Index

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M

MAGENTA - inra.ijpb.color.CommonColors

The magenta color

MAGENTA - inra.ijpb.util.CommonColors

Deprecated.

The magenta color

MAIN_COLORS - inra.ijpb.color.ColorMaps.CommonLabelMaps

Colormap containing only few main colors

mapChannels(ImageStack) - Static method in class inra.ijpb.data.image.ColorImages

Splits the channels of the 3D color image into three new instances of ImageStack containing ByteProcessors.

mapChannels(ImageProcessor) - Static method in class inra.ijpb.data.image.ColorImages

Splits the channels of the color image and returns the new ByteImages into a Map, using channel names as key.

mapLabelIndices(int[]) - Static method in class inra.ijpb.label.LabelImages

Creates an associative array to retrieve the index corresponding to each label.

MarkerControlledWatershed3DPlugin - Class in inra.ijpb.plugins

A plugin to perform marker-controlled watershed on a 2D or 3D image.

MarkerControlledWatershed3DPlugin() - Constructor for class inra.ijpb.plugins.MarkerControlledWatershed3DPlugin

MarkerControlledWatershedTransform2D - Class in inra.ijpb.watershed

Marker-controlled version of the watershed transform in 2D.

MarkerControlledWatershedTransform2D(ImageProcessor, ImageProcessor, ImageProcessor) - Constructor for class inra.ijpb.watershed.MarkerControlledWatershedTransform2D

Initialize a marker-controlled watershed transform

MarkerControlledWatershedTransform2D(ImageProcessor, ImageProcessor, ImageProcessor, double) - Constructor for class inra.ijpb.watershed.MarkerControlledWatershedTransform2D

Initialize a marker-controlled watershed transform.

MarkerControlledWatershedTransform2D(ImageProcessor, ImageProcessor, ImageProcessor, int) - Constructor for class inra.ijpb.watershed.MarkerControlledWatershedTransform2D

Initialize a marker-controlled watershed transform

MarkerControlledWatershedTransform2D(ImageProcessor, ImageProcessor, ImageProcessor, int, double) - Constructor for class inra.ijpb.watershed.MarkerControlledWatershedTransform2D

Initialize a marker-controlled watershed transform.

MarkerControlledWatershedTransform3D - Class in inra.ijpb.watershed

Marker-controlled version of the watershed transform (works for 2D and 3D images).

MarkerControlledWatershedTransform3D(ImagePlus, ImagePlus, ImagePlus) - Constructor for class inra.ijpb.watershed.MarkerControlledWatershedTransform3D

Initialize a marker-controlled watershed transform

MarkerControlledWatershedTransform3D(ImagePlus, ImagePlus, ImagePlus, int) - Constructor for class inra.ijpb.watershed.MarkerControlledWatershedTransform3D

Initialize a marker-controlled watershed transform

MarkerControlledWatershedTransform3D(ImagePlus, ImagePlus, ImagePlus, int, double) - Constructor for class inra.ijpb.watershed.MarkerControlledWatershedTransform3D

Initialize a marker-controlled watershed transform

mask() - Method in interface inra.ijpb.binary.distmap.ChamferDistanceTransform2D

Return the chamfer mask used by this distance transform algorithm.

mask() - Method in class inra.ijpb.binary.distmap.ChamferDistanceTransform2DFloat

mask() - Method in class inra.ijpb.binary.distmap.ChamferDistanceTransform2DShort

mask() - Method in interface inra.ijpb.binary.distmap.ChamferDistanceTransform3D

mask() - Method in class inra.ijpb.binary.distmap.ChamferDistanceTransform3DFloat

mask() - Method in class inra.ijpb.binary.distmap.ChamferDistanceTransform3DShort

mask() - Method in interface inra.ijpb.label.distmap.ChamferDistanceTransform2D

Return the chamfer mask used by this distance transform algorithm.

mask() - Method in class inra.ijpb.label.distmap.ChamferDistanceTransform2DFloat

mask() - Method in class inra.ijpb.label.distmap.ChamferDistanceTransform2DShort

mask() - Method in interface inra.ijpb.label.distmap.ChamferDistanceTransform3D

MAX - inra.ijpb.morphology.directional.DirectionalFilter.Type

Keep the maximum value over all possible orientations

MAX - Static variable in interface inra.ijpb.math.ImageCalculator.Operation

Max operator, that computes the maximum of the values from the two images

MAX_DIST - Static variable in class inra.ijpb.binary.geodesic.GeodesicDistanceTransformFloat

The value used to initialize the distance map, corresponding to positive infinity.

MAX_DIST - Static variable in class inra.ijpb.binary.geodesic.GeodesicDistanceTransformFloat5x5

Deprecated.

The value used to initialize the distance map, corresponding to positive infinity.

