Short Description

Set of block (for graphical programming with Protocols) to perform different operations on ROI (Region Of Interest).

Team: Bio Image Analysis
Institution: Institut Pasteur
Website: http://icy.bioimageanalysis.org/

Documentation

Bundle of blocks (Protocols) to perform different operations on ROI (Region Of Interest).

Supported operations:

  • Create rectangular ROI (2D, 3D, 4D or 5D)
  • Filter / sort / color from ROI descriptor
  • Perform boolean / logical operation between two set of ROI
  • Separate ROIs (into connected components) -> “Separate ROI Components”
  • Split ROIs (using Watersheds) -> “Separate ROI Watershed”
  • Get / set ROI position (either box top-left position or box center)
  • Get / set ROI size
  • Get / set ROI properties (name, color, opacity…)
  • Load ROI(s) from file
  • Save ROI(s) to file

The Filter ROI block

The Filter ROI block support filtering on any descriptor. It’s why the Value field accepts text so you can specify any text (regexp are accepted) if you want to filter on a text type descriptor as Name (in which case only EQUAL or NOT_EQUAL comparison operator make sense). For number type descriptors (a large majority of them) you can of course input any number as text in Value field and the number will be correctly interpreted.

When filtering ROIs by Color, use the following format when expressing the color in hexadecimal values:

AARRGGBB

where AA is the alpha value, RR is the red value, GG, is the green value, and BB is the blue value.

To find the hexadecimal color code of a given ROI, select this ROI in the list, click on its color in Properties and go to the rightmost tab called “Xoetrope color wheel”. The hexadecimal code is FF + the code you see above the Hue, Saturation and Brightness values.

For instance, the hexadecimal code of this orange rectangle2D is FFFF9933. The protocol shown in the two screenshots removes ROIs of a given color.

Note that you can indicate the code in upper of lower case. Don’t put any space and don’t forget to specify the alpha (always equal to “FF”).

ROI position

position X, Y, Z, T, C: the position of the upper left corner of the bounding box around the ROI along each axis (x, y, z, frame and channel)

position X(center), Y(center), Z(center) or Set XYZ Center: coordinates (in pixels) of the center of mass of the ROI

position Z, T and C equal to -1 by default, which means the ROI appear on all Z slices, all frames and all channels.

Example on Get/Set ROI position

Let’s take a ROI example:

Position X = 100
Position Y = 190
Size X = 150
Size Y = 90
Position X (center) = 175
Position Y (center) = 235

Let’s get the ROI position of the upper left corner and center of mass with the block Get ROI position:

Now let’s move the ROI center of mass to the upper right corner of the image. To do so, we use the Set ROI position block, tick the Set XYZ Center box and indicate the new coordinates of the center of mass in position X and position Y.

2 reviews on “ROI blocks

  1. Extremely useful plugin, just the "color" part has a bug, it doesn't save the color with the protocol - loading the protocol has all colors set back to the default value.
  2. IcyLyd
    Thanks Stephane for this bundles of tools. I am using them in most of my protocols particularly roi colors and Boolean operation.

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Changelog

  • Version 1.4.10.0 • Released on: 2021-07-21 17:00:00
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    Description:

    Updated 'Create Rectangular ROI' block to use the new ROI3DBox, get rid of size T and size C information (we don't want ROI4D or ROI5D)

  • Version 1.4.9.0 • Released on: 2021-06-08 09:15:37
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    Description:

    Added Watershed ROI separation plugin

  • Version 1.4.8.0 • Released on: 2021-01-26 16:00:00
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    Description:

    Optimized processing time of ROI logical operation block (not yet blazing fast but still an improvement)

  • Version 1.4.7.0 • Released on: 2020-08-18 15:48:00
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    Description:

    Added feature to ROI Position (set or get): Now it is possible to use the center of the object's bounding box.

  • Version 1.4.6.0 • Released on: 2020-06-23 12:00:00
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    Description:

    Fixed color text comparison in FilterROI block. now comparing lowercase converted values.

  • Version 1.4.5.0 • Released on: 2020-05-29 10:54:00
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    Description:

    Added option to generate ROI copies when performing logical opertations on ROIs

  • Version 1.4.4.0 • Released on: 2020-05-20 17:40:00
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    Description:

    Fixed number parsing from 'value' field in 'filter ROI' block.

  • Version 1.4.3.0 • Released on: 2020-04-16 11:30:00
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    Description:

    Changed 'value' field to String instead of Mutable to make it easier to use.

  • Version 1.4.2.0 • Released on: 2020-04-15 16:00:00
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    Description:

    * "Filter ROI" block now support comparison on String/Text value (for "Name" or "Color" descriptors for instance)
    * "Get ROI Descriptor" block can now return String/Text result (for "Name" or "Color" descriptors for instance)

  • Version 1.4.1.0 • Released on: 2020-03-18 09:30:00
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    Description:

    Updated due to changes in Icy 2.1 (new exceptions on some methods)

  • Version 1.4.0.0 • Released on: 2019-08-22 18:00:00
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    Description:

    * added new Color ROI block to color a group of ROI from a ROI descriptor and a given colormap (really useful !!).
    * added many static method so coloring / filtering / sorting / logical and boolean operations are easily usable from code.

