) - Method in class ij.process.ShortProcessor
  Performs a convolution operation using the specified kernel.
convolve3x3(int[]) - Method in class ij.process.ByteProcessor
  3x3 convolution contributed by Glynne Casteel.
convolve3x3(int[]) - Method in class ij.process.ColorProcessor
  3x3 convolution contributed by Glynne Casteel.
convolve3x3(int[]) - Method in class ij.process.FloatProcessor
  3x3 convolution contributed by Glynne Casteel.
convolve3x3(int[]) - Method in class ij.process.ImageProcessor
  Convolves the image or ROI with the specified 3x3 integer convolution kernel.
convolve3x3(int[]) - Method in class ij.process.ShortProcessor
  3x3 convolution contributed by Glynne Casteel.
convolveFloat(ImageProcessor, float[], int, int) - Method in class ij.plugin.filter.Convolver
  Convolves the image `ip` with a kernel of width `kw` and height `kh`.
convolveLine(float[], float[], float[][], int, int, int, int, int, int) - Method in class ij.plugin.filter.GaussianBlur
  Convolve a line with a symmetric kernel and write to a separate array, possibly the pixels array of a FloatProcessor (as a row or column or part thereof)
copy(boolean) - Method in class ij.ImagePlus
  Copies the contents of the current selection to the internal clipboard.
copy - Variable in class ij.gui.HistogramWindow
copy(boolean) - Method in class ij.gui.ImageWindow
  Copies the current ROI to the clipboard.
copy() - Method in class ij.measure.Calibration
  Returns a clone of this object.
copyBits(ImageProcessor, int, int, int) - Method in interface ij.process.Blitter
  Copies the image in 'src' to (x,y) using the specified mode.
copyBits(ImageProcessor, int, int, int) - Method in class ij.process.ByteBlitter
  Copies the byte image in 'ip' to (x,y) using the specified mode.
copyBits(ImageProcessor, int, int, int) - Method in class ij.process.ByteProcessor
  Copies the image contained in 'ip' to (xloc, yloc) using one of the transfer modes defined in the Blitter interface.
copyBits(ImageProcessor, int, int, int) - Method in class ij.process.ColorBlitter
  Copies the RGB image in 'ip' to (x,y) using the specified mode.
copyBits(ImageProcessor, int, int, int) - Method in class ij.process.ColorProcessor
  Copies the image contained in 'ip' to (xloc, yloc) using one of the transfer modes defined in the Blitter interface.
copyBits(ImageProcessor, int, int, int) - Method in class ij.process.FloatBlitter
  Copies the float image in 'ip' to (x,y) using the specified mode.
copyBits(ImageProcessor, int, int, int) - Method in class ij.process.FloatProcessor
  Copies the image contained in 'ip' to (xloc, yloc) using one of the transfer modes defined in the Blitter interface.
copyBits(ImageProcessor, int, int, int) - Method in class ij.process.ImageProcessor
  Copies the image contained in 'ip' to (xloc, yloc) using one of the transfer modes defined in the Blitter interface.
copyBits(ImageProcessor, int, int, int) - Method in class ij.process.ShortBlitter
  Copies the 16-bit image in 'ip' to (x,y) using the specified mode.
copyBits(ImageProcessor, int, int, int) - Method in class ij.process.ShortProcessor
  Copies the image contained in 'ip' to (xloc, yloc) using one of the transfer modes defined in the Blitter interface.
copyBits(ImageProcessor, int, int, int) - Method in class ij.process.StackProcessor
copyBits(ImageStack, int, int, int) - Method in class ij.process.StackProcessor
copyScale(ImagePlus) - Method in class ij.ImagePlus
  Copies the calibration of the specified image to this image.
copySelection() - Method in class ij.text.TextPanel
  Copies the current selection to the system clipboard.
copyToClipboard() - Method in class ij.gui.HistogramWindow
count - Variable in class ij.gui.HistogramWindow
create(String, String) - Method in class ij.plugin.frame.Editor
createBlankImage(int, int) - Static method in class ij.gui.GUI
  Creates a white AWT Image image of the specified size.
createByteImage(String, int, int, int, int) - Static method in class ij.gui.NewImage
createColorModel(FileInfo) - Method in class ij.io.FileOpener
  Returns an IndexColorModel for the image specified by this FileInfo.
createEmptyStack() - Method in class ij.ImagePlus
  Returns an empty image stack that has the same width, height and color table as this image.
createFloatImage(String, int, int, int, int) - Static method in class ij.gui.NewImage
createGrayscaleColorModel(boolean) - Static method in class ij.LookUpTable
createImage(String, String, int, int, int) - Static method in class ij.IJ
  Creates a new imagePlus.
createImage(String, int, int, int, int, int) - Static method in class ij.gui.NewImage
createImage() - Method in class ij.process.ByteProcessor
createImage() - Method in class ij.process.ColorProcessor
createImage() - Method in class ij.process.FloatProcessor
createImage() - Method in class ij.process.ImageProcessor
  Returns a copy of this image is the form of an AWT Image.
createImage() - Method in class ij.process.ShortProcessor
  Create an 8-bit AWT image by scaling pixels in the range min-max to 0-255.
createImagePlus() - Method in class ij.ImagePlus
  Returns a new ImagePlus with this ImagePlus' attributes (e.g.
createInputStream(FileInfo) - Method in class ij.io.FileOpener
  Returns an InputStream for the image described by this FileInfo.
createLUT() - Method in class ij.plugin.filter.AVIWriter
createLut() - Method in class ij.ImagePlus
  Creates a LookUpTable object corresponding to this image.
createMacro(String) - Method in class ij.plugin.NewPlugin
createMacro(String, String) - Method in class ij.plugin.frame.Editor
createModelFromColor(Color) - Static method in class ij.CompositeImage
createNewRoi(int, int) - Method in class ij.ImagePlus
  Starts the process of creating a new selection, where sx and sy are the starting screen coordinates.
createPlugin(String, int, String) - Method in class ij.plugin.NewPlugin
createProcessor(int, int) - Method in class ij.process.ByteProcessor
  Returns a new, blank ByteProcessor with the specified width and height.
createProcessor(int, int) - Method in class ij.process.ColorProcessor
  Returns a new, blank ShortProcessor with the specified width and height.
createProcessor(int, int) - Method in class ij.process.FloatProcessor
  Returns a new, blank FloatProcessor with the specified width and height.
createProcessor(int, int) - Method in class ij.process.ImageProcessor
  Returns a new, blank processor with the specified width and height.
createProcessor(int, int) - Method in class ij.process.ShortProcessor
  Returns a new, blank ShortProcessor with the specified width and height.
createRGBImage(String, int, int, int, int) - Static method in class ij.gui.NewImage
createShortImage(String, int, int, int, int) - Static method in class ij.gui.NewImage
  Creates an unsigned short image.
createSubtitle() - Method in class ij.gui.ImageWindow
  Creates the subtitle.
createUnsignedShortImage(String, int, int, int, int) - Static method in class ij.gui.NewImage
  Obsolete.
createWindow() - Method in class ij.gui.ProfilePlot
  Displays this profile plot in a window.
crop() - Method in class ij.process.ByteProcessor
crop() - Method in class ij.process.ColorProcessor
crop() - Method in class ij.process.FloatProcessor
crop() - Method in class ij.process.ImageProcessor
  Creates a new processor containing an image that corresponds to the current ROI.
crop() - Method in class ij.process.ShortProcessor
crop(int, int, int, int) - Method in class ij.process.StackProcessor
  Crops the stack to the specified rectangle.
crosshairCursor - Static variable in class ij.gui.ImageCanvas
currentMemory() - Static method in class ij.IJ
  Returns the amount of memory currently being used by ImageJ.
currentSlice - Variable in class ij.ImagePlus
cx - Variable in class ij.process.ImageProcessor
cy - Variable in class ij.process.ImageProcessor

## D

D2S - Static variable in interface ij.macro.MacroConstants
DATE_TIME - Static variable in class ij.io.TiffDecoder
DEFAULT_FLAGS - Static variable in class ij.gui.Plot
  the default flags
DEFAULT_PORT - Static variable in class ij.ImageJ
  Address of socket where Image accepts commands
DEFAULT_QUALITY - Static variable in class ij.plugin.JpegWriter
DESPECKLE - Static variable in class ij.plugin.filter.RankFilters
DIALOG - Static variable in interface ij.macro.MacroConstants
DICOM - Static variable in class ij.io.FileInfo
DICOM - Static variable in class ij.io.Opener
DICOM - class ij.plugin.DICOM.
  This plugin decodes DICOM files.
DICOM() - Constructor for class ij.plugin.DICOM
  Default constructor.
DICOM(InputStream) - Constructor for class ij.plugin.DICOM
  Constructs a DICOM reader that using an InputStream.
DICOM(BufferedInputStream) - Constructor for class ij.plugin.DICOM
  Constructs a DICOM reader that using an BufferredInputStream.
DICOM_Sorter - class ij.plugin.DICOM_Sorter.
DICOM_Sorter() - Constructor for class ij.plugin.DICOM_Sorter
DIFFERENCE - Static variable in interface ij.process.Blitter
  dst=abs(dst-src)
DIR_IMAGE - Static variable in class ij.Prefs
DISPLAY_SUMMARY - Static variable in class ij.plugin.filter.ParticleAnalyzer
  Display a summary.
DIVIDE - Static variable in interface ij.process.Blitter
  dst=dst/src
DIV_BY_ZERO_VALUE - Static variable in class ij.Prefs
DIV_EQUAL - Static variable in interface ij.macro.MacroConstants
DO - Static variable in interface ij.macro.MacroConstants
DOES_16 - Static variable in interface ij.plugin.filter.PlugInFilter
  Set this flag if the filter handles 16-bit images.
DOES_32 - Static variable in interface ij.plugin.filter.PlugInFilter
  Set this flag if the filter handles float images.
DOES_8C - Static variable in interface ij.plugin.filter.PlugInFilter
  Set this flag if the filter handles 8-bit indexed color images.
DOES_8G - Static variable in interface ij.plugin.filter.PlugInFilter
  Set this flag if the filter handles 8-bit grayscale images.
DOES_ALL - Static variable in interface ij.plugin.filter.PlugInFilter
  Set this flag if the filter handles all types of images.
DOES_RGB - Static variable in interface ij.plugin.filter.PlugInFilter
  Set this flag if the filter handles RGB images.
DOES_STACKS - Static variable in interface ij.plugin.filter.PlugInFilter
  Set this flag if the filter wants its run() method to be called for all the slices in a stack.
DONE - Static variable in interface ij.plugin.filter.PlugInFilter
  Set this flag if the filter does not want its run method called.
DOT - Static variable in class ij.gui.Plot
  Display points using a single pixel.
DOUBLE_CLICK_THRESHOLD - Static variable in class ij.gui.Toolbar
DO_COMMAND - Static variable in interface ij.macro.MacroConstants
DO_WAND - Static variable in interface ij.macro.MacroConstants
DRAW_LINE - Static variable in interface ij.macro.MacroConstants
DRAW_OVAL - Static variable in interface ij.macro.MacroConstants
DRAW_RECT - Static variable in interface ij.macro.MacroConstants
DRAW_STRING - Static variable in interface ij.macro.MacroConstants
DROPPER - Static variable in class ij.gui.Toolbar
DUMP - Static variable in interface ij.macro.MacroConstants
DialogListener - interface ij.gui.DialogListener.
  PlugIns or PlugInFilters that want to listen to changes in a GenericDialog without adding listeners for each dialog field should implement this method.
DirectoryChooser - class ij.io.DirectoryChooser.
  This class displays a dialog box that allows the user can select a directory.
DirectoryChooser(String) - Constructor for class ij.io.DirectoryChooser
  Display a dialog using the specified title.
Distribution - class ij.plugin.Distribution.
  This plugin implements the Analyze/Distribution command.
Distribution() - Constructor for class ij.plugin.Distribution
DragAndDrop - class ij.plugin.DragAndDrop.
  This class opens images, roi's, luts and text files dragged and dropped on the "ImageJ" window.
DragAndDrop() - Constructor for class ij.plugin.DragAndDrop
Duplicater - class ij.plugin.filter.Duplicater.
  This plugin implements ImageJ's Image/Duplicate command.
Duplicater() - Constructor for class ij.plugin.filter.Duplicater
d2s(double) - Static method in class ij.IJ
  Converts a number to a formatted string using 2 digits to the right of the decimal point.
d2s(double, int) - Static method in class ij.IJ
  Converts a number to a rounded formatted string.
darkBlue - Static variable in class ij.plugin.filter.Analyzer
debugInfo - Variable in class ij.io.FileInfo
debugMode - Static variable in class ij.IJ
debugMode - Variable in class ij.io.TiffDecoder
decimalPlaces - Variable in class ij.gui.HistogramWindow
decodeToken(int) - Method in class ij.macro.Program
defaultColorModel - Static variable in class ij.process.ImageProcessor
defaultCursor - Static variable in class ij.gui.ImageCanvas
defaultDirectory - Static variable in class ij.gui.HistogramWindow
defaultText - Variable in class ij.gui.GenericDialog
defaultValues - Variable in class ij.gui.GenericDialog
degreeSymbol - Static variable in class ij.IJ
deleteLastSlice() - Method in class ij.ImageStack
  Deletes the last slice in the stack.
deleteLastSlice() - Method in class ij.VirtualStack
  Deletes the last slice in the stack.
deleteRow(int) - Method in class ij.measure.ResultsTable
  Deletes the specified row.
deleteSlice(int) - Method in class ij.ImageStack
  Deletes the specified slice, were 1<=n<=nslices.
deleteSlice(int) - Method in class ij.VirtualStack
  Deletes the specified slice, were 1<=n<=nslices.
description - Variable in class ij.io.FileInfo
destroy() - Method in class ij.ImageJApplet
dfht3(float[], int, boolean, int) - Method in class ij.process.FHT
  Performs an optimized 1D FHT.
dialogItemChanged(GenericDialog, AWTEvent) - Method in interface ij.gui.DialogListener
  This method is invoked by a Generic Dialog if any of the inputs have changed (CANCEL does not trigger it; OK and running the dialog from a macro only trigger the first DialogListener added to a GenericDialog).
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.plugin.SpecifyROI
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.plugin.filter.Convolver
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.plugin.filter.GaussianBlur
  Listener to modifications of the input fields of the dialog
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.plugin.filter.MaximumFinder
  Read the parameters (during preview or after showing the dialog)
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.plugin.filter.PlugInFilterRunner
  The listener to any change in the dialog.
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.plugin.filter.RankFilters
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.plugin.filter.Rotator
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.plugin.filter.UnsharpMask
digits - Variable in class ij.gui.HistogramWindow
dilate() - Method in class ij.process.ByteProcessor
dilate(int, int) - Method in class ij.process.ByteProcessor
dilate() - Method in class ij.process.ColorProcessor
dilate() - Method in class ij.process.FloatProcessor
  Not implemented.
dilate() - Method in class ij.process.ImageProcessor
  Dilates the image or ROI using a 3x3 minimum filter.
dilate() - Method in class ij.process.ShortProcessor
  Not implemented.
directory - Variable in class ij.io.FileInfo
disableDensityCalibration() - Method in class ij.measure.Calibration
disablePathRecording() - Static method in class ij.plugin.frame.Recorder
  Temporarily disables path recording.
disablePopupMenu(boolean) - Method in class ij.gui.ImageCanvas
  Disable/enable popup menu.
disableRowLabels() - Method in class ij.measure.ResultsTable
  Set the row label column to null.
disableUndo - Static variable in class ij.Prefs
  Disable Edit/Undo command.
display(String, String) - Method in class ij.plugin.frame.Editor
displayComplex - Static variable in class ij.plugin.FFT
displayFHT - Static variable in class ij.plugin.FFT
displayRawPS - Static variable in class ij.plugin.FFT
displayResults() - Method in class ij.plugin.filter.Analyzer
  Writes the last row in the results table to the ImageJ window.
displaySummary - Variable in class ij.plugin.filter.ParticleAnalyzer
divide(FHT) - Method in class ij.process.FHT
  Returns the image resulting from the point by point Hartley division of this image by the specified image.
divideByZeroValue - Static variable in class ij.process.FloatBlitter
dmode - Variable in class ij.process.ImageStatistics
doCommand(String) - Static method in class ij.IJ
  Starts executing a menu command in a separete thread and returns immediately.
doFiltering(FloatProcessor, int, int[], int, int, float) - Method in class ij.plugin.filter.RankFilters
  Filter a FloatProcessor according to filterType
doFit(int) - Method in class ij.measure.CurveFitter
  Perform curve fitting with the simplex method doFit(fitType) just does the fit doFit(fitType, true) pops up a dialog allowing control over simplex parameters alpha is reflection coefficient (-1) beta is contraction coefficient (0.5) gamma is expansion coefficient (2)
doFit(int, boolean) - Method in class ij.measure.CurveFitter
doFit(int) - Method in class ij.plugin.frame.Fitter
doMath(ImagePlus, ImagePlus) - Method in class ij.plugin.FFTMath
doOptions() - Method in class ij.plugin.filter.Profiler
doProjection() - Method in class ij.plugin.ZProjector
  Performs actual projection using specified method.
doProjections(ImagePlus) - Method in class ij.plugin.filter.Projector
doRGBProjection() - Method in class ij.plugin.ZProjector
doRGBProjections(ImagePlus) - Method in class ij.plugin.filter.Projector
doWand(int, int) - Static method in class ij.IJ
  Equivalent to clicking on the current image at (x,y) with the wand tool.
done - Variable in class ij.gui.StackWindow
doubleBuffer - Static variable in class ij.Prefs
  Double buffer display of selections.
dragEnter(DropTargetDragEvent) - Method in class ij.plugin.DragAndDrop
dragExit(DropTargetEvent) - Method in class ij.plugin.DragAndDrop
dragOver(DropTargetDragEvent) - Method in class ij.plugin.DragAndDrop
draw() - Method in class ij.ImagePlus
  Draws the image.
draw(int, int, int, int) - Method in class ij.ImagePlus
  Draws image and roi outline using a clip rect.
draw(Graphics) - Method in class ij.gui.Line
  Draws this line in the image.
draw(Graphics) - Method in class ij.gui.OvalRoi
draw() - Method in class ij.gui.Plot
  Draws the plot specified in the constructor.
draw() - Method in class ij.gui.PlotWindow
  Displays the plot.
draw(Graphics) - Method in class ij.gui.PointRoi
  Draws the points on the image.
draw(Graphics) - Method in class ij.gui.PolygonRoi
draw(Graphics) - Method in class ij.gui.Roi
draw(Graphics) - Method in class ij.gui.ShapeRoi
  Non-destructively draws the shape of this object on the associated ImagePlus.
draw(Graphics) - Method in class ij.gui.TextRoi
  Draws the text on the screen, clipped to the ROI.
draw(ImageProcessor) - Method in class ij.plugin.filter.Filler
drawColorBar(Graphics, int, int, int, int) - Method in class ij.LookUpTable
drawColorBar(ImageProcessor, int, int) - Method in class ij.plugin.filter.CalibrationBar
drawColorBar(ImagePlus, int, int) - Method in class ij.plugin.filter.CalibrationBar
drawDot(int, int) - Method in class ij.process.ImageProcessor
  Draws a dot using the current line width and fill/draw value.
drawDot2(int, int) - Method in class ij.process.ImageProcessor
  Obsolete
drawEllipse(ImageProcessor) - Method in class ij.process.EllipseFitter
  Draws the ellipse on the specified image.
drawEllipse(ImageProcessor) - Method in class ij.process.ImageStatistics
drawHistogram(ImageProcessor, boolean) - Method in class ij.gui.HistogramWindow
drawInfo(Graphics) - Method in class ij.gui.ImageWindow
  Draws the subtitle.
drawLabel(ImagePlus, ImageProcessor, int, Rectangle) - Method in class ij.plugin.filter.Filler
drawLine(int, int, int, int) - Method in class ij.process.ImageProcessor
  Draws a line from (x1,y1) to (x2,y2).
drawOval(int, int, int, int) - Method in class ij.process.ImageProcessor
  Draws an elliptical shape.
drawParticle(ImageProcessor, Roi, ImageStatistics, ImageProcessor) - Method in class ij.plugin.filter.ParticleAnalyzer
  Draws a selected particle in a separate image.
drawPixel(int, int) - Method in class ij.process.ByteProcessor
  Draws a pixel in the current foreground color.
drawPixel(int, int) - Method in class ij.process.ColorProcessor
  Draws a pixel in the current foreground color.
drawPixel(int, int) - Method in class ij.process.FloatProcessor
  Draws a pixel in the current foreground color.
drawPixel(int, int) - Method in class ij.process.ImageProcessor
  Sets the pixel at (x,y) to the current fill/draw value.
drawPixel(int, int) - Method in class ij.process.ShortProcessor
  Draws a pixel in the current foreground color.
drawPixels(ImageProcessor) - Method in class ij.gui.Line
drawPixels(ImageProcessor) - Method in class ij.gui.OvalRoi
  Draws an outline of this OvalRoi on the image.
drawPixels(ImageProcessor) - Method in class ij.gui.PointRoi
drawPixels(ImageProcessor) - Method in class ij.gui.PolygonRoi
drawPixels() - Method in class ij.gui.Roi
  Obsolete, use drawPixels(ImageProcessor)
drawPixels(ImageProcessor) - Method in class ij.gui.Roi
  Draws the selection outline on the specified ImageProcessor.
drawPixels(ImageProcessor) - Method in class ij.gui.ShapeRoi
  Draws the shape of this object onto the specified ImageProcessor.
drawPixels(ImageProcessor) - Method in class ij.gui.TextRoi
  Renders the text on the image.
drawPlot(Plot) - Method in class ij.gui.PlotWindow
  Draws a new plot in this window.
drawPolygon(Polygon) - Method in class ij.process.ImageProcessor
  Draws a polygon.
drawRect(int, int, int, int) - Method in class ij.process.ImageProcessor
  Draws a rectangle.
drawString(String) - Method in class ij.process.ImageProcessor
  Draws a string at the current location using the current fill/draw value.
drawString(String, int, int) - Method in class ij.process.ImageProcessor
  Draws a string at the specified location using the current fill/draw value.
drawUnscaledColorBar(ImageProcessor, int, int, int, int) - Method in class ij.LookUpTable
drawingColor - Variable in class ij.process.ImageProcessor
drop(DropTargetDropEvent) - Method in class ij.plugin.DragAndDrop
dropActionChanged(DropTargetDragEvent) - Method in class ij.plugin.DragAndDrop
dstHeight - Variable in class ij.gui.ImageCanvas
dstWidth - Variable in class ij.gui.ImageCanvas
dumpProgram() - Method in class ij.macro.Program
dumpSymbolTable() - Method in class ij.macro.Program
duplicate(ImagePlus) - Method in class ij.plugin.filter.Duplicater
duplicate() - Method in class ij.process.ByteProcessor
  Returns a duplicate of this image.
duplicate() - Method in class ij.process.ColorProcessor
  Returns a duplicate of this image.
duplicate() - Method in class ij.process.FloatProcessor
  Returns a duplicate of this image.
duplicate() - Method in class ij.process.ImageProcessor
  Returns a duplicate of this image.
duplicate() - Method in class ij.process.ShortProcessor
  Returns a duplicate of this image.
duplicateStack(ImagePlus, String) - Method in class ij.plugin.filter.Duplicater

## E

EDM - class ij.plugin.filter.EDM.
  This plugin implements the Euclidean Distance Map (EDM), Ultimate Eroded Points and Watershed commands in the Process/Binary submenu.
EDM() - Constructor for class ij.plugin.filter.EDM
ELLIPSE - Static variable in interface ij.measure.Measurements
ELLIPSES - Static variable in class ij.plugin.filter.ParticleAnalyzer
ELSE - Static variable in interface ij.macro.MacroConstants
EMBEDDED - Static variable in class ij.ImageJ
ENDS_WITH - Static variable in interface ij.macro.MacroConstants
EOF - Static variable in interface ij.macro.MacroConstants
EOL - Static variable in interface ij.macro.MacroConstants
EQ - Static variable in interface ij.macro.MacroConstants
EVAL - Static variable in interface ij.macro.MacroConstants
EXCLUDE_EDGE_PARTICLES - Static variable in class ij.plugin.filter.ParticleAnalyzer
  Do not measure particles touching edge of image.
EXIT - Static variable in interface ij.macro.MacroConstants
EXP - Static variable in interface ij.macro.MacroConstants
EXPONENTIAL - Static variable in class ij.measure.Calibration
EXPONENTIAL - Static variable in class ij.measure.CurveFitter
EXP_WITH_OFFSET - Static variable in class ij.measure.CurveFitter
Editor - class ij.plugin.frame.Editor.
  This is a simple TextArea based editor for editing and compiling plugins.
Editor() - Constructor for class ij.plugin.frame.Editor
Editor(int, int, int, int) - Constructor for class ij.plugin.frame.Editor
EllipseFitter - class ij.process.EllipseFitter.
  This class fits an ellipse to an ROI.
EllipseFitter() - Constructor for class ij.process.EllipseFitter
Executer - class ij.Executer.
  Runs ImageJ menu commands in a separate thread.
Executer(String) - Constructor for class ij.Executer
  Create an Executer to run the specified menu command in this thread using the active image.
Executer(String, ImagePlus) - Constructor for class ij.Executer
  Create an Executer that runs the specified menu command in a separate thread using the active image image.
ExtendedPlugInFilter - interface ij.plugin.filter.ExtendedPlugInFilter.
  ImageJ plugins that process an image may implement this interface.
east(ImageProcessor) - Method in class ij.plugin.filter.Shadows
enableDebugging() - Method in class ij.io.TiffDecoder
endPaste() - Method in class ij.gui.Roi
equalize(ImagePlus) - Method in class ij.plugin.ContrastEnhancer
equalize(ImageProcessor) - Method in class ij.plugin.ContrastEnhancer
  Changes the tone curves of images.
equals(Object) - Method in class ij.gui.Roi
  Checks whether two rectangles are equal.
equals(Calibration) - Method in class ij.measure.Calibration
  Compares two Calibration objects for equality.
erode() - Method in class ij.process.ByteProcessor
erode(int, int) - Method in class ij.process.ByteProcessor
erode() - Method in class ij.process.ColorProcessor
erode() - Method in class ij.process.FloatProcessor
  Not implemented.
erode() - Method in class ij.process.ImageProcessor
  Erodes the image or ROI using a 3x3 maximum filter.
erode() - Method in class ij.process.ShortProcessor
  Not implemented.
error(String) - Static method in class ij.IJ
  Displays a message in a dialog box titled "ImageJ".
error(String, String) - Static method in class ij.IJ
  Displays a message in a dialog box with the specified title.
escapePressed() - Static method in class ij.IJ
  Returns true if the `Esc` key was pressed since the last ImageJ command started to execute or since resetEscape() was called.
evalSpline(int[], int[], int, double) - Method in class ij.measure.SplineFitter
  Evalutes spline function at given point
excludeEdgeParticles - Variable in class ij.plugin.filter.ParticleAnalyzer
exitWhenQuitting(boolean) - Method in class ij.ImageJ
  ImageJ calls System.exit() when qutting when 'exitWhenQuitting' is true.
exp() - Method in class ij.process.FloatProcessor
exp() - Method in class ij.process.ImageProcessor
  Performs a exponential transform on the image or ROI.
exp() - Method in class ij.process.ShortProcessor
expandImage(ImageProcessor, int, int, int, int) - Method in class ij.plugin.CanvasResizer
expandStack(ImageStack, int, int, int, int) - Method in class ij.plugin.CanvasResizer

## F

FALSE - Static variable in interface ij.macro.MacroConstants
FCOLOR - Static variable in class ij.Prefs
FERET - Static variable in interface ij.measure.Measurements
FERET - Static variable in class ij.measure.ResultsTable
FFT - class ij.plugin.FFT.
  This class implements the FFT, Inverse FFT and Redisplay Power Spectrum commands in the Process/FFT submenu.
FFT() - Constructor for class ij.plugin.FFT
FFTCustomFilter - class ij.plugin.filter.FFTCustomFilter.
  This class implements the Process/FFT/Custom Filter command.
FFTCustomFilter() - Constructor for class ij.plugin.filter.FFTCustomFilter
FFTFilter - class ij.plugin.filter.FFTFilter.
  This class implements the Process/FFT/bandpass Filter command.
FFTFilter() - Constructor for class ij.plugin.filter.FFTFilter
FFTMath - class ij.plugin.FFTMath.
  The class implements the Process/FFT/Math command.
FFTMath() - Constructor for class ij.plugin.FFTMath
FHT - class ij.process.FHT.
  This class contains a Java implementation of the Fast Hartley Transform.
FHT(ImageProcessor) - Constructor for class ij.process.FHT
  Constructs a FHT object from an ImageProcessor.
FILE - Static variable in interface ij.macro.MacroConstants
FILL - Static variable in interface ij.macro.MacroConstants
FILL_BLACK - Static variable in class ij.gui.NewImage
FILL_OVAL - Static variable in interface ij.macro.MacroConstants
FILL_RAMP - Static variable in class ij.gui.NewImage
FILL_RECT - Static variable in interface ij.macro.MacroConstants
FILL_WHITE - Static variable in class ij.gui.NewImage
FILTER - Static variable in class ij.Undo
FILTERS_MENU - Static variable in class ij.Menus
FINAL_PROCESSING - Static variable in interface ij.plugin.filter.PlugInFilter
  Set this flag if the setup method of the filter should be called again after the calls to the run(ip) have finished.
FITS - Static variable in class ij.io.FileInfo
FITS - Static variable in class ij.io.Opener
FITS_Reader - class ij.plugin.FITS_Reader.
  Opens and displays FITS images.
FITS_Reader() - Constructor for class ij.plugin.FITS_Reader
FITS_Writer - class ij.plugin.FITS_Writer.
  This plugin saves a 16 or 32 bit image in FITS format.
FITS_Writer() - Constructor for class ij.plugin.FITS_Writer
FLOOD_FILL - Static variable in interface ij.macro.MacroConstants
FLOOR - Static variable in interface ij.macro.MacroConstants
FOR - Static variable in interface ij.macro.MacroConstants
FPS - Static variable in class ij.Prefs
FREELINE - Static variable in class ij.gui.Roi
FREELINE - Static variable in class ij.gui.Toolbar
FREEROI - Static variable in class ij.gui.Roi
FREEROI - Static variable in class ij.gui.Toolbar
FROM_CHAR_CODE - Static variable in interface ij.macro.MacroConstants
FUNCTION - Static variable in interface ij.macro.MacroConstants
FileInfo - class ij.io.FileInfo.
  This class consists of public fields that describe an image file.
FileInfo() - Constructor for class ij.io.FileInfo
  Creates a FileInfo object with all of its fields set to their default value.
FileOpener - class ij.io.FileOpener.
  Opens or reverts an image specified by a FileInfo object.
FileOpener(FileInfo) - Constructor for class ij.io.FileOpener
FileSaver - class ij.io.FileSaver.
  Saves images in tiff, gif, jpeg, raw, zip and text format.
FileSaver(ImagePlus) - Constructor for class ij.io.FileSaver
  Constructs a FileSaver from an ImagePlus.
Filler - class ij.plugin.filter.Filler.
  This plugin implements ImageJ's Fill, Clear, Clear Outside and Draw commands.
Filler() - Constructor for class ij.plugin.filter.Filler
Filters - class ij.plugin.filter.Filters.
  This plugin implements the Invert, Smooth, Sharpen, Find Edges, and Add Noise commands.
Filters() - Constructor for class ij.plugin.filter.Filters
Fitter - class ij.plugin.frame.Fitter.
  ImageJ plugin that does curve fitting using the modified CurveFitter class.
Fitter() - Constructor for class ij.plugin.frame.Fitter
FloatBlitter - class ij.process.FloatBlitter.
  This class does bit blitting of 32-bit floating-point images.
FloatBlitter(FloatProcessor) - Constructor for class ij.process.FloatBlitter
  Constructs a FloatBlitter from a FloatProcessor.
FloatProcessor - class ij.process.FloatProcessor.
  This is an 32-bit floating-point image and methods that operate on that image.
FloatProcessor(int, int, float[], ColorModel) - Constructor for class ij.process.FloatProcessor
  Creates a new FloatProcessor using the specified pixel array and ColorModel.
FloatProcessor(int, int) - Constructor for class ij.process.FloatProcessor
  Creates a blank FloatProcessor using the default grayscale LUT that displays zero as black.
FloatProcessor(int, int, int[]) - Constructor for class ij.process.FloatProcessor
  Creates a FloatProcessor from an int array using the default grayscale LUT.
FloatProcessor(int, int, double[]) - Constructor for class ij.process.FloatProcessor
  Creates a FloatProcessor from a double array using the default grayscale LUT.
FloatProcessor(float[][]) - Constructor for class ij.process.FloatProcessor
  Creates a FloatProcessor from a float[][] array using the default LUT.
FloatProcessor(int[][]) - Constructor for class ij.process.FloatProcessor
  Creates a FloatProcessor from an int[][] array.
FloatStatistics - class ij.process.FloatStatistics.
  32-bit (float) image statistics, including histogram.
FloatStatistics(ImageProcessor) - Constructor for class ij.process.FloatStatistics
  Constructs an ImageStatistics object from a FloatProcessor using the standard measurement options (area, mean, mode, min and max).
FloatStatistics(ImageProcessor, int, Calibration) - Constructor for class ij.process.FloatStatistics
  Constructs a FloatStatistics object from a FloatProcessor using the specified measurement options.
FloodFiller - class ij.process.FloodFiller.
  This class, which does flood filling, is used by the floodFill() macro function and by the particle analyzer The Wikipedia at "http://en.wikipedia.org/wiki/Flood_fill" has a good description of the algorithm used here as well as examples in C and Java.
FloodFiller(ImageProcessor) - Constructor for class ij.process.FloodFiller
FolderOpener - class ij.plugin.FolderOpener.
  Implements the File/Import/Image Sequence command, which opens a folder of images as a stack.
FolderOpener() - Constructor for class ij.plugin.FolderOpener
Fonts - class ij.plugin.frame.Fonts.
  Displays a window that allows the user to set the font, size and style.
Fonts() - Constructor for class ij.plugin.frame.Fonts
FractalBoxCounter - class ij.plugin.filter.FractalBoxCounter.
  Calculate the so-called "capacity" fractal dimension.
FractalBoxCounter() - Constructor for class ij.plugin.filter.FractalBoxCounter
FreehandRoi - class ij.gui.FreehandRoi.
  Freehand region of interest or freehand line of interest
FreehandRoi(int, int, ImagePlus) - Constructor for class ij.gui.FreehandRoi
Functions - class ij.macro.Functions.
  This class implements the built-in macro functions.
f(int, double[], double) - Static method in class ij.measure.CurveFitter
  Returns "fit" function value for parameters "p" at "x"
f2hex(float) - Static method in class ij.util.Tools
  Converts a float to an 9 byte hex string starting with '#'.
fList - Static variable in class ij.measure.CurveFitter
fileFormat - Variable in class ij.io.FileInfo
fileName - Variable in class ij.io.FileInfo
fileName - Static variable in class ij.plugin.FFT
fileType - Variable in class ij.io.FileInfo
fill(ImageProcessor) - Method in class ij.plugin.filter.Filler
fill(ImageProcessor) - Method in class ij.process.ByteProcessor
  Fills pixels that are within roi and part of the mask.
fill(ImageProcessor) - Method in class ij.process.ColorProcessor
  Fills pixels that are within roi and part of the mask.
fill() - Method in class ij.process.ColorProcessor
  Fills the current rectangular ROI.
fill() - Method in class ij.process.FloatProcessor
  Fills the current rectangular ROI.
fill(ImageProcessor) - Method in class ij.process.FloatProcessor
  Fills pixels that are within roi and part of the mask.
fill(int, int) - Method in class ij.process.FloodFiller
  Does a 4-connected flood fill.
fill() - Method in class ij.process.ImageProcessor
  Fills the image or ROI bounding rectangle with the current fill/draw value.
fill(ImageProcessor) - Method in class ij.process.ImageProcessor
  Fills pixels that are within the ROI and part of the mask (i.e.
fill(ImageProcessor, Rectangle) - Method in class ij.process.PolygonFiller
  Fills the polygon using the ImageProcessor's current drawing color.
fill() - Method in class ij.process.ShortProcessor
  Fills the current rectangular ROI.
fill(ImageProcessor) - Method in class ij.process.ShortProcessor
  Fills pixels that are within roi and part of the mask.
fill8(int, int) - Method in class ij.process.FloodFiller
  Does a 8-connected flood fill.
fillOval(int, int, int, int) - Method in class ij.process.ImageProcessor
  Fills an elliptical shape.
fillPolygon(Polygon) - Method in class ij.process.ImageProcessor
  Fills a polygon.
filter(int) - Method in class ij.process.ByteProcessor
  Filters using a 3x3 neighborhood.
filter(int) - Method in class ij.process.ColorProcessor
  3x3 unweighted smoothing.
filter(int) - Method in class ij.process.FloatProcessor
  Filters using a 3x3 neighborhood.
filter(int) - Method in class ij.process.ImageProcessor
  A 3x3 filter operation, where the argument (BLUR_MORE, FIND_EDGES, etc.) determines the filter type.
filter(int) - Method in class ij.process.ShortProcessor
  Filters using a 3x3 neighborhood.
filterRGB(int, double) - Method in class ij.process.ColorProcessor
  Performs the specified 3x3 filter on the reg, green and blue planes.
findEdges() - Method in class ij.process.ColorProcessor
findEdges() - Method in class ij.process.ImageProcessor
  Finds edges in the image or ROI using a Sobel operator.
findMaxima(ImageProcessor, double, double, int, boolean, boolean) - Method in class ij.plugin.filter.MaximumFinder
  Here the processing is done: Find the maxima of an image (does not find minima)
findMinAndMax() - Method in class ij.process.FloatProcessor
  Calculates the minimum and maximum pixel value for the entire image.
findMinAndMax() - Method in class ij.process.ShortProcessor
findNthLowestNumber(float[], int, int) - Static method in class ij.plugin.filter.RankFilters
  Find the n-th lowest number in part of an array
fit(ImageProcessor, ImageStatistics) - Method in class ij.process.EllipseFitter
  Fits an ellipse to the current ROI.
fitList - Static variable in class ij.measure.CurveFitter
fitSpline(int) - Method in class ij.gui.PolygonRoi
fixNewLines(String) - Static method in class ij.util.Tools
  Converts carriage returns to line feeds.
flags - Variable in class ij.gui.ImageCanvas
flipHorizontal() - Method in class ij.process.ImageProcessor
  Flips the image or ROI horizontally.
flipHorizontal() - Method in class ij.process.StackProcessor
flipVertical() - Method in class ij.process.ByteProcessor
flipVertical() - Method in class ij.process.ColorProcessor
flipVertical() - Method in class ij.process.FloatProcessor
flipVertical() - Method in class ij.process.ImageProcessor
  Flips the image or ROI vertically.
flipVertical() - Method in class ij.process.ShortProcessor
flipVertical() - Method in class ij.process.StackProcessor
floodFill - Variable in class ij.plugin.filter.ParticleAnalyzer
flush() - Method in class ij.ImagePlus
  Sets the image arrays to null to help the garbage collector do its job.
focusGained(FocusEvent) - Method in class ij.gui.GenericDialog
focusGained(FocusEvent) - Method in class ij.gui.ImageWindow
focusGained(FocusEvent) - Method in class ij.plugin.Scaler
focusGained(FocusEvent) - Method in class ij.plugin.frame.PlugInFrame
focusGained(FocusEvent) - Method in class ij.text.TextWindow
focusLost(FocusEvent) - Method in class ij.gui.GenericDialog
focusLost(FocusEvent) - Method in class ij.gui.ImageWindow
focusLost(FocusEvent) - Method in class ij.plugin.Scaler
focusLost(FocusEvent) - Method in class ij.plugin.frame.PlugInFrame
focusLost(FocusEvent) - Method in class ij.text.TextWindow
font - Variable in class ij.process.ImageProcessor
fontMetrics - Variable in class ij.process.ImageProcessor
fps - Variable in class ij.measure.Calibration
  Frame rate in frames per second
frame - Variable in class ij.gui.HistogramWindow
frameInterval - Variable in class ij.io.FileInfo
frameInterval - Variable in class ij.measure.Calibration
  Frame interval in 'timeUnit's
freeMemory() - Static method in class ij.IJ
  Runs the garbage collector and returns a string something like "64K of 256MB (25%)" that shows how much of the available memory is in use.
functionIDs - Static variable in interface ij.macro.MacroConstants
functions - Static variable in interface ij.macro.MacroConstants

