Short Description

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.

Documentation

This plugin is outdated and has been superseded by the "Label Extractor" plugin. 

Resources needing this

3 reviews on “Connected Components

  1. Stephane Dallongeville
    Very nice plugin, almost perfect ;) It would be very nice to have an automatic mode (default) : compute the histogram and extracts values different from the largest bean. Also i would have seen the ROI as the default export format but i guess that is a matter of taste ;)
  2. IcyLyd
    This block is particularly convenient to extract receptor clusters after spot detector in protocol. This is the only plugin allowing filtering by size and it is really powerfull.

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Changelog

  • Version 4.8.5.0 • Released on: 2019-01-31 18:54:25
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    Description:

    Updated to be compatible with volatile Sequence (Icy 2.0)

  • Version 4.8.4.0 • Released on: 2015-12-10 08:57:20
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    Description:

    Fixed issues with ROIs too small to calculate convex envelopes

  • Version 4.8.3.0 • Released on: 2015-10-21 12:10:39
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    Description:

    Fixed issue with ROI-based analysis

  • Version 4.8.2.0 • Released on: 2015-03-19 12:18:15
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    Description:

    * Exported ROIs now have a number for easier identification
    * Removed warnings in code

  • Version 4.8.1.0 • Released on: 2014-06-05 19:45:46
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    Description:

    Moved internal "QuickHull: library away to avoid conflict with the official "ConvexHull" library

  • Version 4.8.0.0 • Released on: 2014-04-21 00:16:12
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    Description:

    New method to export as ROI
    New method to fill inside a sequence
    Fixed perimeter calculation in 2D and 3D (corrects for digitisation artefacts)

  • Version 4.7.0.1 • Released on: 2014-01-13 11:09:58
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    Description:

    * never discard Z edges in 2D
    * fix edge discard label in block mode

  • Version 4.7.0.0 • Released on: 2013-11-04 20:36:42
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    Description:

    New: Connected Components now works on the input sequence ROI

  • Version 4.6.2.1 • Released on: 2013-10-30 19:16:42
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    Description:

    Updated to Icy 1.4.0.0

  • Version 4.6.2.0 • Released on: 2013-10-28 11:12:58
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    Description:

    Optimize the computation of the convex envelope

  • Version 4.6.1.0 • Released on: 2013-07-30 14:30:17
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    Description:

    Optimized intersection calculation

  • Version 4.6.0.0 • Released on: 2013-03-22 14:31:16
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    Description:

    New: 3D ROI support

  • Version 4.5.1.0 • Released on: 2013-02-04 11:18:40
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    Description:

    Sort ellipse fit such that the first value is always the large axis

  • Version 4.5.0.0 • Released on: 2012-11-13 19:14:23
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    Description:

    Added new object measures in the .xls file:
    - 2D perimeter (or 3D surface)
    - ellipse axes (X,Y,Z)
    - hull fill ratio (2D and 3D)

  • Version 4.4.1.1 • Released on: 2012-11-12 15:33:18
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    Description:

    Re-upload jar file (version issue ?)

  • Version 4.4.1.0 • Released on: 2012-11-08 14:59:42
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    Description:

    Excel results are now exported in real metric units (according to the resolution of the input sequence)

  • Version 4.4.0.0 • Released on: 2012-10-31 18:39:23
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    Description:

    New: output the list of ROI in block mode

  • Version 4.3.3.1 • Released on: 2012-10-11 16:43:55
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    Description:

    Automatically add a ".xls" extension to the export file (useful when using a sequence file name as the export file)

  • Version 4.3.3.0 • Released on: 2012-09-26 16:26:47
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    Description:

    * Safety to ensure that the xls export file is not null
    * (Blocks) Removed deprecated BlockInfo implementation

  • Version 4.3.2.1 • Released on: 2012-09-11 11:09:30
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    Description:

    Fixed jar export

  • Version 4.3.2.0 • Released on: 2012-09-11 09:38:33
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    Description:

    Connected Components are now channel-aware (but extraction remains in the first channel)

  • Version 4.3.1.0b • Released on: 2012-09-03 14:45:45
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    Description:

    Added sequence name at the first line of the generated spreadsheet.

  • Version 4.3.0.0b • Released on: 2012-08-09 16:25:03
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    Description:

    New: Added the Excel export functionality to protocols (NOTE: this is experimental and will be replaced by a more stable export system later on)

  • Version 4.2.0.3 • Released on: 2012-08-02 16:13:53
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    Description:

    - throw appropriate errors when working on an empty sequence
    - try to fix a concurrent modification exception when creating ROIs on the original sequence

  • Version 4.2.0.2 • Released on: 2012-07-19 19:04:14
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    Description:

    implemented BlockInfo interface in ConnectedComponentDescriptor (name should be more user friendly in Protocols)

  • Version 4.2.0.1 • Released on: 2012-07-16 14:05:25
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    Description:

