Package inra.ijpb.plugins
Contains plugins, for integration with ImageJ GUI.
The file defining the plugin arborescence in menu is located in
src/main/resources/plugins.config
.

Class Summary Class Description AnalyzeMicrostructure3D Plugin for computing densities of 3D intrinsic volumes (volume, surface area, mean breadth and Euler number) from 3D binary images.AnalyzeRegions Plugin for computing morphology of regions from label images.AnalyzeRegions3D Plugin for measuring geometric quantities such as volume, surface area, and eventually sphericity index.AreaOpeningPlugin Select binary particles in a planar image based on number of pixels.AverageThicknessPlugin BinaryOverlayPlugin BoundingBox3DPlugin Plugin for measuring extend of 3D bounding box from label images.BoundingBoxPlugin Plugin for computing (2D) bounding box of regions from label images.ChamferDistanceMap3DPlugin Compute distance map, with possibility to choose chamfer weights, result type, and to normalize result or not.ChamferDistanceMapPlugin Compute distance map, with possibility to choose chamfer weights, result type, and to normalize result or not.ConvexifyPlugin Computes the Convex equivalent of a binary image.CropLabelPlugin Crops a label image and binarize it to contain only the specified label.DilateLabelsPlugin Dilate all labels within a label image.DirectionalFilteringPlugin Plugin for computing directional filtering.DistanceTransformWatershed This plugin computes watershed on the inverse of the distance map of a binary image.DistanceTransformWatershed3D This plugin computes watershed on the inverse of the distance map of a 3D binary image.DrawTableValuesPlugin Draw the values of a results table column into current image, using specified columns for x and y positions.EquivalentEllipsePlugin Computes equivalent ellipse of each region within a label image.EquivalentEllipsoidPlugin Computes equivalent ellipsoid for each region with a binary or label 3D image.ExpandLabelsPlugin Creates a new image larger than the original one, and copies each label identically but shifted by a given dilation coefficient.ExtendBordersPlugin Pads the current image with the specified value or color.ExtendedMinAndMax3DPlugin Plugin for computing regional minima and maxima in grayscale images.ExtendedMinAndMaxPlugin Plugin for computing extended minima and maxima in grayscale images.FillHolesPlugin Plugin for filling holes (dark holes within bright structures) in 8bits grayscale or binary 2D/3D images.GeodesicDiameter3DPlugin Plugin for computing geodesic distances of 3D particles from label images using chamfer weights.GeodesicDiameterPlugin Plugin for computing geodesic distances of labeled particles using chamfer weights.GeodesicDistanceMap3D Plugin for computing geodesic distance map from binary images using chamfer weights.GeodesicDistanceMap3DPlugin Plugin for computing geodesic distance map from binary 3D images using chamfer weights.GeodesicDistanceMapPlugin Plugin for computing geodesic distance map from binary marker and constrained to binary or label images using chamfer distances propagation.GrayscaleAreaOpeningPlugin Select binary particles in a planar image based on number of pixels.GrayscaleAttributeFiltering3D Plugin to perform between attribute opening, closing, and black or white tophat on a 3D grayscale image.GrayscaleAttributeFilteringPlugin Select binary particles in a planar image based on number of pixels.GrayscaleBoxDiameterOpeningPlugin Select binary particles in a planar image based on number of pixels.ImposeMinAndMax3DPlugin Plugin for imposing minima or maxima on a grayscale 3D image, using a specific connectivity.ImposeMinAndMaxPlugin Plugin for imposing minima or maxima on a grayscale image, using a specific connectivity.InertiaEllipsePlugin Deprecated. replaced by EquivalentEllipsePlugin (since 1.4.2).InertiaEllipsoidPlugin Deprecated. replaced by EquivalentEllipsoidPlugin (since 1.4.1)IntensityMeasures3D This class implements a set of photometric (intensity) measurements over an input grayscale image (2D or 3D) and its set of corresponding labels.InteractiveGeodesicDistanceMap Plugin for computing geodesic distance map from binary images using chamfer weights.InteractiveMarkerControlledWatershed Plugin to perform automatic segmentation of 2D and 3D images using markercontrolled watershed with manually selected seeds.InteractiveMorphologicalReconstruction Plugin for performing interactive morphological reconstruction by dilation or by erosion on grayscale images.InteractiveMorphologicalReconstruction3D Plugin for performing interactive geodesic reconstruction by dilation erosion on grayscale images.InterfaceSurfaceArea3D Plugin for measuring the surface area of the interface between two labels within a 3D label image.KeepLargestLabelPlugin Removes all the labels in a 2D/3D image but the largest one.KeepLargestRegionPlugin Removes all the