## G

GAMMA_VARIATE - Static variable in class ij.measure.Calibration
GAMMA_VARIATE - Static variable in class ij.measure.CurveFitter
GET_ARGUMENT - Static variable in interface ij.macro.MacroConstants
GET_BOOLEAN - Static variable in interface ij.macro.MacroConstants
GET_BOUNDING_RECT - Static variable in interface ij.macro.MacroConstants
GET_BOUNDS - Static variable in interface ij.macro.MacroConstants
GET_COORDINATES - Static variable in interface ij.macro.MacroConstants
GET_COUNT - Static variable in interface ij.macro.MacroConstants
GET_CURSOR_LOC - Static variable in interface ij.macro.MacroConstants
GET_DATE_AND_TIME - Static variable in interface ij.macro.MacroConstants
GET_DIMENSIONS - Static variable in interface ij.macro.MacroConstants
GET_DIRECTORY - Static variable in interface ij.macro.MacroConstants
GET_FILE_LIST - Static variable in interface ij.macro.MacroConstants
GET_FONT_LIST - Static variable in interface ij.macro.MacroConstants
GET_HEIGHT - Static variable in interface ij.macro.MacroConstants
GET_HISTOGRAM - Static variable in interface ij.macro.MacroConstants
GET_ID - Static variable in interface ij.macro.MacroConstants
GET_IMAGE_INFO - Static variable in interface ij.macro.MacroConstants
GET_INFO - Static variable in interface ij.macro.MacroConstants
GET_LINE - Static variable in interface ij.macro.MacroConstants
GET_LIST - Static variable in interface ij.macro.MacroConstants
GET_LOCATION_AND_SIZE - Static variable in interface ij.macro.MacroConstants
GET_LUT - Static variable in interface ij.macro.MacroConstants
GET_METADATA - Static variable in interface ij.macro.MacroConstants
GET_MIN_AND_MAX - Static variable in interface ij.macro.MacroConstants
GET_NUMBER - Static variable in interface ij.macro.MacroConstants
GET_PIXEL - Static variable in interface ij.macro.MacroConstants
GET_PIXEL_SIZE - Static variable in interface ij.macro.MacroConstants
GET_PROFILE - Static variable in interface ij.macro.MacroConstants
GET_RAW_STATISTICS - Static variable in interface ij.macro.MacroConstants
GET_RESULT - Static variable in interface ij.macro.MacroConstants
GET_RESULT_LABEL - Static variable in interface ij.macro.MacroConstants
GET_SLICE_NUMBER - Static variable in interface ij.macro.MacroConstants
GET_STATISTICS - Static variable in interface ij.macro.MacroConstants
GET_STRING - Static variable in interface ij.macro.MacroConstants
GET_THRESHOLD - Static variable in interface ij.macro.MacroConstants
GET_TIME - Static variable in interface ij.macro.MacroConstants
GET_TITLE - Static variable in interface ij.macro.MacroConstants
GET_VERSION - Static variable in interface ij.macro.MacroConstants
GET_VOXEL_SIZE - Static variable in interface ij.macro.MacroConstants
GET_WIDTH - Static variable in interface ij.macro.MacroConstants
GET_ZOOM - Static variable in interface ij.macro.MacroConstants
GIF - Static variable in class ij.io.Opener
GIF_OR_JPG - Static variable in class ij.io.FileInfo
GRAY12_UNSIGNED - Static variable in class ij.io.FileInfo
  12-bit unsigned integer (0-4095).
GRAY16 - Static variable in class ij.ImagePlus
  16-bit grayscale (unsigned)
GRAY16 - Static variable in class ij.gui.NewImage
GRAY16_SIGNED - Static variable in class ij.io.FileInfo
  16-bit signed integer (-32768-32767).
GRAY16_UNSIGNED - Static variable in class ij.io.FileInfo
  16-bit unsigned integer (0-65535).
GRAY24_UNSIGNED - Static variable in class ij.io.FileInfo
  24-bit unsigned integer.
GRAY32 - Static variable in class ij.ImagePlus
  32-bit floating-point grayscale
GRAY32 - Static variable in class ij.gui.NewImage
GRAY32_FLOAT - Static variable in class ij.io.FileInfo
  32-bit floating-point.
GRAY32_INT - Static variable in class ij.io.FileInfo
  32-bit signed integer.
GRAY32_UNSIGNED - Static variable in class ij.io.FileInfo
  32-bit unsigned integer.
GRAY64_FLOAT - Static variable in class ij.io.FileInfo
  64-bit floating-point.
GRAY8 - Static variable in class ij.ImagePlus
  8-bit grayscale (unsigned)
GRAY8 - Static variable in class ij.gui.NewImage
GRAY8 - Static variable in class ij.io.FileInfo
  8-bit unsigned integer (0-255).
GT - Static variable in interface ij.macro.MacroConstants
GTE - Static variable in interface ij.macro.MacroConstants
GUI - class ij.gui.GUI.
  This class consists of static GUI utility methods.
GUI() - Constructor for class ij.gui.GUI
GaussianBlur - class ij.plugin.filter.GaussianBlur.
  This plug-in filter uses convolution with a Gaussian function for smoothing.
GaussianBlur() - Constructor for class ij.plugin.filter.GaussianBlur
  Default constructor
GelAnalyzer - class ij.plugin.GelAnalyzer.
  This plugin generates gel profile plots that can be analyzed using the wand tool.
GelAnalyzer() - Constructor for class ij.plugin.GelAnalyzer
GenericDialog - class ij.gui.GenericDialog.
  This class is a customizable modal dialog box.
GenericDialog(String) - Constructor for class ij.gui.GenericDialog
  Creates a new GenericDialog with the specified title.
GenericDialog(String, Frame) - Constructor for class ij.gui.GenericDialog
  Creates a new GenericDialog using the specified title and parent frame.
GifEncoder - class ij.io.GifEncoder.
  GifEncoder - writes out an image as a GIF.
GifEncoder(int, int, byte[], byte[], byte[], byte[]) - Constructor for class ij.io.GifEncoder
  Constructs a new GifEncoder.
GifEncoder(Image) - Constructor for class ij.io.GifEncoder
  Constructs a new GifEncoder using an 8-bit AWT Image.
gLUT1 - Variable in class ij.process.ImageProcessor
gLUT2 - Variable in class ij.process.ImageProcessor
gamma(double) - Method in class ij.process.FloatProcessor
gamma(double) - Method in class ij.process.ImageProcessor
  Performs gamma correction of the image or ROI.
gamma(double) - Method in class ij.process.ShortProcessor
gapBetweenImages - Variable in class ij.io.FileInfo
get(String, String) - Static method in class ij.Prefs
  Uses the keyword `key` to retrieve a string from the preferences file.
get(String, double) - Static method in class ij.Prefs
  Uses the keyword `key` to retrieve a number from the preferences file.
get(String, boolean) - Static method in class ij.Prefs
  Uses the keyword `key` to retrieve a boolean from the preferences file.
get(int, int) - Method in class ij.process.ByteProcessor
get(int) - Method in class ij.process.ByteProcessor
get(int, int) - Method in class ij.process.ColorProcessor
get(int) - Method in class ij.process.ColorProcessor
get(int, int) - Method in class ij.process.FloatProcessor
get(int) - Method in class ij.process.FloatProcessor
get(int, int) - Method in class ij.process.ImageProcessor
  This is a faster version of getPixel() that does not do bounds checking.
get(int) - Method in class ij.process.ImageProcessor
get(int, int) - Method in class ij.process.ShortProcessor
get(int) - Method in class ij.process.ShortProcessor
getAdditionalFunctions() - Static method in class ij.macro.Interpreter
getAngle() - Method in class ij.gui.PolygonRoi
  Returns the angle in degrees between the first two segments of this polyline.
getAngle(int, int, int, int) - Method in class ij.gui.Roi
  Returns the angle in degrees between the specified line and a horizontal line.
getApplet() - Static method in class ij.IJ
  Returns the Applet that created this ImageJ or null if running as an application.
getArgs() - Static method in class ij.ImageJ
  Returns the command line arguments passed to ImageJ.
getAutoThreshold() - Method in class ij.process.ImageProcessor
  Returns a pixel value (threshold) that can be used to divide the image into objects and background.
getAutoThreshold(int[]) - Method in class ij.process.ImageProcessor
  This is a version of getAutoThreshold() that uses a histogram passed as an argument.
getBackgroundColor() - Static method in class ij.gui.Toolbar
getBatchModeImage(int) - Static method in class ij.macro.Interpreter
getBatchModeImageCount() - Static method in class ij.macro.Interpreter
getBatchModeImageIDs() - Static method in class ij.macro.Interpreter
getBestIndex(Color) - Method in class ij.process.ColorProcessor
  Always returns 0 since RGB images do not use LUTs.
getBestIndex(Color) - Method in class ij.process.ImageProcessor
  Returns the LUT index that's the best match for this color.
getBitDepth() - Method in class ij.ImagePlus
  Returns the bit depth, 8, 16, 24 (RGB) or 32.
getBits(int) - Method in class ij.io.BitBuffer
getBlues() - Method in class ij.LookUpTable
getBoolean(String, boolean) - Static method in class ij.Prefs
  Finds a boolean in IJ_Props or IJ_Prefs.txt.
getBoundingRect() - Method in class ij.gui.Roi
  This obsolete method has been replaced by getBounds().
getBounds() - Method in class ij.gui.Line
  Return the bounding rectangle of this line.
getBounds() - Method in class ij.gui.Roi
  Return this selection's bounding rectangle.
getBrightness() - Method in class ij.process.ColorProcessor
  Returns brightness as a FloatProcessor.
getBrushSize() - Static method in class ij.gui.Toolbar
getByteRow(ImageStack, int, int, int, int, int, int[]) - Method in class ij.plugin.filter.Projector
getBytesPerPixel() - Method in class ij.io.FileInfo
  Returns the number of bytes used per pixel.
getCTable() - Method in class ij.measure.Calibration
  Returns the calibration table.
getCValue(int) - Method in class ij.measure.Calibration
  Converts a raw pixel value to a density calibrated value.
getCValue(double) - Method in class ij.measure.Calibration
  Converts a raw pixel value to a density calibrated value.
getCalibration() - Method in class ij.ImagePlus
  Returns this image's calibration.
getCalibrationTable() - Method in class ij.process.ImageProcessor
  Returns the calibration table or null.
getCanvas() - Method in class ij.ImagePlus
  Returns the ImageCanvas being used to display this image, or null.
getCanvas() - Method in class ij.gui.ImageWindow
getChannelColor() - Method in class ij.CompositeImage
getChannelProcessor() - Method in class ij.CompositeImage
getChannelProcessor() - Method in class ij.ImagePlus
  Returns a reference to the current ImageProcessor.
getCheckboxes() - Method in class ij.gui.GenericDialog
  Returns the Vector containing the Checkboxes.
getChoices() - Method in class ij.gui.GenericDialog
  Returns the Vector containing the Choices.
getClassLoader() - Static method in class ij.IJ
  Returns an instance of the class loader ImageJ uses to run plugins.
getClipboard() - Static method in class ij.ImagePlus
  Returns the internal clipboard or null if the internal clipboard is empty.
getCode() - Method in class ij.macro.Program
getCoefficients() - Method in class ij.measure.Calibration
  Returns the calibration function coefficients.
getColor(String, Color) - Static method in class ij.Prefs
  Finds a color in IJ_Props or IJ_Prefs.txt.
getColor() - Method in class ij.gui.ColorChooser
  Displays a color selection dialog and returns the color selected by the user.
getColor() - Static method in class ij.gui.Roi
  Returns the color used for drawing ROI outlines.
getColor() - Method in class ij.gui.Toolbar
  Obsolete.
getColor(int, int) - Method in class ij.process.ColorProcessor
getColorModel() - Method in class ij.ImageStack
  Returns this stack's color model.
getColorModel() - Method in class ij.LookUpTable
getColorModel() - Method in class ij.process.ImageProcessor
  Returns this processor's color model.
getColumn(int) - Method in class ij.measure.ResultsTable
  Returns a copy of the given column as a float array.
getColumn(int, int, int[], int) - Method in class ij.process.ImageProcessor
  Returns the pixel values down the column starting at (x,y).
getColumnHeading(int) - Method in class ij.measure.ResultsTable
  Returns the heading of the specified column or null if the column is empty.
getColumnHeadings() - Method in class ij.measure.ResultsTable
  Returns a tab-delimited string containing the column headings.
getColumnHeadings() - Method in class ij.text.TextPanel
  Returns the column headings as a tab-delimited string.
getColumnIndex(String) - Method in class ij.measure.ResultsTable
  Returns the index of the first column with the given heading.
getCommand() - Static method in class ij.Executer
  Returns the last command executed.
getCommand() - Static method in class ij.plugin.frame.Recorder
  Returns the name of the command currently being recorded, or null.
getCommandOptions() - Static method in class ij.plugin.frame.Recorder
  Use by GenericDialog to determine if any options have been recorded.
getCommands() - Static method in class ij.Menus
  Returns the hashtable that associates commands with plugins.
getComplexTransform() - Method in class ij.process.FHT
  Converts this FHT to a complex Fourier transform and returns it as a two slice stack.
getCopy() - Method in class ij.process.FHT
  Returns a clone of this FHT.
getCount() - Method in class ij.plugin.frame.RoiManager
  Returns the ROI count.
getCounter() - Method in class ij.measure.ResultsTable
  Returns the current value of the measurement counter.
getCounter() - Static method in class ij.plugin.filter.Analyzer
  Returns the current measurement count.
getCurrentColorModel() - Method in class ij.process.ImageProcessor
  Returns the current color model, which may have been modified by setMinAndMax() or setThreshold().
getCurrentImage() - Static method in class ij.WindowManager
  Returns the active ImagePlus.
getCurrentPasteMode() - Static method in class ij.gui.Roi
  Returns the current paste transfer mode.
getCurrentSlice() - Method in class ij.ImagePlus
  Returns the current stack slice number or 1 if this is a single image.
getCurrentWindow() - Static method in class ij.WindowManager
  Returns the active ImageWindow.
getCursorLoc() - Method in class ij.gui.ImageCanvas
  Returns the current cursor location.
getDecimalPlaces(double, double) - Static method in class ij.util.Tools
  Returns the number of decimal places need to display two numbers.
getDefaultColorModel() - Method in class ij.process.ImageProcessor
  Returns the default grayscale IndexColorModel.
getDefaultDirectory() - Static method in class ij.io.OpenDialog
  Returns the current working directory, which may be null.
getDescriptionString() - Method in class ij.io.FileSaver
  Returns a string containing information about the specified image.
getDimensions() - Method in class ij.ImagePlus
  Returns the dimensions of this image (width, height, nChannels, nSlices, nFrames) as a 5 element int array.
getDir(String) - Static method in class ij.Macro
getDir(String) - Method in class ij.io.Opener
getDirectory(String) - Static method in class ij.IJ
  Returns the path to the home ("user.home"), startup (ImageJ directory), plugins, macros, temp, current or image directory if `title` is "home", "startup", "plugins", "macros", "temp", "current" or "image", otherwise, displays a dialog and returns the path to the directory selected by the user.
getDirectory() - Method in class ij.VirtualStack
  Returns the path to the directory containing the images.
getDirectory() - Method in class ij.io.DirectoryChooser
  Returns the directory selected by the user.
getDirectory() - Method in class ij.io.OpenDialog
  Returns the selected directory.
getDirectory() - Method in class ij.io.SaveDialog
  Returns the selected directory.
getDirectory() - Method in class ij.macro.Functions
getDoScaling() - Static method in class ij.process.ImageConverter
  Returns true if scaling is enabled.
getDouble(String, double) - Static method in class ij.Prefs
  Looks up a real number in IJ_Props or IJ_Prefs.txt.
getEditor() - Method in class ij.plugin.NewPlugin
  Returns the Editor the newly created macro or plugin was opened in.
getErrorMessage() - Method in class ij.gui.GenericDialog
  Returns an error message if getNextNumber was unable to convert a string into a number, otherwise, returns null.
getFeretsDiameter() - Method in class ij.gui.OvalRoi
  Returns Feret's diameter, the greatest distance between any two points along the ROI boundary.
getFeretsDiameter() - Method in class ij.gui.PolygonRoi
  Returns Feret's diameter, the greatest distance between any two points along the ROI boundary.
getFeretsDiameter() - Method in class ij.gui.Roi
  Returns Feret's diameter, the greatest distance between any two points along the ROI boundary.
getFeretsDiameter() - Method in class ij.gui.ShapeRoi
  Returns the maximum Feret diameter (i.e., the largest distance between the shape's boundaries).
getFileInfo() - Method in class ij.ImagePlus
  Returns a FileInfo object containing information, including the pixel array, needed to save this image.
getFileInfo() - Method in class ij.io.ImportDialog
  Displays the dialog and returns a FileInfo object that can be used to open the image.
getFileName(int) - Method in class ij.VirtualStack
  Returns the file name of the specified slice, were 1<=n<=nslices.
getFileName() - Method in class ij.io.OpenDialog
  Returns the selected file name.
getFileName() - Method in class ij.io.SaveDialog
  Returns the selected file name.
getFilePointer() - Method in class ij.io.RandomAccessStream
getFileSeparator() - Static method in class ij.Prefs
  Returns the file.separator system property.
getFileType(String) - Method in class ij.io.Opener
  Attempts to determine the image file type by looking for 'magic numbers' and the file name extension.
getFitGoodness() - Method in class ij.measure.CurveFitter
  Get a measure of "goodness of fit" where 1.0 is best.
getFixedMax() - Static method in class ij.gui.ProfilePlot
  Returns the profile plot y-axis max.
getFixedMin() - Static method in class ij.gui.ProfilePlot
  Returns the profile plot y-axis min.
getFloatArray() - Method in class ij.process.ImageProcessor
getFont() - Static method in class ij.Menus
getFont() - Static method in class ij.gui.TextRoi
  Returns the name of the current font.
getFontMetrics() - Method in class ij.process.ImageProcessor
  Returns the current FontMetrics.
getFontSize() - Static method in class ij.Menus
  Returns the size (in points) used for the fonts in ImageJ menus.
getForegroundColor() - Static method in class ij.gui.Toolbar
getFrame(String) - Static method in class ij.WindowManager
  Returns the frame with the specified title or null if a frame with that title is not found.
getFrameRate() - Static method in class ij.plugin.Animator
  Returns the current animation speed in frames per second.
getFreeColumn(String) - Method in class ij.measure.ResultsTable
  Sets the heading of the the first available column and returns that column's index.
getFrontWindow() - Static method in class ij.WindowManager
  Returns the front most window or null.
getFunction() - Method in class ij.measure.Calibration
  Returns the calibration function ID.
getGlobalCalibration() - Method in class ij.ImagePlus
  Returns the system-wide calibration, or null.
getGlobals() - Method in class ij.macro.Program
getGreens() - Method in class ij.LookUpTable
getHSB(byte[], byte[], byte[]) - Method in class ij.process.ColorProcessor
  Returns hue, saturation and brightness in 3 byte arrays.
getHeight() - Method in class ij.ImagePlus
getHeight() - Method in class ij.ImageStack
getHeight() - Method in class ij.process.ImageProcessor
  Returns the height of this image in pixels.
getHigherZoomLevel(double) - Static method in class ij.gui.ImageCanvas
getHistogram() - Method in class ij.gui.HistogramWindow
getHistogram() - Method in class ij.process.ByteProcessor
getHistogram(ImageProcessor) - Method in class ij.process.ByteProcessor
getHistogram() - Method in class ij.process.ColorProcessor
getHistogram(ImageProcessor) - Method in class ij.process.ColorProcessor
getHistogram() - Method in class ij.process.FloatProcessor
  Not implemented.
getHistogram() - Method in class ij.process.ImageProcessor
  Returns the histogram of the image or ROI.
getHistogram() - Method in class ij.process.ShortProcessor
  Returns 65536 bin histogram of the current ROI, which can be non-rectangular.
getHistogramMax() - Method in class ij.process.ImageProcessor
  Returns the maximum histogram value used for histograms of float images.
getHistogramMin() - Method in class ij.process.ImageProcessor
  Returns the minimum histogram value used for histograms of float images.
getHistogramSize() - Method in class ij.process.ImageProcessor
  Returns the number of float image histogram bins.
getHomeDir() - Static method in class ij.Prefs
  Returns the path to the ImageJ directory.
getID() - Method in class ij.ImagePlus
  Returns this image's unique numeric ID.
getIDList() - Static method in class ij.WindowManager
  Returns a list of the IDs of open images.
getImage() - Method in class ij.CompositeImage
getImage() - Static method in class ij.IJ
  Returns a reference to the active image.
getImage() - Method in class ij.ImagePlus
  Returns the current AWT image.
getImage(int) - Static method in class ij.WindowManager
  For IDs less than zero, returns the ImagePlus with the specified ID.
getImage(String) - Static method in class ij.WindowManager
  Returns the first image that has the specified title or null if it is not found.
getImageArray() - Method in class ij.ImageStack
  Returns the stack as an array of 1D pixel arrays.
getImageArray() - Method in class ij.VirtualStack
  Returns null.
getImageCount() - Static method in class ij.WindowManager
  Returns the number of open images.
getImageInfo(ImagePlus, ImageProcessor) - Method in class ij.plugin.filter.Info
getImagePlus() - Method in class ij.gui.ImageWindow
getImagePlus() - Method in class ij.gui.Plot
  Returns the plot as an ImagePlus.
getImageStack() - Method in class ij.ImagePlus
  Returns the base image stack.
getImageStackSize() - Method in class ij.ImagePlus
  If this is a stack, returns the actual number of images in the stack, else returns 1.
getImagesURL() - Static method in class ij.Prefs
  Returns the URL of the directory that contains the ImageJ sample images.
getIndexSampleModel() - Method in class ij.process.ImageProcessor
getInitialMagnification() - Method in class ij.gui.ImageWindow
getInsets() - Method in class ij.gui.GenericDialog
getInsets() - Method in class ij.gui.ImageWindow
  Override Container getInsets() to make room for some text above the image.
getInstance() - Static method in class ij.IJ
  Returns a reference to the "ImageJ" frame.
getInstance() - Static method in class ij.gui.Toolbar
  Returns a reference to the ImageJ toolbar.
getInstance() - Static method in class ij.macro.Interpreter
getInstance() - Static method in class ij.plugin.frame.RoiManager
  Returns a reference to the ROI Manager or null if it is not open.
getInt(String, int) - Static method in class ij.Prefs
  Finds an int in IJ_Props or IJ_Prefs.txt.
getIntArray() - Method in class ij.process.ImageProcessor
getInterpolate() - Method in class ij.process.ImageProcessor
  Returns the value of the interpolate field.
getInterpolatedPixel(double, double) - Method in class ij.process.ByteProcessor
  Uses bilinear interpolation to find the pixel value at real coordinates (x,y).
getInterpolatedPixel(double, double) - Method in class ij.process.ColorProcessor
  Calls getPixelValue(x,y).
getInterpolatedPixel(double, double) - Method in class ij.process.FloatProcessor
  Uses bilinear interpolation to find the pixel value at real coordinates (x,y).
getInterpolatedPixel(double, double) - Method in class ij.process.ImageProcessor
  Uses bilinear interpolation to find the pixel value at real coordinates (x,y).
getInterpolatedPixel(double, double) - Method in class ij.process.ShortProcessor
  Uses bilinear interpolation to find the pixel value at real coordinates (x,y).
getInterpolatedRGBPixel(double, double) - Method in class ij.process.ColorProcessor
  Uses bilinear interpolation to find the pixel value at real coordinates (x,y).
getInterpolatedValue(double, double) - Method in class ij.process.ImageProcessor
  Uses bilinear interpolation to find the pixel value at real coordinates (x,y).
getIterations() - Method in class ij.measure.CurveFitter
  Get number of iterations performed
getLabel(int) - Method in class ij.measure.ResultsTable
  Returns the label of the specified row.
getLastBatchModeImage() - Static method in class ij.macro.Interpreter
getLastColumn() - Method in class ij.measure.ResultsTable
  Returns the index of the last used column, or -1 if no columns are used.
getLastDirectory() - Static method in class ij.io.OpenDialog
  Returns the path to the last directory opened by the user using a file open or file save dialog, or using drag and drop.
getLastName() - Static method in class ij.io.OpenDialog
  Returns the name of the last file opened by the user using a file open or file save dialog, or using drag and drop.
getLength() - Method in class ij.gui.Line
  Returns the length of this line.
getLength() - Method in class ij.gui.OvalRoi
  Returns the perimeter length.
getLength() - Method in class ij.gui.PolygonRoi
  Returns the perimeter (for ROIs) or length (for lines).
getLength() - Method in class ij.gui.Roi
  Returns the perimeter length.
getLength() - Method in class ij.gui.ShapeRoi
  Returns the length of this shape (perimeter, if shape is closed).
getLine(double, double, double, double) - Method in class ij.process.ImageProcessor
  Returns an array containing the pixel values along the line starting at (x1,y1) and ending at (x2,y2).
getLine(int) - Method in class ij.text.TextPanel
  Returns the specified line as a string.
getLineCount() - Method in class ij.text.TextPanel
  Returns the number of lines of text in this TextPanel.
getList() - Method in class ij.plugin.frame.RoiManager
  Returns the selection list.
getLocalCalibration() - Method in class ij.ImagePlus
  Returns this image's local calibration, ignoring the "Global" calibration flag.
getLocation(String) - Static method in class ij.Prefs
  Uses the keyword `key` to retrieve a location from the preferences file.
getLocationAsString(int, int) - Method in class ij.ImagePlus
  Converts the current cursor location to a string.
getLowerZoomLevel(double) - Static method in class ij.gui.ImageCanvas
getLutUpdateMode() - Method in class ij.process.ImageProcessor
  Returns the LUT update mode, which can be RED_LUT, BLACK_AND_WHITE_LUT, OVER_UNDER_LUT or NO_LUT_UPDATE.
getMacroCount() - Method in class ij.plugin.MacroInstaller
getMacroShortcuts() - Static method in class ij.Menus
  Returns the hashtable that associates keyboard shortcuts with macros.
getMacrosMenu() - Static method in class ij.Menus
getMacrosPath() - Static method in class ij.Menus
  Returns the path to the macros directory or null if the macros directory was not found.
getMagnification() - Method in class ij.gui.ImageCanvas
getMapSize() - Method in class ij.LookUpTable
getMask() - Method in class ij.ImagePlus
  For images with irregular ROIs, returns a byte mask, otherwise, returns null.
getMask() - Method in class ij.gui.OvalRoi
getMask() - Method in class ij.gui.PointRoi
getMask() - Method in class ij.gui.PolygonRoi
  Override Roi.nudge() to support splines.
getMask() - Method in class ij.gui.Roi
  Always returns null for rectangular Roi's
getMask() - Method in class ij.gui.ShapeRoi
  Returns this ROI's mask pixels as a ByteProcessor with pixels "in" the mask set to white (255) and pixels "outside" the mask set to black (0).
getMask() - Method in class ij.process.ImageProcessor
  For images with irregular ROIs, returns a mask, otherwise, returns null.
getMask(int, int) - Method in class ij.process.PolygonFiller
  Returns a byte mask containing a filled version of the polygon.
getMaskArray() - Method in class ij.process.ImageProcessor
  Returns the mask byte array, or null if there is no mask.
getMax(int) - Method in class ij.CompositeImage
getMax() - Method in class ij.gui.ProfilePlot
  Returns the calculated maximum value.
getMax(double[]) - Static method in class ij.measure.CurveFitter
  Gets index of highest value in an array.
getMax() - Method in class ij.process.ByteProcessor
  Returns the largest displayed pixel value.
getMax() - Method in class ij.process.ColorProcessor
  Returns the largest displayed pixel value.
getMax() - Method in class ij.process.FloatProcessor
  Returns the largest displayed pixel value.
getMax() - Method in class ij.process.ImageProcessor
  Returns the largest displayed pixel value.
getMax() - Method in class ij.process.ShortProcessor
  Returns the largest displayed pixel value.
getMaxIterations() - Method in class ij.measure.CurveFitter
  Get maximum number of iterations allowed
getMaxThreshold() - Method in class ij.process.ImageProcessor
  Returns the upper threshold level.
getMaximumBounds() - Method in class ij.gui.ImageWindow
getMeasurements() - Static method in class ij.plugin.filter.Analyzer
getMemorySetting() - Method in class ij.plugin.Memory
getMenuBar() - Static method in class ij.Menus
getMenus() - Method in class ij.macro.Program
getMessage() - Method in class ij.gui.GenericDialog
  Returns a reference to the Label or MultiLineLabel created by addMessage(), or null if addMessage() was not called.
getMin(int) - Method in class ij.CompositeImage
getMin() - Method in class ij.gui.ProfilePlot
  Returns the calculated minimum value.
getMin() - Method in class ij.process.ByteProcessor
  Returns the smallest displayed pixel value.
getMin() - Method in class ij.process.ColorProcessor
  Returns the smallest displayed pixel value.
getMin() - Method in class ij.process.FloatProcessor
  Returns the smallest displayed pixel value.
getMin() - Method in class ij.process.ImageProcessor
  Returns the smallest displayed pixel value.
getMin() - Method in class ij.process.ShortProcessor
  Returns the smallest displayed pixel value.
getMinMax(double[]) - Static method in class ij.util.Tools
getMinMax(float[]) - Static method in class ij.util.Tools
getMinThreshold() - Method in class ij.process.ImageProcessor
  Returns the lower threshold level.
getMinimumSize() - Method in class ij.gui.MultiLineLabel
getMinimumSize() - Method in class ij.gui.Toolbar
getMinimumSize() - Method in class ij.gui.TrimmedButton
getModifiers() - Method in class ij.gui.ImageCanvas
  Returns the mouse event modifiers.
getNChannels() - Method in class ij.ImagePlus
  Returns the number of channels.
getNChannels() - Method in class ij.process.ColorProcessor
  Returns the number of color channels of the image, i.e., 3.
getNChannels() - Method in class ij.process.ImageProcessor
  Returns the number of color channels in the image.
getNCoordinates() - Method in class ij.gui.PolygonRoi
  Returns the number of XY coordinates.
getNFrames() - Method in class ij.ImagePlus
  Returns the number of frames (time-points).
getNSlices() - Method in class ij.ImagePlus
  Returns the image depth (number of z-slices).
getName(String) - Static method in class ij.Macro
getName() - Method in class ij.gui.Roi
  Returns the name of this ROI, or null.
getName(String) - Method in class ij.io.Opener
getName(String) - Method in class ij.plugin.ClassChecker
getName() - Method in class ij.plugin.TextReader
  Returns the file name.
getName(String) - Static method in class ij.plugin.frame.RoiManager
  Returns the name of the selection with the specified index.
getNextBoolean() - Method in class ij.gui.GenericDialog
  Returns the state of the next checkbox.
getNextChoice() - Method in class ij.gui.GenericDialog
  Returns the selected item in the next popup menu.
getNextChoiceIndex() - Method in class ij.gui.GenericDialog
  Returns the index of the selected item in the next popup menu.
getNextNumber() - Method in class ij.gui.GenericDialog
  Returns the contents of the next numeric field.
getNextString() - Method in class ij.gui.GenericDialog
  Returns the contents of the next text field.
getNextText() - Method in class ij.gui.GenericDialog
  Returns the contents of the next text area.
getNonImageWindows() - Static method in class ij.WindowManager
  Returns an array containing a list of the non-image windows.
getNthImageID(int) - Static method in class ij.WindowManager
  Returns the ID of the Nth open image.
getNumParams() - Method in class ij.measure.CurveFitter
  Get number of parameters for current fit function
getNumber(String, double) - Static method in class ij.IJ
  Allows the user to enter a number in a dialog box.
getNumericFields() - Method in class ij.gui.GenericDialog
  Returns the Vector containing the numeric TextFields.
getOpenUsingPlugins() - Static method in class ij.io.Opener
  Returns the state of the openUsingPlugins flag.
getOptions() - Static method in class ij.Macro
  If a command started using run(name, options) is running, returns the options string, otherwise, returns null.
getOriginalFileInfo() - Method in class ij.ImagePlus
  Returns the FileInfo object that was used to open this image.
getParams() - Method in class ij.measure.CurveFitter
  Get the set of parameter values from the best corner of the simplex
getPasteMode() - Method in class ij.gui.Roi
  Returns the current paste transfer mode, or NOT_PASTING (-1) if no paste operation is in progress.
getPixel(int, int) - Method in class ij.ImagePlus
  Returns the pixel value at (x,y) as a 4 element array.
getPixel(int, int) - Method in class ij.process.ByteProcessor
getPixel(int, int) - Method in class ij.process.ColorProcessor
getPixel(int, int, int[]) - Method in class ij.process.ColorProcessor
  Returns the 3 samples for the pixel at (x,y) in an array of int.
getPixel(int, int) - Method in class ij.process.FloatProcessor
  Returns a pixel value that must be converted using Float.intBitsToFloat().
getPixel(int, int, int[]) - Method in class ij.process.FloatProcessor
  Returns the value of the pixel at (x,y) in a one element int array.
getPixel(int, int) - Method in class ij.process.ImageProcessor
  Returns the value of the pixel at (x,y).
getPixel(int, int, int[]) - Method in class ij.process.ImageProcessor
  Returns the samples for the pixel at (x,y) in an int array.
getPixel(int, int) - Method in class ij.process.ShortProcessor
getPixelCount() - Method in class ij.process.ImageProcessor
getPixelValue(int, int) - Method in class ij.process.ByteProcessor
getPixelValue(int, int) - Method in class ij.process.ColorProcessor
  Converts the specified pixel to grayscale using the formula g=(r+g+b)/3 and returns it as a float.
getPixelValue(int, int) - Method in class ij.process.FloatProcessor
  Returns the value of the pixel at (x,y) as a float.
getPixelValue(int, int) - Method in class ij.process.ImageProcessor
  Returns the value of the pixel at (x,y).
getPixelValue(int, int) - Method in class ij.process.ShortProcessor
  Returns the value of the pixel at (x,y) as a float.
getPixels(int) - Method in class ij.ImageStack
  Returns the pixel array for the specified slice, were 1<=n<=nslices.
getPixels(int) - Method in class ij.VirtualStack
  Returns the pixel array for the specified slice, were 1<=n<=nslices.
getPixels() - Method in class ij.gui.Line
  Returns the pixel values along this line.
getPixels() - Method in class ij.process.ByteProcessor
  Returns a reference to the byte array containing this image's pixel data.
getPixels() - Method in class ij.process.ColorProcessor
  Returns a reference to the int array containing this image's pixel data.
getPixels() - Method in class ij.process.FloatProcessor
  Returns a reference to the float array containing this image's pixel data.
getPixels() - Method in class ij.process.ImageProcessor
  Returns a reference to this image's pixel array.
getPixels() - Method in class ij.process.ShortProcessor
  Returns a reference to the short array containing this image's pixel data.
getPixelsCopy() - Method in class ij.process.ByteProcessor
  Returns a copy of the pixel data.
getPixelsCopy() - Method in class ij.process.ColorProcessor
  Returns a copy of the pixel data.
getPixelsCopy() - Method in class ij.process.FloatProcessor
  Returns a copy of the pixel data.
getPixelsCopy() - Method in class ij.process.ImageProcessor
  Returns a copy of the pixel data.
getPixelsCopy() - Method in class ij.process.ShortProcessor
  Returns a copy of the pixel data.
getPlotSize() - Method in class ij.gui.ProfilePlot
  Returns the size of the plot that createWindow() creates.
getPlugInsPath() - Static method in class ij.Menus
  Returns the path to the user plugins directory or null if the plugins directory was not found.
getPlugins() - Static method in class ij.Menus
  Returns a list of the plugins in the plugins menu.
getPolygon() - Method in class ij.gui.Line
getPolygon() - Method in class ij.gui.OvalRoi
  Returns this OvalRoi as a polygon.
getPolygon() - Method in class ij.gui.PolygonRoi
  Returns this PolygonRoi as a Polygon.
getPolygon() - Method in class ij.gui.Roi
  Returns the outline of this selection as a Polygon, or null if this is a straight line selection.
getPopupMenu() - Static method in class ij.Menus
getPort() - Static method in class ij.ImageJ
  Returns the port that ImageJ checks on startup to see if another instance is running.
getPowerSpectrum() - Method in class ij.process.FHT
  Returns an 8-bit power spectrum, log-scaled to 1-254.
getPrecision() - Static method in class ij.plugin.filter.Analyzer
  Returns the number of digits displayed to the right of decimal point.
getPreferredLocation() - Method in class ij.ImageJ
getPreferredSize() - Method in class ij.gui.ImageCanvas
getPreferredSize() - Method in class ij.gui.MultiLineLabel
getPreferredSize() - Method in class ij.gui.ProgressBar
getPreferredSize() - Method in class ij.gui.Toolbar
getPreferredSize() - Method in class ij.gui.TrimmedButton
getPrefsDir() - Static method in class ij.Prefs
  Gets the path to the directory where the preferences file (IJPrefs.txt) is saved.
getPreviewCheckbox() - Method in class ij.gui.GenericDialog
  Returns a reference to the Preview Checkbox.
getProcessor(int) - Method in class ij.CompositeImage
getProcessor() - Method in class ij.ImagePlus
  Returns a reference to the current ImageProcessor.
getProcessor(int) - Method in class ij.ImageStack
  Returns an ImageProcessor for the specified slice, were 1<=n<=nslices.
getProcessor(int) - Method in class ij.VirtualStack
  Returns an ImageProcessor for the specified slice, were 1<=n<=nslices.
getProcessor() - Method in class ij.gui.Plot
  Returns the plot as an ImageProcessor.
getProfile() - Method in class ij.gui.ProfilePlot
  Returns the profile plot data.
getProgram() - Method in class ij.plugin.MacroInstaller
getProgressBar() - Method in class ij.ImageJ
getProjection() - Method in class ij.plugin.ZProjector
  Retrieve results of most recent projection operation.
getProperties() - Method in class ij.ImagePlus
  Returns this image's Properties.
getProperty(String) - Method in class ij.ImagePlus
  Returns the property associated with 'key'.
getQuality() - Static method in class ij.plugin.JpegWriter
getRGB(byte[], byte[], byte[]) - Method in class ij.process.ColorProcessor
  Returns the red, green and blue planes as 3 byte arrays.
getRGBRow(ImageStack, int, int, int, int, int, int[]) - Method in class ij.plugin.filter.Projector
getROIs() - Method in class ij.plugin.frame.RoiManager
  Returns the ROI Hashtable.
getRSquared() - Method in class ij.measure.CurveFitter
  Returns R^2, where 1.0 is best.
getRawLength() - Method in class ij.gui.Line
  Returns the length of this line in pixels.
getRawValue(double) - Method in class ij.measure.Calibration
  Converts a density calibrated value into a raw pixel value.
getRedirectImage(ImagePlus) - Static method in class ij.plugin.filter.Analyzer
  Returns the image selected in the "Redirect To:" popup menu of the Analyze/Set Measurements dialog or null if "None" is selected, the image was not found or the image is not the same size as `currentImage`.
getReds() - Method in class ij.LookUpTable
getResiduals() - Method in class ij.measure.CurveFitter
  Returns residuals array ie.
getResource(String) - Method in class ij.io.PluginClassLoader
  Returns a resource from the path or JAR files as a URL
getResourceAsStream(String) - Method in class ij.io.PluginClassLoader
  Returns a resource from the path or JAR files as an InputStream
getRestarts() - Method in class ij.measure.CurveFitter
  Get number of simplex restarts to do
getResultString() - Method in class ij.measure.CurveFitter
  Get a string description of the curve fitting results for easy output.
getResultsTable() - Static method in class ij.measure.ResultsTable
  Returns the ResultsTable used by the Measure command.
getResultsTable() - Static method in class ij.plugin.filter.Analyzer
  Returns the ImageJ results table.
getRoi() - Method in class ij.ImagePlus
getRoi() - Method in class ij.ImageStack
getRoi() - Method in class ij.io.RoiDecoder
  Returns the ROI.
getRoi() - Method in class ij.process.ImageProcessor
  Returns a Rectangle that represents the current region of interest.
getRois() - Method in class ij.gui.ShapeRoi
  Converts a Shape into Roi object(s).
getRoisAsArray() - Method in class ij.plugin.frame.RoiManager
  Returns the ROIs as an array.
getRoot() - Method in class ij.plugin.ControlPanel
getRow(int, int, int[], int) - Method in class ij.process.ImageProcessor
  Returns the pixel values along the horizontal line starting at (x,y).
getRowAsString(int) - Method in class ij.measure.ResultsTable
  Returns a tab-delimited string representing the given row, where 0<=row<=counter-1.
getSD() - Method in class ij.measure.CurveFitter
  Returns the standard deviation of the residuals.
getSD() - Static method in class ij.plugin.filter.Filters
  Returns the default standard deviation used by Process/Noise/Add Specified Noise.
getScreenSize() - Static method in class ij.IJ
  Returns the size, in pixels, of the primary display.
getSelectionEnd() - Method in class ij.text.TextPanel
  Returns the index of the last selected line, or -1 if there is no slection.
getSelectionStart() - Method in class ij.text.TextPanel
  Returns the index of the first selected line, or -1 if there is no slection.
getShapeAsArray() - Method in class ij.gui.ShapeRoi
  Retrieves the end points and control points of the path as a float array.
getShapeRoi() - Method in class ij.io.RoiDecoder
getShortSliceLabel(int) - Method in class ij.ImageStack
  Returns a shortened version (up to the first 60 characters or first newline and suffix removed) of the label of the specified slice.
getShortTitle() - Method in class ij.ImagePlus
  Returns a shortened version of image name that does not include spaces or a file name extension.
getShortcuts() - Static method in class ij.Menus
  Returns the hashtable that associates shortcuts with commands.
getShowAllROIs() - Method in class ij.gui.ImageCanvas
getSize() - Method in class ij.ImageStack
  Returns the number of slices in this stack.
getSize() - Method in class ij.VirtualStack
  Returns the number of slices in this stack.
getSize() - Static method in class ij.gui.TextRoi
  Returns the current font size.
getSliceLabel(int) - Method in class ij.ImageStack
  Returns the label of the specified slice, were 1<=n<=nslices.
getSliceLabel(int) - Method in class ij.VirtualStack
  Returns the file name of the Nth image.
getSliceLabels() - Method in class ij.ImageStack
  Returns the slice labels as an array of Strings.
getSliceNumber() - Method in class ij.plugin.filter.PlugInFilterRunner
  Return the slice number currently processed by the calling thread.
getSliders() - Method in class ij.gui.GenericDialog
  Returns the sliders (Scrollbars).
getSnapshotPixels() - Method in class ij.process.ByteProcessor
getSnapshotPixels() - Method in class ij.process.ColorProcessor
  Returns a reference to the snapshot pixel array.
getSnapshotPixels() - Method in class ij.process.FloatProcessor
getSnapshotPixels() - Method in class ij.process.ImageProcessor
  Returns a reference to the snapshot (undo) buffer, or null.
getSnapshotPixels() - Method in class ij.process.ShortProcessor
getSrcRect() - Method in class ij.gui.ImageCanvas
getStack() - Method in class ij.ImagePlus
  Returns the image stack.
getStackSize() - Method in class ij.ImagePlus
  If this is a stack, returns the number of slices, else returns 1.
getStartTime() - Method in class ij.ImagePlus
  Returns the time in milliseconds when startTiming() was last called.
getState() - Method in class ij.gui.Roi
getStatistics() - Method in class ij.ImagePlus
  Returns an ImageStatistics object generated using the standard measurement options (area, mean, mode, min and max).
getStatistics(int) - Method in class ij.ImagePlus
  Returns an ImageStatistics object generated using the specified measurement options.
getStatistics(int, int) - Method in class ij.ImagePlus
  Returns an ImageStatistics object generated using the specified measurement options and histogram bin count.
getStatistics(int, int, double, double) - Method in class ij.ImagePlus
  Returns an ImageStatistics object generated using the specified measurement options, histogram bin count and histogram range.
getStatistics(ImageProcessor, int, Calibration) - Static method in class ij.process.ImageStatistics
getString(String, String) - Static method in class ij.IJ
  Allows the user to enter a string in a dialog box.
getString(String) - Static method in class ij.Prefs
  Finds an string in IJ_Props or IJ_Prefs.txt.
getString(String, String) - Static method in class ij.Prefs
  Finds an string in IJ_Props or IJ_Prefs.txt.
getStringFields() - Method in class ij.gui.GenericDialog
  Returns the Vector containing the string TextFields.
getStringWidth(String) - Method in class ij.process.ImageProcessor
  Returns the width in pixels of the specified string.
getStringWidth(String, FontMetrics, Graphics) - Static method in class ij.util.Java2
getStyle() - Static method in class ij.gui.TextRoi
  Returns the current font style.
getSumResidualsSqr() - Method in class ij.measure.CurveFitter
getSymbolTable() - Method in class ij.macro.Program
getTempCurrentImage() - Static method in class ij.WindowManager
  Returns `tempCurrentImage`, which may be null.
getText() - Method in class ij.plugin.frame.Editor
getText() - Method in class ij.text.TextPanel
  Returns all the text as a string.
getTextArea() - Method in class ij.plugin.frame.Editor
getTextArea1() - Method in class ij.gui.GenericDialog
  Returns a reference to textArea1.
getTextArea2() - Method in class ij.gui.GenericDialog
  Returns a reference to textArea2.
getTextPanel() - Static method in class ij.IJ
  Returns a reference to the "Results" window TextPanel.
getTextPanel() - Method in class ij.text.TextWindow
  Returns a reference to this TextWindow's TextPanel.
getThreads() - Static method in class ij.Prefs
  Returns the number of threads used by PlugInFilters to process stacks.
getTiffInfo() - Method in class ij.io.TiffDecoder
getTimeUnit() - Method in class ij.measure.Calibration
  Returns the distance unit (e.g.
getTitle() - Method in class ij.ImagePlus
  Returns the image name.
getToolId() - Static method in class ij.gui.Toolbar
  Returns the ID of the current tool (Toolbar.RECTANGLE, Toolbar.OVAL, etc.).
getToolId(String) - Method in class ij.gui.Toolbar
  Returns the ID of the tool whose name (the description displayed in the status bar) starts with the specified string, or -1 if the tool is not found.
getTransferData(DataFlavor) - Method in class ij.plugin.Clipboard
getTransferDataFlavors() - Method in class ij.plugin.Clipboard
getTransparentPixel() - Method in class ij.io.GifEncoder
getType() - Method in class ij.ImagePlus
  Returns the current image type (ImagePlus.GRAY8, ImagePlus.GRAY16, ImagePlus.GRAY32, ImagePlus.COLOR_256 or ImagePlus.COLOR_RGB).
getType() - Method in class ij.gui.Roi
getTypeAsString() - Method in class ij.gui.Roi
  Convenience method that converts Roi type to a human-readable form.
getUMeans() - Static method in class ij.plugin.filter.Analyzer
  Returns an array containing the first 20 uncalibrated means.
getUniqueName(String) - Static method in class ij.WindowManager
  Returns a unique name by adding, before the extension, -1, -2, etc.
getUnit() - Method in class ij.measure.Calibration
  Returns the length unit (e.g.
getUnits() - Method in class ij.measure.Calibration
  Returns the plural form of the length unit (e.g.
getValue(String, String, String) - Static method in class ij.Macro
getValue(String) - Method in class ij.gui.GenericDialog
getValue(int, int) - Method in class ij.measure.ResultsTable
  Obsolete, replaced by getValueAsDouble.
getValue(String, int) - Method in class ij.measure.ResultsTable
  Returns the value of the specified column and row, where column is the column heading and row is a number greater than or equal zero and less than value returned by getCounter().
getValueAsDouble(int, int) - Method in class ij.measure.ResultsTable
  Returns the value of the given column and row, where column must be less than or equal the value returned by getLastColumn() and row must be greater than or equal zero and less than the value returned by getCounter().
getValueUnit() - Method in class ij.measure.Calibration
  Returns the value unit.
getVersion() - Static method in class ij.IJ
  Returns the ImageJ version number as a string.
getVersion() - Method in class ij.plugin.ControlPanel
getWeightingFactors() - Static method in class ij.process.ColorProcessor
  Returns the three weighting factors used by getPixelValue(), getHistogram() and convertToByte() to do color conversions.
getWidth() - Method in class ij.ImagePlus
getWidth() - Method in class ij.ImageStack
getWidth() - Static method in class ij.gui.Line
getWidth() - Method in class ij.process.ImageProcessor
  Returns the width of this image in pixels.
getWindow() - Method in class ij.ImagePlus
  Returns the ImageWindow that is being used to display this image.
getWindowCount() - Static method in class ij.WindowManager
  Returns the number of open image windows.
getX(double) - Method in class ij.measure.Calibration
  Converts a x-coodinate in pixels to physical units (e.g.
getXCoordinates() - Method in class ij.gui.PolygonRoi
  Returns this ROI's X-coordinates, which are relative to origin of the bounding box.
getXValues() - Method in class ij.gui.PlotWindow
getY(double) - Method in class ij.measure.Calibration
  Converts a y-coodinate in pixels to physical units (e.g.
getY(double, int) - Method in class ij.measure.Calibration
  Converts a y-coodinate in pixels to physical units (e.g.
getYCoordinates() - Method in class ij.gui.PolygonRoi
  Returns this ROI's Y-coordinates, which are relative to origin of the bounding box.
getYValues() - Method in class ij.gui.PlotWindow
getZ(double) - Method in class ij.measure.Calibration
  Converts a z-coodinate in pixels to physical units (e.g.
getf(int, int) - Method in class ij.process.ByteProcessor
getf(int) - Method in class ij.process.ByteProcessor
getf(int, int) - Method in class ij.process.ColorProcessor
getf(int) - Method in class ij.process.ColorProcessor
getf(int, int) - Method in class ij.process.FloatProcessor
getf(int) - Method in class ij.process.FloatProcessor
getf(int, int) - Method in class ij.process.ImageProcessor
getf(int) - Method in class ij.process.ImageProcessor
getf(int, int) - Method in class ij.process.ShortProcessor
getf(int) - Method in class ij.process.ShortProcessor
green - Variable in class ij.plugin.filter.RGBStackSplitter
  These are the three stacks created by the split(ImageStack) method.
greens - Variable in class ij.io.FileInfo
grow(int, int) - Method in class ij.gui.FreehandRoi
grow(int, int) - Method in class ij.gui.Line
grow(int, int) - Method in class ij.gui.PolygonRoi
grow(int, int) - Method in class ij.gui.Roi

