S1000 & SD1000

Fiber Optic Spectrometers

User's Manual
Revision 3, September 1993

SpectraScope version 1.7

S1000 & SD1000 Utility Disk Version C-1.0

Ocean Optics, Inc.

1104 Pinehurst Road
Dunedin, FL 34698

(813) 733-2447
FAX 733-3962

Copyright Notice: This document and all diagrams are the property of Ocean Optics, Inc.
and may not be reproduced or copied by any means for any purpose.

1
 Table of Contents

Quick Set Up 1
Physical Layout 3
Experimental Setups 4
Selecting Accessories 5
Operating Software 7
Programming 10
Spectrometer Alignment 12
Pinouts for S1000 13
Time Control 14
Output Zero Adjust 15
Harness Connections 15
Noise, Signal Averaging & Filtering 16
Control Pin outputs (D9) 17
Computer Interface 17

1
 Quick Set Up
The S1000 is easy to set up and use. This is a quick procedure for those familiar with installing
expansion boards and software in a PC.
ADC Board

The S1000 & SD1000 operating software uses drivers for the Kiethley DAS-16F, the Computer
Boards Inc. CIO-DAS16Jr & CIO-DAS330 boards, or any equivalent protocol ADC board. If
you are using another ADC protocol you must modify the software (see Programming - 'C'
Modules).

You should consult the operating manuals for the DAS-16F or CIO-AD16Jr for instructions on
how to install the boards in the expansion slot and how to make the necessary changes.

The ADC boards should be set as follows:

BASE ADDRESS 300H (768 Decimal)

DMA CHANNEL SELECT 1 (Choices are 1&3. 3 is used
by the hard drive in an XT)
1/10 MHz jumper 10 MHz
8/16 CHANNEL SELECT 16
GAIN/RANGE 0-10Volts (the gain for the
CIO-AD16Jr and many
other boards is under
software control)

Both the BASE ADDRESS and DMA CHANNEL SELECT are the default settings for the ADC
boards and are specified in theSpectraScope operating software. If you get a Mode 0 error
message upon starting the program, it may be due to conflict with another PC board installed at
the same address. If it is necessary to change the base address of the ADC board you will need to
modify the software as well.

The IRQ level for the board is established through software. Type SET SSIRQ=n where n is
3,4,5 or 7 (7 is the default). When you find an IRQ level that works, add the command line to
your AUTOEXEC.BAT file.

The 1/10 MHz jumpers and the 8/16 CHANNEL SELECT must be changed from their default
settings on the ADC boards. The 1/10 MHz jumper controls the counter on the ADC board
which is used to pace the ADC conversion trigger. The 8/16 CHANNEL SELECT configures
the inputs to the ADC board as 8 differential or 16 single ended.

The DAS-16F board has a switch for setting gain (S5) that should be set to 0-10V. S4 should be
set to unipolar. S3 should be set to 16.

1
Installing the interface cable

TURN OFF THE COMPUTER BEFORE INSTALLING THE CABLE!

The 37 pin female connector end of the cable goes to the ADC plug at the back of the computer.
The male 25 pin connector goes to the back of the spectrometer unit (see Physical Layout).

Loading the Software

The operating software diskette contains executable software to run the S1000 or SD1000 and
source code files (*.C) to expedite customization of the software. To install, copy the entire
diskette to the directory of choice on your PC hard drive. The following are required for
operation:

S1000 SD1000
S1000.EXE SD1000.EXE
SETUP2.DAT SETUP.DAT
EGAVGA.BGI EGAVGA.BGI

The S1000 software is written for a single spectrometer system, but will run the master
spectrometer of a dual system. This can be an advantage if only the master unit is being used
because execution speed is faster and data files are smaller.

Installing optical fibers

Single strand optical fibers with SMA terminations are required to input light to the
spectrometer. The input fiber is an integral part of the spectrometer. Spectral resolution is
determined by fiber diameter, and the light transmission efficiency of individual SMA
terminations varies considerably. Also, SMA terminations may not be perfectly symmetrical.
For these reasons it is best to install the input fiber and leave in place throughout the course of an
experiment.

