iCys User Guide

Administrator Tasks Defining Custom Carriers
Carrier Side View
Bottom
Thickness
Base to
Well Height
Outside edge of carrier
{
Rooms
If you do not know the measurements for Base to Well Height or Bottom
Thickness, use the method described in “Determining the Freeform Z
Parameters” on page C-22. When you have entered these measurements,
return to Focus Methods, below.
✧ Retraction Offset—The Retraction Offset is only needed if you have a
carrier that may be bumped by the microscope when moving from room
to room (the only standard carrier for which this is an issue is the 3 Room
Petri Dish). If a Retraction Offset is required, but you do not know it, you
can find it as follows:
– Click on Instrument ⇒ Home Objective. Manually move the stage to a
position between rooms using the touchpad or Remote Control unit
knobs.
– As described in “Finding the Base to Well Height” on page C-22, use
the Remote Control unit knobs and the autofocus monitor to focus on the
top of the carrier.
– When you have a clear focus, click Set from Z for the Retraction Offset
value.
❍ Focus Methods—Specify the preferred (or required) focus method.
✧ Bottom then Top—For thicker plastic-bottomed plates (greater than
400µ) especially; iCys will focus first on the plate bottom, then translate
up by the bottom thickness to the plate top and refocus.
✧ Bottom Only—For glass-bottomed or thinner plastic-bottomed (less than
400µ) plates, iCys focuses directly on the bottom then moves up by the
bottom thickness plus other offsets to bring the sample into focus.
✧ Default—If you want to allow your users to select a focus method (as
discussed in “Focus and Performance” on page 3-33), select both focus
methods and then select the method that you want to use as a default
setting.
Note: If the Bottom Thickness is less than 400µ, select Bottom Only as the only
available focus method. iCys will set the default focus method to match.
❍ Test Autofocus—To test whether you have the values for your carrier set
correctly, you can run Test Autofocus. To test under working conditions,
CompuCyte suggests that you fill the test wells with water or another buffered
solution (such as phosphate-buffered saline [PBS].)
C-20 iCys Research Imaging Cytometer User Guide Revision B