## H

HAND - Static variable in class ij.gui.Toolbar
HANDLE_SIZE - Static variable in class ij.gui.Roi
HEIGHT_KEY - Static variable in class ij.text.TextWindow
HTMLDialog - class ij.gui.HTMLDialog.
  This is modal dialog box that displays HTML formated text.
HTMLDialog(String, String) - Constructor for class ij.gui.HTMLDialog
Histogram - class ij.plugin.Histogram.
  This plugin implements the Analyze/Histogram command.
Histogram() - Constructor for class ij.plugin.Histogram
HistogramWindow - class ij.gui.HistogramWindow.
  This class is an extended ImageWindow that displays histograms.
HistogramWindow(ImagePlus) - Constructor for class ij.gui.HistogramWindow
  Displays a histogram using the title "Histogram of ImageName".
HistogramWindow(String, ImagePlus, int) - Constructor for class ij.gui.HistogramWindow
  Displays a histogram using the specified title and number of bins.
HistogramWindow(String, ImagePlus, int, double, double) - Constructor for class ij.gui.HistogramWindow
  Displays a histogram using the specified title, number of bins and histogram range.
HistogramWindow(String, ImagePlus, int, double, double, int) - Constructor for class ij.gui.HistogramWindow
  Displays a histogram using the specified title, number of bins, histogram range and yMax.
HistogramWindow(String, ImagePlus, ImageStatistics) - Constructor for class ij.gui.HistogramWindow
  Displays a histogram using the specified title and ImageStatistics.
Hotkeys - class ij.plugin.Hotkeys.
  Implements the Plugins/Hotkeys/Install and Remove commands.
Hotkeys() - Constructor for class ij.plugin.Hotkeys
handCursor - Static variable in class ij.gui.ImageCanvas
handleColor - Variable in class ij.gui.Roi
handleMouseDown(int, int) - Method in class ij.gui.Roi
handleMouseDrag(int, int, int) - Method in class ij.gui.Roi
handleMouseUp(int, int) - Method in class ij.gui.FreehandRoi
handleMouseUp(int, int) - Method in class ij.gui.PointRoi
handleMouseUp(int, int) - Method in class ij.gui.PolygonRoi
handleMouseUp(int, int) - Method in class ij.gui.Roi
handleMouseUp(int, int) - Method in class ij.gui.TextRoi
handlePopupMenu(MouseEvent) - Method in class ij.gui.ImageCanvas
hasVars() - Method in class ij.macro.Program
height - Variable in class ij.ImagePlus
height - Variable in class ij.io.FileInfo
height - Variable in class ij.process.ImageProcessor
height - Variable in class ij.process.ImageStatistics
hexDigits - Static variable in class ij.util.Tools
  This array contains the 16 hex digits '0'-'F'.
hide() - Method in class ij.ImagePlus
  Closes the window, if any, that is displaying this image.
hideErrorMessages() - Method in class ij.plugin.TextReader
hideProcessStackDialog - Static variable in class ij.IJ
hideProgress() - Method in class ij.process.ImageProcessor
histMax - Variable in class ij.process.ImageStatistics
histMin - Variable in class ij.process.ImageStatistics
histYMax - Variable in class ij.process.ImageStatistics
histogram - Variable in class ij.gui.HistogramWindow
histogram - Variable in class ij.process.ImageStatistics
histogram16 - Variable in class ij.process.ImageStatistics
  65536 element histogram (16-bit images only)
histogramMax - Variable in class ij.process.ImageProcessor
histogramMin - Variable in class ij.process.ImageProcessor
histogramSize - Variable in class ij.process.ImageProcessor

## I

IF - Static variable in interface ij.macro.MacroConstants
IJ - class ij.IJ.
  This class consists of static utility methods.
IJ() - Constructor for class ij.IJ
IMAGEIO - Static variable in class ij.io.FileInfo
IMAGE_DESCRIPTION - Static variable in class ij.io.TiffDecoder
IMAGE_LENGTH - Static variable in class ij.io.TiffDecoder
IMAGE_WIDTH - Static variable in class ij.io.TiffDecoder
IMPORT_MENU - Static variable in class ij.Menus
INCLUDE_HOLES - Static variable in class ij.plugin.filter.ParticleAnalyzer
  Flood fill to ignore interior holes.
INDEX_OF - Static variable in interface ij.macro.MacroConstants
INTEGRATED_DENSITY - Static variable in interface ij.measure.Measurements
INTEGRATED_DENSITY - Static variable in class ij.measure.ResultsTable
INVALID_SHORTCUT - Static variable in class ij.Menus
INVERT - Static variable in interface ij.macro.MacroConstants
INVERT_Y - Static variable in interface ij.measure.Measurements
IN_TOLERANCE - Static variable in class ij.plugin.filter.MaximumFinder
  Output type all points around the maximum within the tolerance
IPLAB - Static variable in class ij.io.TiffDecoder
IS - Static variable in interface ij.macro.MacroConstants
IS_ACTIVE - Static variable in interface ij.macro.MacroConstants
IS_KEY_DOWN - Static variable in interface ij.macro.MacroConstants
IS_NAN - Static variable in interface ij.macro.MacroConstants
IS_OPEN - Static variable in interface ij.macro.MacroConstants
ImageCalculator - class ij.plugin.ImageCalculator.
  This plugin implements the Process/Image Calculator command.
ImageCalculator() - Constructor for class ij.plugin.ImageCalculator
ImageCanvas - class ij.gui.ImageCanvas.
  This is a Canvas used to display images in a Window.
ImageCanvas(ImagePlus) - Constructor for class ij.gui.ImageCanvas
ImageConverter - class ij.process.ImageConverter.
  This class converts an ImagePlus object to a different type.
ImageConverter(ImagePlus) - Constructor for class ij.process.ImageConverter
  Constructs an ImageConverter based on an ImagePlus object.
ImageJ - class ij.ImageJ.
  This frame is the main ImageJ class.
ImageJ() - Constructor for class ij.ImageJ
  Creates a new ImageJ frame that runs as an application.
ImageJ(Applet) - Constructor for class ij.ImageJ
  Creates a new ImageJ frame that runs as an applet.
ImageJ(Applet, int) - Constructor for class ij.ImageJ
  If 'applet' is not null, creates a new ImageJ frame that runs as an applet.
ImageJApplet - class ij.ImageJApplet.
  Runs ImageJ as an applet and optionally opens up to nine images using URLs passed as a parameters.
ImageJApplet() - Constructor for class ij.ImageJApplet
ImageLayout - class ij.gui.ImageLayout.
  This is a custom layout manager that supports resizing of zoomed images.
ImageLayout(ImageCanvas) - Constructor for class ij.gui.ImageLayout
  Creates a new ImageLayout with center alignment and 5 pixel horizontal and vertical gaps.
ImageListener - interface ij.ImageListener.
ImageMath - class ij.plugin.filter.ImageMath.
  This plugin implements ImageJ's Process/Math submenu.
ImageMath() - Constructor for class ij.plugin.filter.ImageMath
ImagePlus - class ij.ImagePlus.
  This is an extended image class that supports 8-bit, 16-bit, 32-bit (real) and RGB images.
ImagePlus() - Constructor for class ij.ImagePlus
  Constructs an uninitialized ImagePlus.
ImagePlus(String, Image) - Constructor for class ij.ImagePlus
  Constructs an ImagePlus from an AWT Image.
ImagePlus(String, ImageProcessor) - Constructor for class ij.ImagePlus
  Constructs an ImagePlus from an ImageProcessor.
ImagePlus(String) - Constructor for class ij.ImagePlus
  Constructs an ImagePlus from a TIFF, BMP, DICOM, FITS, PGM, GIF or JPRG specified by a path or from a TIFF, DICOM, GIF or JPEG specified by a URL.
ImagePlus(String, ImageStack) - Constructor for class ij.ImagePlus
  Constructs an ImagePlus from a stack.
ImageProcessor - class ij.process.ImageProcessor.
  This abstract class is the superclass for classes that process the four data types (byte, short, float and RGB) supported by ImageJ.
ImageProcessor() - Constructor for class ij.process.ImageProcessor
ImageProperties - class ij.plugin.filter.ImageProperties.
ImageProperties() - Constructor for class ij.plugin.filter.ImageProperties
ImageReader - class ij.io.ImageReader.
  Reads raw 8-bit, 16-bit or 32-bit (float or RGB) images from a stream or URL.
ImageReader(FileInfo) - Constructor for class ij.io.ImageReader
  Constructs a new ImageReader using a FileInfo object to describe the file to be read.
ImageStack - class ij.ImageStack.
  This class represents an expandable array of images.
ImageStack(int, int) - Constructor for class ij.ImageStack
  Creates a new, empty image stack.
ImageStack(int, int, ColorModel) - Constructor for class ij.ImageStack
  Creates a new, empty image stack.
ImageStatistics - class ij.process.ImageStatistics.
  Statistics, including the histogram, of an image or image roi.
ImageStatistics() - Constructor for class ij.process.ImageStatistics
ImageWindow - class ij.gui.ImageWindow.
  A frame for displaying images.
ImageWindow(String) - Constructor for class ij.gui.ImageWindow
ImageWindow(ImagePlus) - Constructor for class ij.gui.ImageWindow
ImageWindow(ImagePlus, ImageCanvas) - Constructor for class ij.gui.ImageWindow
ImageWriter - class ij.io.ImageWriter.
  Writes a raw image described by a FileInfo object to an OutputStream.
ImageWriter(FileInfo) - Constructor for class ij.io.ImageWriter
ImportDialog - class ij.io.ImportDialog.
  This is a dialog box used to imports raw 8, 16, 24 and 32-bit images.
ImportDialog(String, String) - Constructor for class ij.io.ImportDialog
ImportDialog() - Constructor for class ij.io.ImportDialog
Info - class ij.plugin.filter.Info.
  This plugin implements the Image/Show Info command.
Info() - Constructor for class ij.plugin.filter.Info
Installer - class ij.plugin.Installer.
  Implements the Plugins/Shortcuts/Install...
Installer() - Constructor for class ij.plugin.Installer
Interpreter - class ij.macro.Interpreter.
  This is the recursive descent parser/interpreter for the ImageJ macro language.
Interpreter() - Constructor for class ij.macro.Interpreter
IterFactor - Static variable in class ij.measure.CurveFitter
ic - Variable in class ij.gui.ImageWindow
ic - Variable in class ij.gui.Roi
ij - package ij
ij - Variable in class ij.gui.ImageCanvas
ij - Variable in class ij.gui.ImageWindow
ij.gui - package ij.gui
ij.io - package ij.io
ij.macro - package ij.macro
ij.measure - package ij.measure
ij.plugin - package ij.plugin
ij.plugin.filter - package ij.plugin.filter
ij.plugin.frame - package ij.plugin.frame
ij.process - package ij.process
ij.text - package ij.text
ij.util - package ij.util
image - Variable in class ij.process.ImageProcessor
imageClosed(ImagePlus) - Method in interface ij.ImageListener
imageHeight - Variable in class ij.gui.ImageCanvas
imageOpened(ImagePlus) - Method in interface ij.ImageListener
imageUpdate(Image, int, int, int, int, int) - Method in class ij.ImagePlus
  Used by ImagePlus to monitor loading of images.
imageUpdated(ImagePlus) - Method in interface ij.ImageListener
imageUpdated - Variable in class ij.gui.ImageCanvas
imageWidth - Variable in class ij.gui.ImageCanvas
img - Variable in class ij.ImagePlus
img - Variable in class ij.process.ImageProcessor
imp - Variable in class ij.gui.ImageCanvas
imp - Variable in class ij.gui.ImageWindow
imp - Variable in class ij.gui.ProfilePlot
imp - Variable in class ij.gui.Roi
imp - Variable in class ij.plugin.filter.ParticleAnalyzer
in - Variable in class ij.io.TiffDecoder
incrementCounter() - Method in class ij.measure.ResultsTable
  Increments the measurement counter by one.
info - Variable in class ij.io.FileInfo
info - Variable in class ij.measure.Calibration
  Plugin writers can use this string to store information about the image.
init() - Method in class ij.ImageJApplet
  Starts ImageJ if it's not already running.
inputStream - Variable in class ij.io.FileInfo
insert(ImageProcessor, int, int) - Method in class ij.process.ImageProcessor
  Inserts the image contained in 'ip' at (xloc, yloc).
install(String) - Method in class ij.plugin.MacroInstaller
install(String, Menu) - Method in class ij.plugin.MacroInstaller
installFile(String) - Method in class ij.plugin.MacroInstaller
installFromIJJar(String) - Method in class ij.plugin.MacroInstaller
  Installs a macro set contained in ij.jar.
installLibrary(String) - Method in class ij.plugin.MacroInstaller
installPlugin(String, char, String, String, ImageJ) - Static method in class ij.Menus
  Adds a plugin based command to the end of a specified menu.
instanceColor - Variable in class ij.gui.Roi
intelByteOrder - Static variable in class ij.Prefs
  Export Raw using little-endian byte order.
intelByteOrder - Variable in class ij.io.FileInfo
interpolate - Static variable in class ij.gui.PlotWindow
  Interpolate line profiles.
interpolate - Variable in class ij.process.ImageProcessor
interpolateScaledImages - Static variable in class ij.Prefs
  Display images scaled <100% using bilinear interpolation
invalidNumber() - Method in class ij.gui.GenericDialog
  Returns true if one or more of the numeric fields contained an invalid number.
inverseTransform() - Method in class ij.process.FHT
  Performs an inverse transform, converting this image into the space domain.
inversionTested - Variable in class ij.process.ImageProcessor
invert() - Method in class ij.process.FloatProcessor
invert() - Method in class ij.process.ImageProcessor
  Inverts the image or ROI.
invert() - Method in class ij.process.ShortProcessor
invert() - Method in class ij.process.StackProcessor
invertLut() - Method in class ij.process.ColorProcessor
  Does nothing since RGB images do not use LUTs.
invertLut() - Method in class ij.process.ImageProcessor
  Inverts the values in this image's LUT (indexed color model).
invertedLut - Variable in class ij.process.ImageProcessor
ip - Variable in class ij.ImagePlus
isAntialiased() - Static method in class ij.gui.TextRoi
isArea() - Method in class ij.gui.Roi
  Returns true if this is an area selection.
isAutoRunAndHide() - Method in class ij.plugin.MacroInstaller
  Returns true if an "AutoRunAndHide" macro was run/installed.
isBatchMode() - Static method in class ij.macro.Interpreter
isClosed() - Method in class ij.gui.ImageWindow
  Has this window been closed?
isColorLut() - Method in class ij.process.ImageProcessor
  Returns true if this image uses a color LUT.
isDataFlavorSupported(DataFlavor) - Method in class ij.plugin.Clipboard
isGrayscale() - Method in class ij.LookUpTable
  Returns `true` if this is a 256 entry grayscale LUT.
isHSB() - Method in class ij.ImageStack
  Returns true if this is a 3-slice HSB stack.
isHandle(int, int) - Method in class ij.gui.Line
  Returns a handle number if the specified screen coordinates are inside or near a handle, otherwise returns -1.
isHandle(int, int) - Method in class ij.gui.OvalRoi
  Returns a handle number if the specified screen coordinates are inside or near a handle, otherwise returns -1.
isHandle(int, int) - Method in class ij.gui.PolygonRoi
  Returns a handle number if the specified screen coordinates are inside or near a handle, otherwise returns -1.
isHandle(int, int) - Method in class ij.gui.Roi
  Returns a handle number if the specified screen coordinates are inside or near a handle, otherwise returns -1.
isInvertedLut() - Method in class ij.ImagePlus
  Returns true is this image uses an inverting LUT that displays zero as white and 255 as black.
isInvertedLut() - Method in class ij.process.ColorProcessor
  Always returns false since RGB images do not use LUTs.
isInvertedLut() - Method in class ij.process.ImageProcessor
  Returns true if this image uses an inverting LUT that displays zero as white and 255 as black.
isJava14() - Static method in class ij.IJ
  Returns true if ImageJ is running on a Java 1.4 or greater JVM.
isJava15() - Static method in class ij.IJ
  Returns true if ImageJ is running on a Java 1.5 or greater JVM.
isJava16() - Static method in class ij.IJ
  Returns true if ImageJ is running on a Java 1.6 or greater JVM.
isJava2() - Static method in class ij.IJ
  Returns true if ImageJ is running on Java 2.
isKillable() - Method in class ij.process.ImageProcessor
  Obsolete.
isLine() - Method in class ij.gui.Roi
  Returns true if this is a line selection.
isLinux() - Static method in class ij.IJ
  Returns true if ImageJ is running on Linux.
isLocked() - Method in class ij.ImagePlus
  Returns 'true' if the image is locked.
isMacOSX() - Static method in class ij.IJ
  Returns true if this machine is a Macintosh running OS X.
isMacintosh() - Static method in class ij.IJ
  Returns true if this machine is a Macintosh.
isProcessor() - Method in class ij.ImagePlus
isPseudoColorLut() - Method in class ij.process.ImageProcessor
  Returns true if this image uses a pseudocolor or grayscale LUT, in other words, is this an image that can be filtered.
isRGB() - Method in class ij.ImageStack
  Returns true if this is a 3-slice RGB stack.
isRedirectImage() - Static method in class ij.plugin.filter.Analyzer
  Returns `true` if an image is selected in the "Redirect To:" popup menu of the Analyze/Set Measurements dialog box.
isResultsWindow() - Static method in class ij.IJ
  Returns true if the "Results" window is open.
isSigned16Bit() - Method in class ij.measure.Calibration
  Returns true if this is a signed 16-bit image.
isVirtual() - Method in class ij.ImageStack
  Returns true if this is a virtual (disk resident) stack.
isVirtual() - Method in class ij.VirtualStack
  Always return true.
isVisible() - Method in class ij.gui.Roi
  Returns true if this ROI is currently displayed on an image.
isVista() - Static method in class ij.IJ
  Returns true if ImageJ is running on Windows Vista.
isWindows() - Static method in class ij.IJ
  Returns true if this machine is running Windows.
itemStateChanged(ItemEvent) - Method in class ij.ImageJ
  Handles CheckboxMenuItem state changes.
itemStateChanged(ItemEvent) - Method in class ij.gui.GenericDialog
itemStateChanged(ItemEvent) - Method in class ij.gui.Toolbar
itemStateChanged(ItemEvent) - Method in class ij.plugin.Colors
itemStateChanged(ItemEvent) - Method in class ij.plugin.filter.Resizer
itemStateChanged(ItemEvent) - Method in class ij.plugin.frame.ContrastAdjuster
itemStateChanged(ItemEvent) - Method in class ij.plugin.frame.Editor
itemStateChanged(ItemEvent) - Method in class ij.plugin.frame.Fitter
itemStateChanged(ItemEvent) - Method in class ij.plugin.frame.Fonts
itemStateChanged(ItemEvent) - Method in class ij.plugin.frame.PasteController
itemStateChanged(ItemEvent) - Method in class ij.plugin.frame.RoiManager
itemStateChanged(ItemEvent) - Method in class ij.plugin.frame.ThresholdAdjuster
itemStateChanged(ItemEvent) - Method in class ij.text.TextWindow