System Checkout

Start the software by typing S1000 or SD1000 and ENTER. The main menu should appear.
Type 1 for "Oscilloscope Mode". A trace should appear on the screen after a few seconds. This
is the zero light level and should be near the bottom of the graph. If it is not you may need to
adjust the zero level (see ZERO ADJUST SECTION). Use a flashlight or some other light source
to illuminate the end of the input fiber(s). The trace should move upward in response to the
light. If you saturate the array the trace may be difficult to notice as it will lie on the top margin
of the graph. If you have any problems or questions, please call us.

2
 Physical Layout

SMA optical connectors for SD1000

Rear view - electrical connections

3
 Experimental Setups
The S1000 and SD1000 fiber optic spectrometers permit easy configuration for measuring
absorbance, reflection, fluorescence and light energy. The standard SMA input allows you use

probes and accessories from any manufacturer as lo ng as single strand fibers are specified. The
following are some suggested setups:

4
 Selecting Accessories
Input Fiber
The spectral resolution of the spectrometer is determined by the grating, the input fiber diameter
and numerical aperture. We recommend all silica UV quality 0.2 NA fiber.

For routine spectrophotometry, 50 µm or 100 µm fibers provide more than adequate light and
give the best spectral resolution. For reflectance spectrophotometry 200 µm fibers work best.
For very low light applications, larger fibers can be considered. Fibers are available in three
versions each suitable for a different wavelength range: SR is HOH fiber suitable for the
UV/VIS range (200 - 750nm). GR is gradient index fiber, available in 50 and 100 µm diameter
only (400 - 1000nm). LR is LOH fiber suitable for the NIR range (500 - 1000nm).

Grating Fiber Cat. # Fiber Resolution Spectral

(lines/mm) Diameter (FWHM) Range (nm)
(µm)
1200.00 16-50-? 50.00 1.2 250.00
" 16-100-? 100.00 2.5 "
" 16-200-? 200.00 5.0 "
" 16-400-? 400.00 10.0 "
600.00 16-50-? 50.00 2.5 500.00
" 16-100-? 100.00 5.0 "
" 16-200-? 200.00 10.0 "

Accessories
Device Catalogue # Uses
PC plug- in A/D board CIODAS-16Jr 12 bit ADC, 125 KHz
" " " CIODAS-330 12 bit ADC, 330 KHz

5
fiber splitter 16-200R/2:1-2-SMA-? divides light from single
fiber into 2 fibers
bifurcated fiber BIF16-200SR-2-SMA/3 delivers light from light
source to master & slave
spectrometers
7 fiber probe 11-1006000020-SMA/F central read fiber
surrounded by 6
illumination fibers, used
for reflectance.
cuvette holder CUV-4 1 cm cuvette holder,
requires collimating
lenses
light source 5600 DCR tungsten halogen lamp,
regulated power supply
& SMA adapter
Collimating lenses 74-05-SMA/.250 (UV) Collimating lenses are
74-04-SMA/.250 (VIS) useful for making cuvette
sample compartments
Couplers 21-02 SMA Couple two SMA
terminated fiber together,
can be used as crude
attenuators by loosening
the SMA connectors
Bulkhead Bushings 21-01 Couple an SMA fiber to a
solid plate. Useful for
positioning fiber near a
light source.
plug filters SCH-??? order sorting Schott
glass, can be mounted in
an SMA bulkhead
connector or directly in
the spectrometer. Used to
block short wavelengths
that cause 2nd order
overlap of spectra.

Light Sources

A Hg vapor lamp (Oriel 6035 or equivalent) is recommended for checking the calibration of the
spectrometer. Ordinary office fluorescent lights have distinct mercury lines and can be used as
well. Quartz tungsten halogen bulbs (e.g. Welch Allyn 01079) or high pressure xenon flash
lamps can be used for most VIS -NIR applications.

