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 morphological feature of regions from label images.
AnalyzeRegions.Features	The list of features to compute.
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
BinaryOrLabelOverlayPlugin	Display a label map or a binary image as overlay onto a grayscale image.
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 3D distance map, with possibility to choose the chamfer mask, the result type (integer or floating point), and to normalize result or not.
ChamferDistanceMapPlugin	Compute distance map, with possibility to choose the chamfer mask, the result type (integer or floating point), 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.
DrawLabelsAsOverlayPlugin	Draw the labels of the regions as overlay.
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 8-bits grayscale or binary 2D/3D images.
FillLabelHolesPlugin	Fills the holes within the region of a label image.
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	Deprecated. use GeodesicDistanceMap3DPlugin instead
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 top-hat 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 marker-controlled 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 8-bits 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.
LabelMapMorphologicalFilteringPlugin	Applies morphological filtering on a label image.
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 marker-controlled 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 AnalyzeRegions3D
RegionAdjacencyGraphPlugin
RegionalMinAndMax3DPlugin	Plugin for computing regional minima and maxima in grayscale images.
RegionalMinAndMaxPlugin	Plugin for computing regional minima and maxima in grayscale images.
RegionBoundariesLabelingPlugin
RegionMorphometryPlugin	Deprecated. replaced by AnalyzeRegions
RemapLabelsPlugin	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 modes
LabelMapMorphologicalFilteringPlugin.Operation	A pre-defined set of basis morphological operations, that can be easily used with a GenericDialog.
LabelSizeFilteringPlugin.Operation	A pre-defined set of Labels for populating plugin.
MorphologicalReconstruction3DPlugin.Operation	A pre-defined set of operations for geodesic reconstruction.
MorphologicalReconstructionPlugin.Operation	A pre-defined set of operations for geodesic reconstruction.
MorphologicalSegmentation.ResultMode	enumeration of result modes
RegionalMinAndMax3DPlugin.Operation	A customized enumeration to choose between regional minima or maxima.
RegionalMinAndMaxPlugin.Operation	A customized enumeration to choose between regional minima or maxima.