## J

JAVA_OR_TEXT - Static variable in class ij.io.Opener
JPEG - Static variable in class ij.Prefs
JPEG - Static variable in class ij.io.Opener
Java2 - class ij.util.Java2.
  This class contains static methods that use the Java 2 API.
Java2() - Constructor for class ij.util.Java2
JavaProperties - class ij.plugin.JavaProperties.
  Displays the Java system properties in a text window.
JavaProperties() - Constructor for class ij.plugin.JavaProperties
JpegWriter - class ij.plugin.JpegWriter.
  The File->Save As->Jpeg command (FileSaver.saveAsJpeg()) uses this plugin to save images in JPEG format when running Java 2.
JpegWriter() - Constructor for class ij.plugin.JpegWriter
jarFiles - Variable in class ij.io.PluginClassLoader
justification - Variable in class ij.process.ImageProcessor

## K

KEEP_PREVIEW - Static variable in interface ij.plugin.filter.ExtendedPlugInFilter
  Set this flag if the last preview image may be kept as a result.
KEY_PREFIX - Static variable in class ij.Prefs
KURTOSIS - Static variable in interface ij.measure.Measurements
KURTOSIS - Static variable in class ij.measure.ResultsTable
kNPoints - Variable in class ij.plugin.filter.RankFilters
kRadius - Variable in class ij.plugin.filter.RankFilters
keyPressed(KeyEvent) - Method in class ij.ImageJ
keyPressed(KeyEvent) - Method in class ij.gui.GenericDialog
keyPressed(KeyEvent) - Method in class ij.gui.MessageDialog
keyPressed(KeyEvent) - Method in class ij.gui.SaveChangesDialog
keyPressed(KeyEvent) - Method in class ij.gui.YesNoCancelDialog
keyPressed(KeyEvent) - Method in class ij.text.TextPanel
keyReleased(KeyEvent) - Method in class ij.ImageJ
keyReleased(KeyEvent) - Method in class ij.gui.GenericDialog
keyReleased(KeyEvent) - Method in class ij.gui.MessageDialog
keyReleased(KeyEvent) - Method in class ij.gui.SaveChangesDialog
keyReleased(KeyEvent) - Method in class ij.gui.YesNoCancelDialog
keyReleased(KeyEvent) - Method in class ij.text.TextPanel
keyTyped(KeyEvent) - Method in class ij.ImageJ
keyTyped(KeyEvent) - Method in class ij.gui.GenericDialog
keyTyped(KeyEvent) - Method in class ij.gui.MessageDialog
keyTyped(KeyEvent) - Method in class ij.gui.SaveChangesDialog
keyTyped(KeyEvent) - Method in class ij.gui.YesNoCancelDialog
keyTyped(KeyEvent) - Method in class ij.text.TextPanel
keywordIDs - Static variable in interface ij.macro.MacroConstants
keywords - Static variable in interface ij.macro.MacroConstants
killProcessor() - Method in class ij.ImagePlus
  Obsolete.
killRoi() - Method in class ij.ImagePlus
  Deletes the current region of interest.
killStack() - Method in class ij.ImagePlus
kurtosis - Variable in class ij.process.ImageStatistics

## L

LABELS - Static variable in interface ij.measure.Measurements
LAST_INDEX_OF - Static variable in interface ij.macro.MacroConstants
LEFT_JUSTIFY - Static variable in class ij.process.ImageProcessor
  Left justify text.
LEFT_MARGIN - Static variable in class ij.gui.Plot
  the margin width left of the plot frame (enough for 5-digit numbers such as unscaled 16-bit data
LENGTH_OF - Static variable in interface ij.macro.MacroConstants
LIMIT - Static variable in interface ij.measure.Measurements
LINE - Static variable in class ij.gui.Plot
  Connect points with solid lines.
LINE - Static variable in class ij.gui.PlotWindow
  Connect points with solid lines.
LINE - Static variable in class ij.gui.Roi
LINE - Static variable in class ij.gui.Toolbar
LINE_TO - Static variable in interface ij.macro.MacroConstants
LOC_KEY - Static variable in class ij.plugin.frame.ContrastAdjuster
LOC_KEY - Static variable in class ij.plugin.frame.ThresholdAdjuster
LOC_KEY - Static variable in class ij.text.TextWindow
LOG - Static variable in interface ij.macro.MacroConstants
LOG - Static variable in class ij.measure.Calibration
LOG - Static variable in class ij.measure.CurveFitter
LOG2 - Static variable in class ij.measure.Calibration
LOG2 - Static variable in class ij.measure.CurveFitter
LOGICAL_AND - Static variable in interface ij.macro.MacroConstants
LOGICAL_OR - Static variable in interface ij.macro.MacroConstants
LT - Static variable in interface ij.macro.MacroConstants
LTE - Static variable in interface ij.macro.MacroConstants
LUT - Static variable in class ij.io.Opener
LUT_Editor - class ij.plugin.LUT_Editor.
LUT_Editor() - Constructor for class ij.plugin.LUT_Editor
LZW - Static variable in class ij.io.FileInfo
LZW_WITH_DIFFERENCING - Static variable in class ij.io.FileInfo
Line - class ij.gui.Line.
  This class represents a straight line selection.
Line(int, int, int, int) - Constructor for class ij.gui.Line
  Creates a new straight line selection using the specified starting and ending screen coordinates.
Line(int, int, ImagePlus) - Constructor for class ij.gui.Line
  Starts the process of creating a new user-generated straight line selection.
Line(int, int, int, int, ImagePlus) - Constructor for class ij.gui.Line
  Obsolete
LineGraphAnalyzer - class ij.plugin.filter.LineGraphAnalyzer.
  Implements ImageJ's Analyze/Analyze Line Graph command.
LineGraphAnalyzer() - Constructor for class ij.plugin.filter.LineGraphAnalyzer
LineWidthAdjuster - class ij.plugin.frame.LineWidthAdjuster.
  Adjusts the width of line selections.
LineWidthAdjuster() - Constructor for class ij.plugin.frame.LineWidthAdjuster
LookUpTable - class ij.LookUpTable.
  This class represents a color look-up table.
LookUpTable(Image) - Constructor for class ij.LookUpTable
  Constructs a LookUpTable object from an AWT Image.
LookUpTable(ColorModel) - Constructor for class ij.LookUpTable
  Constructs a LookUpTable object from a ColorModel.
LutApplier - class ij.plugin.filter.LutApplier.
  This plugin implements the Image/Lookup Tables/Apply LUT command.
LutApplier() - Constructor for class ij.plugin.filter.LutApplier
LutLoader - class ij.plugin.LutLoader.
  Opens NIH Image look-up tables (LUTs), 768 byte binary LUTs (256 reds, 256 greens and 256 blues), LUTs in text format, or generates the LUT specified by the string argument passed to the run() method.
LutLoader() - Constructor for class ij.plugin.LutLoader
LutViewer - class ij.plugin.filter.LutViewer.
  Displays the active image's look-up table.
LutViewer() - Constructor for class ij.plugin.filter.LutViewer
label - Variable in class ij.gui.MessageDialog
label(ImageProcessor) - Method in class ij.plugin.filter.Filler
layoutContainer(Container) - Method in class ij.gui.ImageLayout
  Lays out the container and calls ImageCanvas.resizeCanvas() to adjust the image canvas size as needed.
lineRadius - Variable in class ij.plugin.filter.RankFilters
lineTo(int, int) - Method in class ij.process.ImageProcessor
  Draws a line from the current drawing location to (x,y).
lineWidth - Variable in class ij.process.ImageProcessor
list - Variable in class ij.gui.HistogramWindow
listAllThreads(PrintWriter) - Static method in class ij.plugin.ThreadLister
listCommands() - Method in class ij.plugin.CommandLister
listShortcuts() - Method in class ij.plugin.CommandLister
listValues - Static variable in class ij.gui.PlotWindow
  Display the XY coordinates in a separate window.
load(Object, Applet) - Static method in class ij.Prefs
  Finds and loads the ImageJ configuration file, "IJ_Props.txt".
load(BufferedReader) - Method in class ij.text.TextWindow
  Appends the text in the specified file to the end of this TextWindow.
loadClass(String) - Method in class ij.io.PluginClassLoader
  Returns a Class from the path or JAR files.
loadClass(String, boolean) - Method in class ij.io.PluginClassLoader
  Returns a Class from the path or JAR files.
loadClassBytes(String) - Method in class ij.io.PluginClassLoader
  This does the actual work of loading the bytes from the disk.
lock() - Method in class ij.ImagePlus
  Locks the image so other threads can test to see if it is in use.
lockSilently() - Method in class ij.ImagePlus
  Similar to lock, but doesn't beep and display an error message if the attempt to lock the image fails.
locked - Variable in class ij.ImagePlus
log(String) - Static method in class ij.IJ
log - Variable in class ij.gui.HistogramWindow
log() - Method in class ij.process.FloatProcessor
log() - Method in class ij.process.ImageProcessor
  Performs a log transform on the image or ROI.
log() - Method in class ij.process.ShortProcessor
logScale - Variable in class ij.gui.HistogramWindow
longOffset - Variable in class ij.io.FileInfo
loop - Variable in class ij.measure.Calibration
  Loop back and forth when animating stack
lostOwnership(Clipboard, Transferable) - Method in class ij.gui.HistogramWindow
lostOwnership(Clipboard, Transferable) - Method in class ij.gui.PlotWindow
lostOwnership(Clipboard, Transferable) - Method in class ij.plugin.frame.Editor
lostOwnership(Clipboard, Transferable) - Method in class ij.text.TextPanel
lut - Variable in class ij.gui.HistogramWindow
lutAnimation - Variable in class ij.process.ImageProcessor
lutMessage - Static variable in class ij.plugin.ZProjector
lutSize - Variable in class ij.io.FileInfo
lutUpdateMode - Variable in class ij.process.ImageProcessor
lzwUncompress(byte[]) - Method in class ij.io.ImageReader
  Utility method for decoding an LZW-compressed image strip.

## M

MACRO - Static variable in interface ij.macro.MacroConstants
MACRO - Static variable in class ij.plugin.NewPlugin
MACRO_CANCELED - Static variable in class ij.Macro
MAGNIFIER - Static variable in class ij.gui.Toolbar
MAJOR - Static variable in class ij.measure.ResultsTable
MAKE_LINE - Static variable in interface ij.macro.MacroConstants
MAKE_OVAL - Static variable in interface ij.macro.MacroConstants
MAKE_POLYGON - Static variable in interface ij.macro.MacroConstants
MAKE_RECTANGLE - Static variable in interface ij.macro.MacroConstants
MAKE_SELECTION - Static variable in interface ij.macro.MacroConstants
MASKS - Static variable in class ij.plugin.filter.ParticleAnalyzer
MAX - Static variable in class ij.measure.ResultsTable
MAX - Static variable in class ij.plugin.filter.RankFilters
MAX - Static variable in interface ij.process.Blitter
  dst=max(dst,src)
MAX_COLUMNS - Static variable in class ij.measure.ResultsTable
  Obsolete; use getLastColumn().
MAX_MACROS - Static variable in class ij.plugin.MacroInstaller
MAX_MACROS - Static variable in class ij.plugin.frame.Editor
MAX_METHOD - Static variable in class ij.plugin.ZProjector
MAX_OF - Static variable in interface ij.macro.MacroConstants
MAX_OPEN_RECENT_ITEMS - Static variable in class ij.Menus
MAX_SIZE - Static variable in class ij.plugin.MacroInstaller
MAX_SIZE - Static variable in class ij.plugin.frame.Editor
MAX_SLIDERS - Static variable in class ij.gui.GenericDialog
MAX_STANDARDS - Static variable in interface ij.measure.Measurements
  Maximum number of calibration standard (20)
MEAN - Static variable in interface ij.measure.Measurements
MEAN - Static variable in class ij.measure.ResultsTable
MEAN - Static variable in class ij.plugin.filter.RankFilters
MEDIAN - Static variable in interface ij.measure.Measurements
MEDIAN - Static variable in class ij.measure.ResultsTable
MEDIAN - Static variable in class ij.plugin.filter.RankFilters
MEDIAN_METHOD - Static variable in class ij.plugin.ZProjector
MENU_BAR - Static variable in class ij.plugin.frame.Editor
MENU_SIZE - Static variable in class ij.Prefs
METAMORPH1 - Static variable in class ij.io.TiffDecoder
METAMORPH2 - Static variable in class ij.io.TiffDecoder
META_DATA - Static variable in class ij.io.TiffDecoder
META_DATA_BYTE_COUNTS - Static variable in class ij.io.TiffDecoder
METHODS - Static variable in class ij.plugin.ZProjector
MIN - Static variable in class ij.measure.ResultsTable
MIN - Static variable in class ij.plugin.filter.RankFilters
MIN - Static variable in interface ij.process.Blitter
  dst=min(dst,src)
MINOR - Static variable in class ij.measure.ResultsTable
MINUS_EQUAL - Static variable in interface ij.macro.MacroConstants
MINUS_MINUS - Static variable in interface ij.macro.MacroConstants
MIN_HEIGHT - Static variable in class ij.gui.ImageWindow
MIN_MAX - Static variable in interface ij.measure.Measurements
MIN_METHOD - Static variable in class ij.plugin.ZProjector
MIN_OF - Static variable in interface ij.macro.MacroConstants
MIN_WIDTH - Static variable in class ij.gui.ImageWindow
MODE - Static variable in interface ij.measure.Measurements
MODE - Static variable in class ij.measure.ResultsTable
MONOSPACED - Static variable in class ij.plugin.frame.Editor
MOVE_TO - Static variable in interface ij.macro.MacroConstants
MOVING - Static variable in class ij.gui.Roi
MOVING_HANDLE - Static variable in class ij.gui.Roi
MULTIPLY - Static variable in interface ij.process.Blitter
  dst=src*src
MUL_EQUAL - Static variable in interface ij.macro.MacroConstants
Macro - class ij.Macro.
  The class contains static methods that perform macro operations.
Macro() - Constructor for class ij.Macro
MacroConstants - interface ij.macro.MacroConstants.
MacroInstaller - class ij.plugin.MacroInstaller.
  This plugin implements the Plugins/Macros/Install Macros command.
MacroInstaller() - Constructor for class ij.plugin.MacroInstaller
MacroRunner - class ij.macro.MacroRunner.
  This class runs macros in a separate thread.
MacroRunner() - Constructor for class ij.macro.MacroRunner
  Create a MacrRunner.
MacroRunner(String) - Constructor for class ij.macro.MacroRunner
  Create a new object that interprets macro source in a separate thread.
MacroRunner(String, String) - Constructor for class ij.macro.MacroRunner
  Create a new object that interprets macro source in a separate thread, and also passing a string argument.
MacroRunner(File) - Constructor for class ij.macro.MacroRunner
  Create a new object that interprets a macro file using a separate thread.
MacroRunner(Program, int, String) - Constructor for class ij.macro.MacroRunner
  Create a new object that runs a tokenized macro in a separate thread.
MacroRunner(Program, int, String, String) - Constructor for class ij.macro.MacroRunner
  Create a new object that runs a tokenized macro in a separate thread, passing a string argument.
Macro_Runner - class ij.plugin.Macro_Runner.
  Opens and runs a macro file.
Macro_Runner() - Constructor for class ij.plugin.Macro_Runner
MaximumFinder - class ij.plugin.filter.MaximumFinder.
  This ImageJ plug-in filter creates a mask where the local maxima of the current image are marked (255; unmarked pixels 0).
MaximumFinder() - Constructor for class ij.plugin.filter.MaximumFinder
Measurements - interface ij.measure.Measurements.
MeasurementsWriter - class ij.plugin.MeasurementsWriter.
  Writes measurements to a tab-delimited text file.
MeasurementsWriter() - Constructor for class ij.plugin.MeasurementsWriter
MedianCut - class ij.process.MedianCut.
  Converts an RGB image to 8-bit index color using Heckbert's median-cut color quantization algorithm.
MedianCut(int[], int, int) - Constructor for class ij.process.MedianCut
MedianCut(ColorProcessor) - Constructor for class ij.process.MedianCut
Memory - class ij.plugin.Memory.
  This plugin implements the Edit/Options/Memory command.
Memory() - Constructor for class ij.plugin.Memory
MemoryMonitor - class ij.plugin.MemoryMonitor.
  This plugin continuously plots ImageJ's memory utilization.
MemoryMonitor() - Constructor for class ij.plugin.MemoryMonitor
Menus - class ij.Menus.
  This class installs and updates ImageJ's menus.
MessageDialog - class ij.gui.MessageDialog.
  A modal dialog box that displays information.
MessageDialog(Frame, String, String) - Constructor for class ij.gui.MessageDialog
MontageMaker - class ij.plugin.MontageMaker.
  Implements the Image/Stacks/Make Montage command.
MontageMaker() - Constructor for class ij.plugin.MontageMaker
MultiLineLabel - class ij.gui.MultiLineLabel.
  Custom component for displaying multiple lines.
MultiLineLabel(String) - Constructor for class ij.gui.MultiLineLabel
macroCount() - Method in class ij.macro.Program
macroRunning() - Static method in class ij.IJ
  Returns true if either of the IJ.run() methods is executing.
mag - Variable in class ij.gui.Roi
magnification - Variable in class ij.gui.ImageCanvas
magnification - Variable in class ij.gui.ProfilePlot
main(String[]) - Static method in class ij.ImageJ
major - Variable in class ij.process.EllipseFitter
  Length of major axis
major - Variable in class ij.process.ImageStatistics
  Length of major axis of fitted ellipse
make16bitEDM(ImageProcessor) - Method in class ij.plugin.filter.EDM
  Calculates a 16-bit grayscale Euclidean Distance Map for a binary 8-bit image.
makeDefaultColorModel() - Method in class ij.process.ImageProcessor
makeGaussianKernel(double, double, int) - Method in class ij.plugin.filter.GaussianBlur
  Create a 1-dimensional normalized Gaussian kernel with standard deviation sigma and the running sum over the kernel Note: this is one side of the kernel only, not the full kernel as used by the Convolver class of ImageJ.
makeKernel(double) - Method in class ij.plugin.filter.RankFilters
  Create a circular kernel of a given radius.
makeLine(int, int, int, int) - Static method in class ij.IJ
  Creates a straight line selection.
makeMask(ImageProcessor, Rectangle) - Method in class ij.plugin.filter.Filler
makeMontage(ImagePlus) - Method in class ij.plugin.MontageMaker
makeMontage(ImagePlus, int, int, double, int, int, int, int, boolean) - Method in class ij.plugin.MontageMaker
makeOval(int, int, int, int) - Static method in class ij.IJ
  Creates an elliptical selection.
makeRectangle(int, int, int, int) - Static method in class ij.IJ
  Creates a rectangular selection.
makeRoi(ImageProcessor) - Method in class ij.process.EllipseFitter
  Generates the xCoordinates, yCoordinates public arrays that can be used to create an ROI.
makeSurfacePlot(ImageProcessor) - Method in class ij.plugin.SurfacePlotter
makeThumbnail(int, int, double) - Method in class ij.process.ColorProcessor
  Uses averaging to creates a new ColorProcessor containing a scaled copy of this image or selection.
makeUniqueName(String) - Static method in class ij.WindowManager
  If 'name' is not unique, adds -1, -2, etc.
markWidth - Static variable in class ij.plugin.filter.Analyzer
maskSizeError(ImageProcessor) - Method in class ij.process.ImageProcessor
max(double) - Method in class ij.process.FloatProcessor
max(double) - Method in class ij.process.ImageProcessor
  Pixels greater than 'value' are set to 'value'.
max - Variable in class ij.process.ImageStatistics
max(double) - Method in class ij.process.ShortProcessor
maxCount - Variable in class ij.process.ImageStatistics
maxMemory() - Static method in class ij.IJ
  Returns the maximum amount of memory available to ImageJ or zero if ImageJ is unable to determine this limit.
maxMemory() - Method in class ij.plugin.Memory
  Returns the maximum amount of memory this JVM will attempt to use.
maxPoints - Variable in class ij.gui.PolygonRoi
maxThreshold - Variable in class ij.process.ImageProcessor
maxValue() - Method in class ij.process.FloatProcessor
  Returns the largest possible positive finite pixel value.
maxValue() - Method in class ij.process.ImageProcessor
  Returns the maximum possible pixel value.
maxValue() - Method in class ij.process.ShortProcessor
  Returns the maximum possible pixel value.
maximize() - Method in class ij.gui.ImageWindow
mean - Variable in class ij.process.ImageStatistics
measure() - Method in class ij.gui.MultiLineLabel
median - Variable in class ij.process.ImageStatistics
medianFilter() - Method in class ij.process.ByteProcessor
medianFilter() - Method in class ij.process.ColorProcessor
medianFilter() - Method in class ij.process.FloatProcessor
  Not implemented.
medianFilter() - Method in class ij.process.ImageProcessor
  A 3x3 median filter.
medianFilter() - Method in class ij.process.ShortProcessor
  Not implemented.
mergeStacks() - Method in class ij.plugin.RGBStackMerge
  Combines three grayscale stacks into one RGB stack.
mergeStacks(int, int, int, ImageStack, ImageStack, ImageStack, boolean) - Method in class ij.plugin.RGBStackMerge
metaData - Variable in class ij.io.FileInfo
metaDataTypes - Variable in class ij.io.FileInfo
micronSymbol - Static variable in class ij.IJ
min(double) - Method in class ij.process.FloatProcessor
min(double) - Method in class ij.process.ImageProcessor
  Pixels less than 'value' are set to 'value'.
min - Variable in class ij.process.ImageStatistics
min(double) - Method in class ij.process.ShortProcessor
minThreshold - Variable in class ij.process.ImageProcessor
minValue() - Method in class ij.process.FloatProcessor
  Returns the smallest possible positive nonzero pixel value.
minValue() - Method in class ij.process.ImageProcessor
  Returns the minimum possible pixel value.
minimize() - Method in class ij.gui.ImageWindow
minimumLayoutSize(Container) - Method in class ij.gui.ImageLayout
  Returns the minimum dimensions for this layout.
minor - Variable in class ij.process.EllipseFitter
  Length of minor axis
minor - Variable in class ij.process.ImageStatistics
  Length of minor axis of fitted ellipse
mode - Variable in class ij.process.ImageStatistics
modifiers(int) - Static method in class ij.ImageJ
  Return the current list of modifier keys.
mouseClicked(MouseEvent) - Method in class ij.ImageJ
mouseClicked(MouseEvent) - Method in class ij.gui.ImageCanvas
mouseClicked(MouseEvent) - Method in class ij.gui.Toolbar
mouseClicked(MouseEvent) - Method in class ij.plugin.frame.RoiManager
mouseClicked(MouseEvent) - Method in class ij.text.TextPanel
mouseDownInHandle(int, int, int) - Method in class ij.gui.Line
mouseDownInHandle(int, int, int) - Method in class ij.gui.PolygonRoi
mouseDownInHandle(int, int, int) - Method in class ij.gui.Roi
mouseDragged(MouseEvent) - Method in class ij.gui.ImageCanvas
mouseDragged(MouseEvent) - Method in class ij.gui.Toolbar
mouseDragged(MouseEvent) - Method in class ij.text.TextPanel
mouseEntered(MouseEvent) - Method in class ij.ImageJ
mouseEntered(MouseEvent) - Method in class ij.gui.ImageCanvas
mouseEntered(MouseEvent) - Method in class ij.gui.Toolbar
mouseEntered(MouseEvent) - Method in class ij.plugin.frame.RoiManager
mouseEntered(MouseEvent) - Method in class ij.text.TextPanel
mouseExited(MouseEvent) - Method in class ij.ImageJ
mouseExited(MouseEvent) - Method in class ij.gui.ImageCanvas
mouseExited(MouseEvent) - Method in class ij.gui.Toolbar
mouseExited(MouseEvent) - Method in class ij.plugin.frame.RoiManager
mouseExited(MouseEvent) - Method in class ij.text.TextPanel
mouseMoved(int, int) - Method in class ij.ImagePlus
  Displays the cursor coordinates and pixel value in the status bar.
mouseMoved(int, int) - Method in class ij.gui.HistogramWindow
mouseMoved(MouseEvent) - Method in class ij.gui.ImageCanvas
mouseMoved(int, int) - Method in class ij.gui.ImageWindow
  This method is called by ImageCanvas.mouseMoved(MouseEvent).
mouseMoved(int, int) - Method in class ij.gui.PlotWindow
  Updates the graph X and Y values when the mouse is moved.
mouseMoved(MouseEvent) - Method in class ij.gui.Toolbar
mouseMoved(MouseEvent) - Method in class ij.text.TextPanel
mousePressed(MouseEvent) - Method in class ij.ImageJ
mousePressed(MouseEvent) - Method in class ij.gui.ImageCanvas
mousePressed(MouseEvent) - Method in class ij.gui.Toolbar
mousePressed(MouseEvent) - Method in class ij.plugin.frame.RoiManager
mousePressed(MouseEvent) - Method in class ij.text.TextPanel
mouseReleased(MouseEvent) - Method in class ij.ImageJ
mouseReleased(MouseEvent) - Method in class ij.gui.ImageCanvas
mouseReleased(MouseEvent) - Method in class ij.gui.Toolbar
mouseReleased(MouseEvent) - Method in class ij.plugin.frame.RoiManager
mouseReleased(MouseEvent) - Method in class ij.text.TextPanel
mouseWheelMoved(MouseWheelEvent) - Method in class ij.gui.ImageWindow
mouseWheelMoved(MouseWheelEvent) - Method in class ij.gui.StackWindow
mouseWheelMoved(MouseWheelEvent) - Method in class ij.plugin.frame.RoiManager
mouseWheelMoved(MouseWheelEvent) - Method in class ij.text.TextPanel
moveCursor - Static variable in class ij.gui.ImageCanvas
moveHandle(int, int) - Method in class ij.gui.Line
moveHandle(int, int) - Method in class ij.gui.OvalRoi
moveHandle(int, int) - Method in class ij.gui.PolygonRoi
moveHandle(int, int) - Method in class ij.gui.Roi
moveTo(int, int) - Method in class ij.process.ImageProcessor
  Sets the current drawing location.
multiply(FHT) - Method in class ij.process.FHT
  Returns the image resulting from the point by point Hartley multiplication of this image and the specified image.
multiply(double) - Method in class ij.process.FloatProcessor
multiply(double) - Method in class ij.process.ImageProcessor
  Multiplies each pixel in the image or ROI by 'value'.
multiply(double) - Method in class ij.process.ShortProcessor

## N

NEQ - Static variable in interface ij.macro.MacroConstants
NEW_ARRAY - Static variable in interface ij.macro.MacroConstants
NEW_IMAGE - Static variable in interface ij.macro.MacroConstants
NEW_MENU - Static variable in interface ij.macro.MacroConstants
NEW_SUBFILE_TYPE - Static variable in class ij.io.TiffDecoder
NIH_IMAGE_HDR - Static variable in class ij.io.TiffDecoder
NIMAGES - Static variable in interface ij.macro.MacroConstants
NOISE_SD - Static variable in class ij.Prefs
NONE - Static variable in class ij.measure.Calibration
NOP - Static variable in interface ij.macro.MacroConstants
NORMAL - Static variable in class ij.gui.Roi
NORMAL_RETURN - Static variable in class ij.Menus
NOTHING - Static variable in class ij.Undo
NOTHING - Static variable in class ij.plugin.filter.ParticleAnalyzer
NOT_INSTALLED - Static variable in class ij.Menus
NOT_PASTING - Static variable in class ij.gui.Roi
NO_CHANGES - Static variable in interface ij.plugin.filter.PlugInFilter
  Set this flag if the filter makes no changes to the pixel data and does not require undo.
NO_IMAGE_REQUIRED - Static variable in interface ij.plugin.filter.PlugInFilter
  Set this flag if the filter does not require that an image be open.
NO_LUT_UPDATE - Static variable in class ij.process.ImageProcessor
NO_THRESHOLD - Static variable in class ij.process.ImageProcessor
  Value returned by getMinThreshold() when thresholding is not enabled.
NO_UNDO - Static variable in interface ij.plugin.filter.PlugInFilter
  Set this flag if the filter does not require undo.
NRESULTS - Static variable in interface ij.macro.MacroConstants
NSLICES - Static variable in interface ij.macro.MacroConstants
NUMBER - Static variable in interface ij.macro.MacroConstants
NUMERIC_FUNCTION - Static variable in interface ij.macro.MacroConstants
NaN - Static variable in interface ij.macro.MacroConstants
NewImage - class ij.gui.NewImage.
  New image dialog box plus several static utility methods for creating images.
NewImage() - Constructor for class ij.gui.NewImage
NewPlugin - class ij.plugin.NewPlugin.
  This class creates a new macro or the Java source for a new plugin.
NewPlugin() - Constructor for class ij.plugin.NewPlugin
NextImageOpener - class ij.plugin.NextImageOpener.
NextImageOpener() - Constructor for class ij.plugin.NextImageOpener
n(double) - Method in class ij.plugin.filter.Analyzer
  Converts a number to a formatted string with a tab at the end.
nBins - Static variable in class ij.gui.HistogramWindow
nBins - Variable in class ij.process.ImageStatistics
nCoordinates - Variable in class ij.process.EllipseFitter
  Initialized by makeRoi()
nImages - Variable in class ij.io.FileInfo
nPoints - Variable in class ij.gui.PolygonRoi
name - Variable in class ij.gui.Roi
newImage(String, String, int, int, int) - Static method in class ij.IJ
  Opens a new image.
newMaxCount - Variable in class ij.gui.HistogramWindow
newPixels - Variable in class ij.process.ImageProcessor
newWindowCreated - Static variable in class ij.plugin.Converter
  obsolete
noBorder - Static variable in class ij.Prefs
  Do not draw black border around image.
noGridLines - Static variable in class ij.gui.PlotWindow
  Add grid lines to plots
noImage() - Static method in class ij.IJ
  Displays a "no images are open" dialog box.
noPointLabels - Static variable in class ij.Prefs
  Do not label multiple points created using point tool.
noise(double) - Method in class ij.process.ByteProcessor
noise(double) - Method in class ij.process.ColorProcessor
noise(double) - Method in class ij.process.FloatProcessor
noise(double) - Method in class ij.process.ImageProcessor
  Adds random noise to the image or ROI.
noise(double) - Method in class ij.process.ShortProcessor
north(ImageProcessor) - Method in class ij.plugin.filter.Shadows
northeast(ImageProcessor) - Method in class ij.plugin.filter.Shadows
northwest(ImageProcessor) - Method in class ij.plugin.filter.Shadows
not(ShapeRoi) - Method in class ij.gui.ShapeRoi
  Unary subtraction operator.
notifyListeners(int) - Method in class ij.ImagePlus
npoints - Variable in class ij.gui.Wand
  The number of points in the generated outline.
nudge(int) - Method in class ij.gui.Roi
  Nudge ROI one pixel on arrow key press.
nudgeCorner(int) - Method in class ij.gui.Line
  Nudge end point of line by one pixel.
nudgeCorner(int) - Method in class ij.gui.Roi
  Nudge lower right corner of rectangular and oval ROIs by one pixel based on arrow key press.
numberField - Variable in class ij.gui.GenericDialog
numericFunctionIDs - Static variable in interface ij.macro.MacroConstants
numericFunctions - Static variable in interface ij.macro.MacroConstants

