Short Description

This segmentation method performs a N-class thresholding based on a K-Means classification of the image histogram, then extracts objects in a bottom-up manner using user-defined minimum and maximum object sizes. Very useful to detect clustered objects in fluorescence microscopy.

Documentation

Original publication:
A. Dufour, V. Meas-Yedid, A. Grassart, and J.-C. Olivo-Marin, "Automated Quantification of Cell Endocytosis Using Active Contours and Wavelet", Proc. ICPR 2008, Tampa, FL, USA.

Resources needing this

One review on “HK-Means

  1. IcyLyd
    Very usefull to set threshold manually or automatically using protocols. The export in color coded ROI is great and visual.

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Changelog

  • Version 2.9.0.0 • Released on: 2019-01-31 18:53:25
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    Description:

    Updated to be compatible with volatile Sequence (Icy 2.0)

  • Version 2.8.2.0 • Released on: 2016-08-30 17:22:09
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    Description:

    Fixed an issue when filtering by minimum intensity

  • Version 2.8.1.0 • Released on: 2016-02-03 17:55:29
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    Description:

    Fixed an issue when processing multi-channel images

  • Version 2.8.0.0 • Released on: 2016-02-02 19:59:00
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    Description:

    * Switched to the ROI-based implementation (connected components must die!)
    * Fixed an issue with the color map of the labeled sequence
    * ROIs are now coloured based on the color map of the channel they were detected in
    * Added status bar and console output
    * A bit more documentation in the GUI
    * Some cleaning and fixes

  • Version 2.7.4.0 • Released on: 2015-07-31 11:57:06
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    Description:

    Added the frame parameter in block mode

  • Version 2.7.3.0 • Released on: 2015-06-26 13:06:27
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    Description:

    * Added an option in standalone mode to process only a single frame
    * Use a channel selector instead of a dimension picker
    * Fixed the removal of 3D ROIs produced by the plugin before running again

  • Version 2.7.2.0 • Released on: 2015-05-28 17:17:11
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    Description:

    Fixed an issue causing where the labeled output was missing in Protocol mode.

  • Version 2.7.1.0 • Released on: 2015-05-22 14:08:13
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    Description:

    * Fixed extraction on single channel sequences
    * Fixed swimmingpool output

  • Version 2.7.0.0 • Released on: 2015-05-22 13:58:19
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    Description:

    * Extracted core methods into class HKMeans with static access (useful for scripting)
    * Export to swimming pool now includes full mask information (useful for intensity measurement after tracking)

  • Version 2.6.0.0 • Released on: 2013-10-30 18:24:23
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    Description:

    Updated to Icy 1.4.0.0 (new support for 3D ROI)

  • Version 2.5.0.0 • Released on: 2013-10-30 15:47:18
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    Description:

    Added final threshold parameter in block version

  • Version 2.4.0.0 • Released on: 2013-06-12 16:52:22
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    Description:

    3D ROI export

  • Version 2.3.1.0 • Released on: 2012-11-16 16:53:52
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    Description:

    Display a message dialog indicating that ROIs cannot be exported in 3D

  • Version 2.3.0.0 • Released on: 2012-10-31 17:28:21
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    Description:

    New: output the extracted objects as a list of ROI in block mode

  • Version 2.2.0.0 • Released on: 2012-09-11 09:42:24
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    Description:

    HK-Means is channel aware

  • Version 2.1.2.0 • Released on: 2012-08-03 10:42:00
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    Description:

    Fixed the output file name generation

  • Version 2.1.1.0 • Released on: 2012-08-02 17:02:14
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    Description:

    * Show appropriate error when given an incorrect class number
    * Adjust the output file name to the input name + a suffix (and a incremental number if used via EzPlug)

  • Version 2.1.0.0 • Released on: 2012-06-28 17:57:52
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    Description:

    * fix: throw handled exception if input is null (obviously…)
    * blocks: updated output to use VarGenericArray

  • Version 2.0.0.0 • Released on: 2012-06-21 13:35:29
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    Description:

    Support for Blocks programming.

  • Version 1.4.2.0 • Released on: 2012-05-31 16:30:48
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    Description:

    fixed: trying to access an EzGUI when running within Blocks

  • Version 1.4.1.0 • Released on: 2012-05-31 15:18:02
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    Description:

    adjusted classpath and field visibility

  • Version 1.4.0.0 • Released on: 2012-05-11 18:58:29
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    Description:

    new: changed internal structures and output to use integers instead of shorts
    new: updated to ConnectedComponents v.3.2.0.0 (components sorting)

  • Version 1.3.3.0 • Released on: 2012-04-12 13:56:01
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    Description:

    Updated to Filter toolbox 2.1.0.0

  • Version 1.3.2.0 • Released on: 2012-04-06 18:50:43
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    Description:

    Results names are incremental for easier differentiation.

  • Version 1.3.1.1 • Released on: 2012-02-20 11:54:00
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    Description:

    Updated to EzPlug 1.6.4.1 (no logic change)

  • Version 1.3.1.0 • Released on: 2011-11-29 17:15:16
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    Description:

    * added label on the interface displaying the total number of detected objects

  • Version 1.3.0.0 • Released on: 2011-11-19 16:52:45
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    Description:

    * new: export detections to the swimming pool for tracking purposes
    * new: export detections as ROIs on the input sequence

  • Version 1.2.0.1 • Released on: 2011-11-09 13:27:26
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    Description:

    updated to icy.type.DataType

  • Version 1.2.0.0 • Released on: 2011-09-09 19:12:39
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    Description:

    New: added optional parameter to discard objects below a certain intensity threshold within the extraction process

  • Version 1.1.0.0 • Released on: 2011-05-27 15:57:33
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    Description:

    - New: added a method to output the connected components found in the sequence
    - New: the total number and ID of the components are displayed in the console and the output sequence.

  • Version 1.0.0.1 • Released on: 2011-05-19 17:33:49
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    Description:

    - switched to non-beta state
    - adjusted default parameters

  • Version 1.0.0.0b • Released on: 2011-05-19 17:23:54
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    Description:

    initial submission