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11 Dec 2017 10:38
15 Nov 2017 19:02
Great! Very useful with spot counting within Protocols

ROI Inclusion analysis

by Alexandre Dufour

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.

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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.


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.