## O

ONE - Static variable in class ij.plugin.filter.EDM
  unit in 16-bit EDM image: this value corresponds to a distance of one pixel
OPEN - Static variable in interface ij.macro.MacroConstants
OPENED - Static variable in class ij.ImagePlus
OPTIONS - Static variable in class ij.Prefs
OR - Static variable in interface ij.process.Blitter
  dst=dst OR src
OUTLIERS - Static variable in class ij.plugin.filter.RankFilters
OUTLINES - Static variable in class ij.plugin.filter.ParticleAnalyzer
OVAL - Static variable in class ij.gui.Roi
OVAL - Static variable in class ij.gui.Toolbar
OVER_UNDER_LUT - Static variable in class ij.process.ImageProcessor
OpenDialog - class ij.io.OpenDialog.
  This class displays a dialog window from which the user can select an input file.
OpenDialog(String, String) - Constructor for class ij.io.OpenDialog
  Displays a file open dialog with 'title' as the title.
OpenDialog(String, String, String) - Constructor for class ij.io.OpenDialog
  Displays a file open dialog, using the specified default directory and file name.
Opener - class ij.io.Opener.
  Opens tiff (and tiff stacks), dicom, fits, pgm, jpeg, bmp or gif images, and look-up tables, using a file open dialog or a path.
Opener() - Constructor for class ij.io.Opener
Options - class ij.plugin.Options.
  This plugin implements most of the commands in the Edit/Options sub-menu.
Options() - Constructor for class ij.plugin.Options
OvalRoi - class ij.gui.OvalRoi.
  Oval region of interest
OvalRoi(int, int, int, int) - Constructor for class ij.gui.OvalRoi
  Creates a new OvalRoi.
OvalRoi(int, int, ImagePlus) - Constructor for class ij.gui.OvalRoi
  Starts the process of creating a user-defined OvalRoi.
OvalRoi(int, int, int, int, ImagePlus) - Constructor for class ij.gui.OvalRoi
  Obsolete
offScreenX(int) - Method in class ij.gui.ImageCanvas
  Converts a screen x-coordinate to an offscreen x-coordinate.
offScreenXD(int) - Method in class ij.gui.ImageCanvas
  Converts a screen x-coordinate to a floating-point offscreen x-coordinate.
offScreenY(int) - Method in class ij.gui.ImageCanvas
  Converts a screen y-coordinate to an offscreen y-coordinate.
offScreenYD(int) - Method in class ij.gui.ImageCanvas
  Converts a screen y-coordinate to a floating-point offscreen y-coordinate.
offset - Variable in class ij.io.FileInfo
okForFits(ImagePlus) - Static method in class ij.io.FileSaver
okForGif(ImagePlus) - Static method in class ij.io.FileSaver
okForJpeg(ImagePlus) - Static method in class ij.io.FileSaver
  Always returns true.
oldHeight - Variable in class ij.gui.Roi
oldWidth - Variable in class ij.gui.Roi
oldX - Variable in class ij.gui.Roi
oldY - Variable in class ij.gui.Roi
open() - Static method in class ij.IJ
  Displays a file open dialog box and then opens the tiff, dicom, fits, pgm, jpeg, bmp, gif, lut, roi, or text file selected by the user.
open(String) - Static method in class ij.IJ
  Opens and displays a tiff, dicom, fits, pgm, jpeg, bmp, gif, lut, roi, or text file.
open(String) - Static method in class ij.Macro
open(String, int, int, int, int, int) - Static method in class ij.gui.NewImage
open() - Method in class ij.io.FileOpener
  Opens the image and displays it.
open(boolean) - Method in class ij.io.FileOpener
  Opens the image.
open() - Method in class ij.io.Opener
  Displays a file open dialog box and then opens the tiff, dicom, fits, pgm, jpeg, bmp, gif, lut, roi, or text file selected by the user.
open(String) - Method in class ij.io.Opener
  Opens and displays a tiff, dicom, fits, pgm, jpeg, bmp, gif, lut, roi, or text file.
open(String) - Method in class ij.plugin.DICOM
  Opens the specified file as a DICOM.
open() - Method in class ij.plugin.TextReader
  Displays a file open dialog and opens the specified text file as a float image.
open(String) - Method in class ij.plugin.TextReader
  Opens the specified text file as a float image.
open(String, String) - Method in class ij.plugin.frame.Editor
open100Percent - Static variable in class ij.Prefs
  Open images at 100% magnification
open16bitAsciiImage(StreamTokenizer, int, int) - Method in class ij.plugin.PGM_Reader
open16bitRawImage(InputStream, int, int) - Method in class ij.plugin.PGM_Reader
openAndAddToRecent(String) - Method in class ij.io.Opener
  Opens the specified file and adds it to the File/Open Recent menu.
openAsciiImage(StreamTokenizer, int, byte[]) - Method in class ij.plugin.PGM_Reader
openFile(String) - Method in class ij.plugin.PGM_Reader
openFromIJJar(String) - Method in class ij.plugin.MacroInstaller
  Returns a text file contained in ij.jar.
openHeader(StreamTokenizer) - Method in class ij.plugin.PGM_Reader
openImage(String) - Static method in class ij.IJ
  Open the specified file as a tiff, bmp, dicom, fits, pgm, gif or jpeg image and returns an ImagePlus object if successful.
openImage() - Method in class ij.io.ImportDialog
  Displays the dialog and opens the specified image or images.
openImage(String, String) - Method in class ij.io.Opener
  Attempts to open the specified file as a tiff, bmp, dicom, fits, pgm, gif or jpeg image.
openImage(String) - Method in class ij.io.Opener
  Attempts to open the specified file as a tiff, bmp, dicom, fits, pgm, gif or jpeg.
openMultiple() - Method in class ij.io.Opener
  Displays a JFileChooser and then opens the tiff, dicom, fits, pgm, jpeg, bmp, gif, lut, roi, or text files selected by the user.
openRawImage(InputStream, int, byte[]) - Method in class ij.plugin.PGM_Reader
openRoi(String) - Method in class ij.io.Opener
  Attempts to open the specified ROI, returning null if unsuccessful.
openRoi(String, String) - Method in class ij.plugin.RoiReader
openTiff(String, String) - Method in class ij.io.Opener
  Attempts to open the specified file as a tiff.
openTiff(InputStream, String) - Method in class ij.io.Opener
  Attempts to open the specified inputStream as a TIFF, returning an ImagePlus object if successful.
openTiffStack(FileInfo[]) - Method in class ij.io.Opener
  Attemps to open a tiff file as a stack.
openURL(String) - Method in class ij.io.Opener
  Attempts to open the specified url as a tiff, zip compressed tiff, dicom, gif or jpeg.
openURL(String) - Static method in class ij.plugin.BrowserLauncher
  Attempts to open the default web browser to the given URL.
openZip(String) - Method in class ij.io.Opener
  Opens a single TIFF or DICOM contained in a ZIP archive, or a ZIPed collection of ".roi" files created by the ROI manager.
or(ShapeRoi) - Method in class ij.gui.ShapeRoi
  Unary union operator.
or(int) - Method in class ij.process.FloatProcessor
or(int) - Method in class ij.process.ImageProcessor
  Binary OR of each pixel in the image or ROI with 'value'.
or(int) - Method in class ij.process.ShortProcessor
originalBitDepth - Variable in class ij.process.FHT
  Used by the FFT class.
originalColorModel - Variable in class ij.process.FHT
  Used by the FFT class.
originalHeight - Variable in class ij.process.FHT
  Used by the FFT class.
originalWidth - Variable in class ij.process.FHT
  Used by the FFT class.
outOfMemory(String) - Static method in class ij.IJ
  Displays an "out of memory" message to the "Log" window.
outline() - Method in class ij.process.BinaryProcessor
outline() - Method in class ij.process.ByteProcessor

## P

PARALLELIZE_STACKS - Static variable in interface ij.plugin.filter.PlugInFilter
  Set this flag if the slices of a stack may be processed in parallel threads
PARSE_FLOAT - Static variable in interface ij.macro.MacroConstants
PARSE_INT - Static variable in interface ij.macro.MacroConstants
PASTE - Static variable in class ij.Undo
PERIMETER - Static variable in interface ij.measure.Measurements
PERIMETER - Static variable in class ij.measure.ResultsTable
PGM - Static variable in class ij.io.FileInfo
PGM - Static variable in class ij.io.Opener
PGM_Reader - class ij.plugin.PGM_Reader.
  This plugin opens PxM format images.
PGM_Reader() - Constructor for class ij.plugin.PGM_Reader
PHOTO_INTERP - Static variable in class ij.io.TiffDecoder
PI - Static variable in interface ij.macro.MacroConstants
PLANAR_CONFIGURATION - Static variable in class ij.io.TiffDecoder
PLOT - Static variable in interface ij.macro.MacroConstants
PLUGIN - Static variable in class ij.plugin.NewPlugin
PLUGINS_MENU - Static variable in class ij.Menus
PLUGIN_FILTER - Static variable in class ij.plugin.NewPlugin
PLUGIN_FRAME - Static variable in class ij.plugin.NewPlugin
PLUS_EQUAL - Static variable in interface ij.macro.MacroConstants
PLUS_PLUS - Static variable in interface ij.macro.MacroConstants
PNG - Static variable in class ij.io.Opener
PNG_Writer - class ij.plugin.PNG_Writer.
  Saves in PNG format using the ImageIO class available in java 1.4 or later.
PNG_Writer() - Constructor for class ij.plugin.PNG_Writer
PNM_Writer - class ij.plugin.PNM_Writer.
PNM_Writer() - Constructor for class ij.plugin.PNM_Writer
POINT - Static variable in class ij.gui.Roi
POINT - Static variable in class ij.gui.Toolbar
POINT_SELECTION - Static variable in class ij.plugin.filter.MaximumFinder
  Do not create image, only mark points
POLY2 - Static variable in class ij.measure.Calibration
POLY2 - Static variable in class ij.measure.CurveFitter
POLY3 - Static variable in class ij.measure.Calibration
POLY3 - Static variable in class ij.measure.CurveFitter
POLY4 - Static variable in class ij.measure.Calibration
POLY4 - Static variable in class ij.measure.CurveFitter
POLYGON - Static variable in class ij.gui.Roi
POLYGON - Static variable in class ij.gui.Toolbar
POLYLINE - Static variable in class ij.gui.Roi
POLYLINE - Static variable in class ij.gui.Toolbar
POW - Static variable in interface ij.macro.MacroConstants
POWER - Static variable in class ij.measure.Calibration
POWER - Static variable in class ij.measure.CurveFitter
PREDEFINED_FUNCTION - Static variable in interface ij.macro.MacroConstants
PREDICTOR - Static variable in class ij.io.TiffDecoder
PREFS_NAME - Static variable in class ij.Prefs
PRINT - Static variable in interface ij.macro.MacroConstants
PROPS_NAME - Static variable in class ij.Prefs
PUT_PIXEL - Static variable in interface ij.macro.MacroConstants
ParticleAnalyzer - class ij.plugin.filter.ParticleAnalyzer.
  Implements ImageJ's Analyze Particles command.
ParticleAnalyzer(int, int, ResultsTable, double, double, double, double) - Constructor for class ij.plugin.filter.ParticleAnalyzer
  Constructs a ParticleAnalyzer.
ParticleAnalyzer(int, int, ResultsTable, double, double) - Constructor for class ij.plugin.filter.ParticleAnalyzer
  Constructs a ParticleAnalyzer using the default min and max circularity values (0 and 1).
ParticleAnalyzer() - Constructor for class ij.plugin.filter.ParticleAnalyzer
  Default constructor
PasteController - class ij.plugin.frame.PasteController.
  Implements ImageJ's Paste Control window.
PasteController() - Constructor for class ij.plugin.frame.PasteController
Plot - class ij.gui.Plot.
  This class is an image that line graphs can be drawn on.
Plot(String, String, String, float[], float[], int) - Constructor for class ij.gui.Plot
  Construct a new PlotWindow.
Plot(String, String, String, float[], float[]) - Constructor for class ij.gui.Plot
  This version of the constructor uses the default flags.
Plot(String, String, String, double[], double[], int) - Constructor for class ij.gui.Plot
  This version of the constructor accepts double arrays.
Plot(String, String, String, double[], double[]) - Constructor for class ij.gui.Plot
  This version of the constructor accepts double arrays and uses the default flags
PlotWindow - class ij.gui.PlotWindow.
  This class is an extended ImageWindow that displays line graphs.
PlotWindow(String, String, String, float[], float[]) - Constructor for class ij.gui.PlotWindow
  Construct a new PlotWindow.
PlotWindow(String, String, String, double[], double[]) - Constructor for class ij.gui.PlotWindow
  This version of the constructor excepts double arrays.
PlugIn - interface ij.plugin.PlugIn.
  Plugins that acquire images or display windows should implement this interface.
PlugInFilter - interface ij.plugin.filter.PlugInFilter.
  ImageJ plugins that process an image should implement this interface.
PlugInFilterRunner - class ij.plugin.filter.PlugInFilterRunner.
PlugInFilterRunner(Object, String, String) - Constructor for class ij.plugin.filter.PlugInFilterRunner
  The constructor runs a PlugInFilter or ExtendedPlugInFilter by calling its setup, run, etc.
PlugInFrame - class ij.plugin.frame.PlugInFrame.
  This is a closeable window that plugins can extend.
PlugInFrame(String) - Constructor for class ij.plugin.frame.PlugInFrame
PluginClassLoader - class ij.io.PluginClassLoader.
  ImageJ uses this class loader to load plugins and resources from the plugins directory and immediate subdirectories.
PluginClassLoader(String) - Constructor for class ij.io.PluginClassLoader
  Creates a new PluginClassLoader that searches in the directory path passed as a parameter.
PluginClassLoader(String, boolean) - Constructor for class ij.io.PluginClassLoader
  This version of the constructor is used when ImageJ is launched using Java WebStart.
PointRoi - class ij.gui.PointRoi.
  This class represents a collection of points.
PointRoi(int[], int[], int) - Constructor for class ij.gui.PointRoi
  Creates a new PointRoi using the specified arrays of offscreen coordinates.
PointRoi(int, int) - Constructor for class ij.gui.PointRoi
  Creates a new PointRoi using the specified offscreen coordinates.
PointRoi(int, int, ImagePlus) - Constructor for class ij.gui.PointRoi
  Creates a new PointRoi using the specified screen coordinates.
PolygonFiller - class ij.process.PolygonFiller.
  This class fills polygons using the scan-line filling algorithm described at "http://www.cs.rit.edu/~icss571/filling/".
PolygonFiller() - Constructor for class ij.process.PolygonFiller
  Constructs a PolygonFiller.
PolygonFiller(int[], int[], int) - Constructor for class ij.process.PolygonFiller
  Constructs a PolygonFiller using the specified polygon.
PolygonRoi - class ij.gui.PolygonRoi.
  This class represents a polygon region of interest or polyline of interest.
PolygonRoi(int[], int[], int, int) - Constructor for class ij.gui.PolygonRoi
  Creates a new polygon or polyline ROI from x and y coordinate arrays.
PolygonRoi(Polygon, int) - Constructor for class ij.gui.PolygonRoi
  Creates a new polygon or polyline ROI from a Polygon.
PolygonRoi(int[], int[], int, ImagePlus, int) - Constructor for class ij.gui.PolygonRoi
  Obsolete
PolygonRoi(int, int, ImagePlus) - Constructor for class ij.gui.PolygonRoi
  Starts the process of creating a new user-generated polygon or polyline ROI.
Prefs - class ij.Prefs.
  This class contains the ImageJ preferences, which are loaded from the "IJ_Props.txt" and "IJ_Prefs.txt" files.
Prefs() - Constructor for class ij.Prefs
Printer - class ij.plugin.filter.Printer.
  This plugin implements the File/Page Setup and File/Print commands.
Printer() - Constructor for class ij.plugin.filter.Printer
ProfilePlot - class ij.gui.ProfilePlot.
  Creates a density profile plot of a rectangular selection or line selection.
ProfilePlot() - Constructor for class ij.gui.ProfilePlot
ProfilePlot(ImagePlus) - Constructor for class ij.gui.ProfilePlot
ProfilePlot(ImagePlus, boolean) - Constructor for class ij.gui.ProfilePlot
Profiler - class ij.plugin.filter.Profiler.
  Implements the Process/Plot Profile and Edit/Options/Profile Plot Options commands.
Profiler() - Constructor for class ij.plugin.filter.Profiler
Program - class ij.macro.Program.
  An object of this type is a tokenized macro file and the associated symbol table.
Program() - Constructor for class ij.macro.Program
ProgressBar - class ij.gui.ProgressBar.
  This is the progress bar that is displayed in the lower right hand corner of the ImageJ window.
ProgressBar(int, int) - Constructor for class ij.gui.ProgressBar
  This constructor is called once by ImageJ at startup.
Projector - class ij.plugin.filter.Projector.
  This plugin creates a sequence of projections of a rotating volume (stack of slices) onto a plane using nearest-point (surface), brightest-point, or mean-value projection or a weighted combination of nearest- point projection with either of the other two methods (partial opacity).
Projector() - Constructor for class ij.plugin.filter.Projector
paint(Graphics) - Method in class ij.gui.GenericDialog
paint(Graphics) - Method in class ij.gui.ImageCanvas
paint(Graphics) - Method in class ij.gui.ImageWindow
paint(Graphics) - Method in class ij.gui.MultiLineLabel
paint(Graphics) - Method in class ij.gui.ProgressBar
paint(Graphics) - Method in class ij.gui.Toolbar
paint(Graphics) - Method in class ij.gui.YesNoCancelDialog
parseDouble(String, double) - Static method in class ij.util.Tools
  Returns a double containg the value represented by the specified `String`.
parseDouble(String) - Static method in class ij.util.Tools
  Returns a double containg the value represented by the specified `String`.
particleAnalyzerFill(int, int, double, double, ImageProcessor, Rectangle) - Method in class ij.process.FloodFiller
  This method is used by the particle analyzer to remove interior holes from particle masks.
paste() - Method in class ij.ImagePlus
  Inserts the contents of the internal clipboard into the active image.
paste() - Method in class ij.gui.ImageWindow
pasteMode - Static variable in class ij.gui.Roi
path - Variable in class ij.io.PluginClassLoader
ph - Variable in class ij.process.ImageStatistics
pixelCount - Variable in class ij.process.ImageStatistics
pixelDepth - Variable in class ij.io.FileInfo
pixelDepth - Variable in class ij.measure.Calibration
  Pixel depth in 'unit's
pixelHeight - Variable in class ij.ImagePlus
  Obsolete.
pixelHeight - Variable in class ij.io.FileInfo
pixelHeight - Variable in class ij.measure.Calibration
  Pixel height in 'unit's
pixelWidth - Variable in class ij.ImagePlus
  Obsolete.
pixelWidth - Variable in class ij.io.FileInfo
pixelWidth - Variable in class ij.measure.Calibration
  Pixel width in 'unit's
pixels - Variable in class ij.io.FileInfo
pixels - Variable in class ij.process.ByteProcessor
pixels - Variable in class ij.process.ColorProcessor
plotHeight - Static variable in class ij.gui.PlotWindow
  The height of the plot in pixels.
plotScale - Variable in class ij.gui.HistogramWindow
plotWidth - Static variable in class ij.gui.PlotWindow
  The width of the plot in pixels.
pointAutoMeasure - Static variable in class ij.Prefs
  Point tool auto-measure mode.
pointAutoNextSlice - Static variable in class ij.Prefs
  Point tool auto-next slice mode (not saved in IJ_Prefs).
positionWindow() - Method in class ij.plugin.frame.Editor
powerOf2Size() - Method in class ij.process.FHT
  Returns true of this FHT contains a square image with a width that is a power of two.
precision - Static variable in class ij.plugin.filter.Analyzer
preferredLayoutSize(Container) - Method in class ij.gui.ImageLayout
  Returns the preferred dimensions for this layout.
previewRunning(boolean) - Method in class ij.gui.GenericDialog
  optical feedback whether preview is running by switching from "Preview" to "wait..."
previousRoi - Static variable in class ij.gui.Roi
print(Graphics, PageFormat, int) - Method in class ij.plugin.filter.Printer
processStack - Variable in class ij.plugin.filter.ParticleAnalyzer
processWindowEvent(WindowEvent) - Method in class ij.plugin.frame.RoiManager
processWindowEvent(WindowEvent) - Method in class ij.text.TextWindow
profile - Variable in class ij.gui.ProfilePlot
putBehind() - Static method in class ij.WindowManager
  Activates the next image window on the window list.
putByteRow(ImageStack, int, int, int, int[]) - Method in class ij.plugin.filter.Projector
putColumn(ImageProcessor, int, int, float[], int) - Method in class ij.plugin.Slicer
putColumn(int, int, int[], int) - Method in class ij.process.ImageProcessor
  Inserts the pixels contained in 'data' into a column starting at (x,y).
putPixel(int, int, int) - Method in class ij.process.ByteProcessor
  Stores the specified value at (x,y).
putPixel(int, int, int[]) - Method in class ij.process.ColorProcessor
  Sets a pixel in the image using a 3 element (R, G and B) int array of samples.
putPixel(int, int, int) - Method in class ij.process.ColorProcessor
  Stores the specified value at (x,y).
putPixel(int, int, int[]) - Method in class ij.process.FloatProcessor
  Sets a pixel in the image using a one element int array.
putPixel(int, int, int) - Method in class ij.process.FloatProcessor
  Stores the specified value at (x,y).
putPixel(int, int, int[]) - Method in class ij.process.ImageProcessor
  Sets a pixel in the image using an int array of samples.
putPixel(int, int, int) - Method in class ij.process.ImageProcessor
  Stores the specified value at (x,y).
putPixel(int, int, int) - Method in class ij.process.ShortProcessor
  Stores the specified value at (x,y).
putPixelValue(int, int, double) - Method in class ij.process.ByteProcessor
  Stores the specified real value at (x,y).
putPixelValue(int, int, double) - Method in class ij.process.ColorProcessor
  Stores the specified real grayscale value at (x,y).
putPixelValue(int, int, double) - Method in class ij.process.FloatProcessor
  Stores the specified real value at (x,y).
putPixelValue(int, int, double) - Method in class ij.process.ImageProcessor
  Stores the specified value at (x,y).
putPixelValue(int, int, double) - Method in class ij.process.ShortProcessor
  Stores the specified real value at (x,y).
putRGBRow(ImageStack, int, int, int, int[]) - Method in class ij.plugin.filter.Projector
putRow(ImageProcessor, int, int, float[], int) - Method in class ij.plugin.Slicer
putRow(int, int, int[], int) - Method in class ij.process.ImageProcessor
  Inserts the pixels contained in 'data' into a horizontal line starting at (x,y).
pw - Variable in class ij.process.ImageStatistics

## Q

quadrantSwapNeeded - Variable in class ij.process.FHT
  Used by the FFT class.
quit() - Method in class ij.ImageJ
  Called by ImageJ when the user selects Quit.
quitting() - Method in class ij.ImageJ
  Returns true if ImageJ is exiting.