6
 Operating Software
Ocean Optics announces the first release of SpectraScope(TM) spectroscopy data acquisition
and processing software for the S1000 series of miniature spectrometers. SpectraScope
enhances the fiber optic spectrometers by providing a real time graphical interface to a wide
variety of signal processing algorithms: integration period, auto dark correction, signal
averaging, time based normalization, spectral smoothing, dual beam drift correction,
absorbance, transmittance, and spectral differentiation to name a few.

This user friendly, mouse oriented software features pull down menus, on screen cursors, smart
icons for saving data, control drivers for pulsed light sources, on screen inspection of data files,
printer drivers, x_zoom, y_re-scale, 3-D graphics, single and dual wavelength tracking, and an
incredibly fast RAMDRIVE episodic sampling facility for acquiring large sets of spectral scans
for time series analysis. Operating parameters, reference and sample spectra can be stored as
complete experiments as well as individual files, and can be recalled for post experiment signal
processing.

The executable version is free to all S1000 users with source code options starting at $519 to
permit customization to your particular applications. Contract programming is also available.

While SpectraScope operates best on a 33 MegaHertz or higher Intel 486 PC equipped with
VGA, mouse and 2 Meg RAM, it will operate on a 286 PC equipped with EGA, 1 Meg RAM,
and MathCoprocessor.

In addition to SpectraScope, a simpler operating software (S1000.EXE & SD1000.EXE) along

with source code is supplied free of charge on a separate diskette. This software which acquires
data, outputs graphs to the monitor, calculates absorbance and transmission, and saves ASCII
files can be used without
restriction.

Installing SpectraScope

To install the SpectraScope software on your IBM PC compatible, create a new directory, then
copy the entire diskette into the new directory. For example, under Dos you would type:
MD SS then press enter to make a new Directory named SS.
CD SS then press enter to Change Directory to the new SS.
COPY B:*.* then press enter to copy all files from the diskette in floppy drive B.
SS then press enter to start SpectraScope.

SpectraScope supports online help files which describe the operation of the various menu
features. The help files contents are listed below.

7
General Help Menu Summary:

Panic icon: Clicking this area (top of screen, just left of the data cursor rectangles) will cause
the system to reset to average settings, in case you want instant relief from slow response. It
affects the ADC data sample frequency (-> 100 KHz) and the number of samples to
average (-> 1).

Save icons: Clicking these areas (top left of screen) allow the same operation as File -> Save for
the sample (data & file type depends on mode), dark (setup with no light), and reference (e.g.
white for reflection, solvent for absorption).

Data Cursor: The data cursor is a verticle line which can be moved from left to right or right to
left along the data scan. The data value at the cursor location is displayed in the top status bar.

Movement is controlled by selecting one of the four rectangles (top right of screen) with a mouse
click. Alternately, the keypad keys will perform similarly:

Home (fast left) PgUp (fast right)

End (left) PgDn (right)
Del (remove cursor)

Interrupts: The Adc (Analog to Digital Converter) adapter needs the use of an interrupt request
(IRQ) in the PC plug in bus. SS defaults to IRQ7, however if you are having problems you may
change this to IRQ3, IRQ4, or IRQ5 (try this first). At the Dos
prompt type "SET SSIRQ=5" (if this works just put the same line in your AUTOEXEC.BAT
file).

Speed Up Episode: The episodic data capture function initiated via the Setup -> Episode menu
option writes continuous data to disk when there is no episode delay(0) or inter scan delays.
Since your disk has a rather large seek time as compaired to rapid data capture requirements, you
may need speed up this process. Install the Dos RAMDRIVE.sys command in your config.sys
file. Example:
dos=umb,high
device=\dos\himem.sys
device=\dos\ramdrive.sys 2048 /e
device=\dos\emm386.exe

This installs a 2 meg ramdisk in extended memory. This will hold approx 200 episode samples.

You must tell SS where the ram drive is located by typing "SET SSRAMD=D" at the Dos
prompt (also put this line in your AUTOEXEC.BAT file. "D" indicates that your ramdrive is
drive "D". The ramdrive will always be the next letter above your last drive.

