Repair notes for Spex Fluorolog 2 Fluorescence Spectrophotometer

This page contains information we discovered when repairing our Spex Fluorolog 2 spectrofluorometer (model no. CM1T11I) in room 341. Although this is a fine instrument, it is almost 20 years old and the technical support people at the vendor are no longer able to repair it or provide information about it. However, we were able to repair it on our own. The purpose of this document is to serve as a reference for when the chewing gum and twine wear out, and we have to repair it again.
Spex Fluorolog 2
Fig. 1. The dual emission version of the Spex Fluorolog 2.

Jumper settings and I/O connections

The controller contains two CTI cards and two high voltage cards. (Some models may have only one of each). The CTI card has digital I/O ports along the top, and two DB15 connectors on the back for analog input from the photomultipliers. One CTI card is needed for each emission monochromator / photomultiplier combination. If there are two CTI cards, all the I/O connections are made to the master card, and the two cards are connected by a short jumper cable. Jumpers J1 to J9 on both cards must be properly set for the cards to work.

The high voltage cards supply 950 and 400 VDC for the photomultipliers.

We are interested in purchasing spare CTI cards and high-voltage cards. If you have one, please contact me at the address above.
Spex CTI Card
Fig. 2. Spex CTI card

  1. The I/O connections at the top of the card are made through the blue plastic connectors (See Fig. 3) to DB9 connectors on the back of the computer. Do not connect the blue cable from card 1 to card 2 upside-down, or it will blow out the card.
  2. Older cards have numerous fuses on each card. These are small white squares with a thin wire visible through a window. They are easily blown, and blowing a fuse is a common source of problems. These fuses can be safely replaced with wire jumpers. On later cards, these fuses were replaced by wire jumpers.
  3. The monochromators are 1681B single-grating monochromators. When powered on, they supply a potential of 3 volts to the blue connectors on the CTI card. The monochromators should be turned off before connecting or disconnecting cables to the CTI card.
  4. The blue connector for the shutter at locations 220 and 210 should be aligned to the far edge of the card. The number of pins on the card does not match with the connector. When the spectrofluorometer is first powered up, there should be an audible click from the shutter if the card is functioning.
  5. If there are two CTI cards, one must be set to Master and one set to Slave. Setting jumpers 9,8, and 4 makes it a master. Setting jumpers 9 and 7 makes it a slave. This also sets the IRQ to 5. If the IRQ is wrong, or if both cards are set the same, the software will either hang, or it will say "CTI board interrupt timeout error." The boards can be in any slot; as with any ISA card, moving to another slot is unlikely to fix a problem.
  6. Both of our CTI boards are only partially functional. If a board does not cause the shutter to click, it still might be able to control the monochromators. Do not swap the boards on the Spex in room 341.
  7. Make sure the CTI boards and power supply cards are not touching each other. This can cause the board to short out. We placed a sheet of cardboard between them to prevent contact.
Location Connection
220, 210 Shutter (through adapter)
200 Monochromator 4 (through DB9)
190 Monochromator 3 (through DB9)
180 Monochromator 2 (through DB9)
170 Monochromator 1 (through DB9)
160 To board #2
150 Chopper
Jumper Setting
(Master)		 Setting
(Slave)
J17-18 J17 (top) J17 (top)
J19-20 1 to 3 (wire) 1 to 3 (wire)
J23-24 J23 (bottom) J23 (bottom)
J21-22 J22 (right) J22 (right)
J9 1 1
J8 1 0
J7 0 1
J1 0 0
J2 0 0
J3 0 0
J4 1 0
J5 0 0
J6 0 0
Jumpers and board connections

Software

  1. At least some versions of the DM3000 software check the serial number on the CTI board. If the board is changed, it will say: 
    Serial number(s) on interface board(s) 
do not match the expected values.
    The software then says: 
    Hardware key does not return proper value. 
Please check your printer for error conditions. 
Access denied.
    and dumps you to a DOS prompt. The serial number is encoded in a PAL chip on the board. In other words, the board has a form of copy protection that seems to be designed to prevent people from repairing the spectrometer. We could find no way to specify the board's serial number in any of the configuration files or in the dm3000 executable itself. We have not yet figured out how to get around this. The vendor expressed surprise when asked about this feature, saying it is not present in more recent versions of the software.
  2. The monochromator should move back and forth when the software starts up, before the software asks for the starting wavelengths. If the monochromator does not move, the board is not functioning.
  3. The number of CTI cards and the IRQ must be correctly specified in the hardware.ini file.
  4. If the CHOPOFF.SYS driver is loaded in config.sys, it will print out the I/O addresses of each CTI card. This is helpful in determining whether the cards are present. The driver appears to serve no other function.
  5. The software was originally supplied on 5¼" floppy disks. All floppy disks become unreadable over time (as have our original floppies). Be sure to make copies on a more up-to-date medium.

1681B Monochromators

Each monochromator has its own power supply, which is fed to the CTI card through a serial cable. The CTI card makes contact closures that turn a stepper motor in the monochromator. Inside the monochromator, the motor is connected to the power supply by an 8-pin nylon connector. The eight pins connect to each end of the four coils in sequence (i.e., 1,1,2,2,3,3,4,4). There is no common wire. On the DB9 end of the serial cable, pin 4 and 5 should have 2.4 volts with respect to pin 3, pins 6-9 should have 3 volts with respect to pin 3, and pins 1 and 2 should have 0 volts with respect to each other. A sequence of momentary contacts between pin 3 and pins 4-9 rotates the motor.

