Short Description

  • computes ROI measurements. Measures include geometric (bounding box) and intensity information
  • updates measurements live when ROIs are modified
  • exports the measures to 3rd-party sheet edition softwares.

For 3D measurements, you could be interested as well by the 3D Analysis plugin.

Team: Bio Image Analysis Unit
Institution: Institut Pasteur
Website: https://research.pasteur.fr/en/team/bioimage-analysis/

Documentation

This plugin computes measurements (also called descriptors or features) on the Regions Of Interest (ROI), and exports these measures to a text or spreadsheet file.

It currently has three working modes:

  1. Standalone interface
  2. As a tab called “ROI tab” in the side pane on the right of the GUI of Icy
  3. As Protocols block

Data can be saved 2 formats:

  1. Spreadsheet: produces a “.xlsx” file, compatible with most spreadsheet software. For the ROI color descriptor, the color of the ROI is used to fill the background of the cell and the cell is filled with the hexadecimal code (see ROI blocks for more info on the ROI color). Note that the stored color may differ slightly from the actual ROI color, due to XLS format restrictions on color palettes.
  2. Text: produces a “.txt” file, where each cell is delimited with a tabulation character (“t”). Preferred format to process further the data with R or Python programming languages. Note that the name of each sheet is inserted inside the text file before the actual sheet contents, with beginning and ending “==” symbol (e.g. “== ROI Statistics ==”).

We detail below the specificities of each mode and give the definition of each descriptor.

Standalone interface

Type “roistatistics” in the search bar of Icy to access it.

call plugin ROIstats from search bar

  • To compute measurements on ROIs, click on “Select features…” and tick the measurements you would like to compute.
  • To save the measurements, click on the floppy disk and select “Export as text file” or “Export as Excel file”, this open a dialog box with which you can indicate the path to save the data (folder and name of the file). Note that the plugin generates a spreadsheet view with one sheet per opened image.
  • To make plots, click on the three stacked lines next to the floppy disk to display histograms or scatterplots of the measurements.

ROI tab

The ROI tab is located in the side pane on the right side of the graphical user interface (GUI) or Icy. It automatically stores measurements from ROIs. Click on the spreasheet with an arrow to export the measurements. Click on the wheel to choose the measurements to display in the tab and the ones to export.

Clicking on the wheel displays two tables:

  • on the right: what is displayed in the tab
  • on the left: what is exported (in .txt or .xls)

Tick the box on the upper left corner to tick/untick all descriptors. Click on “Columns to display” to re-order unticked descriptors. Move a descriptor up or down the list: click on the name of the descriptor to select it, then click on the arrows in the upper right corner.

Protocols block

The block generates a spreadsheet with a single sheet or “workbook” named “ROI Statistics”. The spreadsheet can be saved to disk using the “Workbook to file” block with the following options:

  • format: “Spreadsheet” or “Text” to export the data to .xlsx (Spreadsheet file format) or .tsv (Text file format)
  • output file: opens a dialog box, in which you need to provide the full path to save the data (including the file name)
  • merge: if file exists “Overwrite” (to replace the file), “Merge sheets” (to merge files when processing files in batch),  or “Merge sheets excluding first row” (also to merge files but without repeating the first row, which usually contains the name of the columns)