## R

RANDOM - Static variable in interface ij.macro.MacroConstants
RAW - Static variable in class ij.io.FileInfo
RECORD_STARTS - Static variable in class ij.plugin.filter.ParticleAnalyzer
  Record starting coordinates so outline can be recreated later using doWand(x,y).
RECT - Static variable in interface ij.measure.Measurements
RECTANGLE - Static variable in class ij.gui.Roi
RECTANGLE - Static variable in class ij.gui.Toolbar
RED_LUT - Static variable in class ij.process.ImageProcessor
RENAME - Static variable in interface ij.macro.MacroConstants
REPLACE - Static variable in interface ij.macro.MacroConstants
REQUIRES - Static variable in interface ij.macro.MacroConstants
RESET - Static variable in interface ij.macro.MacroConstants
RESET_MIN_MAX - Static variable in interface ij.macro.MacroConstants
RESET_THRESHOLD - Static variable in interface ij.macro.MacroConstants
RESIZING - Static variable in class ij.gui.Roi
RESOLUTION_UNIT - Static variable in class ij.io.TiffDecoder
RESTORE_PREVIOUS_TOOL - Static variable in interface ij.macro.MacroConstants
RESTORE_SETTINGS - Static variable in interface ij.macro.MacroConstants
RETURN - Static variable in interface ij.macro.MacroConstants
RGB - Static variable in class ij.gui.NewImage
RGB - Static variable in class ij.io.FileInfo
  24-bit interleaved RGB.
RGB48 - Static variable in class ij.io.FileInfo
  48-bit interleaved RGB.
RGB48_PLANAR - Static variable in class ij.io.FileInfo
  48-bit planar RGB.
RGBStackConverter - class ij.plugin.RGBStackConverter.
  Converts a 2 or 3 slice stack to RGB.
RGBStackConverter() - Constructor for class ij.plugin.RGBStackConverter
RGBStackMerge - class ij.plugin.RGBStackMerge.
RGBStackMerge() - Constructor for class ij.plugin.RGBStackMerge
RGBStackSplitter - class ij.plugin.filter.RGBStackSplitter.
  Splits an RGB image or stack into three 8-bit grayscale images or stacks.
RGBStackSplitter() - Constructor for class ij.plugin.filter.RGBStackSplitter
RGB_DILATE - Variable in class ij.process.ColorProcessor
RGB_ERODE - Variable in class ij.process.ColorProcessor
RGB_FIND_EDGES - Variable in class ij.process.ColorProcessor
RGB_MEDIAN - Variable in class ij.process.ColorProcessor
RGB_NOISE - Variable in class ij.process.ColorProcessor
RGB_PLANAR - Static variable in class ij.io.FileInfo
  24-bit planer RGB.
RGB_THRESHOLD - Variable in class ij.process.ColorProcessor
RIGHT_JUSTIFY - Static variable in class ij.process.ImageProcessor
  Right justify text.
RIGHT_MARGIN - Static variable in class ij.gui.Plot
  the margin width right of the plot frame
RODBARD - Static variable in class ij.measure.Calibration
RODBARD - Static variable in class ij.measure.CurveFitter
RODBARD2 - Static variable in class ij.measure.Calibration
RODBARD2 - Static variable in class ij.measure.CurveFitter
ROI - Static variable in class ij.io.Opener
ROICOLOR - Static variable in class ij.Prefs
ROIColor - Static variable in class ij.gui.Roi
ROI_HEIGHT - Static variable in class ij.measure.ResultsTable
ROI_MANAGER - Static variable in interface ij.macro.MacroConstants
ROI_REQUIRED - Static variable in interface ij.plugin.filter.PlugInFilter
  Set this flag if the filter requires an ROI.
ROI_WIDTH - Static variable in class ij.measure.ResultsTable
ROI_X - Static variable in class ij.measure.ResultsTable
ROI_Y - Static variable in class ij.measure.ResultsTable
ROUND - Static variable in interface ij.macro.MacroConstants
ROWS_PER_STRIP - Static variable in class ij.io.TiffDecoder
RUN - Static variable in interface ij.macro.MacroConstants
RUN_MACRO - Static variable in interface ij.macro.MacroConstants
RandomAccessStream - class ij.io.RandomAccessStream.
  This is a class that uses a memory cache to allow seeking within an InputStream.
RandomAccessStream(InputStream) - Constructor for class ij.io.RandomAccessStream
  Constructs a RandomAccessStream from an InputStream.
RandomAccessStream(RandomAccessFile) - Constructor for class ij.io.RandomAccessStream
  Constructs a RandomAccessStream from an RandomAccessFile.
RankFilters - class ij.plugin.filter.RankFilters.
  This plugin implements the Mean, Minimum, Maximum, Variance, Median, Remove Outliers and Despeckle commands.
RankFilters() - Constructor for class ij.plugin.filter.RankFilters
Raw - class ij.plugin.Raw.
  This plugin implements the File/Import/Raw command.
Raw() - Constructor for class ij.plugin.Raw
RecentOpener - class ij.RecentOpener.
  Opens, in a separate thread, files selected from the File/Open Recent submenu.
Recorder - class ij.plugin.frame.Recorder.
  This is ImageJ's macro recorder.
Recorder() - Constructor for class ij.plugin.frame.Recorder
Resizer - class ij.plugin.filter.Resizer.
  This plugin implements ImageJ's Resize command.
Resizer() - Constructor for class ij.plugin.filter.Resizer
ResultsTable - class ij.measure.ResultsTable.
  This is a table for storing measurement results as columns of numeric values.
ResultsTable() - Constructor for class ij.measure.ResultsTable
  Constructs an empty ResultsTable with the counter=0 and no columns.
Roi - class ij.gui.Roi.
  A rectangular region of interest and superclass for the other ROI classes.
Roi(int, int, int, int) - Constructor for class ij.gui.Roi
  Creates a new rectangular Roi.
Roi(Rectangle) - Constructor for class ij.gui.Roi
  Creates a new rectangular Roi.
Roi(int, int, ImagePlus) - Constructor for class ij.gui.Roi
  Starts the process of creating a user-defined rectangular Roi, where sx and sy are the starting screen coordinates.
Roi(int, int, int, int, ImagePlus) - Constructor for class ij.gui.Roi
  Obsolete
RoiDecoder - class ij.io.RoiDecoder.
  Decodes an ImageJ, NIH Image or Scion Image ROI.
RoiDecoder(String) - Constructor for class ij.io.RoiDecoder
  Constructs an RoiDecoder using a file path.
RoiDecoder(byte[], String) - Constructor for class ij.io.RoiDecoder
  Constructs an RoiDecoder using a byte array.
RoiEncoder - class ij.io.RoiEncoder.
  Saves an ROI to a file or stream.
RoiEncoder(String) - Constructor for class ij.io.RoiEncoder
  Creates an RoiEncoder using the specified path.
RoiEncoder(OutputStream) - Constructor for class ij.io.RoiEncoder
  Creates an RoiEncoder using the specified OutputStream.
RoiManager - class ij.plugin.frame.RoiManager.
  This plugin implements the Analyze/Tools/ROI Manager command.
RoiManager() - Constructor for class ij.plugin.frame.RoiManager
RoiReader - class ij.plugin.RoiReader.
  Opens ImageJ, NIH Image and Scion Image for windows ROI outlines.
RoiReader() - Constructor for class ij.plugin.RoiReader
RoiWriter - class ij.plugin.filter.RoiWriter.
  Saves the current ROI outline to a file.
RoiWriter() - Constructor for class ij.plugin.filter.RoiWriter
Rotator - class ij.plugin.filter.Rotator.
  This plugin implements the Image/Rotate/Arbitrarily command.
Rotator() - Constructor for class ij.plugin.filter.Rotator
rLUT1 - Variable in class ij.process.ImageProcessor
rLUT2 - Variable in class ij.process.ImageProcessor
rand(int, int) - Method in class ij.plugin.filter.SaltAndPepper
raster - Variable in class ij.process.ImageProcessor
rc2DFHT(float[], boolean, int) - Method in class ij.process.FHT
  Performs a 2D FHT (Fast Hartley Transform).
read() - Method in class ij.io.RandomAccessStream
read(byte[], int, int) - Method in class ij.io.RandomAccessStream
readDouble() - Method in class ij.io.RandomAccessStream
readFloat() - Method in class ij.io.RandomAccessStream
readFully(byte[]) - Method in class ij.io.RandomAccessStream
readFully(byte[], int) - Method in class ij.io.RandomAccessStream
readInt() - Method in class ij.io.RandomAccessStream
readLong() - Method in class ij.io.RandomAccessStream
readPixels(InputStream) - Method in class ij.io.ImageReader
  Reads the image from the InputStream and returns the pixel array (byte, short, int or float).
readPixels(InputStream, long) - Method in class ij.io.ImageReader
  Skips the specified number of bytes, then reads an image and returns the pixel array (byte, short, int or float).
readPixels(String) - Method in class ij.io.ImageReader
  Reads the image from a URL and returns the pixel array (byte, short, int or float).
readShort() - Method in class ij.io.RandomAccessStream
record - Static variable in class ij.plugin.frame.Recorder
  This variable is true if the recorder is running.
record(String) - Static method in class ij.plugin.frame.Recorder
record(String, String) - Static method in class ij.plugin.frame.Recorder
record(String, String, String) - Static method in class ij.plugin.frame.Recorder
record(String, String, String, String) - Static method in class ij.plugin.frame.Recorder
record(String, int) - Static method in class ij.plugin.frame.Recorder
record(String, int, int) - Static method in class ij.plugin.frame.Recorder
record(String, double, double) - Static method in class ij.plugin.frame.Recorder
record(String, int, int, int) - Static method in class ij.plugin.frame.Recorder
record(String, String, int) - Static method in class ij.plugin.frame.Recorder
record(String, String, int, int) - Static method in class ij.plugin.frame.Recorder
record(String, int, int, int, int) - Static method in class ij.plugin.frame.Recorder
record(String, String, String, int, int, int, int, int) - Static method in class ij.plugin.frame.Recorder
recordInMacros - Static variable in class ij.plugin.frame.Recorder
  Set this variable true to allow recording within IJ.run() calls.
recordOption(String, String) - Static method in class ij.plugin.frame.Recorder
recordOption(String) - Static method in class ij.plugin.frame.Recorder
recordPath(String, String) - Static method in class ij.plugin.frame.Recorder
recordRoi(Polygon, int) - Static method in class ij.plugin.frame.Recorder
recordStarts - Variable in class ij.plugin.filter.ParticleAnalyzer
recordString(String) - Static method in class ij.plugin.frame.Recorder
red - Variable in class ij.plugin.filter.RGBStackSplitter
  These are the three stacks created by the split(ImageStack) method.
redirectErrorMessages() - Static method in class ij.IJ
  Causes IJ.error() and IJ.showMessage() output to be temporarily redirected to the "Log" window.
redirectingErrorMessages() - Static method in class ij.IJ
  Returns the state of the 'redirectErrorMessages' flag.
reds - Variable in class ij.io.FileInfo
register(Class) - Static method in class ij.IJ
  Adds the specified class to a Vector to keep it from being garbage collected, which would cause the classes static fields to be reset.
register(Class) - Method in class ij.ImageJ
  Adds the specified class to a Vector to keep it from being garbage collected, causing static fields to be reset.
removeBatchModeImage(ImagePlus) - Static method in class ij.macro.Interpreter
removeImageListener(ImageListener) - Static method in class ij.ImagePlus
removeLayoutComponent(Component) - Method in class ij.gui.ImageLayout
  Not used by this class.
removeWindow(Frame) - Static method in class ij.WindowManager
  Removes the specified window from the Window menu.
repaintImageWindows() - Static method in class ij.WindowManager
  Repaints all open image windows.
repaintWindow() - Method in class ij.ImagePlus
  Calls draw to draw the image and also repaints the image window to force the information displayed above the image (dimension, type, size) to be updated.
requireControlKey - Static variable in class ij.Prefs
  Require control or command key for keybaord shortcuts.
reset() - Static method in class ij.Undo
reset() - Method in class ij.measure.ResultsTable
  Clears all the columns and sets the counter to zero.
reset() - Method in class ij.process.ByteProcessor
  Reset the image from snapshot.
reset(ImageProcessor) - Method in class ij.process.ByteProcessor
  Restore pixels that are within roi but not part of mask.
reset() - Method in class ij.process.ColorProcessor
reset(ImageProcessor) - Method in class ij.process.ColorProcessor
reset() - Method in class ij.process.FloatProcessor
reset(ImageProcessor) - Method in class ij.process.FloatProcessor
reset() - Method in class ij.process.ImageProcessor
  Restores the pixel data from the snapshot (undo) buffer.
reset(ImageProcessor) - Method in class ij.process.ImageProcessor
  Restores pixels from the snapshot buffer that are within the rectangular roi but not part of the mask.
reset() - Method in class ij.process.ShortProcessor
reset(ImageProcessor) - Method in class ij.process.ShortProcessor
resetBinaryThreshold() - Method in class ij.process.ImageProcessor
  Resets the threshold if minThreshold=maxThreshold and lutUpdateMode=NO_LUT_UPDATE.
resetClipboard() - Static method in class ij.ImagePlus
  Clears the internal clipboard.
resetCounter() - Static method in class ij.plugin.filter.Analyzer
  Sets the measurement counter to zero.
resetCounter - Variable in class ij.plugin.filter.ParticleAnalyzer
resetEscape() - Static method in class ij.IJ
  This method sets the `Esc` key to the "up" position.
resetMinAndMax() - Static method in class ij.IJ
  Resets the minimum and maximum displayed pixel values to be the same as the min and max pixel values.
resetMinAndMax() - Method in class ij.process.ByteProcessor
  Resets this image's LUT.
resetMinAndMax() - Method in class ij.process.FloatProcessor
  Recalculates the min and max values used to scale pixel values to 0-255 for display.
resetMinAndMax() - Method in class ij.process.ImageProcessor
  For short and float images, recalculates the min and max image values needed to correctly display the image.
resetMinAndMax() - Method in class ij.process.ShortProcessor
  Recalculates the min and max values used to scale pixel values to 0-255 for display.
resetOutOfRoi(ImageProcessor, int) - Static method in class ij.plugin.filter.GaussianBlur
  Set the processed pixels above and below the roi rectangle back to their previous value (i.e., snapshot buffer).
resetRoi() - Method in class ij.process.ImageProcessor
  Sets the ROI (Region of Interest) and clipping rectangle to the entire image.
resetSelection() - Method in class ij.text.TextPanel
  Clears the selection, if any.
resetThreshold() - Static method in class ij.IJ
  Disables thresholding.
resetThreshold() - Method in class ij.process.ImageProcessor
  Disables thresholding.
resize(int, int) - Method in class ij.process.ByteProcessor
  Creates a new ByteProcessor containing a scaled copy of this image or selection.
resize(int, int) - Method in class ij.process.ColorProcessor
  Creates a new ColorProcessor containing a scaled copy of this image or selection.
resize(int, int) - Method in class ij.process.FloatProcessor
  Creates a new FloatProcessor containing a scaled copy of this image or selection.
resize(int, int) - Method in class ij.process.ImageProcessor
  Creates a new ImageProcessor containing a scaled copy of this image or ROI.
resize(int) - Method in class ij.process.ImageProcessor
  Creates a new ImageProcessor containing a scaled copy of this image or ROI, with the aspect ratio maintained.
resize(int, int) - Method in class ij.process.ShortProcessor
  Creates a new ShortProcessor containing a scaled copy of this image or selection.
resize(int, int) - Method in class ij.process.StackProcessor
  Creates a new stack with dimensions 'newWidth' x 'newHeight'.
reslice(ImagePlus) - Method in class ij.plugin.Slicer
restorePreviousTool() - Method in class ij.gui.Toolbar
restoreRoi() - Method in class ij.ImagePlus
revert() - Method in class ij.ImagePlus
  Implements the File/Revert command.
revertToSaved(ImagePlus) - Method in class ij.io.FileOpener
  Restores original disk or network version of image.
rgb - Variable in class ij.process.FHT
  Used by the FFT class.
rh - Variable in class ij.process.ImageStatistics
roi - Variable in class ij.ImagePlus
roiHeight - Variable in class ij.process.ImageProcessor
roiHeight - Variable in class ij.process.ImageStatistics
roiWidth - Variable in class ij.process.ImageProcessor
roiWidth - Variable in class ij.process.ImageStatistics
roiX - Variable in class ij.process.ImageProcessor
roiX - Variable in class ij.process.ImageStatistics
roiY - Variable in class ij.process.ImageProcessor
roiY - Variable in class ij.process.ImageStatistics
rotate(double) - Method in class ij.process.ByteProcessor
  Rotates the image or ROI 'angle' degrees clockwise.
rotate(double) - Method in class ij.process.ColorProcessor
  Rotates the image or ROI 'angle' degrees clockwise.
rotate(double) - Method in class ij.process.FloatProcessor
  Rotates the image or ROI 'angle' degrees clockwise.
rotate(double) - Method in class ij.process.ImageProcessor
  Rotates the image or selection 'angle' degrees clockwise.
rotate(double) - Method in class ij.process.ShortProcessor
  Rotates the image or ROI 'angle' degrees clockwise.
rotateLeft() - Method in class ij.process.ImageProcessor
  Rotates the entire image 90 degrees counter-clockwise.
rotateLeft() - Method in class ij.process.StackProcessor
rotateRight() - Method in class ij.process.ImageProcessor
  Rotates the entire image 90 degrees clockwise.
rotateRight() - Method in class ij.process.StackProcessor
rt - Variable in class ij.plugin.filter.ParticleAnalyzer
run() - Method in class ij.Executer
run(String) - Static method in class ij.IJ
  Runs an ImageJ command.
run(String, String) - Static method in class ij.IJ
  Runs an ImageJ command, with options that are passed to the GenericDialog and OpenDialog classes.
run() - Method in class ij.ImageJ
  Quit using a separate thread, hopefully avoiding thread deadlocks.
run() - Method in class ij.RecentOpener
  Open the file and move the path to top of the submenu.
run() - Method in class ij.SocketListener
run() - Method in class ij.gui.StackWindow
run(String) - Method in class ij.macro.Interpreter
  Interprets the specified string.
run(String, String) - Method in class ij.macro.Interpreter
  Runs the specified macro, passing it a string argument and returning a string value.
run(Program) - Method in class ij.macro.Interpreter
  Interprets the specified tokenized macro file starting at location 0.
run() - Method in class ij.macro.MacroRunner
run(String) - Method in class ij.plugin.AboutBox
run(String) - Method in class ij.plugin.Animator
  Set 'arg' to "set" to display a dialog that allows the user to specify the animation speed.
run(String) - Method in class ij.plugin.BMP_Reader
run(String) - Method in class ij.plugin.BMP_Writer
run(String) - Method in class ij.plugin.BrowserLauncher
  Opens the specified URL (default is the ImageJ home page).
run(String) - Method in class ij.plugin.CanvasResizer
run(String) - Method in class ij.plugin.ClassChecker
run(String) - Method in class ij.plugin.Clipboard
run(String) - Method in class ij.plugin.ColorPicker
run(String) - Method in class ij.plugin.Colors
run(String) - Method in class ij.plugin.CommandLister
run(String) - Method in class ij.plugin.Commands
run(String) - Method in class ij.plugin.Compiler
run(String) - Method in class ij.plugin.Composite_Image
run(String) - Method in class ij.plugin.ContrastEnhancer
run(String) - Method in class ij.plugin.ControlPanel
  Creates a panel with the hierarchical tree structure of (some of the) ImageJ's commands according to the structure of the String argument (see below).
run(String) - Method in class ij.plugin.Converter
run(String) - Method in class ij.plugin.DICOM
run(String) - Method in class ij.plugin.DICOM_Sorter
run(String) - Method in class ij.plugin.Distribution
run(String) - Method in class ij.plugin.DragAndDrop
run() - Method in class ij.plugin.DragAndDrop
run(String) - Method in class ij.plugin.FFT
run(String) - Method in class ij.plugin.FFTMath
run(String) - Method in class ij.plugin.FITS_Reader
run(String) - Method in class ij.plugin.FITS_Writer
run(String) - Method in class ij.plugin.FolderOpener
run(String) - Method in class ij.plugin.GelAnalyzer
run(String) - Method in class ij.plugin.Histogram
run(String) - Method in class ij.plugin.Hotkeys
run(String) - Method in class ij.plugin.ImageCalculator
run(String) - Method in class ij.plugin.Installer
run(String) - Method in class ij.plugin.JavaProperties
run(String) - Method in class ij.plugin.JpegWriter
run(String) - Method in class ij.plugin.LUT_Editor
run(String) - Method in class ij.plugin.LutLoader
  If 'arg'="", displays a file open dialog and opens the specified LUT.
run(String) - Method in class ij.plugin.MacroInstaller
run(String) - Method in class ij.plugin.Macro_Runner
  Opens and runs the specified macro file on the current thread.
run(String) - Method in class ij.plugin.MeasurementsWriter
run(String) - Method in class ij.plugin.Memory
run(String) - Method in class ij.plugin.MemoryMonitor
run(String) - Method in class ij.plugin.MontageMaker
run(String) - Method in class ij.plugin.NewPlugin
run(String) - Method in class ij.plugin.NextImageOpener
run(String) - Method in class ij.plugin.Options
run(String) - Method in class ij.plugin.PGM_Reader
run(String) - Method in class ij.plugin.PNG_Writer
run(String) - Method in class ij.plugin.PNM_Writer
run(String) - Method in interface ij.plugin.PlugIn
  This method is called when the plugin is loaded.
run(String) - Method in class ij.plugin.RGBStackConverter
run(String) - Method in class ij.plugin.RGBStackMerge
  Merges one, two or three 8-bit or RGB stacks into a single RGB stack.
run(String) - Method in class ij.plugin.Raw
run(String) - Method in class ij.plugin.RoiReader
run(String) - Method in class ij.plugin.ScaleBar
run(String) - Method in class ij.plugin.Scaler
run(String) - Method in class ij.plugin.ScreenGrabber
run(String) - Method in class ij.plugin.Selection
run(String) - Method in class ij.plugin.SimpleCommands
run(String) - Method in class ij.plugin.Slicer
run(String) - Method in class ij.plugin.SpecifyROI
run(String) - Method in class ij.plugin.StackEditor
  'arg' must be "add", "delete" or "convert".
run(String) - Method in class ij.plugin.StackWriter
run(String) - Method in class ij.plugin.SurfacePlotter
run(String) - Method in class ij.plugin.TextFileReader
run(String) - Method in class ij.plugin.TextReader
run(String) - Method in class ij.plugin.TextWriter
run(String) - Method in class ij.plugin.ThreadLister
run(String) - Method in class ij.plugin.Thresholder
run(String) - Method in class ij.plugin.Timer
run(String) - Method in class ij.plugin.URLOpener
  If 'urlOrName' is a URL, opens the image at that URL.
run(String) - Method in class ij.plugin.WindowOrganizer
run(String) - Method in class ij.plugin.XYCoordinates
run(String) - Method in class ij.plugin.ZProjector
run(String) - Method in class ij.plugin.Zoom
  'arg' must be "in", "out", "100%" or "orig".
run(ImageProcessor) - Method in class ij.plugin.filter.AVIWriter
run(ImageProcessor) - Method in class ij.plugin.filter.Analyzer
run(ImageProcessor) - Method in class ij.plugin.filter.BackgroundSubtracter
run(ImageProcessor) - Method in class ij.plugin.filter.Benchmark
run(ImageProcessor) - Method in class ij.plugin.filter.Binary
run(ImageProcessor) - Method in class ij.plugin.filter.BinaryFiller
run(ImageProcessor) - Method in class ij.plugin.filter.CalibrationBar
run(ImageProcessor) - Method in class ij.plugin.filter.Calibrator
run(ImageProcessor) - Method in class ij.plugin.filter.Convolver
run(ImageProcessor) - Method in class ij.plugin.filter.Duplicater
run(ImageProcessor) - Method in class ij.plugin.filter.EDM
run(ImageProcessor) - Method in class ij.plugin.filter.FFTCustomFilter
run(ImageProcessor) - Method in class ij.plugin.filter.FFTFilter
run(ImageProcessor) - Method in class ij.plugin.filter.Filler
run(ImageProcessor) - Method in class ij.plugin.filter.Filters
run(ImageProcessor) - Method in class ij.plugin.filter.FractalBoxCounter
run(ImageProcessor) - Method in class ij.plugin.filter.GaussianBlur
  This method is invoked for each slice during execution
run(ImageProcessor) - Method in class ij.plugin.filter.ImageMath
run(ImageProcessor) - Method in class ij.plugin.filter.ImageProperties
run(ImageProcessor) - Method in class ij.plugin.filter.Info
run(ImageProcessor) - Method in class ij.plugin.filter.LineGraphAnalyzer
run(ImageProcessor) - Method in class ij.plugin.filter.LutApplier
run(ImageProcessor) - Method in class ij.plugin.filter.LutViewer
run(ImageProcessor) - Method in class ij.plugin.filter.MaximumFinder
  The plugin is inferred from ImageJ by this method
run(ImageProcessor) - Method in class ij.plugin.filter.ParticleAnalyzer
run(ImageProcessor) - Method in interface ij.plugin.filter.PlugInFilter
  Filters use this method to process the image.
run() - Method in class ij.plugin.filter.PlugInFilterRunner
  The dispatcher for the background threads
run(ImageProcessor) - Method in class ij.plugin.filter.Printer
run(ImageProcessor) - Method in class ij.plugin.filter.Profiler
run(ImageProcessor) - Method in class ij.plugin.filter.Projector
run(ImageProcessor) - Method in class ij.plugin.filter.RGBStackSplitter
run(ImageProcessor) - Method in class ij.plugin.filter.RankFilters
run(ImageProcessor) - Method in class ij.plugin.filter.Resizer
run(ImageProcessor) - Method in class ij.plugin.filter.RoiWriter
run(ImageProcessor) - Method in class ij.plugin.filter.Rotator
run(ImageProcessor) - Method in class ij.plugin.filter.SaltAndPepper
run(ImageProcessor) - Method in class ij.plugin.filter.ScaleDialog
run(ImageProcessor) - Method in class ij.plugin.filter.Shadows
run(ImageProcessor) - Method in class ij.plugin.filter.ThresholdToSelection
run(ImageProcessor) - Method in class ij.plugin.filter.Transformer
run(ImageProcessor) - Method in class ij.plugin.filter.UnsharpMask
  This method is invoked for each slice or color channel.
run(ImageProcessor) - Method in class ij.plugin.filter.Writer
run(ImageProcessor) - Method in class ij.plugin.filter.XYWriter
run(ImageProcessor) - Method in class ij.plugin.filter.ZAxisProfiler
run(String) - Method in class ij.plugin.frame.ContrastAdjuster
run() - Method in class ij.plugin.frame.ContrastAdjuster
run() - Method in class ij.plugin.frame.LineWidthAdjuster
run(String) - Method in class ij.plugin.frame.PlugInFrame
run() - Method in class ij.plugin.frame.ThresholdAdjuster
run() - Method in class ij.text.TextPanel
  For better performance, open double-clicked files on separate thread instead of on event dispatch thread.
runCommand(String) - Method in class ij.plugin.frame.RoiManager
  Executes the ROI Manager "Add", "Add & Draw", "Update", "Delete", "Measure", "Draw", "Fill", "Deselect", "Select All", "Combine", "Split" or "Sort" command.
runCommand(String, String) - Method in class ij.plugin.frame.RoiManager
  Executes the ROI Manager "Open", "Save" or "Rename" command.
runFilterPlugIn(Object, String, String) - Method in class ij.ImageJ
runMacro(String) - Static method in class ij.IJ
  Runs the macro contained in the string `macro`.
runMacro(String, String) - Static method in class ij.IJ
  Runs the macro contained in the string `macro`.
runMacro(Program, int, String) - Method in class ij.macro.Interpreter
  Interprets the specified tokenized macro starting at the specified location.
runMacro(String) - Method in class ij.plugin.MacroInstaller
runMacro(String, String) - Method in class ij.plugin.Macro_Runner
  Opens and runs the specified macro on the current thread.
runMacroCommand(String) - Static method in class ij.plugin.MacroInstaller
runMacroFile(String, String) - Static method in class ij.IJ
  Runs the specified macro file.
runMacroFile(String) - Static method in class ij.IJ
  Runs the specified macro file.
runMacroFile(String, String) - Method in class ij.plugin.Macro_Runner
  Opens and runs the specified macro file on the current thread.
runMacroFromIJJar(String, String) - Method in class ij.plugin.Macro_Runner
runMacroShortcut(String) - Static method in class ij.plugin.MacroInstaller
runMacroTool(String) - Method in class ij.plugin.MacroInstaller
runMenuTool(String, String) - Method in class ij.plugin.MacroInstaller
runPlugIn(String, String) - Static method in class ij.IJ
  Runs the specified plugin and returns a reference to it.
runShortcut(Program, int, String) - Method in class ij.macro.MacroRunner
  Runs tokenized macro on current thread if pgm.queueCommands is true.
runUserPlugIn(String, String, String, boolean) - Method in class ij.ImageJ
running - Variable in class ij.gui.ImageWindow
  This variable is set false if the user presses the escape key or closes the window.
running2 - Variable in class ij.gui.ImageWindow
  This variable is set false if the user clicks in this window, presses the escape key, or closes the window.
rw - Variable in class ij.process.ImageStatistics
rx - Variable in class ij.process.ImageStatistics
ry - Variable in class ij.process.ImageStatistics

