Adjusting Mask And Collecting Well Factors; Preparation; Capturing The Image - BIO RAD iCycler iQ Packing List And Installation Manual

4. Open the CD-ROM directory and open the Utilities folder. Open the folder called
Firmware Upgrade and copy the files Upgrade.exe and icycupdt.bin to the Firmware
Upgrade folder.
5. From the Explorer, open the Upgrade folder on the C drive and double click on
Upgrade.exe. The utility will open and automatically download the new version of the
firmware over the serial port.
6. When the upgrade is complete, a message will be displayed telling you that the upgrade
has been successfully completed. You must turn the iCycler off and back on to
implement the new version of firmware.
Section 6
Adjusting the Mask
It is necessary to align the optical unit over the reaction module whenever any of the
following occur:
• a new Optical Module is installed,
• the software is reloaded,
• the system is moved or subjected to a shock.
This procedure involves adjusting the "mask" that defines the area of the CCD assigned
to each of the 96 wells. The mask is a software template, stored in the mask96.ini file, with
96 "holes" which overlay the CCD. The mask identifies the location of the wells relative to
the CCDs. The mask adjustment procedure centers each of these holes over the wells of the
plate.
The process of adjusting the mask requires:
1. Capturing an image.
2. Optimizing the DC offset.
3. Positioning the individual masks.
All these operations are carried out using the utility iQconfig.
Typically mask adjustment is done at initial installation and will not require adjustment
unless the iQ Detector is removed, or if the instrument is moved.

6.1 Capturing the Image

1. Make an appropriate dilution (15–50 nM) of sodium fluorescein and aliquot 50 µl into each
of the 96 wells. Place the plate inside the iCycler reaction block and close the lid.
2. From the Start menu, select iQconfig or use the Explorer to open the file
c:\Program Files\Bio-Rad\iCycler\Ini\iQconfig.exe
This brings up the iQ Configuration window and two dialog boxes: the Image dialog box
and the Gain dialog box (see Figure 6.1.)
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