8
File Menu Help summary:

New - allows the experiment name to be changed. The current experiment name is shown in the
upper right status bar. The experiment name indicates the next filename to be used when
performing a file save. The experiment name is the first six characters of the filename. The next
two characters are the filenumber (00..99).

The file number can be changed too. The file number is automatically incremented when doing
successive file saves of the same file type. The file types cannot be changed as these are
automatically selected for the context of the data. The file type is the last three characters after
the period in the complete dos filename. Here are experiment files generated by SS:

Format: data [if dual_unit] , data

eeeeeenn.cfg - contains setup configuration
eeeeeenn.drk - dark data
eeeeeenn.ref - reference data
eeeeeenn.sam - sample data
eeeeeenn.ep - episode data

Format: wavelength, data [if dual_unit] ,wavelength,data

eeeeeenn.abs - absorbance data
eeeeeenn.trm - transmission data
eeeeeenn.rfs - reference spectra data
eeeeeenn.ssm - sample data

Open - allow the user to select various files to be read back in which were previously saved.
These include an entire experiment (*.cfg, *.drk, *.ref, *.sam), or individually setup (*.cfg), or
sample (*.sam), or dark (*.drk) or reference (*.ref).

When combined with View -> Data graph STATIC selection, the *.sam files can be opened,
graphed, and then plotted. Using this technique, sample data can be loaded, reprocessed (via
setup options) and then saved as new samples in Scope, Absorbance and Transmission modes!

Save - allows the user to save data to files. This includes an entire experiment or selective files
as described above in Open. Normally you would first Save -> Dark then Save -> Reference.
These are required for the other view modes (ie: absorbance, transmission, ref spectra). The Dark
and Reference data is not immediately saved to a file, so they can be repeated easily. This is
different when selecting Save -> saMple, as it immediately generates *.ssm and *.sam in Scope
mode! ( * is the current experiment name and file number as indicated in the upper right status
line). NOTE!!! Save -> saMple in other View modes (ie: absorbance, transmission, ref
spectra), generate data files for that modes data type (*.abs,*.trm,*.rfs). These files can

9
be looked at with File -> View. Optionally, these files can be graphed using File -> Graph
menu, including samples (*.ssm) taken in Scope mode. The save icons on the top
left of the screen perform the same functions as above, but very quickly: File -> Save ->
(sample) (dark) (reference)
Plot - allows the user to plot the currently selected screen on the connected printer device.
First use setup->printer configuration to select output resolution, output port, and type
of print device. SS will remember your setup even after power off via the SS.cfg file. Plot
provides an option to draw xy grid lines.
View - allows the user to look at the context of selected files.
Graph - allows the user to graph selected files on screen. These data files are: *.abs
(absorbance), *.trm (transmission), *.rfs (reference spectra), *.ssm (scope sample), and
*.ep (episode data).
This selection may be sucessively repeated allowing many different files on the same
graph. Only the first graph is automatically y_scaled. Each new graph overlay is
selected as a different color.
When graphing episode data, many scans will overlay from a single file selection.
Again each scan will become a new color. The colors will cycle over if the number of
scan episodes exceed the number of available colors. If you select the 3D graph, each scan in
the episode will be
offset to fit the graph verticle axis. The scaling is set to accomodate all scans. When
combined with the View -> X_zoom you can graph a selected range of the episode
wavelengths. You must first select X_zoom the perform the File -> Graph -> Episode.
The New graph selection allows the next graph to first be cleared and then rescaled.
This is automatic when repeating Episode graphs. After a graph has been drawn, the
system is left in a STATIC mode. To restore realtime operation, you must select View -
> Data in REALTIME. A small "s" appears on bottom left of the graph to tell you the
system is in STATIC mode.
Exit - back to where you came from (Dos or Windows).

