Short Description

This tool compute measures on the ROIs of the chosen sequence, updates the measures live when ROIs are changed and allows to copy/paste the measures to 3rd-party sheet edition softwares. Measures include geometric (bounding box) and intensity information.

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

Documentation

General description:

This plug-in measures a (increasingly) large number of descriptors from the Regions Of Interest (ROI) in the opened images, and export these measures to a text or spreadsheet file. It currently has two working modes:

  1. Standalone interface: the plug-in will generate a spreadsheet view with one sheet per opened image.
  2. Via Protocols: the corresponding block will generate a spreadsheet with a single sheet named “ROI Statistics”, which can in turn be saved to disk using the “Workbook to file” block (this latter block offers an additional option to merge files together when processing files in batch).

This plug-in is able to save the data in 2 formats:

  1. Spreadsheet: this option will produce a “.xls” file, compatible with most spreadsheet software. In this format, the ROI color will be used to fill the background of the cell containing its name (NB: the stored color may differ slightly from the actual ROI color, due to XLS format restrictions on color palettes).
  2. Text: this option will produce a “.txt” file, where each cell is delimited with a tabulation character (“t”), so as to be easily read by many other software. Furthermore, the name of each sheet will be inserted inside the text file before the actual sheet contents, with beginning and ending “==” symbol (e.g. “== ROI Statistics ==”).

Available descriptors:

  • Dataset: the name of the dataset (typically the name of the image or sequence)
  • ROI: the name of the region of interest (this can be changed from the “ROI” panel in the Insepctor window)
  • X, Y, Z: the coordinates (in pixels) representing the center of the bounding box
  • Box width, height, depth: the size (in pixels) of the bounding box along each axis
  • Contour: the perimeter (in 2D) or surface area (in 3D), expressed in pixels
  • Interior: the area (in 2D) or volume (in 3D), expressed in pixels
  • Sphericity (as defined by H. Wadell in 1935): the normalised ratio between the contour and interior, expressed as a percentage (100% for a circle or sphere).
  • Roundness (following the ISO 1101 standard): the normalised ratio between the radius of the minimum inscribed and largest cicrcumbscribed circles (or spheres), expressed as a percentage (100% for a circle or sphere). This measure is somewhat similar to the sphericity measure, but it much more sensitive to small shape variations (it is used in the manufacturing industry to guarantee the roundness of “round” objects)
  • Convexity: the ratio between the volume and the volume of the smallest convex envelope containing the ROI, expressed as a percentage (100% for a convex object)
  • Max. Feret diameter: the maximum distance between any 2 points of the surface, expressed in pixels.
  • Major (or first), Minor 2D (or second), Minor 3D (or third) diameters: the diameter (along each axis) of the best fitting ellipse (or ellipsoid), expressed in pixels. They are always ordered such that Major > Minor 2D > Minor 3D.
  • Elongation factor: a scale factor given by the ratio between the first and second ellipse diameters (see above). The minimum value is 1 (for a non-elongated object).
  • Flatness factor (3D only): a scale factor given by the ratio between the second and third diameters (see above). The minimum vaue is 1 (for an object with perfectly circular section perpendicularly to the major axis)
  • Intensity statistics: minimum, average, maximum, sum, and standard deviation of the intensity distribution in all channels inside the ROI

Note:

The maximum number of ROI that this plugin can currently handle is 65536 (strange number equal to 16th power of 2). This limit is imposed by pre-2010 Excel spreadsheets.

Resources needing this

6 reviews on “ROI Statistics

  1. Hello, I would like to ask what the output from this plugin is actually measuring? There seems to be three channel outputs (0,1 and 2) but I do not know what it is these channels have actually measured. Can anyone tell me please? I would also like to ask what the min x and min y are as well please.
  2. MRC LMCB
    Only giving it a 4 because it's missing some of the measures that ImageJ can compute. Is it possible to export the ROIs into ImageJ to get these other measures, or add our own equations as measures based on these ROIs?
  3. Debora Keller
    Yaya, but the time column and channel columns are missing (and the plot button would be great) :-)
  4. Thank you for addressing reported bugs quickly... Working great now!!! Keep up the good work.
  5. IcyLyd
    The new update allowing the selection of the measured parameters that can be specified in the tab and exported to excel is really convenient and user friendly. Thanks a lot.

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Changelog

  • Version 5.8.2.0 • Released on: 2019-10-17 11:00:00
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    Description:

    minor change to have 'micro' unit representation consistent with Icy application (Stephane).

