iCys User Guide

Generating Analytical Data Contours
Contours
Contouring is the automated process of setting boundaries to segment and define
individual events. The Channel, Threshold, and Contour sections of the Protocol ⇒
Contour menu and the Protocol ⇒ Event menu allow you to define contours. (see
“Protocol” on page 3-30.) The features of these menus are summarized below.
❍ Channel—The first step in defining a Contour is choosing the Channel on
which to base the definition. Select a Channel from the Protocol ⇒Contour ⇒
Channel menu. For more information on selecting a channel see “Channel” on
page 3-52.
❍ Threshold—The Threshold and Channel determine what qualifies as an
event. The Threshold defines the contiguous pixels whose values are equal to
the calculated background for the event plus the threshold value for that
channel. This contour defines the presence of the event at that location.
Threshold settings are available in the Protocol ⇒ Threshold menu. Primary
(Threshold) contour settings are found in the Protocol ⇒ Contour menu. For
more information on setting the Threshold see “Threshold” on page 3-52.
❍ Integration—Defines the boundary within which the total fluorescence of the
event will be calculated (integrated). Settings for the Integration contour are
found in the Contour tab of the Protocol ⇒ Event menu. For additional
information on setting the Integration contour, see “Defining the Integration
Contour” on page 4-7
❍ Background—Defines two boundary lines that are used to calculate the
background fluorescence for an event. Setting for the Background contour are
found in the Background tab or the Protocol ⇒ Event menu. For information
on defining the Background contour see “Generating Background Contours”
on page 4-8
❍ Peripheral—Defines two boundary lines that are used to determine the
periphery of an event. For additional information on Peripheral contours, see
“Peripheral Contouring and Background Correction” on page 4-13
❍ Phantom—Defines contour lines based on non-event criteria. Phantom
contours are described in “Phantom Contours” on page 4-11.
The figure below shows a magnified view of an event with the various contours
displayed. Note the gradations of grayscale colors in the individual squares. Each of
these squares is a pixel. By moving the cursor around in the Field Image window, you
can read the individual values of each pixel in the status bar.
4-2 iCys Research Imaging Cytometer User Guide Revision B