The operating software has been written in two versions, S1000.EXE and SD1000.EXE, for the
single spectrometer and dual spectrometer systems respectively. The software is menu driven
and provides for observing data in real time, calculating absorbance or % transmittance,
displaying data graphically and saving data as ASCII data files on your harddrive.

S1000.EXE
To start the program type S1000 and RETURN. SETUP.DAT and EGAVGA.BGI files must be
in the same directory.

MAIN MENU

Functions are selected by typing in the appropriate number, a 9 is used to exit the program.

1. Oscilloscope This function directs the spectrometer to take scans until interrupted by the
ESC key. Each scan is plotted on the monitor as a plot of 12 bit amplitude (0 to 4096 counts)
versus pixel number. The purpose of this mode is to facilitate setting of operating parameters.

10
The CCD array output should be optimized by changing illumination, fiber size and or the
sampling frequency (which controls the exposure time). The exposure period in ms is displayed
before ent ering the graph mode. NOTE: The rate at which scans are presented depends on the
software execution period and the CCD array integration period. The software execution speed
depends on the computer speed. A math co-processor is recommended. No data is stored during
oscilloscope mode.

2. Take dark (background) data This function directs the spectrometer to signal average n
number of scans and store the values in a data array DARK[1100]. The 1100 values include
'dead' pixels at the beginning and end of the scan, and 1024 active pixels. The values of these
dead pixels reflect the zero offset voltage. The dark output voltage of the array is required for
calculation of absorbance or % transmittance and is obtained by running this function with the
light blocked or turned off at the source. The dark value changes with integration period and
with ambient temperature, so it should be re-run whenever sampling rate is changed and
occasionally throughout the day. The initial values in DARK are set to 0. After signal
averaging, the mean values and variance are displayed to the screen for 5 seconds. The mean
variance is reported in the upper left corner. Mean values and variance are also saved in a data
file SDARK.RAW. Each time the function is run, the contents of DARK[1100] and
SDARK.RAW are replaced.

3. Take reference (blank) data This function takes n number of scans and stores the mean
values in the data array REF[1100], and the mean and variance in SREF.RAW. The reference
data represents the values of a known or reference sample, for example the solvent without
absorbing species for absorbance measurements, or a 'white' standard for reflectance
measurements.

4. Take sample data This function takes n number of scans and stores the mean values in the
data array SAM[1100], and the mean and variance values in SSAM.RAW.
5. Calculate, display and save absorbance The values in the data arrays are used to calculate
absorbance (A):

A = -log{(SAM-DARK)/(REF-DARK)}

Logs of negative numbers and zero denominators are reported as 0 values for absorbance.

A plot of absorbance versus wavelength is displayed on the terminal. Auto-scaling operates

between 0.3 - 4 Absorbance Units. The values of individual pixels can be queried by using an on
screen cursor. The left arrow, right arrow, page down and page up keys move the cursor.
Absorbance values, pixel number and wavelength are displayed in the upper left corner. The
ESC key causes the data to be stored as an ASCII file, the name of the file is displayed in the
upper left corner. The name is derived from the experiment code and a sequence number,
followed by a .ABS extension. The raw data is stored in *.RAW files. If the program is re-
started, the sequencing begins again.

6. Calculate, display and save transmission The values in the data arrays are used to
calculate %T:

11
 %T = 100 x (SAM-DARK)/(REF-DARK)

If zero occurs in the denominator, a value of 100%T is assigned.

The scale for the %T plot is set at 0 - 100%. The cursor function works as in the absorbance
mode. Data files are saved as *.TRM and *.RAW.

7. Display & save reference spectra The values in the data arrays are used to calculate a dark
corrected spectra (S):

S = REF - DARK

The interactive cursor is available for obtaining values at particular pixels. Data files are stored
with a *.SP extension.

8. Change default settings The operating parameters are stored in a file named
SETUP2.DAT. Changes are automatically written to the data file and become the default
settings:

1. Data sampling frequency - sets the ADC conversion rate and also establishes
integration period (doubling the rate decreases integration period by 2). Rates from <1 KHz to
330 KHz are available with the CIODAS-330 board, or <1-110 KHz for the CIODAS-16Jr
board. Top speed may be limited by the PC that is used, a 33 MHz 386 computer is
recommended. Setting the rate above this value will cause the program to crash.

