iCys User Guide

Using the iNovator Toolkit Multi-scale Scanning
Image Hierarchy
The first scale Mosaic Scan image is displayed in the Well Image window. As the
second scale Field Scan progresses a mosaic image of each Dynamic Scan Area is
displayed in the Region Image window. Each scan field image is displayed in the Field
Image window.
From the Well Image, clicking on a particular Scan Area Event will display that event
in the Region image window. Similarly, clicking on a particular scan field location in
the Region Image will display that scan field in the Field Image window.
Analysis Modes for Multi-scale Scans
New Runs
When setting up a new run or re-running an existing run, the user has several
operating modes to choose from. What is meant by operating modes is this: Will the
systems be acquiring new data by scanning a sample or will the system be reanalyzing
previously acquired images by performing a virtual scan of those images? With multiscale
scanning, certain combinations of these two modes are possible. All of these
options are described below.
Live-Live
With a new run, data must be acquired with a live scan. If a fully automated run is
chosen then data will be acquired for both scales by live scanning of the sample. To set
up a fully automated 2 scale scan, make sure the bridge between the two Scan modules
is NOT set to pause by clicking on the box on the bridge until it appears blank, as
shown in the figure below.
Test scans should be made to set the hardware and software protocol parameters for
both scale scans. To set up the protocol for both scales create an abbreviated scout
scan area, turn on the pause between scales and select the Test Scan button or the
Next button (single field). During the scout scanning make the desired changes to the
PMT settings. (NOTE: This may take several iterations of starting and stopping the
test scan.) When the PMT settings are complete, stop the scan and then acquire
another Scout scan using the correct PMT settings. During the Pause, use the View
Image tool as described in “Using the Protocol Menu View Image Feature with
iNovator” of this appendix. Once you are satisfied with the contouring protocol, select
or create Dynamic Scan Areas in the Well Image window to use for setting up the 2nd
scale hardware and contouring protocol. Delete any unnecessary dynamic scan areas.
(NOTE: You may want to increase the size of the dynamic scan areas to be large
enough to complete the 2nd scale setup.) Once you have selected the dynamic scan
areas, press the Paused button to continue the test scan in the 2nd scale. During test
scanning of the 2nd scale make the necessary hardware and contouring protocol
changes. (Note: It may take several iterations of test scanning to accomplish the
setup).
B-34 iCys Research Imaging Cytometer User Guide Revision B