iCys User Guide

May 6, 2005 iCys Cytometric Analysis Software Application Overview
Width—The distance between the first and second background contour. Set
the width such that the outer contour line includes the dimmest pixels adjacent
to an event.
Use pixels between—When determining the background, you usually want to use
those pixels that represent the mean pixel value, such as 30-70%. If, however, the
background is very bright, you might want use a lower threshold, such as 20-50%.
Color—Select the color of the background contour lines. If color is set to None,
no visible contours will be drawn.
Corrected Channels—Allows you to select the individual channels that will use
the background correction.
Peripheral Tab
Selecting the Peripheral tab opens the following menu.
Peripheral contour—Defines two boundary lines that are used to determine the
periphery of an event.
Distance—Specifies the distance between the integration contour and the first
peripheral contour. Set the first peripheral contour such that it picks up the
brighter peripheral pixels.
Width—Specifies the distance between the first and second peripheral
contour. Set the width such that the outer contour line includes the dimmer
pixels that are still within the periphery of an event.
Details on the Contour, Background, and Peripheral tabs are found in “Integration
Contours” on page 4-7, “Background Contours” on page 4-8, and “Peripheral
Contours” on page 4-9.
Phantom
Phantom contours are events generated by iCys from circular contours applied
over the laser-scanned image.
Creating or clicking on a Phantom module opens the following menu.
Revision B iCys Research Imaging Cytometer User Guide 3-57