regions in a binary 2D or 3D image but the largest one.KillBordersPlugin Plugin for removing borders in 8bits grayscale or binary 2D or 3D image.LabelAreaOpeningPlugin LabelBoundariesPlugin LabelEdition Plugin for the manual edition of label images (2D and 3D).LabelingPlugin Computes label image of connected components in a binary planar image or 3D stack.LabelOverlapMeasures This class implements a plugin to calculate overlap measurements over an source and a target label image (2D or 3D).LabelSizeFilteringPlugin Filter labels within a label image using a size criterion.LabelToRgbPlugin Creates a new Color Image that associate a given color to each label of the input image.LabelToValuePlugin Combines a label image and the values within a column of a results table to create a new image with intensity corresponding to the vales in the table column.MarkerControlledWatershed3DPlugin A plugin to perform markercontrolled watershed on a 2D or 3D image.MaxFeretDiameterPlugin Computes Maximum Feret Diameters of a binary or label image.MaxInscribedCirclePlugin Plugin for max inscribed circle of regions from label images.MaxInscribedSpherePlugin Plugin for computing largest inscribed balls within 3D regions.MergeLabelsPlugin MicrostructureAnalysisPlugin Plugin for quantifying microstructures from binary or label images.MorphologicalFilter3DPlugin Various morphological filters for 3D images.MorphologicalFilterCross3DPlugin A simple plugin to test the Cross 3D strel.MorphologicalFilterPlugin Plugin for computing various morphological filters on gray scale or color images.MorphologicalReconstruction3DPlugin Plugin for performing geodesic reconstruction by dimation or by erosion on grayscale images.MorphologicalReconstructionPlugin Plugin for performing morphological reconstruction by dilation or by erosion on grayscale images.MorphologicalSegmentation Plugin to perform automatic segmentation of 2D and 3D images based on morphological operations, mainly extended minima and watershed transforms.NeighborLabelsPlugin Extract the neighbor regions within a label image from a region label, or a list of region labels.OrientedBoundingBoxPlugin Plugin for computing oriented bounding box.ParticleAnalysis3DPlugin Deprecated. replaced by AnalyzeRegions3DRegionAdjacencyGraphPlugin RegionalMinAndMax3DPlugin Plugin for computing regional minima and maxima in grayscale images.RegionalMinAndMaxPlugin Plugin for computing regional minima and maxima in grayscale images.RegionMorphometryPlugin Deprecated. replaced by AnalyzeRegionsRemapLabelsPlugin Ensures the labels in the current label image are numbered between 1 and LMax, where LMax is the number of labels.RemoveBorderLabelsPlugin Removes all labels that touch the selected border, and replace them with value 0.RemoveLargestLabelPlugin Removes all the labels in a 2D/3D image but the largest one.RemoveLargestRegionPlugin Removes the largest region of a binary 2D or 3D image.ReplaceLabelValuesPlugin Replaces the value of selected label(s) by a given value, for 2D/3D images, for gray8, gray16 and float images.ReplaceValuePlugin Simple plugin to replace a value by another one, for 2D/3D images, for gray8, gray16 and float images.SelectLabelsPlugin Creates a new binary image containing only the selected label(s).SetLabelMapPlugin Changes the current LUT such that each label is associated to a different color, and specifies color of background.SizeOpeningPlugin Select binary particles in a 2D or 3D image based on number of pixels.Watershed3DPlugin A plugin to perform watershed on a 3D image using flooding simulations, as described by Soille, Pierre, and Luc M. 
Enum Summary Enum Description Connectivity2D An enumeration of connectivity options for 2D Mathematical Morphology operators.Connectivity3D An enumeration of connectivity options for 3D Mathematical Morphology operators.ExtendedMinAndMax3DPlugin.Operation A customized enumeration to choose between extended minima or maxima.ExtendedMinAndMaxPlugin.Operation A customized enumeration to choose between extended minima or maxima.ImposeMinAndMax3DPlugin.Operation A customized enumeration to choose between minima or maxima imposition.ImposeMinAndMaxPlugin.Operation A customized enumeration to choose between minima or maxima imposition.InteractiveMarkerControlledWatershed.ResultMode enumeration of result modesLabelSizeFilteringPlugin.Operation A predefined set of Labels for populating plugin.MorphologicalReconstruction3DPlugin.Operation A predefined set of operations for geodesic reconstruction.MorphologicalReconstructionPlugin.Operation A predefined set of operations for geodesic reconstruction.MorphologicalSegmentation.ResultMode enumeration of result modesRegionalMinAndMax3DPlugin.Operation A customized enumeration to choose between regional minima or maxima.RegionalMinAndMaxPlugin.Operation A customized enumeration to choose between regional minima or maxima.