MorphoLibJ_-1.6.4

This is release 1.6.4 of MorphoLibJ, a library for Mathematical Morphology with ImageJ/Fiji. This release mostly introduces some refactoring, and fixes some bugs.

New features (from 1.6.1)

• Added the "Skeleton Geodesic Diameter" Plugin, that computes the geodesic diameter on the result of skeletonization
• Added the "Label Map to ROIs" plugins, that computes boundary polygons of regions within a label map (f8e3cc5)

Enhancement / bug fixes

• Analyze Regions 3D Plugin: fixed a bug in computation of equivalent ellipsoid table (d31b5d8)
• the KillBordersPlugin now keeps display settings
• fixed a problem in choice of gradient in plugins/MorphologicalSegmentation
• fixed computation of structuring element offset in morphology/strel/EllipsoidStrel
• fixed computation of BinaryConfigurationsHistogram2D for specific list of labels (a5a21d2)
• several updates in the user manual

Refactoring

• refactored the "AnalyzeRegions" plugin by using the new MorphometricFeatures2D class
• refactored the AnalyzeRegions3D plugin based on the new MorphometricFeatures3D class
• renamed IntrinsicVolumesAnalyzer2D.java into IntrinsicVolumes2D.java
• renamed IntrinsicVolumesAnalyzer3D.java into IntrinsicVolumes3D.java

MorphoLibJ 1.6.3

This is release 1.6.3 of MorphoLibJ, a library for Mathematical Morphology with ImageJ/Fiji. This release mostly introduces some refactoring, and fixes some bugs.

New feature

• added the "Skeleton Geodesic Diameter" Plugin, that computes geodesic diameter on the result of skeletonization

Enhancement / bug fixes

• the KillBordersPlugin now keeps display settings
• fixed a problem in choice of gradient in plugins/MorphologicalSegmentation
• fixed computation of structuring element offset in morphology/strel/EllipsoidStrel
• several updates in the user manual

Refactoring

• refactored the "AnalyzeRegions" plugin by using the new MorphometricFeatures2D class
• refactored the AnalyzeRegions3D plugin based on the new MorphometricFeatures3D class
• renamed IntrinsicVolumesAnalyzer2D.java into IntrinsicVolumes2D.java
• renamed IntrinsicVolumesAnalyzer3D.java into IntrinsicVolumes3D.java

MorphoLibJ 1.6.1

This is release 1.6.1 of MorphoLibJ, a library for Mathematical Morphology with ImageJ/Fiji.

Feature enhancements

• Added new option for morphological filtering of label maps. Can choose to erode only froim background pixels, or from pixels with different label.
• Cropping label images now keeps spatial calibration
• added several logo images (in the "doc/logo" directory)
• user manual updated

Bug fixes

• Fixed bug in computation of Euler number with connectivity 26
• DrawTableValues plugin now correctly manages spatial calibration
• Made Microstructure Analysis 3D more robust to management of large images

Under the hood

• Simplified Uint tests o
• Add ImageShape.subsample(...) methods
• Added ImageUtils.fill(...) methods based on lambda functions

MorphoLibJ 1.6.2

This is release 1.6.2 of MorphoLibJ, a library for Mathematical Morphology with ImageJ/Fiji.
This release is mostly the same as MorphoLibJ-1.6.1, except that it was succesfully created with the continuous integration system. Therefore it is available as a maven artifact from Nexus repository.

Note also that this release contains a logo for MorphoLibJ!!

Feature enhancements

• Added new option for morphological filtering of label maps. Can choose to erode only from background pixels, or from pixels with different label (issue #76)
• Cropping label images now keeps spatial calibration (issue #63)
• Added several logo images (in the "doc/logo" directory)
• User manual updated

Bug fixes

• Fixed bug in computation of Euler number with connectivity 26
• DrawTableValues plugin now correctly manages spatial calibration (issue #78)
• Made Microstructure Analysis 3D more robust to management of large images

Under the hood

• Simplified JUnit tests cases
• Add ImageShape.subsample(...) methods
• Added ImageUtils.fill(...) methods based on lambda functions

MorphoLibJ 1.6.1 beta

MorphoLibJ-1.6.1-beta

The next release is approaching; this beta release if for those who want to try recent bug fixes.

some updates

• cropping label images keeps spatial calibration
• DrawTableValues plugin now correctly manages spatial calibration
• made Microstructure Analysis 3D more robust to management of large images
• updated morphological erosion of label maps
• fixed bug in computation of Euler number with connectivity 26

under the hood

• simplified test cases
• add ImageShape.subsample(...) methods
• added ImageUtils.fill(...) methods based on lambda functions

MorphoLibJ v1.6.0 that fixes bug in microstructure analysis 3D

fixes analysis of 3D microstructures within large 3D images.

MorphoLibJ 1.6.0 (Updated label map filtering)

Add new option for morphological filtering of label maps. Can choose to erode only froim background pixels, or from pixels with different label.

MorphoLibJ v1.6.0

This is release 1.6.0 of MorphoLibJ, a library for Mathematical Morphology with ImageJ/Fiji.

New Features:

• added plugin "Label Morphological Filter"
• added "Fill Label Holes" Plugin
• added "Region Boundaries Labeling" plugin
• added "Binary/Label Overlay" plugin, that provides an opacity option
• added "Draw Labels as Overlay" plugin

Enhancements:

• LabelToValuePlugin should now support macro recording
• AnalyzeRegions Plugin should now be more convenient to script
• Updated the user manual with new plugins, and expanded the explanation of basic concepts
• added region connected component labeling for label maps
• added Glasbey-Dark and Glasbey_Bright colormaps for better visualization of label images
• Change default color map of connected component labeling plugin result
• AverageThickness uses image calibration, and includes unit name within column name
• updated order of plugins in ImageJ "MorphoLibJ -> Label Images" menu

Bug Fixes:

• Fixed edge effects when performing morphologial opening or closing with large structuring elements and structures close to image border
• fixed bug in computation of OctagonStrel mask

Under the hood:

• added MorphologicalFilter abstract class and several specialized classes, to perform morphological filters on 2D/3D images and simplify code of the "Morphology" class.
• Morphology: added static methods for processing ImagePlus instances
• refactored default implementations of Strel interface
• code clean up of FloodFill algorithms
• added GeodesicDistanceTransformFloatHybrid, for performing computation of geodesic distance transform using hybrid algorithm (faster on complex images)
• added the "inra.ijpb.data.image.ImageUtils" utility class, for gathering image edition recurrent tasks
• added the "inra.ijpb.label.LabelUtils" utility class

MorphoLibJ v1.5.1 with Fill Label Holes (V2)

Updates the Fill Label Holes plugin to add a dialog for choosing 1) connectivity of backgroundregions and 2) bit depth of the background connected components.

MorphoLibJ v1.5.1 with Label Morphological Filtering

Added a new plugin "Plugins -> MorphoLibJ -> Labels -> Label Morphological Filters", that applies morphological filters to labels, while avoiding to overlap existing labels.
See also discussion in issue #68.