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User reviews

(6)
5 star
1
4 star
4
3 star
1
2 star
0
1 star
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average rating: 4


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IcyLyd
12 Jul 2015 02:49
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.
Judite Costa
30 Jun 2015 13:59
Thank you for addressing reported bugs quickly... Working great now!!! Keep up the good work.
Debora Keller
27 Jan 2015 19:59
Yaya, but the time column and channel columns are missing (and the plot button would be great) :-)
MRC LMCB
16 Jul 2014 19:34
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?
Biomedical Imaging Group
25 Oct 2013 11:22
Super useful! When is the 3D version coming along?
Hydrogel
04 Oct 2012 12:12
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.

ROI Statistics

by Alexandre Dufour

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.

Publication Id
ICY-W5T6J4
See technical details
View complete changelog

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.