iCys User Guide

Using the iNovator Toolkit iNovator-specific Protocol Modules
iNovator-specific Protocol Modules
The iNovator toolkit provides you with a variety of protocol modules not found in the
basic iCys. Each module’s function and available parameters are explained below. The
module descriptions are organized by the category in which they are found in the
protocol tool box.
Scan
Mosaic Scan Module
The MosaicScan module is similar to the Field Scan module (see page 3-49) with
some exceptions as described here. The MosaicScan module stitches together all of
the scan fields within a given Scan Area prior to segmenting events, developing event
features and displaying data for that scan field. This allows the MosaicScan to
segment events (or draw phantom contours) that cross scan field boundaries.
MosaicScan also reformats the data to provide a 1:1 aspect ratio of the X:Y resolution.
❑ General Tab—Under the General tab you can specify the objective you are using,
the X-step size for the scan, and the field size as shown below:
❍ Objective—Allows you to select which microscope objective lens you will
use for this scale of the run. When not actively scanning, the objective is
moved out of the way of the motorized stage to prevent a carrier from being
bumped by the objective.
❍ X Step size—Determines the size of a single stage step in the X direction.
From the X Step pull-down, select any value from .5µm to 20µm (in .5µm
steps). For a low-resolution scan, select 20µm, the default value.
❍ Field size—Determines the number of X steps that iCys will take when
scanning. You can choose a percentage (100%, 50%, or 25%) or choose to
generate a square scan field. The scan field and pixel size are determined by
the dimensions you select and are displayed in the Scan field dimension
window below. A 100% scan field is 1000 scan lines wide, a 50 % one is 500
B-8 iCys Research Imaging Cytometer User Guide Revision B