Available descriptors

Name    Definition
1st axis (um) The 3D coordinates of the first principal axis of the ROI shape. Perpendicular to both the second and third principal axes.
1st Diameter (um) The diameter (along each axis) of the best fitting ellipse (or ellipsoid), expressed in pixels.
2nd axis (um) The 3D coordinates of the second principal axis of the ROI shape. Perpendicular to both the first and third principal axes.
2nd Diameter (um) The diameter (along each axis) of the best fitting ellipse (or ellipsoid), expressed in pixels.
3rd axis (um) The 3D coordinates of the third principal axis of the ROI shape. Perpendicular to both the first and second principal axes.
3rd Diameter (um) The diameter (along each axis) of the best fitting ellipse (or ellipsoid), expressed in pixels.
Angle (°) Visible only when plugin Angle Descriptor is installed and a polyline with 3 points is drawn. Angle between the 3 points.
Area (um2) Area given in real units computed from the pixel size information from the image.
Center C The coordinates (in pixels) of the center of mass of the ROI along each axis.
Center T The coordinates (in pixels) of the center of mass of the ROI along each axis.
Center X The coordinates (in pixels) of the center of mass of the ROI along each axis.
Center Y The coordinates (in pixels) of the center of mass of the ROI along each axis.
Center Z The coordinates (in pixels) of the center of mass of the ROI along each axis.
Color ROI color, with hexadecimal code, see the documentation on ROI blocks for more information on the hexadecimal color coding in Icy.
Contained The amount of ROIs that are completely inside the current ROI. If an ROI is partially inside the current ROI, it is not counted (use Intersected instead).
Contour (px) The perimeter (in 2D) or surface area (in 3D), expressed in pixels.
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).
Dataset The name of the dataset (typically the name of the image or sequence)  (plugin and block only).
Elongation 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).
Flatness3D 3D only, a scale factor given by the ratio between the second and third diameters (see above). The minimum value is 1 (for an object with perfectly circular section perpendicularly to the major axis).
Folder The name of the folder containing the image file  (plugin and block only).
Full path The full path of the folder containing the image file (plugin and block only).
Global center X (px) The coordinates (in microns) of the center of mass of the ROI along X on the sequence, taking into account the pixel size and the sequence position (plugin and block only).
Global center Y (px) The coordinates (in microns) of the center of mass of the ROI along Y on the sequence, taking into account the pixel size and the sequence position (plugin and block only).
Global center Z (px) The coordinates (in microns) of the center of mass of the ROI along Z on the sequence, taking into account the pixel size and the sequence position (plugin and block only).
Icon Image of the ROI type.
Id Internal identifier for the current ROI. WARNING: This identifier is not stable as it changes with each instance of Icy. It’s just for internal use only.
Intensity center X (px) (ch0) Mean intensity-weighted x position of the ROI.
Intensity center Y (px) (ch0) Mean intensity-weighted y position of the ROI.
Intensity center Z (px) (ch0) Mean intensity-weighted z position of the ROI.
Interior (px) The area (in 2D) or volume (in 3D), expressed in pixels.
Intersected The amount of ROIs intersecting the current ROI. Contrary to the Contained descriptor, partially contained ROIs are counted with this descriptor.
Max Feret diameter (um) The maximum distance between any 2 points of the surface.
Max Intensity (ch 0) Maximum intensity.
Mean Intensity (ch 0) Average intensity.
Min Intensity (ch 0) Minimum intensity.
Name The name of the region of interest (this can be changed from the “ROI” panel in the Inspector window), by default ROIs are called according to their shape, for instance “Polygon2D”.
Opacity The opacity level of the ROI. A value of one means no transparency, a value of zero means that the ROI is completely transparent
Perimeter (um) Perimeter given in real units computed from the pixel size information from the image.
Pitch (°) The counter-clockwise angle of the object main axis on the x-z plane (around the y+ axis). Equal to 0 when aligned with the x-y plane, the sign follows the z axis. See https://en.wikipedia.org/wiki/Ship_motions
Position 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 T 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 The position of the upper left corner of the bounding box around the ROI along each axis (x, y, z, frame and channel).
Position Y The position of the upper left corner of the bounding box around the ROI along each axis (x, y, z, frame and channel).
Position Z The position of the upper left corner of the bounding box around the ROI along each axis (x, y, z, frame and channel).
Read Only The edition state of the ROI. True means no changes can be made to the ROI. False means the ROI can be modified (shape and color modifications).
Roll (°) The counter-clockwise angle around the object principal axis. See (https://en.wikipedia.org/wiki/Ship_motions)
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).
Size C The size (in pixels) of the bounding box around the ROI along each axis (width, height, depth, number of frames and channels).
Size T The size (in pixels) of the bounding box around the ROI along each axis (width, height, depth, number of frames and channels).
Size X The size (in pixels) of the bounding box around the ROI along each axis (width, height, depth, number of frames and channels).
Size Y The size (in pixels) of the bounding box around the ROI along each axis (width, height, depth, number of frames and channels).
Size Z The size (in pixels) of the bounding box around the ROI along each axis (width, height, depth, number of frames and channels).
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).
Standard Deviation (ch 0) Standard deviation of the intensity distribution for each channel inside the ROI.
Sum Intensity (ch 0) Sum of the intensity distribution for each channel inside the ROI.
Surface Area (um2) 3D only, the surface of the element, generally using the contour pixels.
Texture angular second moment (ch 0) Energy, also called “Angular Second Moment” or “Uniformity” is a measure of textural Uniformity of an image. Energy reaches its highest value when grey level distribution has either a constant or a periodic form. An homogenous image contains very few dominant grey tone transitions. Therefore the GLCM (Gray level co-occurrence matrix) for this image will have fewer entries of larger magnitude resulting in large value for energy feature. In contrast, if the GLCM contains a large number of small entries, the energy feature will have a smaller value.
Texture contrast (ch 0) Measure of the local (neighboring) gray level variations. Computed using a gray-level co-occurrence matrix
Texture entropy (ch 0) Entropy measures the disorder of an image. it reaches its smallest value when all elements in the image are equal. When the image is not texturally uniform, many GLCM (Gray-level co-occurrence matrix) elements have very small values, which imply that entropy is very large. Therefore, entropy is inversely proportional to GLCM energy.
Texture homogeneity (ch 0) It can be described as an inverse to the contrast of an image: only entries close to the diagonal of the GLCM (Gray-level co-occurrence matrix) have a big impact on the homogeneity value.
Volume (um3) 3D only, volume given in real units computed from the pixel size information from the image
Yaw (°) The counter-clockwise angle of the object main axis on the x-y plane (around the z+ axis). Equal to 0 when aligned with the positive x axis. See https://en.wikipedia.org/wiki/Ship_motions