Replacing the computer

The most common repair on the Spex is replacing the PC that acts as a controller. Computers with ISA slots are now only available as "industrial computers" from several Internet vendors for about US$ 1000.

We replaced our original PC with an RSI 4U rackmount system (Fig. 1 at right) with 9 ISA slots, from www.interloper.com. This vendor is highly recommended. Their technical support and service were excellent. The quality of the PC that we purchased from Interloper is much higher than the original PC-AT that came with the spectrometer.

Power connections

Computer board and cabling inside RSI 4U rackmount
Fig. 3. Computer board and cabling inside RSI 4U rackmount

When replacing the computer, three 120VAC leads (hot, ground, neutral) must be connected to the inside of the new PC's power supply. This connection should be downstream of the PC power supply switch. This 120 volt supply connects through a diamond-shaped Molex connector to a small Spex power supply, which needs to be saved from the old computer and mounted inside the new one.

The power supply supplies 15 and 30 VDC to the CTI cards and high voltage cards through small white 3-wire connectors (Fig. 4) that plug into the top of each card. The PC should be unplugged before attaching the connectors, because the connector sometimes arcs to the card.

Wiring of 15/30V power connector
Fig. 4. Wiring of 15/30V power connector

Bios settings

The correct BIOS settings are critical for these ISA cards. If they are set incorrectly, the software will hang with no error messages. DO NOT load "Optimized defaults" or "Fail-safe defaults" in the BIOS. This will make the CTI card appear to be non-functional. This is the most difficult aspect of repairing the Spex, because the common defaults do not recognize Spex's cards, and it is very difficult to distinguish between a bad card and an incorrect Bios setting. In both cases, the software just hangs.

Below is a known good BIOS configuration on our RSI rackmount.
Standard
floppy 3 mode Disabled
video VGA/EGA
halt on no errs
total memory 523254k
Advanced
virus Disabled
cpu cache Disabled
quick size test On
1st boot HD0
2nd boot Floppy
3rd boot CDROM
other On
skip floppy Disabled
numlock off
A20 fast
typematic Disabled
security Disabled
APIC Disabled
OS non-OS2
Report no FDD no
EPA off
Advanced chipset
DRAM by SPD
mem freq DDR333
system bios cache on
video bios cache on
memory hole on
delayed trans on
delay thermal 16 min
on-chip vga on
frame buffer 1 MB
boot display auto
onboard lan Disabled
Integrated peripherals
primary pci ide on
ide 1 master PIO auto
ide 1 slave PIO auto
ide 1 master UDMA auto
ide 1 slave UDMA auto
secondary pci ide Disabled
usb Disabled
AC97 Disabled
init display pci slot
idd hdd block on
power on button only
onboard fdc on
serial 1 3F8/IRQ4
serial 2 2F8/IRQ3
uart normal
parallel port 278/IRQ5
parallel port mode normal
pwr non after fail Disabled
midi Disabled
watch dog Disabled
doc D8000-D9FFF
Power management
acpi Disabled
acpi type s1(POS)
pwr mgt user define
video off blank screen
video off suspend no
suspend type stop grant
suspend mode Disabled
hdd power down Disabled
soft off inst off
cpu throttle 87.5%
wake up lan Disabled
pwr on by ring Disabled
resume alarm Disabled
timer events all Disabled
PNP / PCI
PNP OS no
reset config Disabled
resources manual
IRQ all=Legacy ISA
DMA all=Legacy ISA
pci/vga snoop Disabled
assign irq for vga Disabled
Int Pin 1 5
Int Pin 2 5
Int Pin 3 5
Int Pin 4 5
Int Pin 5 5
Int Pin 6 5
Int Pin 7 5
Int Pin 8 5
PCI Health status
cpu warning temp Disabled
cpu throttle temp Disabled
CPU Voltage control
auto detect Enabled
spread spectrum Disabled

Power-up Sequence

  1. The shutter should make a clicking noise when the PC is first turned on.
  2. The DM3000 logo is displayed for 20 sec. During this time, the wavelength settings on the monochromators should move as the hardware is initialized.
  3. After 20 sec, the DM3000 software then checks for error conditions. If no errors are found, it will proceed to the wavelength input screen.

Miscellaneous

  1. The photomultipliers use un-cooled Hamamatsu R508 photomultipliers, which are sensitive from 185 to 810 nm. The extra red sensitivity is a trade-off with noise, and we get about 2000 photons/sec compared with 200 photons/sec from a normal photomultiplier. This type of photomultiplier tube is still in use today.
  2. Spex is now known as Horiba Jobin Yvon.
  3. An excellent alternative vendor is PTI (Photon Technology International).
  4. It is very difficult to get the vendor to repair their products, even when the products are relatively new. We also had no success in convincing the manufacturer to provide a price quotation for a replacement controller. However, the vendor was very responsive to inquiries about purchasing a new instrument.
  5. Although the software capabilities of new instruments are vastly improved, basic spectrofluorometer technology has not changed much in 20 years.

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