iCys User Guide

May 6, 2005 Using the iNovator Toolkit
There are three options for generating dynamic scan areas and events: Whole section,
Rectangle and Random.
❑ Whole section—generates a contour that meets the segmentation criteria in the
protocol around the entire event. This contour becomes the event boundary and
the dynamic scan area boundary.
❑ Rectangle—generates a contour around the entire event as above. iCys then
generates a rectangular scan area within this Whole section contour, centered on
the centroid of the Whole section contour.
❑ Random—generates a contour around the entire event as above. iCys then
generates a specified number rectangular scan areas placed randomly within the
Whole section contour. This is pictured below for a Tissue Micro-Array element.
Additional Parameters are:
❑ Component name—Specify the name of the component (as in the Event module,
see page 3-56.)
❑ Size—If either Rectangle or Random is selected, the Height and Width of the
rectangle must be specified in microns.
❑ Count—If Random is selected the number of scan areas to be generated within
each threshold contour is specified.
❑ Color—The color of the contour line is specified.
❑ Show event name—Checking this option displays the event ID number (or
ordered pair if the Array Alignment module is used.)
Revision B iCys Research Imaging Cytometer User Guide B-25