Short Description

Fills the holes in all the ROI of the active sequence (also works in Protocols).

Team: Bio Image Analysis Unit
Institution: Institut Pasteur
Website: https://icy.bioimageanalysis.org
Source code: https://gitlab.pasteur.fr/bia/icy-fillholesinroi

Documentation

This plugin will take each ROI in the active sequence, and fill the holes (empty areas) detected inside.

Note that ROI with holes that are defined by control points (e.g., by creating an exclusive union of two overlapping ROI) while be converted to area ROI for the hole(s) to be filled.

Holes touching the edge of the image are not considered as actual holes, and will not be filled.

When working in 3D ROIs each z-slice is processed independently from the others.

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One review on “Fill holes in ROI”

  1. X
    XHeiligenstein
    A nice tool, however, I have a problem using it: when I work on a Zstack, containing multiple 2D ROIs (one for each Z), and press fill holes, it turns my ROI into Z=All, T=All and C=All. How could I fix the Z,T and C for each ROI ? So it does not combine all my ROIs into Z All, making a big mess ? Thanks

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Changelog

  • Version 1.3.3.0 • Released on: 2021-06-22 17:00:00
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    Description:

    Fixed duplicated ROI bug in Protocols mode

  • Version 1.3.2.0 • Released on: 2021-04-26 15:13:11
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    Description:

    Updated internal parent POM file.

  • Version 1.3.0.0 • Released on: 2020-08-07 10:48:00
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    Description:

    Now 3DROIAreas are supported!. However the hole filling is performed on each z slice independently

  • Version 1.2.0.0 • Released on: 2020-03-24 10:50:00
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    Description:

    - declared fillHoles(..) method as static so it can be used directly from code.
    - removed Spherical Harmonic sample from package

  • Version 1.1.3.0 • Released on: 2015-03-19 00:21:54
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    Description:

    Fixed incorrect Z/T/C values in processed ROI

  • Version 1.1.2.0 • Released on: 2014-05-13 19:07:33
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    Description:

    Fixed issue causing the number of ROI to grow at each protocol run

  • Version 1.1.1.2 • Released on: 2014-05-12 22:45:04
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    Description:

    Fixed class name again!!

  • Version 1.1.1.1 • Released on: 2014-05-12 22:41:49
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    Description:

    Fixed issue in the class name

  • Version 1.1.1.0 • Released on: 2014-05-12 22:33:31
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    Description:

    Adjusted package name (seemed to cause updating issues)

  • Version 1.1.0.0 • Released on: 2014-05-12 21:30:22
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    Description:

    * Updated to Icy 1.4.3.5
    * Moved to a new package (without breaking backward compatibility)

  • Version 1.0.0.0 • Released on: 2013-07-03 10:00:45
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    Description:

    Handle dummy cases (no sequence opened)

  • Version 0.0.1.0 • Released on: 2013-05-30 15:40:20
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