2. Number of scans - number of data scans to signal average (2 or more).

3. Calibration slopes - the dispersion of the spectrometer, determined from a 2nd order
linear regression analysis of a calibration data set. Enter first coefficient (nm/pixel), return, then
enter the second coefficient (nm/pix^2) and hit return.

4. Calibration intercept (nm) - the wavelength of pixel number 0, determined from

calibration experiment.

5. Experiment code - a 3 character code that is added to file names.

6. Time setting (1 or 4) - Sets the number of clock cycles in the exposure period. A value
of 1 = 8192 clock ticks, a value of 3 = 32768 clock ticks (4 times longer).

7. Gain (1, 2, 4, or 8) The gain on the CIO-AD16Jrboard is under software control. A

setting of 1 matches the 0-10 volt output of the detector with a 0-10 volt ADC range. Settings 2,
4 and 8 set the ADC range to 0-5, 0-2.5, and 0-1.25 volts respectively. This function is ignored
by the DAS-16F board.
8. Set colors Change color of graphics display elements.
9. Quit Exit and save changes.

12
 SD1000.EXE

SD1000.EXE requires the data file SETUP.DAT and EGAVGA.BGI to operate.

The SD1000 software performs all functions on master and slave spectrometers simultaneously
and independently. Data is stored in DARK[1100][2], SAM[1100][2] and REF[1100][2] data
arrays and used to calculate the absorbance or %T of the master and slave
spectrometers. Raw data is stored in files named DARK.RAW, SAM.RAW and REF.RAW. An
additional option is available in the default settings labeled:

9. Correction for drift (y/n) ?

This selection runs the SD1000 as a dual beam unit where the sample is measured by the Master
spectrometer, and the source illumination is monitored by the Slave. If 'y' is selected the
absorbance values of the slave spectrometer (which are zero if the source has remained constant)
are digitally filtered (10 pixel moving boxcar average). The filtered slave values are subtracted
from the master absorbance values. Absorbance data files are written with corrected values for
master and filtered slave values. This function presumes that both spectrometers are set to the
same wavelength range. It does not matter if the wavelength ranges differ slightly as long as
changes in the source experienced over the course of an experiment are small, or if changes are
in intensity and not spectral distribution. Drift correction does not affect %T calculations.

Programming

Source code ANSI standard 'C' files are provided to facilitate customization of software. The
files and their functions are listed below:

S1000.C SD1000.C Main Program, main menu

SOSPLOT.C OSPLOT.C Gets data from CCD array(s), plots on monitor
STAKEDATA TAKEDATA Gets data from CCD array(s), returns average data in
data array specified by a flag, either DARK, REF, or
SAM
SINIT.C INIT.C Initializes ADC board - gain, base address, DMA level,
and interrupt level
DOUT.C DOUT.C a 4 bit bus to initiate one or more functions: strobe
initiate, lamp enable, enable ADC gates
GETDDAT GETDDAT tells ADC board to convert 1100 values from detector
and transfer to memory, loads values from memory into
data array DATA[1100]. Values of q passed work with
DOUT to affect data taking sequence: 0 - lamp stays

13
 DOUT to affect data taking sequence: 0 - lamp stays
on; 1 - strobe is fired along with ADC read; 2 - data
taking is enabled, no strobe or lamp is initiated.
DASG.LIB DASAG.LIB drivers supplied by ADC manufacturer to control the
board.
SCALABS.C CALABS.C calculates, displays and saves absorbance data
SCHANGEDEF.C CHANGEDEF.C changes default settings for operating parameters
SCALTRAN.C CALTRAN.C calculates, displays and saves transmittance data
SSPEC.C SPEC.C display and save spectra saved in REF data array
COLOR.C COLOR.C sets up colors for graphics displays

The object files supplied are compiled in Turbo C version 2.1. Options should be set to "medium
memory model", "case sensitive link off". The DASG.LIB and TCALLOC.C files must be
present. The source code can be recompiled in other versions of C with minimal changes.