MAX_DIST - Static variable in class inra.ijpb.binary.geodesic.GeodesicDistanceTransformFloatHybrid

The value used to initialize the distance map, corresponding to positive infinity.

MAX_DIST - Static variable in class inra.ijpb.binary.geodesic.GeodesicDistanceTransformShort

The value used to initialize the distance map.

MAX_DIST - Static variable in class inra.ijpb.binary.geodesic.GeodesicDistanceTransformShort5x5

Deprecated.

The value used to initialize the distance map.

MAX_DIST - Static variable in class inra.ijpb.binary.geodesic.GeodesicDistanceTransformShortHybrid

The value used to initialize the distance map.

maxFeretDiameter - Variable in class inra.ijpb.plugins.AnalyzeRegions.Features

The boolean flag for computing maximum Feret diameter.

maxFeretDiameter(ArrayList<? extends Point3D>) - Static method in class inra.ijpb.measure.region3d.MaxFeretDiameter3D

Computes Maximum Feret diameter of a set of points.

maxFeretDiameter(ArrayList<? extends Point2D>) - Static method in class inra.ijpb.geometry.FeretDiameters

Computes Maximum Feret diameter of a set of points.

MaxFeretDiameter - Class in inra.ijpb.measure.region2d

Computes maximum Feret Diameter for each region of a binary or label image.

MaxFeretDiameter() - Constructor for class inra.ijpb.measure.region2d.MaxFeretDiameter

Default constructor

MaxFeretDiameter3D - Class in inra.ijpb.measure.region3d

Computes maximum Feret Diameter for each region of a 3D binary or label image.

MaxFeretDiameter3D() - Constructor for class inra.ijpb.measure.region3d.MaxFeretDiameter3D

Default constructor

MaxFeretDiameterPlugin - Class in inra.ijpb.plugins

Computes Maximum Feret Diameters of a binary or label image.

MaxFeretDiameterPlugin() - Constructor for class inra.ijpb.plugins.MaxFeretDiameterPlugin

maxFeretDiameters(ImageStack, int[], Calibration) - Static method in class inra.ijpb.measure.region3d.MaxFeretDiameter3D

Computes Feret diameters as a PointPair3D for each of the specified regions within a label map.

maxFeretDiameters(ImageProcessor, int[], Calibration) - Static method in class inra.ijpb.measure.region2d.MaxFeretDiameter

Computes Feret diameters as a PointPair2D for each of the specified regions within a label map.

MAXIMA - inra.ijpb.morphology.extrema.ExtremaType

The type for maxima

MAXIMUM - inra.ijpb.morphology.strel.LocalExtremum.Type

Type for Maximum

maximumInscribedCircle(ImageProcessor) - Static method in class inra.ijpb.measure.GeometricMeasures2D

Deprecated.

use class inra.ijpb.measure.region2d.largestInscribedCircle instead

maximumInscribedCircle(ImageProcessor, double[]) - Static method in class inra.ijpb.measure.GeometricMeasures2D

Deprecated.

use class inra.ijpb.measure.region2d.largestInscribedCircle instead

maximumInscribedSphere(ImageStack, double[]) - Static method in class inra.ijpb.measure.GeometricMeasures3D

Deprecated.

use LargestInscribedBall instead

maximumInscribedSphere(ImageStack, int[], double[]) - Static method in class inra.ijpb.measure.GeometricMeasures3D

Deprecated.

Radius of maximum inscribed sphere of each particle within a label image.

MaxInscribedCirclePlugin - Class in inra.ijpb.plugins

Plugin for max inscribed circle of regions from label images.

MaxInscribedCirclePlugin() - Constructor for class inra.ijpb.plugins.MaxInscribedCirclePlugin

maxInscribedDisc - Variable in class inra.ijpb.plugins.AnalyzeRegions.Features

The boolean flag for computing largest inscribed disc.

MaxInscribedSpherePlugin - Class in inra.ijpb.plugins

Plugin for computing largest inscribed balls within 3D regions.

MaxInscribedSpherePlugin() - Constructor for class inra.ijpb.plugins.MaxInscribedSpherePlugin

maxValues(ImageStack, ImageStack, int[]) - Static method in class inra.ijpb.label.LabelValues

Find maximum value in intensity image for each label.

maxValues(ImageProcessor, ImageProcessor, int[]) - Static method in class inra.ijpb.label.LabelValues

Find maximum value in intensity image for each label.

maxValueWithinLabels(ImageStack, ImageStack) - Static method in class inra.ijpb.label.LabelValues

Computes the largest value within the valueImage, using the strictly positive values in labelImage as mask.

maxValueWithinLabels(ImageProcessor, ImageProcessor) - Static method in class inra.ijpb.label.LabelValues

Computes the largest value within the valueImage, using the strictly positive values in labelImage as mask.

mean(ImageProcessor, Strel) - Static method in class inra.ijpb.morphology.directional.DirectionalFilter

Computes the average value among the neighbors.