  • Version 5.8.1.0 • Released on: 2019-09-27 16:00:00
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    Description:

    Minor change so Icy is able to find main class of plugin (Stephane)

  • Version 5.8.0.0 • Released on: 2019-08-28 15:20:00
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    Description:

    Added "Box X", "Box Y" and "Box Z" fields (can be useful sometime - Stephane)

  • Version 5.7.1.0 • Released on: 2019-05-06 18:00:00
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    Description:

    * reverted "full path" to show full *folder* path (no filename)
    * fixed "parent folder" field so it just display the "parent folder" (without full path)
    (Stephane)

  • Version 5.7.0.0 • Released on: 2019-05-06 12:00:00
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    Description:

    * "full path" field now returns real full path of dataset (and not only the folder path)
    * "parent folder" field changed to "folder" and now return folder of dataset (and not the parent folder of dataset which is easily deductible from folder)
    (Stephane)

  • Version 5.6.12.0 • Released on: 2019-03-07 14:23:29
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    Description:

    Added Elongation and Flatness3D ROI descriptors so they are available through the ROI table (Stephane)

  • Version 5.6.11.0 • Released on: 2018-12-27 10:34:02
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    Description:

    Fixed a minor issue while updating feature selection check boxes (Stephane).

  • Version 5.6.10.0 • Released on: 2018-09-25 17:55:49
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    Description:

    minor change for the ROI 3D Mesh plugin update (Stephane).

  • Version 5.6.9.1 • Released on: 2018-08-29 18:33:13
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    Description:

    Fixed value conversion with Perimeter, Area, Surface Area and Volume (Stephane).

  • Version 5.6.9.0 • Released on: 2018-08-29 18:03:11
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    Description:

    Reintroduced Perimeter, Area, Surface Area and Volume statistics (Stephane).

  • Version 5.6.8.0 • Released on: 2018-08-03 16:41:37
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    Description:

    Fixed a memory leak due to internal use of EzDialog

  • Version 5.6.7.0 • Released on: 2018-06-01 15:29:06
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    Description:

    Fixed max feret diameter descriptor when VTK is not loaded

  • Version 5.6.6.0 • Released on: 2018-03-26 13:08:00
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    Description:

    Fixed initial loading of selected features with Protocols.

  • Version 5.6.5.0 • Released on: 2018-03-22 17:55:20
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    Description:

    * Better statistics for no area type of ROI.
    * Try to use pixel size information if possible for feret / diameter / distance computations.

  • Version 5.6.4.1 • Released on: 2018-02-26 16:34:57
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    Description:

    Minor fix on load/restore selected features

  • Version 5.6.4.0 • Released on: 2018-02-26 16:04:06
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    Description:

    Added support for correct load/save of selected features in Protocols.

  • Version 5.6.3.1 • Released on: 2018-02-13 16:00:48
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    Description:

    Removed warning for ellipse fit error...

  • Version 5.6.3.0 • Released on: 2018-02-13 15:57:30
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    Description:

    Fixed major / minor axis calculation.

  • Version 5.6.2.0 • Released on: 2018-02-12 18:17:24
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    Description:

    Compiled with Java 7

  • Version 5.6.1.1 • Released on: 2018-01-28 09:45:31
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    Description:

    Fix for headless mode.

  • Version 5.6.1.0 • Released on: 2018-01-28 01:35:25
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    Description:

    - fixed headless mode (measureSelector was creating a graphical component)
    - compatible with java 7 or above

  • Version 5.6.0.2 • Released on: 2017-08-12 19:06:26
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    Description:

    Re-uploaded correct jar file

  • Version 5.6.0.1 • Released on: 2017-08-11 17:51:55
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    Description:

    Rollback minimum Icy version required

  • Version 5.6.0.0 • Released on: 2017-07-20 11:49:20
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    Description:

    New measures: global position of the centre of mass (relative to the dataset, stage, etc.)

  • Version 5.5.8.0 • Released on: 2017-07-05 11:33:07
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    Description:

    Fixed the dataset name for loooooooooong filenameeeeeeees :)

  • Version 5.5.7.0 • Released on: 2017-04-04 18:00:58
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    Description:

    Fixed an issue with Feret diameter computation not working on "flat" 3D regions of interest (i.e. living on a single Z slice)

  • Version 5.5.6.0 • Released on: 2017-01-18 17:36:22
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    Description:

    Fixed an issue with texture descriptors not working in some instances (no image associated to the ROI)

  • Version 5.5.5.0 • Released on: 2016-12-22 15:30:05
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    Description:

    Fixed an issue in the texture analysis where the step would not be taken into account

  • Version 5.5.4.0 • Released on: 2016-12-12 17:36:06
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    Description:

    Fixed contour computation on lines (was reading 0)

  • Version 5.5.3.1 • Released on: 2016-12-06 17:39:36
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    Description:

    Re-uploaded previous jar file

  • Version 5.5.3.0 • Released on: 2016-12-06 17:31:55
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    Description:

    Added multi-step texture analysis (API only, no GUI interface yet)

  • Version 5.5.2.0 • Released on: 2016-10-19 12:27:01
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    Description:

    Fixed an issue in the Track Processor (not displaying the plots correctly)

  • Version 5.5.1.1 • Released on: 2016-08-23 15:49:23
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    Description:

    Re-uploaded JAR file (for investigation purposes)

  • Version 5.5.1.0 • Released on: 2016-07-19 17:28:32
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    Description:

    Fixed issue causing texture descriptor to remain stuck at "N.A."

  • Version 5.5.0.0 • Released on: 2016-07-19 13:59:27
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    Description:

    New: texture descriptors (Haralick)

  • Version 5.4.5.0 • Released on: 2016-06-15 17:51:22
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    Description:

    Fixed track processor to take filters into account (from ROI gate, time clip, motion profiler, etc.)

  • Version 5.4.4.0 • Released on: 2016-04-28 19:11:02
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    Description:

    Feret calculation in 3D now uses the convex hull algorithm => *much* faster computation

  • Version 5.4.3.0 • Released on: 2016-04-28 17:16:26
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    Description:

    Re-optimised the Feret diameter calculation

  • Version 5.4.2.0 • Released on: 2016-04-18 17:47:25
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    Description:

    Optimised the Feret diameter calculation

  • Version 5.4.1.0 • Released on: 2016-03-25 10:44:48
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    Description:

    Select all features by default

  • Version 5.4.0.0 • Released on: 2016-03-18 16:08:06
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    Description:

    * New: ROI Statistics is now compatible with the Track Manager.
    * Rotation angles can now be accessed from the standalone GUI as well as inside protocols

  • Version 5.3.0.0 • Released on: 2016-03-10 23:47:21
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    Description:

    Switched to the new ROIDescriptor implementation

  • Version 5.2.5.0 • Released on: 2016-03-08 20:42:20
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    Description:

    New columns: full path and parent folder

  • Version 5.2.4.0 • Released on: 2016-02-11 09:09:07
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    Description:

    Fixed several under-the-hood issues related to row deletion

  • Version 5.2.3.1 • Released on: 2016-02-10 10:10:58
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    Description:

    Re-uploaded the jar file

  • Version 5.2.3.0 • Released on: 2016-01-14 12:45:13
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    Description:

    Use the legacy Excel (.xls) format for backward compatibility reasons

  • Version 5.2.2.0 • Released on: 2016-01-12 12:40:04
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    Description:

    Added script access for the shape descriptors

  • Version 5.2.1.0 • Released on: 2015-09-28 15:37:12
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    Description:

    Improved plug-in shutdown logic when it is running

  • Version 5.2.0.0 • Released on: 2015-07-11 19:55:53
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    Description:

    * Added color column (requires Workbooks 3.1)
    * Reworked multi-threading computations (performance might decrease but behaviour is much more stable)

  • Version 5.1.1.0 • Released on: 2015-07-06 11:26:05
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    Description:

    * Fixed color export when saving as spreadsheet
    * Fixed issues when exporting the file within a protocol

  • Version 5.1.0.0 • Released on: 2015-07-05 00:17:09
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    Description:

    * Statistics are now always computed in background threads
    * Multiple change events on ROI will only induce a single calculation (useful when editing a ROI)
    * Each ROI is (internally) converted into its area version to speed up computations
    * Changes to ROI name and color are now taken into account

  • Version 5.0.4.0 • Released on: 2015-07-03 18:47:27
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    Description:

    Reverted "perimeter" and "volume" back to "contour" and "interior"

  • Version 5.0.3.0 • Released on: 2015-07-01 15:32:03
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    Description:

    Fixed an issue with headless processing

  • Version 5.0.2.0 • Released on: 2015-06-30 16:11:21
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    Description:

    Fixed issues when exporting files in protocol mode

  • Version 5.0.1.0 • Released on: 2015-06-30 15:09:49
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    Description:

    Fixed an issue caused when adding or deleting multiple ROI at once

  • Version 5.0.0.0 • Released on: 2015-06-30 01:33:46
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    Description:

    A major update for major features!
    * Measures can now be selected from the interface
    * Selected measures are remembered in the preferences
    * Upgraded to Workbooks v.3.0 (much smoother interface)