    Show an error message if the input is null

  • Version 4.2.0.0 • Released on: 2012-07-10 11:20:42
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    Description:

    * Replaced deprecated VarArray by VarGenericArray
    * new methods in ConnectedComponent: intersects, paintOnSequence
    * ShapeDescriptor methods not static anymore
    * Merged CCShape (block) and ShapeDescriptor into ConnectedComponentDescriptor (block)

  • Version 4.0.0.0 • Released on: 2012-06-21 13:30:55
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    Description:

    Support for Blocks programming.
    First available blocks: connected components (main plugin) + minimal shape descriptor

  • Version 3.3.0.0 • Released on: 2012-05-31 15:23:27
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    Description:

    fix: catch error when computing 3D ellipse fit
    adjusted fields visibility (changed from private to protected)

  • Version 3.2.1.0 • Released on: 2012-05-21 11:06:51
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    Description:

    caught exception when computing the ellipse in 2D (singular matrix)

  • Version 3.2.0.0 • Released on: 2012-05-11 18:57:48
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    Description:

    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)

  • Version 3.0.0.0 • Released on: 2012-04-17 20:01:31
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    Description:

    NEW: shape measurement toolbox with numerous descriptors (accessible via static methods, or automatically included when exporting results to .xls files)

  • Version 2.4.1.0 • Released on: 2012-03-22 17:20:27
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    Description:

    renamed internal methods to add/remove points
    new method to add points manually

  • Version 2.4.0.0 • Released on: 2012-03-22 16:47:03
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    Description:

    new: added method to extract contour points from a component
    fix: component's (mass center) coords weren't updated correctly

  • Version 2.3.0.2 • Released on: 2012-02-29 19:19:08
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    Description:

    Amend to the previous update (jar issue ?)

  • Version 2.3.0.1 • Released on: 2012-02-20 13:07:23
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    Description:

    Updated to EzPlug 1.6.4.1

  • Version 2.3.0.0 • Released on: 2012-02-15 19:31:05
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    Description:

    New: Export the list of components to a .xls file for further manipulation with your favorite sheet software.

  • Version 2.2.2.1 • Released on: 2011-12-07 16:20:07
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    Description:

    new build to reflect Detection API changes

  • Version 2.2.2.0 • Released on: 2011-11-28 15:39:29
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    Description:

    added computeMinIntensity(...) methods

  • Version 2.2.1.0 • Released on: 2011-11-19 19:17:50
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    Description:

    Minor speed improvement in the pixel scanning process

  • Version 2.2.0.0 • Released on: 2011-11-16 23:07:41
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    Description:

    New feature: objects can now be exported as ROIs on the original image

  • Version 2.1.0.0 • Released on: 2011-11-14 22:45:41
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    Description:

    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

  • Version 2.0.5.0 • Released on: 2011-11-09 13:20:27
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    Description:

    updated to icy.type.DataType
    outputs components to console

  • Version 2.0.4.0 • Released on: 2011-09-09 19:20:44
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    Description:

    new: added method to compute the major axis of a component by returning the vector between the two most distant points

  • Version 2.0.3.1 • Released on: 2011-07-15 14:21:03
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    Description:

    updated build to Icy 1.0.6.0 (replaced deprecated method call by new one)

  • Version 2.0.3.0 • Released on: 2011-05-20 13:51:16
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    Description:

    added method to compute the maximum distance between a connected component and a user-defined point

  • Version 2.0.2.2 • Released on: 2011-04-27 17:12:23
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    Description:

    minor revision: removed display of the temporary labeling (after first pass)

  • Version 2.0.2.1 • Released on: 2011-04-27 17:08:19
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    Description:

    revised version that removes debug information

  • Version 2.0.2.0 • Released on: 2011-04-27 17:05:54
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    Description:

    Fixed bug in the labeling algorithm, which occurs only in very rare geometrical configurations

  • Version 2.0.1.0 • Released on: 2011-04-21 11:57:02
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    Description:

    - Z flag disappears automatically for 2D images
    - Added description label to explain extraction modes to the user
    - javadoc improved

  • Version 2.0.0.0 • Released on: 2011-04-19 16:29:31
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    Description:

    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

  • Version 1.3.0.0 • Released on: 2011-02-04 17:02:20
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    Description:

    Possibility to compute a component's average intensity in a given sequence

  • Version 1.2.0.2 • Released on: 2011-01-31 18:14:22
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    Description:

    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

  • Version 1.2.0.1 • Released on: 2011-01-31 13:35:58
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    Description:

    Regression from version 1.1.0.0

  • Version 1.2.0.0 • Released on: 2011-01-31 13:06:59
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    Description:

    - 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

  • Version 1.1.0.0 • Released on: 2011-01-26 20:41:35
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    Description:

    - New feature: discard components on the image edge (in XY or XYZ)
    - Object count is printed on the interface for convenience purposes

  • Version 1.0.0.0 • Released on: 2011-01-25 16:11:01
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