Use case

  1. Download these images of fluorescent cells.
  2. Open the image_1.tif.
  3. Do a quick segmentation with the plugin HK-Means
    1. search for HK-Means in the search bar
    2. select the channel 1
    3. set the max object size to 600
    4. set the min object intensity to 30
    5. leave other parameters to default value
  4. Click on the wheel to select descriptors of choice, for instance, Area, Color, Icon, Mean intensity and Name. Click on “Columns to display” to reorder the descriptors by alphabetical order. Use the arrows to move up and down a descriptor in the list (it will change its position in the columns).

Note that here the Mean intensity measure is present three times because there is 3 channels but used only once because the segmentation was done on the channel 1.

To go further, notably on the use of ROI Statistics in protocol blocks, you can explore the protocol associated to these images. The block ROI Statistics (renamed “Compute statistics” is associated to the block Workbook to file to export the results to a spreadsheet). This protocol works in batch on a folder of images.

Resources needing this

6 reviews on “ROI Statistics

  1. H
    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. m
    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. d
    Debora Keller
    Yaya, but the time column and channel columns are missing (and the plot button would be great) :-)
  4. J
    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 5.11.1.0 • Released on: 2022-05-24 11:00:00
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    Description:

    Fixed a small bug in "ROI Statistics Track Processor" + updated for Icy 2.4.0.0

  • Version 5.11.0.0 • Released on: 2021-09-22 17:15:00
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    Description:

    Added Protocols support for "ROI Statistics Track Processor" + some tweaks and fixes.

  • Version 5.10.0.0 • Released on: 2021-08-30 15:30:00
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    Description:

    Fixed statistics export when having no sequence as input (only possible with Protocols).

  • Version 5.9.0.0 • Released on: 2021-06-23 11:10:00
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    Description:

    Fixed missing tracks with ROI statistics track processor.

  • Version 5.8.16.0 • Released on: 2021-03-25 13:53:33
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    Description:

    Fixed UI thread violation

  • Version 5.8.15.0 • Released on: 2021-03-24 15:03:26
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    Description:

    Fixing minor bugs.

  • Version 5.8.14.0 • Released on: 2021-03-11 18:00:00
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    Description:

    - changed "NA" to "ALL" for descriptors Size Z, T, C.
    - changed micro symbol to 'u'
    - fixed NPE bug when using tracks loaded from XML file (ROI Statistics Track Processor)
    - fixed plot display with NaN values ((ROI Statistics Track Processor).

  • Version 5.8.11.0 • Released on: 2020-10-28 10:46:00
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    Description:

    Fixed wrong parameter loading and saving in protocols and javadoc warnings

  • Version 5.8.10.0 • Released on: 2020-10-28 08:16:00
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    Description:

    Fixed wrong parameter loading and saving in protocols

  • Version 5.8.9.0 • Released on: 2020-10-22 10:15:00
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    Description:

    Fixed NPE in updateStatistics() method

  • Version 5.8.8.0 • Released on: 2020-10-19 10:23:00
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    Description:

    Refactoring of the plugin ROIMeasures for better readability

    Added Intensity Center for X Y and Z

  • Version 5.8.7.0 • Released on: 2020-08-12 14:20:00
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    Description:

    Renaming some descriptors names
    Fixed global position to microns taking into account the sequence position

  • Version 5.8.6.0 • Released on: 2020-04-16 14:00:00
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    Description:

    Color export also export color code (hexa string format)

  • Version 5.8.5.0 • Released on: 2020-04-15 18:30:00
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    Description:

    Fixed incorrect selected statistics from Protocols in headless mode (Stephane).

  • Version 5.8.4.0 • Released on: 2020-03-18 18:00:00
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    Description:

    Updated for Icy 2.1 (new exceptions for ROI descriptor interface)

  • Version 5.8.3.0 • Released on: 2019-11-08 19:00:00
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    Description:

    Increased tasks queue size to fix issues when processing many ROI (Stephane)

  • 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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