## S

SAMPLES_PER_PIXEL - Static variable in class ij.io.TiffDecoder
SAMPLE_FORMAT - Static variable in class ij.io.TiffDecoder
SAVE - Static variable in interface ij.macro.MacroConstants
SAVE_AS - Static variable in interface ij.macro.MacroConstants
SAVE_AS_MENU - Static variable in class ij.Menus
SAVE_SETTINGS - Static variable in interface ij.macro.MacroConstants
SCREEN_HEIGHT - Static variable in interface ij.macro.MacroConstants
SCREEN_WIDTH - Static variable in interface ij.macro.MacroConstants
SD_METHOD - Static variable in class ij.plugin.ZProjector
SEGMENTED - Static variable in class ij.plugin.filter.MaximumFinder
  Output type watershed-segmented image
SELECT - Static variable in interface ij.macro.MacroConstants
SELECTION_NAME - Static variable in interface ij.macro.MacroConstants
SELECTION_TYPE - Static variable in interface ij.macro.MacroConstants
SELECT_IMAGE - Static variable in interface ij.macro.MacroConstants
SETUP_UNDO - Static variable in interface ij.macro.MacroConstants
SET_AUTO_THRESHOLD - Static variable in interface ij.macro.MacroConstants
SET_BACKGROUND - Static variable in interface ij.macro.MacroConstants
SET_BATCH_MODE - Static variable in interface ij.macro.MacroConstants
SET_COLOR - Static variable in interface ij.macro.MacroConstants
SET_FONT - Static variable in interface ij.macro.MacroConstants
SET_FOREGROUND - Static variable in interface ij.macro.MacroConstants
SET_JUSTIFICATION - Static variable in interface ij.macro.MacroConstants
SET_KEY_DOWN - Static variable in interface ij.macro.MacroConstants
SET_LINE_WIDTH - Static variable in interface ij.macro.MacroConstants
SET_LOCATION - Static variable in interface ij.macro.MacroConstants
SET_LUT - Static variable in interface ij.macro.MacroConstants
SET_METADATA - Static variable in interface ij.macro.MacroConstants
SET_MIN_MAX - Static variable in interface ij.macro.MacroConstants
SET_OPTION - Static variable in interface ij.macro.MacroConstants
SET_PASTE_MODE - Static variable in interface ij.macro.MacroConstants
SET_PIXEL - Static variable in interface ij.macro.MacroConstants
SET_RESULT - Static variable in interface ij.macro.MacroConstants
SET_RGB_WEIGHTS - Static variable in interface ij.macro.MacroConstants
SET_SELECTION_LOC - Static variable in interface ij.macro.MacroConstants
SET_SELECTION_NAME - Static variable in interface ij.macro.MacroConstants
SET_SLICE - Static variable in interface ij.macro.MacroConstants
SET_THRESHOLD - Static variable in interface ij.macro.MacroConstants
SET_TOOL - Static variable in interface ij.macro.MacroConstants
SET_VOXEL_SIZE - Static variable in interface ij.macro.MacroConstants
SET_Z_COORDINATE - Static variable in interface ij.macro.MacroConstants
SHIFT_LEFT - Static variable in interface ij.macro.MacroConstants
SHIFT_RIGHT - Static variable in interface ij.macro.MacroConstants
SHORTCUTS_MENU - Static variable in class ij.Menus
SHORTCUT_IN_USE - Static variable in class ij.Menus
SHOW_MESSAGE - Static variable in interface ij.macro.MacroConstants
SHOW_MESSAGE_WITH_CANCEL - Static variable in interface ij.macro.MacroConstants
SHOW_NONE - Static variable in class ij.plugin.filter.ParticleAnalyzer
  Do not display particle outline image.
SHOW_OUTLINES - Static variable in class ij.plugin.filter.ParticleAnalyzer
  Display image containing outlines of measured paticles.
SHOW_PROGRESS - Static variable in interface ij.macro.MacroConstants
SHOW_PROGRESS - Static variable in class ij.plugin.filter.ParticleAnalyzer
  Display a progress bar.
SHOW_RESULTS - Static variable in class ij.plugin.filter.ParticleAnalyzer
  Display results in the ImageJ console.
SHOW_STATUS - Static variable in interface ij.macro.MacroConstants
SHOW_SUMMARY - Static variable in class ij.plugin.filter.ParticleAnalyzer
  Obsolete
SHOW_TEXT - Static variable in interface ij.macro.MacroConstants
SIN - Static variable in interface ij.macro.MacroConstants
SINGLE_POINTS - Static variable in class ij.plugin.filter.MaximumFinder
  Output type single points
SKEWNESS - Static variable in interface ij.measure.Measurements
SKEWNESS - Static variable in class ij.measure.ResultsTable
SLICE - Static variable in interface ij.measure.Measurements
SLICE - Static variable in class ij.measure.ResultsTable
SNAPSHOT - Static variable in interface ij.macro.MacroConstants
SNAPSHOT - Static variable in interface ij.plugin.filter.PlugInFilter
  Set this flag if the filter requires a snapshot (copy of the pixels array).
SOFTWARE - Static variable in class ij.io.TiffDecoder
SPARE1 - Static variable in class ij.gui.Toolbar
SPARE2 - Static variable in class ij.gui.Toolbar
SPARE3 - Static variable in class ij.gui.Toolbar
SPARE4 - Static variable in class ij.gui.Toolbar
SPARE5 - Static variable in class ij.gui.Toolbar
SPARE6 - Static variable in class ij.gui.Toolbar
SPARE7 - Static variable in class ij.gui.Toolbar
SPARE8 - Static variable in class ij.gui.Toolbar
SPARE9 - Static variable in class ij.gui.Toolbar
SPLIT - Static variable in interface ij.macro.MacroConstants
SQRT - Static variable in interface ij.macro.MacroConstants
SQRT2 - Static variable in class ij.plugin.filter.EDM
  in 16-bit EDM image this value corresponds to a pixel distance of sqrt(2)
SQRT5 - Static variable in class ij.plugin.filter.EDM
  in 16-bit EDM image this value corresponds to a pixel distance of sqrt(2)
STACK_REQUIRED - Static variable in interface ij.plugin.filter.PlugInFilter
  Set this flag if the filter requires a stack.
STANDALONE - Static variable in class ij.ImageJ
STARTS_WITH - Static variable in interface ij.macro.MacroConstants
STD_DEV - Static variable in interface ij.measure.Measurements
STD_DEV - Static variable in class ij.measure.ResultsTable
STRAIGHT_LINE - Static variable in class ij.measure.Calibration
STRAIGHT_LINE - Static variable in class ij.measure.CurveFitter
STRING - Static variable in interface ij.macro.MacroConstants
STRING_CONSTANT - Static variable in interface ij.macro.MacroConstants
STRING_FUNCTION - Static variable in interface ij.macro.MacroConstants
STRIP_BYTE_COUNT - Static variable in class ij.io.TiffDecoder
STRIP_OFFSETS - Static variable in class ij.io.TiffDecoder
SUBSTRING - Static variable in interface ij.macro.MacroConstants
SUBTRACT - Static variable in interface ij.process.Blitter
  dst=dst-src
SUM_METHOD - Static variable in class ij.plugin.ZProjector
SUPPORTS_MASKING - Static variable in interface ij.plugin.filter.PlugInFilter
  Set this flag if the filter wants ImageJ, for non-rectangular ROIs, to restore that part of the image that's inside the bounding rectangle but outside of the ROI.
SaltAndPepper - class ij.plugin.filter.SaltAndPepper.
  Implements ImageJ's Process/Noise/Salt and Pepper command.
SaltAndPepper() - Constructor for class ij.plugin.filter.SaltAndPepper
SansSerif12 - Static variable in class ij.ImageJ
  SansSerif, 12-point, plain font.
SaveChangesDialog - class ij.gui.SaveChangesDialog.
  A modal dialog box with a one line message and "Don't Save", "Cancel" and "Save" buttons.
SaveChangesDialog(Frame, String) - Constructor for class ij.gui.SaveChangesDialog
SaveDialog - class ij.io.SaveDialog.
  This class displays a dialog window from which the user can save a file.
SaveDialog(String, String, String) - Constructor for class ij.io.SaveDialog
  Displays a file save dialog with 'title' as the title, 'defaultName' as the initial file name, and 'extension' (e.g.
SaveDialog(String, String, String, String) - Constructor for class ij.io.SaveDialog
  Displays a file save dialog, using the specified default directory and file name and extension.
ScaleBar - class ij.plugin.ScaleBar.
  This plugin implements the Analyze/Tools/Draw Scale Bar command.
ScaleBar() - Constructor for class ij.plugin.ScaleBar
ScaleDialog - class ij.plugin.filter.ScaleDialog.
  Implements the Analyze/Set Scale command.
ScaleDialog() - Constructor for class ij.plugin.filter.ScaleDialog
Scaler - class ij.plugin.Scaler.
  This plugin implements the Edit/Scale command.
Scaler() - Constructor for class ij.plugin.Scaler
ScreenGrabber - class ij.plugin.ScreenGrabber.
  Implements the Plugins/Utilities/Capture Screen command.
ScreenGrabber() - Constructor for class ij.plugin.ScreenGrabber
Selection - class ij.plugin.Selection.
  This plugin implements the commands in the Edit/Section submenu.
Selection() - Constructor for class ij.plugin.Selection
Shadows - class ij.plugin.filter.Shadows.
  Implements the commands in the Process/Shadows submenu.
Shadows() - Constructor for class ij.plugin.filter.Shadows
ShapeRoi - class ij.gui.ShapeRoi.
  A subclass of `ij.gui.Roi` (2D Regions Of Interest) implemented in terms of java.awt.Shape.
ShapeRoi(Roi) - Constructor for class ij.gui.ShapeRoi
  Constructs a ShapeRoi from an Roi.
ShapeRoi(Shape) - Constructor for class ij.gui.ShapeRoi
  Constructs a ShapeRoi from a Shape.
ShapeRoi(int, int, Shape) - Constructor for class ij.gui.ShapeRoi
  Constructs a ShapeRoi from a Shape.
ShapeRoi(float[]) - Constructor for class ij.gui.ShapeRoi
  Constructs a ShapeRoi from an array of variable length path segments.
ShortBlitter - class ij.process.ShortBlitter.
  This class does bit blitting of 16-bit images.
ShortBlitter(ShortProcessor) - Constructor for class ij.process.ShortBlitter
  Constructs a ShortBlitter from a ShortProcessor.
ShortProcessor - class ij.process.ShortProcessor.
  Objects of the class contain a 16-bit unsigned image and methods that operate on that image.
ShortProcessor(int, int, short[], ColorModel) - Constructor for class ij.process.ShortProcessor
  Creates a new ShortProcessor using the specified pixel array and ColorModel.
ShortProcessor(int, int) - Constructor for class ij.process.ShortProcessor
  Creates a blank ShortProcessor using the default grayscale LUT that displays zero as black.
ShortProcessor(BufferedImage) - Constructor for class ij.process.ShortProcessor
  Creates a ShortProcessor from a TYPE_USHORT_GRAY BufferedImage.
ShortProcessor(int, int, short[], ColorModel, boolean) - Constructor for class ij.process.ShortProcessor
  Obsolete.
ShortProcessor(int, int, boolean) - Constructor for class ij.process.ShortProcessor
  Obsolete.
ShortStatistics - class ij.process.ShortStatistics.
  16-bit image statistics, including histogram.
ShortStatistics(ImageProcessor) - Constructor for class ij.process.ShortStatistics
  Construct an ImageStatistics object from a ShortProcessor using the standard measurement options (area, mean, mode, min and max).
ShortStatistics(ImageProcessor, int, Calibration) - Constructor for class ij.process.ShortStatistics
  Constructs a ShortStatistics object from a ShortProcessor using the specified measurement options.
SimpleCommands - class ij.plugin.SimpleCommands.
  This plugin implements the Plugins/Utilities/Unlock, Image/Rename and Plugins/Utilities/Search commands.
SimpleCommands() - Constructor for class ij.plugin.SimpleCommands
Slicer - class ij.plugin.Slicer.
  Implements the Image/Stacks/Reslice command.
Slicer() - Constructor for class ij.plugin.Slicer
SocketListener - class ij.SocketListener.
  Runs commands sent to the port returned by ImageJ.getPort().
SocketListener() - Constructor for class ij.SocketListener
SpecifyROI - class ij.plugin.SpecifyROI.
  This plugin implements the Edit/Selection/Specify command.
SpecifyROI() - Constructor for class ij.plugin.SpecifyROI
SplineFitter - class ij.measure.SplineFitter.
  This class fits a spline function to a set of points.
SplineFitter(int[], int[], int) - Constructor for class ij.measure.SplineFitter
StackConverter - class ij.process.StackConverter.
  This class does stack type conversions.
StackConverter(ImagePlus) - Constructor for class ij.process.StackConverter
StackEditor - class ij.plugin.StackEditor.
  Implements the AddSlice, DeleteSlice and "Convert Windows to Stack" commands.
StackEditor() - Constructor for class ij.plugin.StackEditor
StackProcessor - class ij.process.StackProcessor.
  This class processes stacks.
StackProcessor(ImageStack, ImageProcessor) - Constructor for class ij.process.StackProcessor
  Constructs a StackProcessor from a stack.
StackStatistics - class ij.process.StackStatistics.
  Statistics, including the histogram, of a stack.
StackStatistics(ImagePlus) - Constructor for class ij.process.StackStatistics
StackStatistics(ImagePlus, int, double, double) - Constructor for class ij.process.StackStatistics
StackWindow - class ij.gui.StackWindow.
  This class is an extended ImageWindow used to display image stacks.
StackWindow(ImagePlus) - Constructor for class ij.gui.StackWindow
StackWindow(ImagePlus, ImageCanvas) - Constructor for class ij.gui.StackWindow
StackWriter - class ij.plugin.StackWriter.
  Writes the slices of stack as separate files.
StackWriter() - Constructor for class ij.plugin.StackWriter
StringSorter - class ij.util.StringSorter.
  A simple QuickSort for String arrays.
StringSorter() - Constructor for class ij.util.StringSorter
SurfacePlotter - class ij.plugin.SurfacePlotter.
SurfacePlotter() - Constructor for class ij.plugin.SurfacePlotter
Symbol - class ij.macro.Symbol.
  Objects of this class are used as entries in the macro language symbol table.
s2ints(String) - Method in class ij.plugin.ControlPanel
  Breaks the specified string into an array of ints.
s2ints(String) - Method in class ij.plugin.filter.FractalBoxCounter
  Breaks the specified string into an array of ints.
sCalibrated - Variable in class ij.ImagePlus
  Obsolete.
sampleModel - Variable in class ij.process.ImageProcessor
save(String) - Static method in class ij.IJ
  Saves an image, lookup table, selection or text window to the specified file path.
save - Variable in class ij.gui.HistogramWindow
save() - Method in class ij.io.FileSaver
  Resaves the image.
save(String) - Method in class ij.plugin.MeasurementsWriter
save(PrintWriter) - Method in class ij.text.TextPanel
  Writes all the text in this TextPanel to a file.
saveAs(String, String) - Static method in class ij.IJ
saveAs(String) - Static method in class ij.Macro
saveAs(String) - Method in class ij.text.TextPanel
  Saves all the text in this TextPanel to a file.
saveAsBmp() - Method in class ij.io.FileSaver
  Save the image in BMP format using a save file dialog.
saveAsBmp(String) - Method in class ij.io.FileSaver
  Save the image in BMP format using the specified path.
saveAsFits() - Method in class ij.io.FileSaver
  Save the image in FITS format using a save file dialog.
saveAsFits(String) - Method in class ij.io.FileSaver
  Save the image in FITS format using the specified path.
saveAsGif() - Method in class ij.io.FileSaver
  Save the image in GIF format using a save file dialog.
saveAsGif(String) - Method in class ij.io.FileSaver
  Save the image in Gif format using the specified path.
saveAsJpeg() - Method in class ij.io.FileSaver
  Save the image in JPEG format using a save file dialog.
saveAsJpeg(String) - Method in class ij.io.FileSaver
  Save the image in JPEG format using the specified path.
saveAsLut() - Method in class ij.io.FileSaver
  Save the current LUT using a save file dialog.
saveAsLut(String) - Method in class ij.io.FileSaver
  Save the current LUT using the specified path.
saveAsPgm() - Method in class ij.io.FileSaver
  Saves grayscale images in PGM (portable graymap) format and RGB images in PPM (portable pixmap) format, using a save file dialog.
saveAsPgm(String) - Method in class ij.io.FileSaver
  Saves grayscale images in PGM (portable graymap) format and RGB images in PPM (portable pixmap) format, using the specified path.
saveAsPng() - Method in class ij.io.FileSaver
  Save the image in PNG format using a save file dialog.
saveAsPng(String) - Method in class ij.io.FileSaver
  Save the image in PNG format using the specified path.
saveAsRaw() - Method in class ij.io.FileSaver
  Save the image or stack as raw data using a save file dialog.
saveAsRaw(String) - Method in class ij.io.FileSaver
  Save the image as raw data using the specified path.
saveAsRawStack(String) - Method in class ij.io.FileSaver
  Save the stack as raw data using the specified path.
saveAsText() - Method in class ij.io.FileSaver
  Save the image as tab-delimited text using a save file dialog.
saveAsText(String) - Method in class ij.io.FileSaver
  Save the image as tab-delimited text using the specified path.
saveAsTiff() - Method in class ij.io.FileSaver
  Save the image or stack in TIFF format using a save file dialog.
saveAsTiff(String) - Method in class ij.io.FileSaver
  Save the image in TIFF format using the specified path.
saveAsTiffStack(String) - Method in class ij.io.FileSaver
  Save the stack as a multi-image TIFF using the specified path.
saveAsZip() - Method in class ij.io.FileSaver
  Uses a save file dialog to save the image or stack as a TIFF in a ZIP archive.
saveAsZip(String) - Method in class ij.io.FileSaver
  Save the image or stack in TIFF/ZIP format using the specified path.
saveBitmap(String, Image, int, int) - Method in class ij.plugin.BMP_Writer
saveCommand() - Static method in class ij.plugin.frame.Recorder
  Writes the current command and options to the Recorder window.
saveGlobals(Program) - Method in class ij.macro.Interpreter
  Saves global variablesk.
saveImageDescription(byte[], FileInfo) - Method in class ij.io.TiffDecoder
  Save the image description in the specified FileInfo.
saveLocation(String, Point) - Static method in class ij.Prefs
  Saves the Point `loc` in the preferences file as a string using the keyword `key`.
savePreferences(Properties) - Method in class ij.ImageJ
  Called once when ImageJ quits.
savePreferences(Properties) - Static method in class ij.Menus
  Called once when ImageJ quits.
savePreferences() - Static method in class ij.Prefs
  Saves user preferences in the IJ_Prefs.txt properties file.
savePreferences(Properties) - Static method in class ij.gui.NewImage
  Called when ImageJ quits.
savePreferences(Properties) - Static method in class ij.gui.PlotWindow
  Called once when ImageJ quits.
savePreferences(Properties) - Static method in class ij.io.ImportDialog
  Called once when ImageJ quits.
savePreferences(Properties) - Static method in class ij.plugin.GelAnalyzer
  Called once when ImageJ quits.
savePreferences(Properties) - Static method in class ij.plugin.filter.Analyzer
  Called once when ImageJ quits.
savePreferences(Properties) - Static method in class ij.plugin.filter.ParticleAnalyzer
  Called once when ImageJ quits.
savePrefs(Properties, String) - Static method in class ij.Prefs
savePressed() - Method in class ij.gui.SaveChangesDialog
  Returns true if the user dismissed dialog by pressing "Save".
saveResults(ImageStatistics, Roi) - Method in class ij.plugin.filter.Analyzer
  Saves the measurements specified in the "Set Measurements" dialog, or by calling setMeasurments(), in the system results table.
saveResults(ImageStatistics, Roi) - Method in class ij.plugin.filter.ParticleAnalyzer
  Saves statistics for one particle in a results table.
saveRoi() - Method in class ij.ImagePlus
saveRoi(ImagePlus) - Method in class ij.plugin.filter.RoiWriter
saveXValues - Static variable in class ij.gui.PlotWindow
  Save x-values only.
saveXYCoordinates(ImagePlus) - Method in class ij.plugin.filter.XYWriter
scale(double, double) - Method in class ij.process.ByteProcessor
  Scales the image or selection using the specified scale factors.
scale(double, double) - Method in class ij.process.ColorProcessor
  Scales the image or selection using the specified scale factors.
scale(double, double) - Method in class ij.process.FloatProcessor
  Scales the image or selection using the specified scale factors.
scale(double, double) - Method in class ij.process.ImageProcessor
  Scales the image by the specified factors.
scale(double, double) - Method in class ij.process.ShortProcessor
  Scales the image or selection using the specified scale factors.
scale(double, double) - Method in class ij.process.StackProcessor
scale(double, double, double) - Method in class ij.process.StackProcessor
scaled() - Method in class ij.measure.Calibration
  Returns true if this image is spatially calibrated.
screenX(int) - Method in class ij.gui.ImageCanvas
  Converts an offscreen x-coordinate to a screen x-coordinate.
screenXD(double) - Method in class ij.gui.ImageCanvas
  Converts a floating-point offscreen x-coordinate to a screen x-coordinate.
screenY(int) - Method in class ij.gui.ImageCanvas
  Converts an offscreen y-coordinate to a screen y-coordinate.
screenYD(double) - Method in class ij.gui.ImageCanvas
  Converts a floating-point offscreen x-coordinate to a screen x-coordinate.
scroll(int, int) - Method in class ij.gui.ImageCanvas
seek(int) - Method in class ij.io.RandomAccessStream
select(int) - Method in class ij.plugin.frame.RoiManager
select(int, boolean, boolean) - Method in class ij.plugin.frame.RoiManager
selectAll() - Method in class ij.text.TextPanel
  Selects all the lines in this TextPanel.
selectWindow(int) - Static method in class ij.IJ
  For IDs less than zero, activates the image with the specified ID.
selectWindow(String) - Static method in class ij.IJ
  Activates the window with the specified title.
separator - Static variable in class ij.Prefs
  file.separator system property
set(String, String) - Static method in class ij.Prefs
  Saves the value of the string `text` in the preferences file using the keyword `key`.
set(String, int) - Static method in class ij.Prefs
  Saves `value` in the preferences file using the keyword `key`.
set(String, double) - Static method in class ij.Prefs
  Saves `value` in the preferences file using the keyword `key`.
set(String, boolean) - Static method in class ij.Prefs
  Saves the boolean variable `value` in the preferences file using the keyword `key`.
set(int, int, int) - Method in class ij.process.ByteProcessor
set(int, int) - Method in class ij.process.ByteProcessor
set(int, int, int) - Method in class ij.process.ColorProcessor
set(int, int) - Method in class ij.process.ColorProcessor
set(int, int, int) - Method in class ij.process.FloatProcessor
set(int, int) - Method in class ij.process.FloatProcessor
set(int, int, int) - Method in class ij.process.ImageProcessor
  This is a faster version of putPixel() that does not clip out of range values and does not do bounds checking.
set(int, int) - Method in class ij.process.ImageProcessor
set(int, int, int) - Method in class ij.process.ShortProcessor
set(int, int) - Method in class ij.process.ShortProcessor
setActivated() - Method in class ij.ImagePlus
  Called by ImageWindow.windowActivated().
setAdditionalFunctions(String) - Static method in class ij.macro.Interpreter
  The specified string, if not null, is added to strings passed to the run() method.
setAntialiased(Graphics, boolean) - Static method in class ij.util.Java2
setAntialiasedText(boolean) - Method in class ij.process.ImageProcessor
  Specifies whether or not text is drawn using antialiasing.
setAntialiasedText(Graphics, boolean) - Static method in class ij.util.Java2
setBackgroundColor(int, int, int) - Static method in class ij.IJ
  Sets the background color.
setBackgroundColor(Color) - Static method in class ij.gui.Toolbar
setBackgroundValue(double) - Method in class ij.process.ByteProcessor
  Sets the background fill value, where 0<=value<=255.
setBackgroundValue(double) - Method in class ij.process.ColorProcessor
  Sets the background fill value, where `value` is interpreted as an RGB int.
setBackgroundValue(double) - Method in class ij.process.FloatProcessor
  Does nothing.
setBackgroundValue(double) - Method in class ij.process.ImageProcessor
  Sets the background fill value used by the rotate() and scale() methods.
setBackgroundValue(double) - Method in class ij.process.ShortProcessor
  Does nothing.
setBilinearInterpolation(Graphics, boolean) - Static method in class ij.util.Java2
setBrightness(FloatProcessor) - Method in class ij.process.ColorProcessor
  Updates the brightness using the pixels in the specified FloatProcessor).
setCTable(float[], String) - Method in class ij.measure.Calibration
  Sets the calibration table.
setCalibration(Calibration) - Method in class ij.ImagePlus
  Sets this image's calibration.
setCalibrationTable(float[]) - Method in class ij.process.ImageProcessor
  Set a lookup table used by getPixelValue(), getLine() and convertToFloat() to calibrate pixel values.
setClipRect(Rectangle) - Method in class ij.process.ImageProcessor
  Updates the clipping rectangle used by lineTo(), drawLine(), drawDot() and drawPixel().
setColor(Color) - Method in class ij.ImagePlus
  Sets current foreground color.
setColor(Color) - Method in class ij.gui.Plot
  Changes the drawing color.
setColor(Color) - Method in class ij.gui.PlotWindow
  Changes the drawing color.
setColor(Color) - Static method in class ij.gui.Roi
  Sets the color used for ROI outlines to the specified value.
setColor(Color) - Method in class ij.gui.Toolbar
  Obsolete.
setColor(Color) - Method in class ij.process.ByteProcessor
  Sets the foreground drawing color.
setColor(Color) - Method in class ij.process.ColorProcessor
  Sets the foreground color.
setColor(Color) - Method in class ij.process.FloatProcessor
  Sets the foreground fill/draw color.
setColor(Color) - Method in class ij.process.ImageProcessor
  Sets the default fill/draw value to the pixel value closest to the specified color.
setColor(int) - Method in class ij.process.ImageProcessor
  Obsolete (use setValue)
setColor(Color) - Method in class ij.process.ShortProcessor
  Sets the foreground fill/draw color.
setColorModel(ColorModel) - Method in class ij.ImageStack
  Assigns a new color model to this stack.
setColorModel(ColorModel) - Method in class ij.process.ImageProcessor
  Sets the color model.
setColumnHeadings(String) - Static method in class ij.IJ
  Clears the "Results" window and sets the column headings to those in the tab-delimited 'headings' String.
setColumnHeadings(String) - Method in class ij.text.TextPanel
  Clears this TextPanel and sets the column headings to those in the tab-delimited 'headings' String.
setCommand(String) - Static method in class ij.plugin.frame.Recorder
  Starts recording a command.
setCurrentWindow(ImageWindow) - Static method in class ij.WindowManager
  Makes the image contained in the specified window the active image.
setCursor(int, int, int, int) - Method in class ij.gui.ImageCanvas
  Sets the cursor based on the current tool and cursor location.
setDefaultDirectory(String) - Static method in class ij.io.OpenDialog
  Sets the current working directory.
setDefaultDirectory(String) - Static method in class ij.plugin.frame.Editor
setDefaultHeadings() - Method in class ij.measure.ResultsTable
  Sets the headings used by the Measure command ("Area", "Mean", etc.).
setDefaultHeadings() - Static method in class ij.plugin.filter.Analyzer
  Sets the default headings ("Area", "Mean", etc.).
setDialog(GenericDialog) - Method in class ij.plugin.filter.PlugInFilterRunner
setDimensions(int, int, int) - Method in class ij.ImagePlus
  Sets the 3rd, 4th and 5th dimensions, where `nChannels`*`nSlices`*`nFrames` must be the same as the stack size.
setDisplayList(Vector) - Method in class ij.gui.ImageCanvas
setDisplayList(Shape, Color, BasicStroke) - Method in class ij.gui.ImageCanvas
setDoScaling(boolean) - Static method in class ij.process.ImageConverter
  Set true to scale to 0-255 when converting short to byte or float to byte and to 0-65535 when converting float to short.
setDrawingColor(int, int, boolean) - Method in class ij.gui.ImageCanvas
setDrawingSize(int, int) - Method in class ij.gui.ImageCanvas
setFileInfo(FileInfo) - Method in class ij.ImagePlus
  Saves this image's FileInfo so it can be later retieved using getOriginalFileInfo().
setFileName(String) - Method in class ij.plugin.MacroInstaller
setFloatArray(float[][]) - Method in class ij.process.ImageProcessor
setFont(Font) - Method in class ij.gui.MultiLineLabel
setFont(String, int, int) - Static method in class ij.gui.TextRoi
  Sets the font face, size and style.
setFont(String, int, int, boolean) - Static method in class ij.gui.TextRoi
  Sets the font face, size, style and antialiasing mode.
setFont(Font) - Method in class ij.plugin.frame.Editor
setFont(Font) - Method in class ij.process.ImageProcessor
  Sets the font used by drawString().
setFont(Font, boolean) - Method in class ij.text.TextPanel
setFontSize(int) - Static method in class ij.Menus
  Set the size (in points) used for the fonts in ImageJ menus.
setForegroundColor(int, int, int) - Static method in class ij.IJ
  Sets the foreground color.
setForegroundColor(Color) - Static method in class ij.gui.Toolbar
setFromFloatArrays(float[][]) - Method in class ij.process.ByteProcessor
setFromFloatProcessors(FloatProcessor[]) - Method in class ij.process.ByteProcessor
setFunction(int, double[], String) - Method in class ij.measure.Calibration
  Sets the calibration function, coefficient table and unit (e.g.
setFunction(int, double[], String, boolean) - Method in class ij.measure.Calibration
setGlobalCalibration(Calibration) - Method in class ij.ImagePlus
  Sets the system-wide calibration.
setHSB(byte[], byte[], byte[]) - Method in class ij.process.ColorProcessor
  Sets the current pixels from 3 byte arrays (hue, saturation and brightness).
setHeading(int, String) - Method in class ij.measure.ResultsTable
  Changes the heading of the given column.
setHistogramRange(double, double) - Method in class ij.process.ImageProcessor
  Set the range used for histograms of float images.
setHistogramSize(int) - Method in class ij.process.ImageProcessor
  Set the number of bins to be used for histograms of float images.
setIgnoreFlush(boolean) - Method in class ij.ImagePlus
  Set `ignoreFlush true` to not have the pixel data set to null when the window is closed.
setImage(Image) - Method in class ij.ImagePlus
  Replaces the image, if any, with the one specified.
setImage(ImagePlus) - Method in class ij.gui.Roi
setImage(ImagePlus) - Method in class ij.measure.Calibration
  Disables the density calibation if the specified image has a differenent bit depth.
setImage(ImagePlus) - Method in class ij.plugin.ZProjector
  Explicitly set image to be projected.
setImageUpdated() - Method in class ij.gui.ImageCanvas
  ImagePlus.updateAndDraw calls this method to get paint to update the image from the ImageProcessor.
setImagesURL(String) - Static method in class ij.Prefs
  Sets the URL of the directory that contains the ImageJ sample images.
setInitialParameters(double[]) - Method in class ij.measure.CurveFitter
  Sets the initial parameters, which override the default initial parameters.
setInputEvent(InputEvent) - Static method in class ij.IJ
setInsets(int, int, int) - Method in class ij.gui.GenericDialog
  Set the insets (margins), in pixels, that will be used for the next component added to the dialog.
setInstanceColor(Color) - Method in class ij.gui.Roi
  Sets the color used by this ROI to draw its outline.
setIntArray(int[][]) - Method in class ij.process.ImageProcessor
setInterpolate(boolean) - Method in class ij.process.ImageProcessor
  Setting 'interpolate' true causes scale(), resize(), rotate() and getLine() to do bilinear interpolation.
setInvertY(boolean) - Method in class ij.measure.Calibration
  Sets the 'invertY' flag.
setIsMacroWindow(boolean) - Method in class ij.plugin.frame.Editor
setJustification(int) - Method in class ij.gui.Plot
  Sets the justification used by addLabel(), where `justification` is ImageProcessor.LEFT, ImageProcessor.CENTER or ImageProcessor.RIGHT.
setJustification(int) - Method in class ij.process.ImageProcessor
  Sets the justification used by drawString(), where `justification` is CENTER_JUSTIFY, RIGHT_JUSTIFY or LEFT_JUSTIFY.
setKeyDown(int) - Static method in class ij.IJ
setKeyUp(int) - Static method in class ij.IJ
setLabel(String, int) - Method in class ij.measure.ResultsTable
  Adds a label to the beginning of the specified row, or updates an existing lable, where 0<=rowsetLastDirectory(String) - Static method in class ij.io.OpenDialog
  Sets the path to the directory containing the last file opened by the user.
setLastName(String) - Static method in class ij.io.OpenDialog
  Sets the name of the last file opened by the user.
setLimits(double, double, double, double) - Method in class ij.gui.Plot
  Sets the x-axis and y-axis range.
setLimits(double, double, double, double) - Method in class ij.gui.PlotWindow
  Sets the x-axis and y-axis range.
setLine(int, String) - Method in class ij.text.TextPanel
  Replaces the contents of the specified line, where 'index' must be greater than or equal to zero and less than the value returned by getLineCount().
setLineWidth(int) - Method in class ij.gui.Plot
  Changes the line width.
setLineWidth(int) - Method in class ij.gui.PlotWindow
  Changes the line width.
setLineWidth(int) - Method in class ij.process.ImageProcessor
  Sets the line width used by lineTo() and drawDot().
setLocation(int, int) - Method in class ij.gui.Roi
setLutAnimation(boolean) - Method in class ij.process.ImageProcessor
  For 16 and 32 bit processors, set 'lutAnimation' true to have createImage() use the cached 8-bit version of the image.
setMagnification(double) - Method in class ij.gui.ImageCanvas
setMask(ImageProcessor) - Method in class ij.process.ImageProcessor
  Defines a byte mask that limits processing to an irregular ROI.
setMaxIterations(int) - Method in class ij.measure.CurveFitter
  Set maximum number of iterations allowed
setMeasurements(int) - Static method in class ij.plugin.filter.Analyzer
setMethod(int) - Method in class ij.plugin.ZProjector
setMinAndMax(double, double) - Static method in class ij.IJ
  Sets the minimum and maximum displayed pixel values.
setMinAndMax(double, double) - Static method in class ij.gui.ProfilePlot
  Sets the y-axis min and max.
setMinAndMax(double, double) - Method in class ij.process.ByteProcessor
  Maps the entries in this image's LUT from min-max to 0-255.
setMinAndMax(double, double) - Method in class ij.process.ColorProcessor
  Uses a table look-up to map the pixels in this image from min-max to 0-255.
setMinAndMax(double, double, int) - Method in class ij.process.ColorProcessor
setMinAndMax(double, double) - Method in class ij.process.FloatProcessor
  Sets the min and max variables that control how real pixel values are mapped to 0-255 screen values.
setMinAndMax(double, double) - Method in class ij.process.ImageProcessor
  This image will be displayed by mapping pixel values in the range min-max to screen values in the range 0-255.
setMinAndMax(double, double) - Method in class ij.process.ShortProcessor
  Sets the min and max variables that control how real pixel values are mapped to 0-255 screen values.
setNPasses(int) - Method in class ij.plugin.filter.Convolver
setNPasses(int) - Method in interface ij.plugin.filter.ExtendedPlugInFilter
  This method is called by ImageJ to inform the plugin-filter about the passes to its run method.
setNPasses(int) - Method in class ij.plugin.filter.GaussianBlur
  Set the number of passes of the blur1Direction method.
setNPasses(int) - Method in class ij.plugin.filter.MaximumFinder
  unused method required by interface ExtendedPlugInFilter
setNPasses(int) - Method in class ij.plugin.filter.RankFilters
  This method is called by ImageJ to set the number of calls to run(ip) corresponding to 100% of the progress bar
setNPasses(int) - Method in class ij.plugin.filter.Rotator
setNPasses(int) - Method in class ij.plugin.filter.UnsharpMask
  Since most computing time is spent in GaussianBlur, forward the information about the number of passes to Gaussian Blur.
setName(String) - Method in class ij.gui.Roi
  Sets the name of this ROI.
setNormalize(boolean) - Method in class ij.plugin.filter.Convolver
setOpenUsingPlugins(boolean) - Static method in class ij.io.Opener
  Open all images using HandleExtraFileTypes.
setOptions(String) - Static method in class ij.Macro
setPasteMode(String) - Static method in class ij.IJ
  Sets the transfer mode used by the Edit/Paste command, where mode is "Copy", "Blend", "Average", "Difference", "Transparent", "AND", "OR", "XOR", "Add", "Subtract", "Multiply", or "Divide".
setPasteMode(int) - Static method in class ij.gui.Roi
  Sets the Paste transfer mode.
setPixels(Object, int) - Method in class ij.ImageStack
  Assigns a pixel array to the specified slice, were 1<=n<=nslices.
setPixels(Object, int) - Method in class ij.VirtualStack
  Assigns a pixel array to the specified slice, were 1<=n<=nslices.
setPixels(Object) - Method in class ij.process.ByteProcessor
setPixels(int, FloatProcessor) - Method in class ij.process.ByteProcessor
  Sets the pixels from a FloatProcessor, no scaling.
setPixels(Object) - Method in class ij.process.ColorProcessor
setPixels(int, FloatProcessor) - Method in class ij.process.ColorProcessor
  Sets the pixels of one color channel from a FloatProcessor.
setPixels(Object) - Method in class ij.process.FloatProcessor
setPixels(int, FloatProcessor) - Method in class ij.process.FloatProcessor
  Sets the pixels, and min&max values from a FloatProcessor.
setPixels(Object) - Method in class ij.process.ImageProcessor
  Sets a new pixel array for the image.
setPixels(int, FloatProcessor) - Method in class ij.process.ImageProcessor
  Sets the pixels (of one color channel for RGB images) from a FloatProcessor.
setPixels(Object) - Method in class ij.process.ShortProcessor
setPixels(int, FloatProcessor) - Method in class ij.process.ShortProcessor
  Sets the pixels from a FloatProcessor, no scaling.
setPolygon(int[], int[], int) - Method in class ij.process.PolygonFiller
  Specifies the polygon to be filled.
setPrecision(int) - Method in class ij.measure.ResultsTable
  Sets the number of digits to the right of decimal point.
setPrecision(int) - Static method in class ij.plugin.filter.Analyzer
  Sets the number of digits displayed to the right of decimal point.
setProcessor(String, ImageProcessor) - Method in class ij.ImagePlus
  Replaces the ImageProcessor, if any, with the one specified.
setProgressBar(ProgressBar) - Method in class ij.process.ImageProcessor
  Assigns a progress bar to this processor.
setProperty(String, Object) - Method in class ij.ImagePlus
  Adds a key-value pair to this image's properties.
setQuality(int) - Static method in class ij.plugin.JpegWriter
  Specifies the image quality (0-100).
setRGB(byte[], byte[], byte[]) - Method in class ij.process.ColorProcessor
  Sets the current pixels from 3 byte arrays (reg, green, blue).
setRestarts(int) - Method in class ij.measure.CurveFitter
  Set number of simplex restarts to do
setResultsTable(ResultsTable) - Method in class ij.text.TextPanel
  Sets the ResultsTable associated with this TextPanel.
setRoi(Roi) - Method in class ij.ImagePlus
  Assigns the specified ROI to this image and displays it.
setRoi(int, int, int, int) - Method in class ij.ImagePlus
  Creates a rectangular selection.
setRoi(Rectangle) - Method in class ij.ImagePlus
  Creates a rectangular selection.
setRoi(Rectangle) - Method in class ij.ImageStack
setRoi(Rectangle) - Method in class ij.process.ImageProcessor
  Defines a rectangular region of interest and sets the mask to null if this ROI is not the same size as the previous one.
setRoi(int, int, int, int) - Method in class ij.process.ImageProcessor
  Defines a rectangular region of interest and sets the mask to null if this ROI is not the same size as the previous one.
setRoi(Roi) - Method in class ij.process.ImageProcessor
  Defines a non-rectangular region of interest that will consist of a rectangular ROI and a mask.
setRoi(Polygon) - Method in class ij.process.ImageProcessor
  Defines a polygonal region of interest that will consist of a rectangular ROI and a mask.
setShowAllROIs(boolean) - Method in class ij.gui.ImageCanvas
setShowCursorStatus(boolean) - Method in class ij.gui.ImageCanvas
  Called by IJ.showStatus() to prevent status bar text from being overwritten until the cursor moves at least 12 pixels.
setShowProgress(boolean) - Method in class ij.process.FHT
  Enables/disables display of the progress bar during transforms.
setSilentMode(boolean) - Method in class ij.io.Opener
  The "Opening: path" status message is not displayed in silent mode.
setSize(int, int) - Method in class ij.gui.Plot
  Sets the canvas size (i.e., size of the resulting ImageProcessor).
setSlice(int) - Static method in class ij.IJ
  Switches to the specified stack slice, where 1<='slice'<=stack-size.
setSlice(int) - Method in class ij.ImagePlus
  Activates the specified slice.
setSliceLabel(String, int) - Method in class ij.ImageStack
  Sets the label of the specified slice, were 1<=n<=nslices.
setSliceLabel(String, int) - Method in class ij.VirtualStack
  Does nothing.
setSnapshotCopyMode(boolean) - Method in class ij.process.ImageProcessor
  The getPixelsCopy() method returns a reference to the snapshot buffer if it is not null and 'snapshotCopyMode' is true.
setSnapshotPixels(Object) - Method in class ij.process.ByteProcessor
setSnapshotPixels(Object) - Method in class ij.process.ColorProcessor
setSnapshotPixels(Object) - Method in class ij.process.FloatProcessor
setSnapshotPixels(Object) - Method in class ij.process.ImageProcessor
  Sets a new pixel array for the snapshot (undo) buffer.
setSnapshotPixels(Object) - Method in class ij.process.ShortProcessor
setStack(String, ImageStack) - Method in class ij.ImagePlus
  Replaces the stack, if any, with the one specified.
setStartSlice(int) - Method in class ij.plugin.ZProjector
setStopSlice(int) - Method in class ij.plugin.ZProjector
setSystemLookAndFeel() - Static method in class ij.util.Java2
  Sets the Swing look and feel to the system look and feel.
setTempCurrentImage(ImagePlus) - Static method in class ij.WindowManager
  Makes the specified image temporarily the active image.
setTextPanel(TextPanel) - Static method in class ij.IJ
  TextWindow calls this method with a null argument when the "Results" window is closed.
setThreads(int) - Static method in class ij.Prefs
  Sets the number of threads (1-32) used by PlugInFilters to process stacks.
setThreshold(double, double) - Static method in class ij.IJ
  Sets the lower and upper threshold levels and displays the image using red to highlight thresholded pixels.
setThreshold(double, double, String) - Static method in class ij.IJ
  Sets the lower and upper threshold levels and displays the image using the specified `displayMode` ("Red", "Black & White", "Over/Under" or "No Update").
setThreshold(double, double, int) - Method in class ij.process.FloatProcessor
setThreshold(double, double, int) - Method in class ij.process.ImageProcessor
  Sets the lower and upper threshold levels.
setThreshold(double, double, int) - Method in class ij.process.ShortProcessor
setTimeUnit(String) - Method in class ij.measure.Calibration
  Sets the time unit (e.g.
setTitle(String) - Method in class ij.ImagePlus
  Sets the image name.
setTitle(String) - Method in class ij.text.TextPanel
setTool(int) - Static method in class ij.IJ
  Switches to the specified tool, where id = Toolbar.RECTANGLE (0), Toolbar.OVAL (1), etc.
setTool(int) - Method in class ij.gui.Toolbar
setTransparentColor(Color) - Method in interface ij.process.Blitter
  Sets the transparent color used in the COPY_TRANSPARENT mode (default is Color.white).
setTransparentColor(Color) - Method in class ij.process.ByteBlitter
setTransparentColor(Color) - Method in class ij.process.ColorBlitter
setTransparentColor(Color) - Method in class ij.process.FloatBlitter
setTransparentColor(Color) - Method in class ij.process.ShortBlitter
setTransparentPixel(int) - Method in class ij.io.GifEncoder
setType(int) - Method in class ij.ImagePlus
setUnit(String) - Method in class ij.measure.Calibration
  Sets the length unit (e.g.
setUnsavedMeasurements(boolean) - Static method in class ij.plugin.filter.Analyzer
setValue(String, int, double) - Method in class ij.measure.ResultsTable
  Sets the value of the given column and row, where where 0<=row<counter.
setValue(int, int, double) - Method in class ij.measure.ResultsTable
  Sets the value of the given column and row, where where 0<=column<=(lastRow+1 and 0<=row<counter.
setValue(double) - Method in class ij.process.ByteProcessor
  Sets the default fill/draw value, where 0<=value<=255.
setValue(double) - Method in class ij.process.ColorProcessor
  Sets the default fill/draw value, where `value` is interpreted as an RGB int.
setValue(double) - Method in class ij.process.FloatProcessor
  Sets the default fill/draw value.
setValue(double) - Method in class ij.process.ImageProcessor
  Sets the default fill/draw value.
setValue(double) - Method in class ij.process.ShortProcessor
  Sets the default fill/draw value, where 0<=value<=65535).
setValueUnit(String) - Method in class ij.measure.Calibration
  Sets the value unit.
setWeightingFactors(double, double, double) - Static method in class ij.process.ColorProcessor
  Sets the weighting factors used by getPixelValue(), getHistogram() and convertToByte() to do color conversions.
setWidth(int) - Static method in class ij.gui.Line
setWindow(ImageWindow) - Method in class ij.ImagePlus
  This method should only be called from an ImageWindow.
setWindow(Frame) - Static method in class ij.WindowManager
  The specified frame becomes the front window, the one returnd by getFrontWindow().
setf(int, int, float) - Method in class ij.process.ByteProcessor
setf(int, float) - Method in class ij.process.ByteProcessor
setf(int, int, float) - Method in class ij.process.ColorProcessor
setf(int, float) - Method in class ij.process.ColorProcessor
setf(int, int, float) - Method in class ij.process.FloatProcessor
setf(int, float) - Method in class ij.process.FloatProcessor
setf(int, int, float) - Method in class ij.process.ImageProcessor
setf(int, float) - Method in class ij.process.ImageProcessor
setf(int, int, float) - Method in class ij.process.ShortProcessor
setf(int, float) - Method in class ij.process.ShortProcessor
setup(int, ImagePlus) - Static method in class ij.Undo
setup() - Method in class ij.gui.GenericDialog
setup() - Method in class ij.gui.HistogramWindow
setup(String, ImagePlus) - Method in class ij.plugin.filter.AVIWriter
setup(String, ImagePlus) - Method in class ij.plugin.filter.Analyzer
setup(String, ImagePlus) - Method in class ij.plugin.filter.BackgroundSubtracter
setup(String, ImagePlus) - Method in class ij.plugin.filter.Benchmark
setup(String, ImagePlus) - Method in class ij.plugin.filter.Binary
setup(String, ImagePlus) - Method in class ij.plugin.filter.BinaryFiller
setup(String, ImagePlus) - Method in class ij.plugin.filter.CalibrationBar
setup(String, ImagePlus) - Method in class ij.plugin.filter.Calibrator
setup(String, ImagePlus) - Method in class ij.plugin.filter.Convolver
setup(String, ImagePlus) - Method in class ij.plugin.filter.Duplicater
setup(String, ImagePlus) - Method in class ij.plugin.filter.EDM
setup(String, ImagePlus) - Method in class ij.plugin.filter.FFTCustomFilter
setup(String, ImagePlus) - Method in class ij.plugin.filter.FFTFilter
setup(String, ImagePlus) - Method in class ij.plugin.filter.Filler
setup(String, ImagePlus) - Method in class ij.plugin.filter.Filters
setup(String, ImagePlus) - Method in class ij.plugin.filter.FractalBoxCounter
setup(String, ImagePlus) - Method in class ij.plugin.filter.GaussianBlur
  Method to return types supported
setup(String, ImagePlus) - Method in class ij.plugin.filter.ImageMath
setup(String, ImagePlus) - Method in class ij.plugin.filter.ImageProperties
setup(String, ImagePlus) - Method in class ij.plugin.filter.Info
setup(String, ImagePlus) - Method in class ij.plugin.filter.LineGraphAnalyzer
setup(String, ImagePlus) - Method in class ij.plugin.filter.LutApplier
setup(String, ImagePlus) - Method in class ij.plugin.filter.LutViewer
setup(String, ImagePlus) - Method in class ij.plugin.filter.MaximumFinder
  Method to return types supported
setup(String, ImagePlus) - Method in class ij.plugin.filter.ParticleAnalyzer
setup(String, ImagePlus) - Method in interface ij.plugin.filter.PlugInFilter
  This method is called once when the filter is loaded.
setup(String, ImagePlus) - Method in class ij.plugin.filter.Printer
setup(String, ImagePlus) - Method in class ij.plugin.filter.Profiler
setup(String, ImagePlus) - Method in class ij.plugin.filter.Projector
setup(String, ImagePlus) - Method in class ij.plugin.filter.RGBStackSplitter
setup(String, ImagePlus) - Method in class ij.plugin.filter.RankFilters
  Setup of the PlugInFilter.
setup(String, ImagePlus) - Method in class ij.plugin.filter.Resizer
setup(String, ImagePlus) - Method in class ij.plugin.filter.RoiWriter
setup(String, ImagePlus) - Method in class ij.plugin.filter.Rotator
setup(String, ImagePlus) - Method in class ij.plugin.filter.SaltAndPepper
setup(String, ImagePlus) - Method in class ij.plugin.filter.ScaleDialog
setup(String, ImagePlus) - Method in class ij.plugin.filter.Shadows
setup(String, ImagePlus) - Method in class ij.plugin.filter.ThresholdToSelection
setup(String, ImagePlus) - Method in class ij.plugin.filter.Transformer
setup(String, ImagePlus) - Method in class ij.plugin.filter.UnsharpMask
  Method to return types supported
setup(String, ImagePlus) - Method in class ij.plugin.filter.Writer
setup(String, ImagePlus) - Method in class ij.plugin.filter.XYWriter
setup(String, ImagePlus) - Method in class ij.plugin.filter.ZAxisProfiler
setupDialog(ImagePlus, int) - Static method in class ij.IJ
  Displays a "Process all slices?" dialog.
setupScroll(int, int) - Method in class ij.gui.ImageCanvas
shapeToRoi() - Method in class ij.gui.ShapeRoi
  Attempts to convert this ShapeRoi into a non-composite Roi.
sharpen() - Method in class ij.process.ImageProcessor
  Sharpens the image or ROI using a 3x3 convolution kernel.
sharpenFloat(FloatProcessor, double, float) - Method in class ij.plugin.filter.UnsharpMask
  Unsharp Mask filtering of a float image.
shiftKeyDown() - Static method in class ij.IJ
  Returns true if the shift key is down.
shortcutInUse(String) - Static method in class ij.Menus
show() - Method in class ij.ImagePlus
  Opens a window to display this image and clears the status bar.
show(String) - Method in class ij.ImagePlus
  Opens a window to display this image and displays 'statusMessage' in the status bar.
show() - Method in class ij.gui.Plot
  Displays the plot in a PlotWindow and returns a reference to the PlotWindow.
show(double) - Method in class ij.gui.ProgressBar
  Updates the progress bar, where percent should run from 0 to 1.
show(double, boolean) - Method in class ij.gui.ProgressBar
  Updates the progress bar, where percent should run from 0 to 1.
show(String) - Method in class ij.measure.ResultsTable
  Displays the contents of this ResultsTable in a window with the specified title.
show() - Method in class ij.plugin.ColorPicker
  Overrides ImagePlus.show().
showChoice - Static variable in class ij.plugin.filter.ParticleAnalyzer
showDialog() - Method in class ij.gui.GenericDialog
  Displays this dialog box.
showDialog() - Method in class ij.plugin.FFTMath
showDialog() - Method in class ij.plugin.NewPlugin
showDialog() - Method in class ij.plugin.filter.BackgroundSubtracter
showDialog(ImagePlus) - Method in class ij.plugin.filter.Calibrator
showDialog(ImagePlus, String, PlugInFilterRunner) - Method in class ij.plugin.filter.Convolver
showDialog(ImagePlus, String, PlugInFilterRunner) - Method in interface ij.plugin.filter.ExtendedPlugInFilter
  This method is called after `setup(arg, imp)` unless the `DONE` flag has been set.
showDialog(ImagePlus, String, PlugInFilterRunner) - Method in class ij.plugin.filter.GaussianBlur
  Ask the user for the parameters
showDialog(ImagePlus, String, PlugInFilterRunner) - Method in class ij.plugin.filter.MaximumFinder
showDialog() - Method in class ij.plugin.filter.ParticleAnalyzer
  Displays a modal options dialog.
showDialog() - Method in class ij.plugin.filter.Projector
showDialog(ImagePlus, String, PlugInFilterRunner) - Method in class ij.plugin.filter.RankFilters
showDialog(ImagePlus, String, PlugInFilterRunner) - Method in class ij.plugin.filter.Rotator
showDialog(ImagePlus, String, PlugInFilterRunner) - Method in class ij.plugin.filter.UnsharpMask
  Ask the user for the parameters
showHistogram(ImagePlus, int) - Method in class ij.gui.HistogramWindow
  Draws the histogram using the specified title and number of bins.
showHistogram(ImagePlus, int, double, double) - Method in class ij.gui.HistogramWindow
  Draws the histogram using the specified title, number of bins and histogram range.
showHistogram(ImagePlus, ImageStatistics) - Method in class ij.gui.HistogramWindow
  Draws the histogram using the specified title and ImageStatistics.
showList() - Method in class ij.gui.HistogramWindow
showMessage(String) - Static method in class ij.IJ
  Displays a message in a dialog box titled "Message".
showMessage(String, String) - Static method in class ij.IJ
  Displays a message in a dialog box with the specified title.
showMessageWithCancel(String, String) - Static method in class ij.IJ
  Displays a message in a dialog box with the specified title.
showProgress(double) - Static method in class ij.IJ
  Updates the progress bar, where 0<=progress<=1.0.
showProgress(int, int) - Static method in class ij.IJ
  Updates the progress bar, where the length of the bar is set to (`currentValue+1)/finalValue` of the maximum bar length.
showProgress - Variable in class ij.plugin.filter.ParticleAnalyzer
showProgress(double) - Method in class ij.process.ImageProcessor
showResults - Variable in class ij.plugin.filter.ParticleAnalyzer
showSizeDistribution - Variable in class ij.plugin.filter.ParticleAnalyzer
showSlice(int) - Method in class ij.gui.StackWindow
  Displays the specified slice and updates the stack scrollbar.
showStatus(String) - Static method in class ij.IJ
  Displays a message in the ImageJ status bar.
showStatus() - Method in class ij.gui.Roi
showTime(ImagePlus, long, String) - Static method in class ij.IJ
showTime(ImagePlus, long, String, int) - Static method in class ij.IJ
skeletonize() - Method in class ij.process.BinaryProcessor
  Uses a lookup table to repeatably removes pixels from the edges of objects in a binary image, reducing them to single pixel wide skeletons.
skeletonize() - Method in class ij.process.ByteProcessor
skewness - Variable in class ij.process.ImageStatistics
slice - Variable in class ij.gui.StackWindow
slice - Variable in class ij.plugin.filter.ParticleAnalyzer
sliceLabels - Variable in class ij.io.FileInfo
sliceSelector - Variable in class ij.gui.StackWindow
slider - Variable in class ij.gui.GenericDialog
smooth() - Method in class ij.process.ImageProcessor
  Replaces each pixel with the 3x3 neighborhood mean.
snapshot() - Method in class ij.process.ByteProcessor
  Make a snapshot of the current image.
snapshot() - Method in class ij.process.ColorProcessor
snapshot() - Method in class ij.process.FloatProcessor
snapshot() - Method in class ij.process.ImageProcessor
  Makes a copy of this image's pixel data that can be later restored using reset() or reset(mask).
snapshot() - Method in class ij.process.ShortProcessor
snapshotHeight - Variable in class ij.process.ImageProcessor
snapshotPixels - Variable in class ij.process.ByteProcessor
snapshotPixels - Variable in class ij.process.ColorProcessor
snapshotWidth - Variable in class ij.process.ImageProcessor
sort(ImageStack) - Method in class ij.plugin.DICOM_Sorter
sort(String[]) - Static method in class ij.util.StringSorter
  Sorts the array.
sortFileList(String[]) - Method in class ij.plugin.FolderOpener
  Sorts the file names into numeric order.
source - Variable in class ij.process.ImageProcessor
south(ImageProcessor) - Method in class ij.plugin.filter.Shadows
southeast(ImageProcessor) - Method in class ij.plugin.filter.Shadows
southwest(ImageProcessor) - Method in class ij.plugin.filter.Shadows
spaceBarDown() - Static method in class ij.IJ
  Returns true if the space bar is down.
splinePoints - Variable in class ij.gui.PolygonRoi
split(ImagePlus) - Method in class ij.plugin.filter.RGBStackSplitter
  Splits the specified RGB image or stack into three 8-bit grayscale images or stacks.
split(ImageStack, boolean) - Method in class ij.plugin.filter.RGBStackSplitter
  Splits the specified RGB stack into three 8-bit grayscale stacks.
split(String) - Static method in class ij.util.Tools
  Splits a string into substrings using the default delimiter set, which is " \t\n\r" (space, tab, newline and carriage-return).
split(String, String) - Static method in class ij.util.Tools
  Splits a string into substring using the characters contained in the second argument as the delimiter set.
sqr() - Method in class ij.process.FloatProcessor
sqr() - Method in class ij.process.ImageProcessor
  Performs a square transform on the image or ROI.
sqr() - Method in class ij.process.ShortProcessor
sqrt() - Method in class ij.process.FloatProcessor
sqrt() - Method in class ij.process.ImageProcessor
  Performs a square root transform on the image or ROI.
sqrt() - Method in class ij.process.ShortProcessor
srcRect - Variable in class ij.gui.ImageCanvas
startPaste(ImagePlus) - Method in class ij.gui.Roi
startTiming() - Method in class ij.ImagePlus
  Calls System.currentTimeMillis() to save the current time so it can be retrieved later using getStartTime() to calculate the elapsed time of an operation.
stats - Variable in class ij.gui.HistogramWindow
stdDev - Variable in class ij.process.ImageStatistics
str - Variable in class ij.macro.Symbol
stretchHistogram(ImagePlus, double) - Method in class ij.plugin.ContrastEnhancer
stretchHistogram(ImageProcessor, double) - Method in class ij.plugin.ContrastEnhancer
stretchHistogram(ImageProcessor, double, ImageStatistics) - Method in class ij.plugin.ContrastEnhancer
stringField - Variable in class ij.gui.GenericDialog
stringFunctionIDs - Static variable in interface ij.macro.MacroConstants
stringFunctions - Static variable in interface ij.macro.MacroConstants
stripLengths - Variable in class ij.io.FileInfo
stripOffsets - Variable in class ij.io.FileInfo
subtractBackround(ImageProcessor, int) - Method in class ij.plugin.filter.BackgroundSubtracter
  Implements a rolling-ball algorithm for the removal of smooth continuous background from a two-dimensional gel image.
subtractCircle(String, String, String) - Static method in class ij.gui.ShapeRoi
subtractPoints(Roi) - Method in class ij.gui.PointRoi
  Subtract the points that intersect the specified ROI and return the result.
subtractRGBBackround(ColorProcessor, int) - Method in class ij.plugin.filter.BackgroundSubtracter
summarize() - Method in class ij.plugin.filter.Analyzer
suppressPluginNotFoundError() - Static method in class ij.IJ
  Temporarily suppress "plugin not found" errors.
swapQuadrants(ImageProcessor) - Method in class ij.process.FHT
  Swap quadrants 1 and 3 and 2 and 4 of the specified ImageProcessor so the power spectrum origin is at the center of the image.
swapQuadrants() - Method in class ij.process.FHT
  Swap quadrants 1 and 3 and 2 and 4 of the image contained in this FHT.

