Short Description

Compute and display the intensity evolution for regions of interests (ROIs) through time. Results can be refreshed automatically as ROIs are changed.

Multiple channels are handled separately. Multiple criteria can be computed: mean intensity in the ROI, total intensity, variance, median, etc.

The results are displayed in a dedicated GUI and can be exported to some Excel files.

Team: Bio Image Analysis Unit
Institution: Institut PAsteur
Website: https://icy.bioimageanalysis.org
Source code: https://gitlab.pasteur.fr/bia/roi-intensify-evolution

Documentation

Main steps

This plugin aims at monitoring over time the intensity properties of regions of interest (ROIs) in 2D image sequences. The user-interactions have been as easy and intuitive as possible. Just follow those simple steps:

  1. One should use first the standard tools for ROI creation shipped by ICY. To do so, go the “File & ROI tools” tab in ICY main interface, select the wanted type of ROI and create it by mouse interactions with the image sequence of interest.
  2. Go to the “ROI Intensity Evolution” interface and select the sequence of interest in the box on the right hand side.
  3. Choose the criterion to display in the dedicated box.
  4. Select the ROIs for which this criterion have to be computed in the “Region of interests” list.
  5. Visualize evolution of the criterion over time as a plot “criterion vs. frame number”. If ROIs are changed (e.g. moved) the criterion values and the display are automatically refreshed.
  6. Export results in a Microsoft Excel (XLS) file.

Multicolor images

Multiple channels are handled separately and will be displayed in different plots.

3D stacks

Only the first image of each stack ( z = 0) is processed for now. 3D ROIs are not yet handled.

Criteria

The criterion for the selected ROIs should then be drawn as a curve criterion vs. frame number in the main working area of the plugin.

For the criteria, multiple options are possible:

  • Mean intensity in the area defined by each ROI
  • Maximum intensity
  • Minimum intensity
  • Median intensity
  • Sum of the intensity
  • Variance of the intensity
  • Area over or below a user-defined threshold.

For the latter criterion, the threshold can be defined in a dedicated window which can be accessed through the menu “Options/Set thresholding options”. One can then decide whether pixels over or below the threshold should be counted. Also, it is possible, for the area calculation, to use real image scales (defined as “Pixel Size” in the “Sequence Properties” of each sequence) by checking the dedicated box.

Results export

All the results can be exported to a specified XLS file (Microsoft Excel) via the menu “Save/Save results to XLS file”. The file will consist of a series of sheets, each of which corresponds to a criterion. Each sheet contains a table of the value of the criterion for each ROI at each time frame.

Extra series display

It is possible to overlay extra series to the current plot. The series should be available in the “SwimmingPool” of ICY and be of type org.jfree.data.xy.XYSeries. Extra series can be selected for display via the menu “Options/Display extra series from SwimmingPool”

Author and License

Nicolas Chenouard is the author of the plugin.

Please post questions or suggestions to the ICY forum, or via the email adress nicolas.chenouard.dev@gmail.com.

The code is distributed under the GPLv3 licence and can be accessed by unzipping the ,jar file of the plugin in the plugin folder structure of ICY.

 

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4 reviews on “ROI Intensity Evolution”

  2. IcyLyd
    Really nice. The excel file could be optimize but all the info are available. I wrote a VBA macro to summarise the data which are a little bit disperse spatially in several sheets. Would be great if one could call it from protocols.
  4. S
    StephO
    Nice plugin. It would be even better if it could be used in protocols!!

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Changelog

  • Version 2.1.0.0 • Released on: 2021-04-14 12:30:00
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    Description:

    * Fixed duplicated ROI in selection list

  • Version 2.0.3.0 • Released on: 2021-01-14 16:00:00
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    Description:

    * Added support for 3D dataset and 3D ROI
    * Tweaked profile display
    * Fixed refresh of ROI list on ROI name change

  • Version 2.0.2.0 • Released on: 2021-01-12 00:00:00
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    Description:

    Update GUI and fix error when using ROIs with the same name

  • Version 2.0.1.0 • Released on: 2020-04-06 11:30:00
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    Description:

    Update dependencies for Icy 2.1

  • Version 2.0.0.2 • Released on: 2015-08-24 19:50:49
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    Description:

    Made some methods and classes public for external calls.

  • Version 2.0.0.1 • Released on: 2015-04-20 17:45:28
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    Description:

    Added static access.

  • Version 2.0.0.0 • Released on: 2014-02-08 20:38:08
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    Description:

    Modified GUI to make it simpler and use of a JMenu.

    New criterion: area of pixels under/below a user-defined threshold value.

    Faster computation through the use of sub sequences.

  • Version 1.0.0.3 • Released on: 2013-11-06 19:47:34
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    Description:

    Bugfix due to kernel update to 1.4.0.2

  • Version 1.0.0.2 • Released on: 2013-01-09 20:12:08
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    Description:

    fixed GUI refreshment bug.

  • Version 1.0.0.1 • Released on: 2013-01-09 17:27:01
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    Description:

    removed painter ability and corrected GUI refreshing bug.

  • Version 1.0.0.0 • Released on: 2012-11-21 19:39:12
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    Description:

    Init commit.

    fixed minor issue with frame packing.

  • Version 0.0.1.0 • Released on: 2012-11-21 19:33:02
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