The first GAIIx parts I bought on Ebay (before I knew they came from the sequencer) were the ASI stages and filter wheel. The set consists of a MS-2000 XY stage, a LS-50 linear stage (used for focus), a FW-1000 filter wheel (8 position, accepts 25mm filters), and an LX-4000 controller.
The stages and filter wheel are off the shelf ASI parts. The controller appears to have been custom made for Illumina. While it uses a standard ASI serial command set, each command set requires a prefix. Luckily, Erich Hoover wrote a patch for the Micro-Manager ASI device drivers (stages, filter wheel) to make the LX-4000 work.
Connecting the LS-4000 is straight forward. The connection to the computer is a standard serial connection which plugs into the port labeled RS-232 on the Z/F card (not the FW-1000 card). The filter wheel connects to W0 or W1 on the FW-1000 card, the linear (Z) stage connects to the Z/F stage connector on the Z/F card, and the XY stage connects to the X/Y stage connector on the X/Y card. As far as I can tell, the linear encoder connection on the X/Y card was used to monitor whether the sliding door on the front of the GAIIx was open or closed.
If the XY stage does not work make sure to turn it on using the settings in Micro-Manager (we set this in the start up settings).
One of the filter wheels we received was slightly out of alignment. You can change the filter wheel offset using this program from ASI (runs on XP, requires installation of the bundled ActiveX control). We have not tested ASI’s newer console software with the LX-4000.