MEAN - inra.ijpb.morphology.directional.DirectionalFilter.Operation

The neighborhood mean (average) operation

MEAN - Static variable in interface inra.ijpb.math.ImageCalculator.Operation

Mean operator, that computes the average of the values from the two images

meanBreadth - Variable in class inra.ijpb.measure.region3d.IntrinsicVolumesAnalyzer3D.Result

The mean breadth of the region (proportional to the integral of average curvature)

meanBreadth(ImageStack, Calibration, int, int) - Static method in class inra.ijpb.measure.IntrinsicVolumes3D

Measures the mean breadth of a single region within a 3D binary image.

meanBreadthDensity(ImageStack, Calibration, int, int) - Static method in class inra.ijpb.measure.IntrinsicVolumes3D

Measures the mean breadth density of a single region within a 3D binary image.

meanBreadthLut(Calibration, int, int) - Static method in class inra.ijpb.measure.region3d.IntrinsicVolumes3DUtils

Computes the Look-up table used to measure mean breadth within 3D images.

meanBreadthLut(Calibration, int, int) - Static method in class inra.ijpb.measure.region3d.IntrinsicVolumesAnalyzer3D

Deprecated.

use IntrinsicVolumes3DUtils instead

meanBreadths(ImageStack, int[], Calibration, int, int) - Static method in class inra.ijpb.measure.IntrinsicVolumes3D

Measures the mean breadth of each region within a label image.

meanDist - Variable in class inra.ijpb.measure.region2d.AverageThickness.Result

Average distance computed along the skeleton

median(ImageProcessor, Strel) - Static method in class inra.ijpb.morphology.directional.DirectionalFilter

Computes the median value among the neighbors.

MEDIAN - inra.ijpb.morphology.directional.DirectionalFilter.Operation

The neighborhood median operation

MERGE_LABELS - Static variable in class inra.ijpb.plugins.InteractiveMarkerControlledWatershed

name of the macro method to merge selected labels

MERGE_LABELS - Static variable in class inra.ijpb.plugins.MorphologicalSegmentation

name of the macro method to merge selected labels

mergeChannels(ImageStack, ImageStack, ImageStack) - Static method in class inra.ijpb.data.image.ColorImages

Creates a new color ImageStack from the red, green and blue ImageStack instances.

mergeChannels(ImageProcessor, ImageProcessor, ImageProcessor) - Static method in class inra.ijpb.data.image.ColorImages

Creates a new ColorProcessor from the red, green and blue channels.

mergeChannels(Collection<ImageProcessor>) - Static method in class inra.ijpb.data.image.ColorImages

Creates a new ColorProcessor from a collection of three channels.

mergeLabels() - Static method in class inra.ijpb.plugins.InteractiveMarkerControlledWatershed

Merge labels that are selected either by a freehand or a point ROI.

mergeLabels() - Static method in class inra.ijpb.plugins.MorphologicalSegmentation

Merge labels that are selected either by a freehand or a point ROI.

mergeLabels(ImagePlus, Roi, boolean) - Static method in class inra.ijpb.label.LabelImages

Merge labels selected by freehand or point tool.

MergeLabelsPlugin - Class in inra.ijpb.plugins

MergeLabelsPlugin() - Constructor for class inra.ijpb.plugins.MergeLabelsPlugin

mergeLabelsWithGap(ImagePlus, float[], float, int) - Static method in class inra.ijpb.label.LabelImages

Merge several regions identified by their label, filling the gap between former regions.

mergeLabelsWithGap(ImagePlus, Roi, int, boolean) - Static method in class inra.ijpb.label.LabelImages

Merge labels selected by freehand or point tool.

mergeLabelsWithGap(ImageStack, float[], float, int) - Static method in class inra.ijpb.label.LabelImages

Merge several regions identified by their label, filling the gap between former regions.

mergeLabelsWithGap(ImageProcessor, float[], float, int) - Static method in class inra.ijpb.label.LabelImages

Merge several regions identified by their label, filling the gap between former regions.

MicrostructureAnalysisPlugin - Class in inra.ijpb.plugins

Plugin for quantifying microstructures from binary or label images.

MicrostructureAnalysisPlugin() - Constructor for class inra.ijpb.plugins.MicrostructureAnalysisPlugin

MIN - inra.ijpb.morphology.directional.DirectionalFilter.Type

Keep the minimum value over all possible orientations

MIN - Static variable in interface inra.ijpb.math.ImageCalculator.Operation

Min operator, that computes the minimum of the values from the two images

minFeretDiameter(ArrayList<? extends Point2D>) - Static method in class inra.ijpb.geometry.FeretDiameters

Computes Minimum Feret diameter of a set of points and returns both the diameter and the corresponding angle.

