iCys User Guide

May 6, 2005 Using the iNovator Toolkit
to find areas of interest for more detailed analysis. For example, a slide will be scouted
to identify the locations of tissue samples. When identified, each tissue can then be
analyzed in detail using a higher resolution Field Scan or Mosaic Scan.
The settings required to locate tissue on a slide may be quite different from the
settings for analyzing the structure within those tissues. Therefore, one might define a
Mosaic Scan with a 10X objective and 20 micron steps to be followed by a Field Scan
with a 40X objective and .5 micron steps.
Scan Area Events and Other Events
Multiple event components may be defined in either the first or second scale scan.
Such a protocol is shown below. One of these event components must be designated a
Scan Area Event. The Scan Area Event module generates event data as any other
event component but additionally the Scan Area Event contours are used as scan areas
for the second scale scan. These scan areas, generated from Scan Area Events, are
called Dynamic Scan Areas.
Manipulating Dynamic Scan Areas
While in the Pause state between scans, you may manipulate the Dynamic Scan Areas
(DSAs) generated by the 1st scale scan or create new DSAs manually. When the
system is Paused between the 1st and 2nd scale scan, the bridge between Scan
modules will appear as shown below, pink and with the word Paused visible.
For more information about getting to a paused state, see “Analysis Modes for Multiscale
Scans” on page B-34.
To manipulate an existing DSA, click on the DSA of interest. "Handles" will appear at
the four corners of the DSA as shown below for the TMA element in the upper left of
the image.
Revision B iCys Research Imaging Cytometer User Guide B-31