## T

TABLE - Static variable in class ij.plugin.NewPlugin
TABLE_FULL - Static variable in class ij.measure.ResultsTable
TAN - Static variable in interface ij.macro.MacroConstants
TEXT - Static variable in class ij.gui.Toolbar
TEXT - Static variable in class ij.io.Opener
TEXT_FILE - Static variable in class ij.plugin.NewPlugin
THREADS - Static variable in class ij.Prefs
TIFF - Static variable in class ij.io.FileInfo
TIFF - Static variable in class ij.io.Opener
TIFF_AND_DICOM - Static variable in class ij.io.Opener
TOK_MASK - Static variable in interface ij.macro.MacroConstants
TOK_SHIFT - Static variable in interface ij.macro.MacroConstants
TOOLS_MENU - Static variable in class ij.Menus
TOOL_ID - Static variable in interface ij.macro.MacroConstants
TOP_MARGIN - Static variable in class ij.gui.Plot
  the margin width above the plot frame
TO_BINARY - Static variable in interface ij.macro.MacroConstants
TO_HEX - Static variable in interface ij.macro.MacroConstants
TO_LOWER_CASE - Static variable in interface ij.macro.MacroConstants
TO_STRING - Static variable in interface ij.macro.MacroConstants
TO_UPPER_CASE - Static variable in interface ij.macro.MacroConstants
TRACED_ROI - Static variable in class ij.gui.Roi
TRANSFORM - Static variable in class ij.Undo
TRIANGLE - Static variable in class ij.gui.Plot
  Display points using an tiangular mark.
TRIANGLE - Static variable in class ij.gui.PlotWindow
  Display points using an tiangular mark.
TRUE - Static variable in interface ij.macro.MacroConstants
TYPE_CONVERSION - Static variable in class ij.Undo
TextEncoder - class ij.io.TextEncoder.
  Saves an image described by an ImageProcessor object as a tab-delimited text file.
TextEncoder(ImageProcessor, Calibration, int) - Constructor for class ij.io.TextEncoder
  Constructs a TextEncoder from an ImageProcessor and optional Calibration.
TextFileReader - class ij.plugin.TextFileReader.
  This plugin displays the contents of a text file in a window.
TextFileReader() - Constructor for class ij.plugin.TextFileReader
TextPanel - class ij.text.TextPanel.
  This is an unlimited size text panel with tab-delimited, labeled and resizable columns.
TextPanel() - Constructor for class ij.text.TextPanel
  Constructs a new TextPanel.
TextPanel(String) - Constructor for class ij.text.TextPanel
  Constructs a new TextPanel.
TextReader - class ij.plugin.TextReader.
  This plugin opens a tab-delimeted text file as an image.
TextReader() - Constructor for class ij.plugin.TextReader
TextRoi - class ij.gui.TextRoi.
  This class is a rectangular ROI containing text.
TextRoi(int, int, ImagePlus) - Constructor for class ij.gui.TextRoi
TextWindow - class ij.text.TextWindow.
  Uses a TextPanel to displays text in a window.
TextWindow(String, String, int, int) - Constructor for class ij.text.TextWindow
  Opens a new single-column text window.
TextWindow(String, String, String, int, int) - Constructor for class ij.text.TextWindow
  Opens a new multi-column text window.
TextWindow(String, int, int) - Constructor for class ij.text.TextWindow
  Opens a new text window containing the contents of a text file.
TextWriter - class ij.plugin.TextWriter.
  This plugin implements the File/Save As/Text command.
TextWriter() - Constructor for class ij.plugin.TextWriter
ThreadLister - class ij.plugin.ThreadLister.
  Displays thread information in a text window.
ThreadLister() - Constructor for class ij.plugin.ThreadLister
ThresholdAdjuster - class ij.plugin.frame.ThresholdAdjuster.
  Adjusts the lower and upper threshold levels of the active image.
ThresholdAdjuster() - Constructor for class ij.plugin.frame.ThresholdAdjuster
ThresholdToSelection - class ij.plugin.filter.ThresholdToSelection.
ThresholdToSelection() - Constructor for class ij.plugin.filter.ThresholdToSelection
Thresholder - class ij.plugin.Thresholder.
  This plugin implements the Process/Binary/Make Binary and Convert to Mask commands.
Thresholder() - Constructor for class ij.plugin.Thresholder
TiffDecoder - class ij.io.TiffDecoder.
  Decodes single and multi-image TIFF files.
TiffDecoder(String, String) - Constructor for class ij.io.TiffDecoder
TiffDecoder(InputStream, String) - Constructor for class ij.io.TiffDecoder
TiffEncoder - class ij.io.TiffEncoder.
  Saves an image described by a FileInfo object as an uncompressed, big-endian TIFF file.
TiffEncoder(FileInfo) - Constructor for class ij.io.TiffEncoder
Timer - class ij.plugin.Timer.
  ImageJ plugin for measuring the speed of various Java operations.
Timer() - Constructor for class ij.plugin.Timer
Tokenizer - class ij.macro.Tokenizer.
  This class converts an imageJ macro file file into a token stream.
Tokenizer() - Constructor for class ij.macro.Tokenizer
Toolbar - class ij.gui.Toolbar.
  The ImageJ toolbar.
Toolbar() - Constructor for class ij.gui.Toolbar
Tools - class ij.util.Tools.
  This class contains static utility methods.
Tools() - Constructor for class ij.util.Tools
Transformer - class ij.plugin.filter.Transformer.
  Implements the flip and rotate commands in the Image/Transformations submenu.
Transformer() - Constructor for class ij.plugin.filter.Transformer
TrimmedButton - class ij.gui.TrimmedButton.
  This is an extended Button class used to reduce the width of the HUGE buttons on Mac OS X.
TrimmedButton(String, int) - Constructor for class ij.gui.TrimmedButton
TypeConverter - class ij.process.TypeConverter.
  This class converts an ImageProcessor to another data type.
TypeConverter(ImageProcessor, boolean) - Constructor for class ij.process.TypeConverter
textArea1 - Variable in class ij.gui.GenericDialog
textArea2 - Variable in class ij.gui.GenericDialog
textValueChanged(TextEvent) - Method in class ij.gui.ColorChooser
textValueChanged(TextEvent) - Method in class ij.gui.GenericDialog
textValueChanged(TextEvent) - Method in class ij.plugin.Distribution
textValueChanged(TextEvent) - Method in class ij.plugin.Histogram
textValueChanged(TextEvent) - Method in class ij.plugin.Scaler
textValueChanged(TextEvent) - Method in class ij.plugin.Slicer
textValueChanged(TextEvent) - Method in class ij.plugin.filter.ImageProperties
textValueChanged(TextEvent) - Method in class ij.plugin.filter.Resizer
textValueChanged(TextEvent) - Method in class ij.plugin.frame.Editor
textValueChanged(TextEvent) - Method in class ij.plugin.frame.LineWidthAdjuster
theLabel - Variable in class ij.gui.GenericDialog
theta - Variable in class ij.process.EllipseFitter
  Angle in radians
thread - Variable in class ij.gui.StackWindow
threshold(int) - Method in class ij.process.ByteProcessor
  Sets pixels less than or equal to level to 0 and all other pixels to 255.
threshold(int) - Method in class ij.process.ColorProcessor
  Not implemented.
threshold(int) - Method in class ij.process.FloatProcessor
  Not implemented.
threshold(int) - Method in class ij.process.ImageProcessor
  Sets pixels less than or equal to level to 0 and all other pixels to 255.
threshold(int) - Method in class ij.process.ShortProcessor
toDouble(float[]) - Static method in class ij.util.Tools
  Converts the float array 'a' to a double array.
toEDM(ImageProcessor) - Method in class ij.plugin.filter.EDM
  Converts a binary image into a 8-bit grayscale Euclidean Distance Map (EDM).
toFloat(int, FloatProcessor) - Method in class ij.process.ByteProcessor
  Returns a FloatProcessor with the same image, no scaling or calibration (pixel values 0 to 255).
toFloat(int, FloatProcessor) - Method in class ij.process.ColorProcessor
  Returns a FloatProcessor with one color channel of the image.
toFloat(int, FloatProcessor) - Method in class ij.process.FloatProcessor
  Returns this FloatProcessor.
toFloat(int, FloatProcessor) - Method in class ij.process.ImageProcessor
  Returns a FloatProcessor with the image or one color channel thereof.
toFloat(int, FloatProcessor) - Method in class ij.process.ShortProcessor
  Returns a FloatProcessor with the same image, no scaling or calibration (pixel values 0 to 65535).
toFloat(double[]) - Static method in class ij.util.Tools
  Converts the double array 'a' to a float array.
toFloatArrays() - Method in class ij.process.ByteProcessor
toFloatProcessors() - Method in class ij.process.ByteProcessor
toString() - Method in class ij.ImagePlus
toString() - Method in class ij.ImageStack
toString() - Method in class ij.gui.ImageWindow
toString() - Method in class ij.gui.Roi
toString() - Method in class ij.io.FileInfo
toString() - Method in class ij.macro.Symbol
toString() - Method in class ij.measure.Calibration
toString() - Method in class ij.measure.ResultsTable
toString() - Method in class ij.process.FHT
  Returns a string containing information about this FHT.
toString() - Method in class ij.process.ImageProcessor
  Returns a string containing information about this ImageProcessor.
tokenize(String) - Method in class ij.macro.Tokenizer
  Uses a StreamTokenizer to convert an ImageJ macro file into a token stream.
transform() - Method in class ij.process.FHT
  Performs a foreward transform, converting this image into the frequency domain.
trim() - Method in class ij.ImageStack
  Frees memory by deleting a few slices from the end of the stack.
trim() - Method in class ij.VirtualStack
  Does nothing.
trimFileList(String[]) - Method in class ij.plugin.FolderOpener
  Removes names that start with "." or end with ".db".
trimKey(String) - Static method in class ij.Macro
trimProcessor() - Method in class ij.ImagePlus
  Frees RAM by setting the snapshot (undo) buffer in the current ImageProcessor to null.
type - Variable in class ij.gui.Roi
type - Variable in class ij.macro.Symbol

## U

UNCALIBRATED_OD - Static variable in class ij.measure.Calibration
UNKNOWN - Static variable in class ij.io.FileInfo
UNKNOWN - Static variable in class ij.io.Opener
UPDATED - Static variable in class ij.ImagePlus
UPDATE_DISPLAY - Static variable in interface ij.macro.MacroConstants
UPDATE_RESULTS - Static variable in interface ij.macro.MacroConstants
URLOpener - class ij.plugin.URLOpener.
  Opens TIFFs, ZIP compressed TIFFs, DICOMs, GIFs and JPEGs using a URL.
URLOpener() - Constructor for class ij.plugin.URLOpener
USER_FUNCTION - Static variable in interface ij.macro.MacroConstants
UTILITIES_MENU - Static variable in class ij.Menus
Undo - class ij.Undo.
  This class consists of static methods and fields that implement ImageJ's Undo command.
Undo() - Constructor for class ij.Undo
UnsharpMask - class ij.plugin.filter.UnsharpMask.
  This plugin-filter implements ImageJ's Unsharp Mask command.
UnsharpMask() - Constructor for class ij.plugin.filter.UnsharpMask
umean - Variable in class ij.process.ImageStatistics
  Uncalibrated mean
undo() - Static method in class ij.Undo
uninstallPlugin(String) - Static method in class ij.Menus
  Deletes a command installed by installPlugin.
unit - Variable in class ij.ImagePlus
  Obsolete.
unit - Variable in class ij.io.FileInfo
units - Variable in class ij.ImagePlus
  Obsolete.
units - Variable in class ij.gui.ProfilePlot
unlock() - Method in class ij.ImagePlus
  Unlocks the image.
unzoom() - Method in class ij.gui.ImageCanvas
update(ImageProcessor) - Method in class ij.ImageStack
  Updates this stack so its attributes, such as min, max, calibration table and color model, are the same as 'ip'.
update(Graphics) - Method in class ij.gui.ImageCanvas
update(Graphics) - Method in class ij.gui.ProgressBar
update(boolean, boolean) - Method in class ij.gui.Roi
  If 'add' is true, adds this selection to the previous one.
update() - Static method in class ij.plugin.frame.ContrastAdjuster
  Updates the ContrastAdjuster.
updateAndDraw() - Method in class ij.ImagePlus
  Updates this image from the pixel data in its associated ImageProcessor, then displays it.
updateAndDraw() - Method in class ij.plugin.frame.ContrastAdjuster
  Resets this ContrastAdjuster and brings it to the front.
updateAndRepaintWindow() - Method in class ij.ImagePlus
  Calls updateAndDraw to update from the pixel data and draw the image, and also repaints the image window to force the information displayed above the image (dimension, type, size) to be updated.
updateChannelAndDraw() - Method in class ij.CompositeImage
updateChannelAndDraw() - Method in class ij.ImagePlus
  Updates this image from the pixel data in its associated ImageProcessor, then displays it.
updateClassName(String, String) - Method in class ij.plugin.frame.Editor
  Changes a plugins class name to reflect a new file name.
updateClipRect() - Method in class ij.gui.Roi
updateFullWindow - Variable in class ij.gui.Roi
updateHeadings() - Method in class ij.plugin.filter.Analyzer
  Updates the displayed column headings.
updateImage() - Method in class ij.CompositeImage
updateImage() - Method in class ij.ImagePlus
  ImageCanvas.paint() calls this method when the ImageProcessor has generated new image.
updateImage(ImagePlus) - Method in class ij.gui.ImageWindow
updateMenus() - Static method in class ij.Menus
  Updates the Image/Type and Window menus.
updatePolygon() - Method in class ij.gui.PolygonRoi
updateSliceSelector() - Method in class ij.gui.StackWindow
  Updates the stack scrollbar.
updateStatusbarValue() - Method in class ij.ImagePlus
  Redisplays the (x,y) coordinates and pixel value (which may have changed) in the status bar.
updateWindowMenuItem(String, String) - Static method in class ij.Menus
  Changes the name of an item in the Window menu.
updateY(int, int) - Static method in class ij.plugin.filter.Analyzer
  Returns an updated Y coordinate based on the current "Invert Y Coordinates" flag.
updateY(double, int) - Static method in class ij.plugin.filter.Analyzer
  Returns an updated Y coordinate based on the current "Invert Y Coordinates" flag.
url - Variable in class ij.io.FileInfo
useInvertingLut - Static variable in class ij.Prefs
  Open 8-bit images with inverting LUT so 0 is white and 255 is black.
useJFileChooser - Static variable in class ij.Prefs
  Use JFileChooser instead of FileDialog to open and save files.
usePointer - Static variable in class ij.gui.ImageCanvas
usePointerCursor - Static variable in class ij.Prefs
  Use pointer cursor instead of cross

## V

VAR - Static variable in interface ij.macro.MacroConstants
VARIANCE - Static variable in class ij.plugin.filter.RankFilters
VERSION - Static variable in class ij.ImageJ
  Plugins should call IJ.getVersion() to get the version string.
VirtualStack - class ij.VirtualStack.
  This class represents an array of disk-resident images.
VirtualStack(int, int, ColorModel, String) - Constructor for class ij.VirtualStack
  Creates a new, empty virtual stack.
value - Variable in class ij.gui.HistogramWindow
value - Variable in class ij.macro.Symbol
valueUnit - Variable in class ij.io.FileInfo
versionLessThan(String) - Static method in class ij.IJ
  Displays an error message and returns false if the ImageJ version is less than the one specified.
verticalColorBar(ImageProcessor, int, int, int, int) - Method in class ij.plugin.filter.CalibrationBar

## W

WAIT - Static variable in interface ij.macro.MacroConstants
WAND - Static variable in class ij.gui.Toolbar
WHILE - Static variable in interface ij.macro.MacroConstants
WIDTH_KEY - Static variable in class ij.text.TextWindow
WINDOW_MENU_ITEMS - Static variable in class ij.Menus
WORD - Static variable in interface ij.macro.MacroConstants
WRITE - Static variable in interface ij.macro.MacroConstants
Wand - class ij.gui.Wand.
  This class implements ImageJ's wand (tracing) tool.
Wand(ImageProcessor) - Constructor for class ij.gui.Wand
  Constructs a Wand object from an ImageProcessor.
WindowManager - class ij.WindowManager.
  This class consists of static methods used to manage ImageJ's windows.
WindowOrganizer - class ij.plugin.WindowOrganizer.
WindowOrganizer() - Constructor for class ij.plugin.WindowOrganizer
Writer - class ij.plugin.filter.Writer.
  This plugin saves an image in tiff, gif, jpeg, bmp, png, text or raw format.
Writer() - Constructor for class ij.plugin.filter.Writer
wait(int) - Static method in class ij.IJ
  Delays 'msecs' milliseconds.
wasCanceled() - Method in class ij.gui.GenericDialog
  Returns true if the user clicks on "Cancel".
wasOKed() - Method in class ij.gui.GenericDialog
  Returns true if the user has clicked on "OK" or a macro is running.
weightedColor - Static variable in class ij.Prefs
  Color to grayscale conversion is weighted (0.299, 0.587, 0.114) if the variable is true.
west(ImageProcessor) - Method in class ij.plugin.filter.Shadows
whiteIsZero - Variable in class ij.io.FileInfo
width - Variable in class ij.ImagePlus
width - Variable in class ij.io.FileInfo
width - Variable in class ij.process.ImageProcessor
width - Variable in class ij.process.ImageStatistics
win - Variable in class ij.ImagePlus
windowActivated(WindowEvent) - Method in class ij.ImageJ
windowActivated(WindowEvent) - Method in class ij.gui.ImageWindow
windowActivated(WindowEvent) - Method in class ij.plugin.frame.ContrastAdjuster
windowActivated(WindowEvent) - Method in class ij.plugin.frame.Editor
  Override windowActivated in PlugInFrame to prevent Mac menu bar from being installed.
windowActivated(WindowEvent) - Method in class ij.plugin.frame.LineWidthAdjuster
windowActivated(WindowEvent) - Method in class ij.plugin.frame.PlugInFrame
windowActivated(WindowEvent) - Method in class ij.plugin.frame.ThresholdAdjuster
windowClosed(WindowEvent) - Method in class ij.ImageJ
windowClosed(WindowEvent) - Method in class ij.gui.ImageWindow
windowClosed(WindowEvent) - Method in class ij.plugin.frame.PlugInFrame
windowClosing(WindowEvent) - Method in class ij.ImageJ
windowClosing(WindowEvent) - Method in class ij.gui.ImageWindow
windowClosing(WindowEvent) - Method in class ij.plugin.frame.ContrastAdjuster
windowClosing(WindowEvent) - Method in class ij.plugin.frame.Editor
windowClosing(WindowEvent) - Method in class ij.plugin.frame.Fonts
windowClosing(WindowEvent) - Method in class ij.plugin.frame.LineWidthAdjuster
windowClosing(WindowEvent) - Method in class ij.plugin.frame.PasteController
windowClosing(WindowEvent) - Method in class ij.plugin.frame.PlugInFrame
windowClosing(WindowEvent) - Method in class ij.plugin.frame.Recorder
windowClosing(WindowEvent) - Method in class ij.plugin.frame.ThresholdAdjuster
windowDeactivated(WindowEvent) - Method in class ij.ImageJ
windowDeactivated(WindowEvent) - Method in class ij.gui.ImageWindow
windowDeactivated(WindowEvent) - Method in class ij.plugin.frame.PlugInFrame
windowDeiconified(WindowEvent) - Method in class ij.ImageJ
windowDeiconified(WindowEvent) - Method in class ij.gui.ImageWindow
windowDeiconified(WindowEvent) - Method in class ij.plugin.frame.PlugInFrame
windowIconified(WindowEvent) - Method in class ij.ImageJ
windowIconified(WindowEvent) - Method in class ij.gui.ImageWindow
windowIconified(WindowEvent) - Method in class ij.plugin.frame.PlugInFrame
windowOpened(WindowEvent) - Method in class ij.ImageJ
windowOpened(WindowEvent) - Method in class ij.gui.ImageWindow
windowOpened(WindowEvent) - Method in class ij.plugin.frame.PlugInFrame
windowStateChanged(WindowEvent) - Method in class ij.gui.ImageWindow
write(String) - Static method in class ij.IJ
  Displays a line of text in the "Results" window.
write(OutputStream) - Method in class ij.io.GifEncoder
  Saves the image as a GIF file.
write(OutputStream) - Method in class ij.io.ImageWriter
  Writes the image to the specified OutputStream.
write(Roi) - Method in class ij.io.RoiEncoder
  Save the Roi to the file of stream.
write(DataOutputStream) - Method in class ij.io.TextEncoder
  Saves the image as a tab-delimited text file.
write(DataOutputStream) - Method in class ij.io.TiffEncoder
  Saves the image as a TIFF file.
writeByteFrame(int) - Method in class ij.plugin.filter.AVIWriter
writeImage(ImagePlus) - Method in class ij.plugin.filter.AVIWriter
writeRGBFrame(int) - Method in class ij.plugin.filter.AVIWriter

## X

X - Static variable in class ij.gui.Plot
  Display points using an X-shaped mark.
X - Static variable in class ij.gui.PlotWindow
  Display points using an X-shaped mark.
XINC - Static variable in class ij.plugin.MacroInstaller
XINC - Static variable in class ij.plugin.frame.Editor
XOR - Static variable in interface ij.process.Blitter
  dst=dst XOR src
XYCoordinates - class ij.plugin.XYCoordinates.
  Writes the XY coordinates and pixel values of all non-background pixels to a tab-delimited text file.
XYCoordinates() - Constructor for class ij.plugin.XYCoordinates
XYWriter - class ij.plugin.filter.XYWriter.
  Saves the XY coordinates of the current ROI boundary.
XYWriter() - Constructor for class ij.plugin.filter.XYWriter
X_CENTER_OF_MASS - Static variable in class ij.measure.ResultsTable
X_CENTROID - Static variable in class ij.measure.ResultsTable
X_FORCE2GRID - Static variable in class ij.gui.Plot
  flag for forcing frame to coincide with the grid/ticks in x direction (results in unused space)
X_GRID - Static variable in class ij.gui.Plot
  flag for drawing vertical grid lines for x-axis ticks
X_NUMBERS - Static variable in class ij.gui.Plot
  flag for numeric labels of x-axis ticks
X_RESOLUTION - Static variable in class ij.io.TiffDecoder
X_TICKS - Static variable in class ij.gui.Plot
  flag for drawing x-axis ticks
x1 - Variable in class ij.gui.Line
x1d - Variable in class ij.gui.Line
x2 - Variable in class ij.gui.Line
x2d - Variable in class ij.gui.Line
xCenter - Variable in class ij.process.EllipseFitter
  X centroid
xCenterOfMass - Variable in class ij.process.ImageStatistics
xCentroid - Variable in class ij.process.ImageStatistics
xCoordinates - Variable in class ij.process.EllipseFitter
  Initialized by makeRoi()
xInc - Variable in class ij.gui.ProfilePlot
xMax - Variable in class ij.gui.Roi
xMax - Variable in class ij.process.ImageProcessor
xMin - Variable in class ij.process.ImageProcessor
xMouse - Variable in class ij.gui.ImageCanvas
xMouseStart - Variable in class ij.gui.ImageCanvas
xOrigin - Variable in class ij.measure.Calibration
  X origin in pixels.
xScreenSpline - Variable in class ij.gui.PolygonRoi
xSpline - Variable in class ij.gui.PolygonRoi
xSrcStart - Variable in class ij.gui.ImageCanvas
xValues - Variable in class ij.gui.ProfilePlot
xor(ShapeRoi) - Method in class ij.gui.ShapeRoi
  Unary exclusive or operator.
xor(int) - Method in class ij.process.FloatProcessor
xor(int) - Method in class ij.process.ImageProcessor
  Binary exclusive OR of each pixel in the image or ROI with 'value'.
xor(int) - Method in class ij.process.ShortProcessor
xp - Variable in class ij.gui.PolygonRoi
xp2 - Variable in class ij.gui.PolygonRoi
xpoints - Variable in class ij.gui.Wand
  The x-coordinates of the points in the outline.

## Y

YINC - Static variable in class ij.plugin.MacroInstaller
YINC - Static variable in class ij.plugin.frame.Editor
Y_CENTER_OF_MASS - Static variable in class ij.measure.ResultsTable
Y_CENTROID - Static variable in class ij.measure.ResultsTable
Y_FORCE2GRID - Static variable in class ij.gui.Plot
  flag for forcing frame to coincide with the grid/ticks in y direction (results in unused space)
Y_GRID - Static variable in class ij.gui.Plot
  flag for drawing horizontal grid lines for y-axis ticks
Y_NUMBERS - Static variable in class ij.gui.Plot
  flag for numeric labels of x-axis ticks
Y_RESOLUTION - Static variable in class ij.io.TiffDecoder
Y_TICKS - Static variable in class ij.gui.Plot
  flag for drawing x-axis ticks
YesNoCancelDialog - class ij.gui.YesNoCancelDialog.
  A modal dialog box with a one line message and "Yes", "No" and "Cancel" buttons.
YesNoCancelDialog(Frame, String, String) - Constructor for class ij.gui.YesNoCancelDialog
y1 - Variable in class ij.gui.Line
y1d - Variable in class ij.gui.Line
y2 - Variable in class ij.gui.Line
y2d - Variable in class ij.gui.Line
yCenter - Variable in class ij.process.EllipseFitter
  X centroid
yCenterOfMass - Variable in class ij.process.ImageStatistics
yCentroid - Variable in class ij.process.ImageStatistics
yCoordinates - Variable in class ij.process.EllipseFitter
  Initialized by makeRoi()
yLabel - Variable in class ij.gui.ProfilePlot
yMax - Variable in class ij.gui.HistogramWindow
yMax - Variable in class ij.gui.Roi
yMax - Variable in class ij.process.ImageProcessor
yMin - Variable in class ij.process.ImageProcessor
yMouse - Variable in class ij.gui.ImageCanvas
yMouseStart - Variable in class ij.gui.ImageCanvas
yOrigin - Variable in class ij.measure.Calibration
  Y origin in pixels.
yScreenSpline - Variable in class ij.gui.PolygonRoi
ySpline - Variable in class ij.gui.PolygonRoi
ySrcStart - Variable in class ij.gui.ImageCanvas
yesPressed() - Method in class ij.gui.YesNoCancelDialog
  Returns true if the user dismissed dialog by pressing "Yes".
yp - Variable in class ij.gui.PolygonRoi
yp2 - Variable in class ij.gui.PolygonRoi
ypoints - Variable in class ij.gui.Wand
  The y-coordinates of the points in the outline.

## Z

ZAxisProfiler - class ij.plugin.filter.ZAxisProfiler.
  Implements the Image/Stack/Plot Z-axis Profile command.
ZAxisProfiler() - Constructor for class ij.plugin.filter.ZAxisProfiler
ZIP - Static variable in class ij.io.Opener
ZIP_ARCHIVE - Static variable in class ij.io.FileInfo
ZProjector - class ij.plugin.ZProjector.
  This plugin performs a z-projection of the input stack.
ZProjector() - Constructor for class ij.plugin.ZProjector
ZProjector(ImagePlus) - Constructor for class ij.plugin.ZProjector
  Construction of ZProjector with image to be projected.
Zoom - class ij.plugin.Zoom.
  This plugin implements the commands in the Image/Zoom submenu.
Zoom() - Constructor for class ij.plugin.Zoom
zOrigin - Variable in class ij.measure.Calibration
  Z origin in pixels.
zeroClip() - Method in class ij.measure.Calibration
  Returns true if zero clipping is enabled.
zoomIn(int, int) - Method in class ij.gui.ImageCanvas
  Zooms in by making the window bigger.
zoomOut(int, int) - Method in class ij.gui.ImageCanvas
  Zooms out by making the source rectangle (srcRect) larger and centering it on (x,y).

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