MINIMA - inra.ijpb.morphology.extrema.ExtremaType

The type for minima

MinimaAndMaxima - Class in inra.ijpb.morphology

A collection of static methods for computing regional and extended minima and maxima.

MinimaAndMaxima3D - Class in inra.ijpb.morphology

A collection of static methods for computing regional and extended minima and maxima on 3D stacks.

MINIMUM - inra.ijpb.morphology.strel.LocalExtremum.Type

Type for Minimum

minus(Vector2D) - Method in class inra.ijpb.geometry.Vector2D

Returns the result of the subtraction of this vector with another vector.

minus(Vector3D) - Method in class inra.ijpb.geometry.Vector3D

Returns the result of the subtraction of this vector with another vector.

minus(Vector3d) - Method in class inra.ijpb.measure.Vector3d

Deprecated.

Returns the result of the subtraction of this vector with another vector.

MINUS - Static variable in interface inra.ijpb.math.ImageCalculator.Operation

Minus operator, that subtracts values of the two images

MIRRORED - inra.ijpb.data.border.BorderManager.Type

uses mirrored image to populate border

MIRRORED - inra.ijpb.data.border.BorderManager3D.Type

uses mirrored image to populate border

MirroringBorder - Class in inra.ijpb.data.border

Periodic border that considers image is mirrored indefinitely in all directions.

MirroringBorder(ImageProcessor) - Constructor for class inra.ijpb.data.border.MirroringBorder

Creates a new Mirroring Border Manager

MirroringBorder3D - Class in inra.ijpb.data.border

Periodic border that considers image is mirrored indefinitely in all directions.

MirroringBorder3D(ImageStack) - Constructor for class inra.ijpb.data.border.MirroringBorder3D

Creates a new Mirroring Border Manager

MIXED_COLORS - inra.ijpb.color.ColorMaps.CommonLabelMaps

Colormap containing mixed colors

Moments3D() - Constructor for class inra.ijpb.measure.region3d.EquivalentEllipsoid.Moments3D

momentsToEllipsoids(EquivalentEllipsoid.Moments3D[]) - Method in class inra.ijpb.measure.region3d.EquivalentEllipsoid

Converts an array of 3D moments into equivalent ellipsoid representation.

monitor(Algo) - Static method in class inra.ijpb.algo.DefaultAlgoListener

Static method that creates a new instance of DefaultAlgoListener, and add it to the given algorithm.

MorphologicalFilter - Class in inra.ijpb.morphology.filter

Base class for morphological filters, based on a structuring element.

MorphologicalFilter3DPlugin - Class in inra.ijpb.plugins

Various morphological filters for 3D images.

MorphologicalFilter3DPlugin() - Constructor for class inra.ijpb.plugins.MorphologicalFilter3DPlugin

MorphologicalFilterCross3DPlugin - Class in inra.ijpb.plugins

A simple plugin to test the Cross 3D strel.

MorphologicalFilterCross3DPlugin() - Constructor for class inra.ijpb.plugins.MorphologicalFilterCross3DPlugin

MorphologicalFilterPlugin - Class in inra.ijpb.plugins

Plugin for computing various morphological filters on gray scale or color images.

MorphologicalFilterPlugin() - Constructor for class inra.ijpb.plugins.MorphologicalFilterPlugin

MorphologicalReconstruction3DPlugin - Class in inra.ijpb.plugins

Plugin for performing geodesic reconstruction by dimation or by erosion on grayscale images.

MorphologicalReconstruction3DPlugin() - Constructor for class inra.ijpb.plugins.MorphologicalReconstruction3DPlugin

MorphologicalReconstruction3DPlugin.Operation - Enum in inra.ijpb.plugins

A pre-defined set of operations for geodesic reconstruction.

MorphologicalReconstructionPlugin - Class in inra.ijpb.plugins

Plugin for performing morphological reconstruction by dilation or by erosion on grayscale images.

MorphologicalReconstructionPlugin() - Constructor for class inra.ijpb.plugins.MorphologicalReconstructionPlugin

MorphologicalReconstructionPlugin.Operation - Enum in inra.ijpb.plugins

A pre-defined set of operations for geodesic reconstruction.

MorphologicalSegmentation - Class in inra.ijpb.plugins

Plugin to perform automatic segmentation of 2D and 3D images based on morphological operations, mainly extended minima and watershed transforms.

MorphologicalSegmentation() - Constructor for class inra.ijpb.plugins.MorphologicalSegmentation

MorphologicalSegmentation.ResultMode - Enum in inra.ijpb.plugins

enumeration of result modes

Morphology - Class in inra.ijpb.morphology

Collection of static methods for morphological filters, as well as an enumeration of available methods.

Morphology.Operation - Enum in inra.ijpb.morphology

A pre-defined set of basis morphological operations, that can be easily used with a GenericDialog.

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