This plugin extracts groups of connected pixels in 2D and 3D based on their intensity and that of the background. Works on both binary and gray-scale data. Output can be pushed to the swimming pool for other plug-ins to further exploit the extracted objects.
This plugin is outdated and has been superseded by the “Label Extractor” plugin.
Updated to be compatible with volatile Sequence (Icy 2.0)
Fixed issues with ROIs too small to calculate convex envelopes
Fixed issue with ROI-based analysis
* Exported ROIs now have a number for easier identification
* Removed warnings in code
Moved internal "QuickHull: library away to avoid conflict with the official "ConvexHull" library
New method to export as ROI
New method to fill inside a sequence
Fixed perimeter calculation in 2D and 3D (corrects for digitisation artefacts)
* never discard Z edges in 2D
* fix edge discard label in block mode
New: Connected Components now works on the input sequence ROI
Updated to Icy 1.4.0.0
Optimize the computation of the convex envelope
Optimized intersection calculation
New: 3D ROI support
Sort ellipse fit such that the first value is always the large axis
Added new object measures in the .xls file:
- 2D perimeter (or 3D surface)
- ellipse axes (X,Y,Z)
- hull fill ratio (2D and 3D)
Re-upload jar file (version issue ?)
Excel results are now exported in real metric units (according to the resolution of the input sequence)
New: output the list of ROI in block mode
Automatically add a ".xls" extension to the export file (useful when using a sequence file name as the export file)
* Safety to ensure that the xls export file is not null
* (Blocks) Removed deprecated BlockInfo implementation
Fixed jar export
Connected Components are now channel-aware (but extraction remains in the first channel)
Added sequence name at the first line of the generated spreadsheet.
New: Added the Excel export functionality to protocols (NOTE: this is experimental and will be replaced by a more stable export system later on)
- throw appropriate errors when working on an empty sequence
- try to fix a concurrent modification exception when creating ROIs on the original sequence
implemented BlockInfo interface in ConnectedComponentDescriptor (name should be more user friendly in Protocols)
Show an error message if the input is null
* Replaced deprecated VarArray by VarGenericArray
* new methods in ConnectedComponent: intersects, paintOnSequence
* ShapeDescriptor methods not static anymore
* Merged CCShape (block) and ShapeDescriptor into ConnectedComponentDescriptor (block)
Support for Blocks programming.
First available blocks: connected components (main plugin) + minimal shape descriptor
fix: catch error when computing 3D ellipse fit
adjusted fields visibility (changed from private to protected)
caught exception when computing the ellipse in 2D (singular matrix)
new: option to sort components in the labeled output (currently by ascending or descending Z)
del: removed ConnectedComponentsPainter class (becomes useless and shows incorrect results after sorting)
NEW: shape measurement toolbox with numerous descriptors (accessible via static methods, or automatically included when exporting results to .xls files)
renamed internal methods to add/remove points
new method to add points manually
new: added method to extract contour points from a component
fix: component's (mass center) coords weren't updated correctly
Amend to the previous update (jar issue ?)
Updated to EzPlug 1.6.4.1
New: Export the list of components to a .xls file for further manipulation with your favorite sheet software.
new build to reflect Detection API changes
added computeMinIntensity(...) methods
Minor speed improvement in the pixel scanning process
New feature: objects can now be exported as ROIs on the original image
Major update:
* fixed bug in the 2D extraction process (error along right-hand vertical edge)
* output available as a DetectionResult to use with the Icy tracker
updated to icy.type.DataType
outputs components to console
new: added method to compute the major axis of a component by returning the vector between the two most distant points
updated build to Icy 1.0.6.0 (replaced deprecated method call by new one)
added method to compute the maximum distance between a connected component and a user-defined point
minor revision: removed display of the temporary labeling (after first pass)
revised version that removes debug information
Fixed bug in the labeling algorithm, which occurs only in very rare geometrical configurations
- Z flag disappears automatically for 2D images
- Added description label to explain extraction modes to the user
- javadoc improved
New milestone (breaks backwards compatibility):
- extracted inner class to multiple files to make code lighter => dependent plugins just need to change the import commands, everything else is compatible
- improved painter
- possibility to compute intersections between components
Possibility to compute a component's average intensity in a given sequence
bug fixes of v.1.2.0.0 to make it (finally) operational.
NOTE: retro-compatibility is broken with version 1.2.0.1 and before 1.2.x
Regression from version 1.1.0.0
- Improved edge discard options
- Components' points list return as vecmath.Point3i[]
NOTE: this version breaks retro-compatibility due to the change in accessors of connected components. Refer to the javadoc of the ConnectedComponent class to see the adjustments to perform in dependent plugins
- New feature: discard components on the image edge (in XY or XYZ)
- Object count is printed on the interface for convenience purposes
3 reviews on “Connected Components”