  • Version 1.3.0.0 • Released on: 2019-06-26 15:00:00
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    Description:

    Added new "Logical Operation ROI" to perform logic operation between 2 set of ROIs (intersected, contained, not contained..)

  • Version 1.2.8.0 • Released on: 2019-02-14 16:55:44
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    Description:

    Added "ROI To Rectangle" bloc to convert ROI(s) to Rectangle type ROI(s)

  • Version 1.2.7.1 • Released on: 2019-02-07 12:58:34
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    Description:

    typo

  • Version 1.2.7.0 • Released on: 2019-02-07 12:54:26
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    Description:

    Added "ROI to point" and "ROI to ellipse" blocks

  • Version 1.2.6.0 • Released on: 2019-01-23 11:53:31
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    Description:

    Added "Scale Shape ROI" and "Scale2x ROI" blocks

  • Version 1.2.5.1 • Released on: 2018-03-01 10:45:32
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    Description:

    Fixed typo in "ROI To Mask" block

  • Version 1.2.5.0 • Released on: 2017-10-18 10:38:22
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    Description:

    Added new "Move ROI To Sequence".
    This block adjusts a set of ROIs coming from a source sequence for a destination sequence. ROIs are translated & scaled according to the origin position & resolution of both sequences.

  • Version 1.2.4.1 • Released on: 2017-07-06 18:08:45
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    Description:

    (much) faster ROI filtering and sorting processing.

  • Version 1.2.4.0 • Released on: 2017-06-06 17:05:23
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    Description:

    Added new blocks :
    - SortROI (sort ROIs on a specific descriptor)
    - SeparateROIComponents (separate connected components from ROI(s))

  • Version 1.2.3.0 • Released on: 2017-04-13 18:40:50
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    Description:

    Added new block "get ROI descriptor value"

  • Version 1.2.2.1 • Released on: 2017-04-13 18:40:20
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    Description:

    Added new block "get ROI descriptor value"

  • Version 1.2.2.0 • Released on: 2016-12-21 16:16:03
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    Description:

    Fixed ROI filter block.

  • Version 1.2.1.0 • Released on: 2016-12-02 16:36:39
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    Description:

    Fixed "filter ROI" block state loading.

  • Version 1.2.0.1 • Released on: 2016-11-16 18:48:52
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    Description:

    Added new ROI filter bloc allowing generic filtering on any descriptor.
    Note than in current Icy version (1.8.6.0) the descriptor list does not display correctly but that will be fixed with Icy 1.8.7.0 or superior.

  • Version 1.2.0.0 • Released on: 2016-07-13 16:54:07
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    Description:

    * added block to load / save ROI(s) from / to a file.
    * added block to specifically set ROI T/Z/C position

  • Version 1.1.7.0 • Released on: 2016-02-16 12:29:18
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    Description:

    Boolean operation does not return anymore empty ROI on intersection when ROI are not intersecting.

  • Version 1.1.6.0 • Released on: 2016-02-10 12:42:49
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    Description:

    fixed a typo with the 'Data type' field of 'Roi to Sequence' block.

  • Version 1.1.5.4 • Released on: 2016-01-13 16:48:42
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    Description:

    Better dataType field in RoiToSequence block.

  • Version 1.1.5.3 • Released on: 2016-01-13 16:39:37
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    Description:

    - added field 'dataType' to RoiToSequence block.

  • Version 1.1.5.2 • Released on: 2016-01-13 16:33:42
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    Description:

    fixed typo with "fillValue" field in RoiToSequence block.

  • Version 1.1.5.1 • Released on: 2016-01-13 16:31:50
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    Description:

    fixed typo in fill value field name.

  • Version 1.1.5.0 • Released on: 2016-01-13 16:01:27
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    Description:

    - added RoiToSequence block to the bundle (old RoiToSequence plugin become deprecated).
    - added "fill value" field to RoiToSequence block.

  • Version 1.1.4.1 • Released on: 2016-01-05 18:41:43
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    Description:

    added persistence for the global visible overlay (only work with a specific plugin)

  • Version 1.1.4.0 • Released on: 2016-01-04 13:11:32
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    Description:

    Added a new "create global visible overlay" block which take a list of overlay as input and create a new Overlay which affect globally the visible property of the given input overlay list.

  • Version 1.1.3.0 • Released on: 2015-10-23 11:20:18
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    Description:

    Better error handling for "Set ROI Name" block.

  • Version 1.1.2.1 • Released on: 2015-02-12 18:49:44
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    Description:

    minors refactoring.

  • Version 1.1.2.0 • Released on: 2015-02-12 18:21:47
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    Description:

    minor refactoring

  • Version 1.1.1.0 • Released on: 2015-02-12 17:56:48
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    Description:

    changed some default parameters values

  • Version 1.1.0.1 • Released on: 2015-02-12 16:50:47
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    Description:

    - added set ROI properties block
    - minors improvements
    - a bit of refactoring

  • Version 1.0.0.0 • Released on: 2015-02-12 15:55:50
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    Description:

    Fix version informations.

  • Version 0.0.1.0 • Released on: 2015-02-12 15:46:34
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