  • Version 4.0.8.0 • Released on: 2015-06-18 19:56:10
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    Description:

    Fixed convexity measure

  • Version 4.0.7.0 • Released on: 2015-03-19 16:04:20
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    Description:

    Removed warning messages when unable to calculate shape features (caused the software to become very slow on large datasets)

  • Version 4.0.6.0 • Released on: 2015-02-13 18:15:53
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    Description:

    Fixed ROI intensity calculations (should now be in line with Icy's ROI panel

  • Version 4.0.5.0 • Released on: 2015-01-28 17:57:08
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    Description:

    * Better support for ROI4D and ROI5D
    * Added "T" and "C" columns
    * show "ALL" instead of "-1" for "Z", "T" and "C" columns
    * show "N/A" for unavailable measures
    * Fixed dataset name for sequences with no file name

  • Version 4.0.4.0 • Released on: 2015-01-23 17:36:16
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    Description:

    Converted another exception into a plain warning message

  • Version 4.0.3.0 • Released on: 2015-01-21 16:01:29
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    Description:

    Improved the reactivity of the graphical interface (notably when using many and/or large ROIs)

  • Version 4.0.2.0 • Released on: 2015-01-21 15:03:09
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    Description:

    * Simplified the code a tiny bit
    * Fixed a NPE during intensity calculations, caused by ROI.getCopy()
    * Converted exceptions into console warnings during ellipse fitting and convex hull calculations

  • Version 4.0.1.0 • Released on: 2015-01-13 11:34:59
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    Description:

    Fixed issue when data set name is unavailable

  • Version 4.0.0.0 • Released on: 2015-01-12 17:21:20
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    Description:

    New: many shape measures in 2D and 3D

  • Version 3.4.0.0 • Released on: 2015-01-11 23:50:27
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    Description:

    * Added dataset name in the result table
    * Updated to Workbooks v.2.3 (ability to merge files when saving)

  • Version 3.3.2.0 • Released on: 2015-01-07 15:47:42
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    Description:

    * Fixed row ordering when updating ROI values
    * Remove extra row properly when deleting a ROI

  • Version 3.3.1.0 • Released on: 2014-12-12 15:09:48
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    Description:

    Fixed an issue dealing with null entries

  • Version 3.3.0.1 • Released on: 2014-11-24 17:53:54
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    Description:

    Re-submitting the JAR file (error messages do not coincide with code)

  • Version 3.3.0.0 • Released on: 2014-10-22 00:04:39
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    Description:

    * Upgraded to Icy 1.5.4.2
    * Added sphericity measure

  • Version 3.2.3.0 • Released on: 2014-08-05 19:14:56
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    Description:

    Hopefully fixed the "4000+" cell style bug

  • Version 3.2.2.0 • Released on: 2014-06-18 13:53:32
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    Description:

    Fixed an issue causing the plugin to crash on second execution

  • Version 3.2.1.0 • Released on: 2014-06-17 19:04:44
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    Description:

    Fixed an issue causing the following error message:
    "java.lang.IllegalStateException: The maximum number of cell styles was exceeded. You can define up to 4000 styles in a .xls workbook"

  • Version 3.2.0.0 • Released on: 2014-05-13 01:10:11
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    Description:

    * Fixed min intensity calculation
    * Added standard deviation intensity

  • Version 3.1.1.0 • Released on: 2014-02-17 22:06:35
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    Description:

    Fixed intensity calculations on multiple channels

  • Version 3.1.0.0 • Released on: 2014-02-17 13:03:59
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    Description:

    * Fixed mass center calculation when no sequence was provided
    * Added methods to compute the mass center of 2D and 3D ROI (NOTE: these methods will be deprecated as soon as they are included in the ROIUtil toolbox)

  • Version 3.0.0.1 • Released on: 2014-02-11 21:24:29
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    Description:

    Fixed class-name issue (preventing the update from being visible)

  • Version 3.0.0.0 • Released on: 2014-02-11 09:46:11
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    Description:

    * Merged the "ROI Measures" plugin and "ROI Statistics" into a single Plugin/Block (fewer code, easier to fix and update)
    * Uses the new Workbooks v.2.0 (more responsive interface)
    * All opened sequences will appear in separate tabs (no more sequence selector)
    * Option to save data as spreadsheet or tab-delimited text file

  • Version 2.3.0.0 • Released on: 2014-01-21 19:57:05
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    Description:

    * Rewrote & fixed intensity calculation
    * Added mass center information
    * Renamed standalone plugin to "ROI Statistics" to match protocol version

