illumina iScan Reference guide

iScanTM System
Quick Reference Card
Starting Up and Shutting Down the iScan System
To... Do this...
Start the iScan
Reader
Press the Power switch on the back of the right-
side panel.
Start the
GenomeScan
software
From the Windows Start menu, select
Programs | Illumina | GenomeScan, or double-
click the GenomeScan icon on the desktop.
Shut down the
iScan System
To close the software, click the Menu button
and select Exit.
To shut down the iScan computer, from the
Windows Start menu, select Shut Down.
Then choose Shut down from the Shut Down
Windows dialog box and click OK.
To shut down the iScan Reader, press the Power
switch on the back of the right-side panel.
For more information, see “Getting Started” in the iScan and AutoLoader2 System
Guide.
iScan Reader Status Lights
Status light Description
Power
(blue)
Steady blue indicates the iScan Reader is on.
Ready
(green check)
Steady green indicates the iScan Reader has
been initialized and is ready to scan. The Ready
light flashes during initialization.
Warning
(amber triangle)
Solid amber indicates an instrument error has
occurred. Try cycling the power.
Scan bar
(vertical - blue)
Steady blue indicates the iScan Reader is
currently scanning. The Scan bar is an LED pipe
to the left of the iScan Reader tray door.
For more information, see “Getting Started” in the iScan and AutoLoader2 System
Guide.
Loading and Ejecting BeadChips
To... Do this...
Eject BeadChips
from the iScan
Reader
Open the GenomeScan software.1
Press the2 Open/Close Tray button, located under
the status LEDs, on the front panel of the iScan
Reader.
Lift the carrier out of the iScan Reader tray to remove3
the entire tray of BeadChips. Press and hold the
Lift button on the BeadChip carrier to raise the
BeadChips up for easier access.
Load BeadChips
into the carrier
Hold the BeadChip by the barcode end.1
Place it in a slot so that the non-barcode end presses2
up against the raised stop.
Place up to four BeadChips this way. They may
not lay evenly in their individual slots, but each
BeadChip should fit between the indented sides of
the slot.
Gently press the3 Lift button to open the latches and
raise the pin beneath each BeadChip, then release it.
The BeadChips should settle down firmly into the
slots. If any remain uneven, press and release the Lift
button again.
Load the carrier
into the iScan
Reader
Open the iScan Reader tray by pressing the
1 Open/
Close Tray button on the iScan Reader or selecting
Scanner l Open Tray from the GenomeScan
software menu. The Open/Close Tray button is
located below the Status LEDs and has an up-arrow
with a line under it.
If there is no adaptor plate in the iScan Reader tray,2
load the adaptor plate using the three orientation
holes in the iScan Reader tray as guides.
Line up the notches on the carrier with the silver3
beads on the adaptor plate.
Lower the carrier gently onto the plate and lightly4
jiggle it from side to side to ensure that it fits
securely. Do not press down on the iScan Reader
tray.
For more information, see the iScan and AutoLoader2 System Guide.
Scanning BeadChips
To... Do this...
Start the GenomeScan
application
Double-click the GenomeScan icon on
your desktop.
Log in to the
GenomeScan application
Enter your username and password (if required).
Scan barcodes Click Start, load BeadChips, and click Next.
Create custom scan
settings
Click the Menu button and select Tools | Options.
Select the Scan Settings tab.
Change scan settings In the Setup screen, click Settings.
Rescan barcodes In the Setup screen, click the Menu button and
select Scanner | Scan Barcodes.
Begin the scan Click Scan.
Scan Progress Indicator Colors
Indicator color Description
Light Blue Section to be scanned.
Orange Section in the process of being scanned or
registered.
Green Scan and registration of section successful.
Red Scan and registration of section failed.
For more information, see the iScan and AutoLoader2 System Guide.
Setting Options
To... Do this...
Change input and output
folder paths
In the Setup screen, click Browse. Navigate to the
desired folder or create a new folder. Click OK.
Configure error handling From the Tools menu, select Options. Select Halt
Scan on Errors or Continue Scan on Errors.

Scan Status Icons
Icon Description
Aligning BeadChips
Software is communicating with the reader
Software is communicating with the reader
Focusing
Performing Checks
Scanning Matrices
Scanning Matrix
Registering Image
Saving
Stopping
Pausing
Idle
Camera
Auto Centering
Auto Tilting
Moving Tray Out
Moving Tray In
Moving X Motor
Moving Y Motor
Moving Z Motor
Moving Several Motors
Viewing Images
To... Do this...
View an image file Click on a scanned section from the Scan Progress
Indicator Window (located on the left side of the screen).
An image of the selected section appears in the Image
Window on the right side of the screen.
Set pixel intensities Use the sliders on the Image control bar to adjust the
pixel intensities of your image.
The pixels with a brightness below the bottom slider
are set to black. Pixels with a brightness above the top
slider are set to full brightness. Pixels whose brightness
falls between the sliders are displayed with enhanced
contrast.
The closer together you place the sliders, the sharper the
image contrast for pixels within that range will become.
Adjust the brightness On the Brightness control bar, click and drag to move
the brightness slider. Move it up to increase image
brightness or down to decrease image brightness.
Adjust the contrast On the Contrast control bar, click and drag to move the
contrast slider. Move the slider up to increase the image
contrast and down to decrease the image contrast.
Adjust the color On the Color control bar, click and drag to move the
color slider. Move the slider up to shift the image color
ratio to be more red. Move the slider down to shift the
image color ratio to be more green.
Zoom in or out on an
image
Place the mouse over the image. Click in the image, in
the area you wish to zoom. Using your mouse’s scroll
wheel, scroll down to zoom in on the image and scroll up
to zoom out.
Pan an image Click and hold on the image. Drag the image in the
direction you want to move the image and away from the
area you want to view.
For more information, see the iScan and AutoLoader2 System Guide.
Copyright © 2008 Illumina, Inc.
All rights reserved
Part # 11313555 Rev. A
Image Toolbar and Image Control Icons
Icon Description
Auto Contrast - Resets the image contrast and brightness to
the default settings.
Zoom Out - Zooms out on the image of the selected section in
the Image Window.
Copy to Clipboard - Copies the image in the Image Window to
the clipboard so it can be pasted into another program.
Overlay Cores - Allows you to confirm the registration of a
specific Red or Green image.
Show Green Channel - Shows only the green channel in the
Image Window for the scanned section.
Show Red Channel - Shows only the red channel in the Image
Window for the scanned section.
Overlay Channels - Shows both the red and green channels
simultaneously in the Image Window for the scanned section.
Display Intensity Threshold Controls - Displays the pixel
intensity and color control bars.
Display Brightness/Contrast Controls - Displays the image
contrast, brightness and color control bars.
For more information, see the iScan and AutoLoader2 System Guide.