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May 2016
Last activity
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Mar 2017

Short Description

This plugin allows fitting ellipsoids in 3D images rapidly. The author provides a few points on the boundary using the orthogonal views. An algorithm then finds the best fitted ellipsoid wrt to a certain criteria. The plugin can be used to: i) analyze the configuration of objects such as nuclei or cells in 3D. ii) generate gold standards for assessing segmentation algorithms performance.

Documentation

To use this plugin, you have to use a 3 dimensional image (Third dimension being either Z or T). You can select the sequence to work on through the plugin's interface, and you then have to confirm it.

 

Once the sequence is confirmed, the plugin will open to viewers : one Orthogonal view where the work will be done, and one 3D one used to visualize your image. These viewers are linked, closing one will result in closing the other one.

 

You can navigate in your image with the Orthogonal view as usual, once you are on a point of interest, you can use the check box "lock" to stay in the current position and start delimiting the points that will generate the ellipsoid. You can do that either by clicking, which will result on a point, or by holding the MAJ key and moving the mouse (for a more approximate delimitation). Right-clicking will cancel the last added point.

You can use the crosshair to define your Region of Interest in every plane of the view. After that, you can either unlock the view to delimitate another region (the first one will be stored), or start the plugin to generate the ellipsoid.

The checkbox "display points" will add the clicked points in the 3D view, if you add points while the option is selected, they will also be displayed as sphere with radius 1 pixel.

You can also save created ellipsoid as XML files to later rebuild them in another image.

Selecting one ellipsoid in the "Layers" page of Icy will allow you to change name and/or color to help you recognise the different ellipsoids.

 

The method Ellipses is a work in progress and can't currently be used

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Changelog

  • Version 0.1.1.12 • Released on: 2017-03-13 15:35:35
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  • Version 0.1.1.11 • Released on: 2017-03-02 00:15:06
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    Description:

    Added number of ellipsoids in orthoview
    Added possibility to remove a given ellipsoid.

  • Version 0.1.1.10 • Released on: 2017-02-26 23:53:37
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    Description:

    Corrected a few bugs.
    Added ellipses in orthoviews.

  • Version 0.1.1.9 • Released on: 2017-02-16 18:44:44
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  • Version 0.1.1.8 • Released on: 2017-02-16 18:38:56
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    Description:

    Modified the class name

  • Version 0.1.1.7 • Released on: 2017-02-16 09:56:46
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  • Version 0.1.1.6 • Released on: 2017-02-15 17:47:56
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    Description:

    Changed the core of the algorithm.
    Corrected a bug related to multi-lock, now only one ellipsoid will be generated even after multiple locks.

  • Version 0.1.1.5 • Released on: 2016-09-20 11:05:14
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    Description:

    -- Fixed several issues with the display of odd dimension images in the Orthogonal View

  • Version 0.1.1.4 • Released on: 2016-06-30 10:06:22
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    Description:

    -- Fixes several issues with the saving of ellipsoids

  • Version 0.1.1.3 • Released on: 2016-06-28 11:04:11
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    Description:

    -- CSV files are now exported with both Pixel and Micrometer units

    -- Several bug fixes

  • Version 0.1.1.2 • Released on: 2016-06-16 11:09:07
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  • Version 0.1.1.1 • Released on: 2016-06-16 10:32:59
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  • Version 0.1.1.0 • Released on: 2016-06-15 16:19:54
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  • Version 0.1.0.7 • Released on: 2016-06-15 16:11:44
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  • Version 0.1.0.6 • Released on: 2016-06-15 16:05:10
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  • Version 0.1.0.5 • Released on: 2016-06-15 15:59:59
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  • Version 0.1.0.4 • Released on: 2016-06-15 15:03:41
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  • Version 0.1.0.3 • Released on: 2016-06-14 10:54:49
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    Description:

    -- Now possible to work only on OrthogonalView if the 3D one couldn't be initialized

  • Version 0.1.0.2 • Released on: 2016-06-14 10:11:10
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  • Version 0.1.0.1 • Released on: 2016-06-09 10:34:55
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    Description:

    -- Added a condition to check the original points

  • Version 0.1.0.0 • Released on: 2016-06-08 14:33:50
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    Description:

    -- First final version

  • Version 0.0.3.6b • Released on: 2016-06-07 11:48:23
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  • Version 0.0.3.5b • Released on: 2016-06-07 10:19:08
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    Description:

    -- Implemented multi-threading to increase speed of creation of the Binary mask

  • Version 0.0.3.4b • Released on: 2016-06-06 14:38:19
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  • Version 0.0.3.3b • Released on: 2016-06-06 12:29:35
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  • Version 0.0.3.2 • Released on: 2016-06-06 10:55:52
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  • Version 0.0.3.1b • Released on: 2016-06-03 14:42:54
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    Description:

    -- Fixed bounding box's implementation

  • Version 0.0.3.0b • Released on: 2016-06-03 13:23:52
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    Description:

    -- Added automated saving (Confirming an image will create an XML file which will be updated at each ellipsoid's creation).

    -- Added exports options :

    - CSV will create a csv file readable by any spreadsheet software, in which will be stored information about every created ellipsoid

    - Binary Mask will create a TIFF image, where every pixel's value is 0, except for the ones that are inside a created ellipsoid

    -- Fixed some minor bugs

  • Version 0.0.2.1b • Released on: 2016-06-01 12:50:23
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    Description:

    -- Implemented scaling transformation (still working on rotation)

    -- Fixed some issues

  • Version 0.0.2.0b • Released on: 2016-06-01 10:35:21
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    Description:

    -- Changed XML behavior (now displays much more information about the ellipsoids)

    -- Ellipsoid now display their intersection with each plane on the OrthoViewer (Still Work in Progress, some bugs to fix)

    -- Fixed some issues with XML loading

    -- Started work on transforming the ellipsoids once created (Only translation so far, still some issues to work on)

  • Version 0.0.1.4b • Released on: 2016-05-27 11:24:35
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    Description:

    -- Fixed XML Saving and Loading of ellipsoids

  • Version 0.0.1.3b • Released on: 2016-05-26 16:55:44
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    Description:

    -- Trying one more thing

  • Version 0.0.1.2b • Released on: 2016-05-26 16:48:54
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    Description:

    -- Still fixing early issues

  • Version 0.0.1.1b • Released on: 2016-05-26 16:43:02
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    Description:

    -- Fixing build path

  • Version 0.0.1.0b • Released on: 2016-05-26 16:22:17
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