  • Version 2.2.3.0 • Released on: 2014-01-08 10:59:13
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    Description:

    ROI Statistics block: Fixed bug in intensity calculation with out of bounds ROI

  • Version 2.2.2.0 • Released on: 2013-11-13 10:08:39
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    Description:

    Fixed ROI calculation in protocols

  • Version 2.2.1.0 • Released on: 2013-11-05 15:33:46
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    Description:

    Fixed an error in the ROI Statistics when calculating intensity measures on 2D ROI

  • Version 2.2.0.0 • Released on: 2013-11-05 00:38:16
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    Description:

    * Intensity measures as well as surface/volume are now computed in 3D as well
    * The same measures are now computed in the plug-in and the block version

  • Version 2.1.1.1 • Released on: 2013-10-04 18:18:30
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    Description:

    Fixed ROI Statistics block not being found in protocols if the ROI Measures plugin is not installed

  • Version 2.1.1.0 • Released on: 2013-06-12 16:49:18
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    Description:

    3D intensity is now saved in the workbook (in block mode)

  • Version 2.1.0.0 • Released on: 2013-06-07 15:44:04
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    Description:

    * Added extra sequence for intensity statistics computation
    * Minor code refactoring

  • Version 2.0.2.0 • Released on: 2013-04-11 21:51:20
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    Description:

    ROI statistics block now works even if the ROI have no sequence attached.

  • Version 2.0.1.0 • Released on: 2013-03-14 17:31:48
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    Description:

    Fixed bug in ROI Statistics block due to oversized workbook sheet names (they now get truncated to 31 characters)

  • Version 2.0.0.0 • Released on: 2013-03-12 20:45:48
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    Description:

    NEW: Block support (ROI Statistics)
    * Minor bug fixes

  • Version 1.5.0.2 • Released on: 2013-01-16 10:41:40
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    Description:

    Re-submission of v.1.5.0.0 (main class was missing from previous archive)

  • Version 1.5.0.1 • Released on: 2013-01-15 20:04:16
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    Description:

    Regression from version 1.4.0.0

  • Version 1.5.0.0 • Released on: 2013-01-15 17:51:19
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    Description:

    New: support for Protocols (uses the Apache POI library to create workbooks)

  • Version 1.4.0.0 • Released on: 2012-03-20 16:57:48
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    Description:

    - fixed minor errors
    - added Z selection

  • Version 1.3.3.2 • Released on: 2012-02-21 11:12:55
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    Description:

    (Re-)updated to EzPlug 1.6.4.1

  • Version 1.3.3.1 • Released on: 2012-02-20 13:06:07
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    Description:

    Updated to EzPlug 1.6.4.1

  • Version 1.3.3.0 • Released on: 2012-02-07 15:20:03
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    Description:

    minor updates and fixes to comply with EzPlug 1.6+

  • Version 1.3.2.1 • Released on: 2011-12-01 16:26:14
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    Description:

    quick fix trying to avoid a bug when the selected sequence has no viewer (really odd situation...)

  • Version 1.3.2.0 • Released on: 2011-11-15 01:53:19
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    Description:

    * added more intensity statistics
    * fixed EDT bug

  • Version 1.3.1.1 • Released on: 2011-10-25 09:57:54
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    Description:

    re-build due to a strange error in the dependencies

  • Version 1.3.1.0 • Released on: 2011-10-16 23:40:29
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    Description:

    adjusted refresh events on sequences having one or more ROIs on load (via persistence)

  • Version 1.3.0.0 • Released on: 2011-09-29 18:36:17
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    Description:

    - New: support for 3D images (ROI is duplicated on all slices)

    - Fixed: computation is made on the currently selected time point of the first sequence's viewer

  • Version 1.2.1.0 • Released on: 2011-08-25 15:20:22
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    Description:

    Fixed bug due to sequences already opened (before the plug-in)

  • Version 1.2.0.0 • Released on: 2011-07-25 13:57:46
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    Description:

    Bugfixes:
    - Errors when using multiple plugin instances (backing file closed more than once, views not updated correctly, etc.)
    Major improvements:
    - Export all measures to a .csv file
    Minor improvements:
    - "run" button renamed to "update"
    - "run" button hidden if auto-update checked
    - interface width increased for better readability

  • Version 1.1.0.0 • Released on: 2011-07-22 19:53:51
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    Description:

    Major improvements:
    - Intensity values in each channel
    - Multiple sequences
    - Multiple windows in parallel
    - Support for "on-request" update instead of live (for slower systems)

  • Version 1.0.0.0 • Released on: 2011-07-20 20:40:34
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