In this post we’ll pull off the decorative trim and start to take a detailed look at what is in the box with a focus on the lasers.

The back of the sequencer has a power plug with two fuses and USB, serial, and camera connections.

 

Removing the blue cosmetic trim panels (they simply pull off) reveals two filtered air intakes, one on each side of the instrument. There must be lots of other ways for air to get in to the sequencer as the instrument we bought had a bunch of dust bunnies in it and many of the parts inside had accumulated a fair amount of dust (evident in the pictures below).

 

The panels on the sides and back are simply screwed on. Removing them reveals the guts of the machine. One side (on the left from the back) contains the imaging core, the lasers, and the main power supply. The other side (on the right from the back) contains the cooler, the pumps and actuator, and heated chamber for the fluidics, the stage controller, a USB hub and a USB to serial port converter, a 24 volt power supply, and one of only two customized circuit boards in the whole sequencer.

 

The laser box contains the controller for the three lasers in the system (the focusing laser and the two TIRF excitation lasers). It is mounted on a shock absorbing mount which doubles as a heat sink to the side of the imaging core. Notice the dust collected on the cooling fan intake on the laser box – the filters on the sides on the GA IIx don’t appear to do a whole lot.

 

The single fiber optic output of the laser box is fed into a shock mounted (the two metal plates have elastomers? between them) multimode scrambler which appears to be a re-branded General Photonics MMS-001B. It functions to generate a uniform and stable light distribution at the fiber output by literally squeezing a long strand of fiber optic at a high frequency in six directions. The output of the scrambler is used for TIRF illumination.

 

Removing the cover of the laser box reveals two lasers (a Laser Quantum GEM 500mW 532nm and a Melles Griot 85-RCA-400 660nm 400mW), each with a controller and a circuit board. Mounted on the circuit board is a Luminos 1×2 fiber optic switch and a Wavelength Electronics WLD3343 2.2A laser diode driver for the focus laser. The green and red lasers are connected to the 2×1 switch which controls which one is active. The output of the switch goes to the scrambler which ensures illumination uniformity.

 

Here are pictures of the lasers, the fiber optic switch, and the laser driver after disassembling the parts in the laser box.

 

These class 3B (Melles Griot) and 4 (Quantum GEM) lasers are high power lasers. They can cause permanent vision loss in a fraction of a second. Even diffuse reflections from class 4 lasers can be eye hazards and these lasers are fire hazards! Please make sure that you familiarize yourself with laser safety (such as this excellent safety overview at Sam’s Laser FAQs) before attempting to use these lasers for any purpose other than as an integrated part of the Illumina GAIIx sequencer.

Detailed information (including pinouts, the RS232 command set, and images of both the laser and controller opened up) needed to operate the Quantum GEM 532 laser can be found here.  The RemoteApp laser control software for controlling the laser remotely can be downloaded from Laser Quantum here.

The  Melles Griot laser is apparently a custom laser but the controller is their standard universal laser controller without an enclosure. The manual for the L44000 controller contains pinout and command set information.