Digital output functions

Digital outputs are available from the ADC board and are initiated with calls to DOUT(x). The
digital output lines are wired through the computer interface cable to the spectrometer and are
designated for the following purposes: Digital Output 0 (DO-0) is strobe initiate, DO-1 is
exposure time control, DO-2 is not used, DO-3 enables the ADC gates. The decimal value of x
and the resulting conditions are:

x Function DO-0 DO-1 DO-2 DO-3

0.00 Disables all 0.00 0.00 0.00 0.00
8.00 enable ADC, short exposure, 0.00 0.00 0.00 1.00
no strobe
9.00 enable ADC & strobe, short 1.00 0.00 0.00 1.00
exposure
10.00 enable ADC, long exposure, 0.00 1.00 0.00 1.00
no strobe
11.00 enable ADC & strobe, long 1.00 1.00 0.00 1.00
exposure

14
exposure

15
 Spectrometer Alignment
PLEASE BE CAREFUL ABOUT STATIC. S1000 IS CMOS CONSTRUCTION

The S1000 spectrometer is designed to be a fixed bandpass system that is preset at the factory to
the wavelength range of interest, and optimized for performance at that region. The optimization
includes choice of grating and the positioning of certain fixed optical elements. However, it is
possible to adjust the bandpass higher or lower within the limits imposed by grating choice and
fixed element position.

The alignment procedure consists of sliding the spectrometer along the circuit board slots
(screws on bottom) for focus and adjusting the two small set screws on the left side of the
spectrometer for bandpass and centering on the CCD array. A .035 inch Allen wrench is
required. The system is in focus when the spectral peaks from an emission source are
symmetrical.

The following steps are suggested:

1. Remove the spectrometer from the mounting posts by removing the bolts located at
the corners. Leave the spectrometer plugged into the 44 pin card edge connector, but
slip a piece of paper underneath the circuit board to prevent contact with the metal
posts.
2. Lift the spectrometer and install an optical fiber in the spectrometer input SMA
connector so that the fiber does not go through the instrument case.
3. Use a Hg vapor or other suitable spectral line source as the light input. Run the
spectrometer in oscilloscope mode.
4. Both set screws change both wavelength and centering and should be adjusted in
small increments with both screws being turned in the same direction. Clockwise
movements shift the observed spectra towards longer wavelengths.
5. When the desired wavelength range is achieved, the spectrometer case should be
adjusted by sliding it closer or further from the detector. Loosen the mounting screws
located on the bottom of the circuit board, slide the case until the best focus is
achieved, then tighten the screws. Best focus is demonstrated by symmetry of line
source peaks.
6. Remove the fiber input and reinstall the spectrometer on the mounting posts. Re-
install the fiber and fine-tune the set-screws if necessary.
7. Re-calibrate the spectrometer. NOTE! The input fiber is part of the optical system.
There are small differences in the position of fibers in the SMA connectors that will
cause small shifts in calibration.

16
 Card Edge Pinouts for S1000 - C series
Pin # Description Pin# Description
1.00 Video out + 23.00 Strobe fire output (TTL)
synchronized with linear
array
2.00 NC 24.00 NC
3.00 Ground * 25.00 External Clock in (TTL) *
4.00 Ground $ 26.00 Time control
5.00 Ground 27.00 Q12 out for integration
time external divider
control
6.00 Ground 28.00 Enable Array Read input @
(buffered)
7.00 NC 29.00 NC
8.00 NC 30.00 NC
9.00 NC 31.00 NC
10.00 +5 VDC in * 32.00 NC
11.00 NC 33.00 NC
12.00 NC 34.00 NC
13.00 phi 10 to pin 13 of slave $ 35.00 NC
14.00 phi RO to pin 14 of slave $ 36.00 NC
15.00 phi TG to pin 15 of slave $ 37.00 NC
16.00 phi SHO to pin 16 of $ 38.00 Integration time input
slave (divided from pin 27)
17.00 NC 39.00 NC
18.00 ADC Trigger output 40.00 NC
19.00 NC 41.00 NC
20.00 Strobe enable in 42.00 NC
21.00 NC 43.00 -12 VDC $
22.00 NC 44.00 +12VDC $

