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ROI Inclusion analysis

Publication ID: ICY-B3M8X7

Short Description

Calculates the number of objects (e.g. spots, bacteria etc.) inside larger objects (e.g. nuclei, cells etc.), as well as their distance to the edge of their enclosure.

Documentation

This method performs the inclusion analysis of a so-called "inner" ROI with respect to a so-called "outer" ROI. It is first determined whether the specified "inner" ROI is contained in (or overlaps with) the specified "outer" ROI. If so, three distance values are measured:

  • An "oriented" distance (in pixels) from the center of the "inner" ROI to the edge of the "outer" ROI, calculated along a ray going from the center of the "outer" ROI through the center of the "inner" ROI
  • The equivalent, relative "oriented" distance from center (0) to edge (1).
  • The "non-oriented" (closest) distance from the center of the "inner" ROI.

 

Parameters:
Outer ROI: In protocols => the list of outer (i.e. enclosing) ROI; In standalone mode => the sequence containing them.
Inner ROI: In protocols => the list of inner (i.e. enclosed) ROI; In standalone mode => the sequence containing them.
Include overlapping ROI: check this box if partially overlapping ROI should be considered as "inside", otherwise they are discarded from the analysis

 

The output is given in the form of a workbook with two pages:
Details: Detailed analysis containing the measured distances for each object with respect to its enclosing region.
Summary: A summary containing for each the total number of inner objects per outer objects, and their average distance to the edge.

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Changelog

  • Version 1.3.0.0 • Released on: 2017-09-27 09:40:11
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    Description:

    Multi-threading for speeeeeeeed

  • Version 1.2.0.0 • Released on: 2017-08-31 09:18:20
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    Description:

    Added time information to the analysis

  • Version 1.1.4.0 • Released on: 2017-07-05 14:27:24
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    Description:

    Fixed the detection of intersecting ROI

  • Version 1.1.3.0 • Released on: 2017-06-15 11:04:19
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    Description:

    Fixed the inclusion analysis on ROI with different channels

  • Version 1.1.2.0 • Released on: 2017-06-08 16:55:45
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    Description:

    Fixed handling of 3D vs 2D ROI

  • Version 1.1.1.0 • Released on: 2017-06-08 16:04:02
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    Description:

    Handle point-lie ROI in 2D

  • Version 1.1.0.0 • Released on: 2016-12-11 15:13:59
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    Description:

    New measure: absolute (i.e. non-oriented) distance to edge

  • Version 1.0.0.0 • Released on: 2016-08-26 11:23:37
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    Description:

    * Bumped version to 1.0
    * Inverted the order of the result pages (summary now comes before details)

  • Version 0.0.1.0 • Released on: 2016-08-26 11:10:27
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