iCys User Guide

iCys Cytometric Analysis Software Application Overview iCys Task Bar
Contour Modules
The Contour section of the Menu Bar allows you to define Contour parameters,
including channel, threshold, color, and name. Additional information on defining
Contours can be found in “Types of Contours” on page 4-3.
Channel
Creating or clicking on a Channel module opens the following menu
.
❍ Channel—The pulldown Channel menu allows you to choose a contour
channel from a list of active channels, including virtual channels.
❍ Scale image—Checking this box will scale the image to the aspect ratio of the
scan.
If selected, the new image is created so that the aspect ratio is always 1 to 1.
If cleared, the new images aspect ratio is based on the X-Step and objective.
The aspect ratio must be selected when the subsequent modules include shapesensitive
operations such as Watershed and morphological filters.
Threshold
Threshold represents the minimum amount of pixel fluorescence required to
generate a contour for an event.
When setting the threshold you can choose Auto, which will automatically set the
threshold, or you can set it manually using a slider.
The threshold module will display either the word Auto or the numerical setting
you have entered.
There are two methods you may use to manually adjust the threshold.
3-52 iCys Research Imaging Cytometer User Guide Revision B