iCys User Guide

Using the iNovator Toolkit Multi-scale Scanning
Multi-scale Scanning
Introduction
Unique Features
Multi-scale scanning involves defining a protocol for two sequential scans referred to
as scales (because they are usually done at different resolutions). Typically, the first
scale is done using the Mosaic Scan module at low resolution. This is referred to as a
scout scan because it is scouting for relatively large structures such as tissue
microarray elements, tissue sections, structures within tissue sections or cell colonies.
Events found in this scout scan may be designated Scan Area Events. These scan area
events become the defined scan areas for the second scale, typically higher resolution
scan. Such a scan is defined in Tutorial 4, the protocol of which is shown below.
Different Detector Module Settings
The two scales' Detector module settings are independent of one another. Data
channels, virtual channels, detector gain and offset, laser selection and (if applicable)
laser power may be independently selected and set for each scale. This allows the user
to set up the system for the very different scan requirements of scout vs. high
resolution scans.
Different Scan Module Settings
The scan module settings are at the heart of defining the operation of each of the two
scales. As was mentioned, the first scale is a Mosaic Scan, typically at low resolution
B-30 iCys Research Imaging Cytometer User Guide Revision B