Code: * Required for operation

@ Required for ADC read
+ Outputs to ADC
$ Slave board interconnections

The S1000 pins are located by looking at edge of card, spectrometer UP:

1 3 5 7 9 11 13 15 17 19 21 23 25 27 29 31 33 35 37 39 41 43
2 4 6 8 10 12 14 16 18 20 22 24 26 28 30 32 34 36 38 40 42 44

17
NOTE: The backs of some 44 pin female connectors are numbered from the back (ie. Sullins
CPZS EZC22DRXH)

B 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22
A 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22

Integration Time Control

PLEASE BE CAREFUL ABOUT STATIC. S1000 IS CMOS CONSTRUCTION

The integration period or exposure time is set through software

Setting # Clock Cycles (C)

1.00 8,192
4.00 32,768

The integration period (T) is the product of the clock period (Tc ) and the number
of clock cycles (C):

T = (Tc) x (C)

The clock period is controlled under software by the data sampling frequency (f) setting for the
ADC board:

Tc = (2f)-1

The output of pin 27 on the card edge is "clock x 8,192". It can be divided externally to lengthen
the integration time beyond this value or as an alternative, the clock input, pin 25, can be
divided to control the integration time. Both these operations are to be inputted to pin 38. If
external control of integration time is to be used, the PEEL deice on the circuit card must be re-
programmed. Please contact our service department for details.

Output Zero Adjust

A 14 turn potentiometer is located on the top of the circuit board to allow for output zero adjust.
It is the only analog adjustment on the spectrometer board. The pot is factory adjusted to
reflect an ADC count of about 20 on the left and right overscan and reflects optical saturation at
near 11 Vdc. One might want to output to a differential ADC or have some alternate requirement
other than the 0 to 10 volt span supplied. This pot can be adjusted to give a baseline of from -12
to +12 Vdc.

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 Harness connections for SD1000 Dual unit
NOTE: S1000 uses same harness
D25 D9 22/44 22/44 Notes
Master Slave
1.00 25.00
2.00 28.00
3.00 18.00
7.00 5.00
9.00 10.00
11.00 1.00 RG 172
12.00 3.00 shield (not connected
to slave)
13.00 1.00 RG 172
20.00 20.00
22.00 26.00
4.00 4.00 ground connect
13.00 13.00
14.00 14.00
15.00 15.00
16.00 16.00
43.00 43.00
44.00 44.00
1.00 6.00
5.00 23.00
7.00 17.00

S1000 Linear Array Spectrometer System

Noise The S1000 has been designed to minimize noise and provide a stable output signal. All
supply voltages are bypassed at the IC and all supplies are filtered to provide minimal noise to
the analog circuits. Analog and digital circuits are separated and lines are located on opposite
sides of the board. Special filters are used in the DC supply to the analog side of the linear array
in order to eliminate noise transfer. The wide band output stage has a CMRR of 90 dB to
virtually eliminate power supply noise effects for in-phase components.

To eliminate switching noise problems in ADC sampling, the gate signal has been delayed to a
quiet point in the sample and held voltage output. The structure on this signal is normal and is
not observed by the ADC. Total CMOS construction (except for the power supply) also aids in

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noise reduction since EMI can only be generated by di/dt not by dv/dt.

The analog power supply is a Burr-Brown regulated DC/DC converter (PWR5905)

which supplies without additional filtering only a few mV of ripple to 10 MHz. The output from
the system is as stable as its power supply. We maintain a line regulation of +/- 0.3% based on an
already regulated +5VDC from your PC. We believe that our AC to DC regulation is on the
order of 10-5 or better. Load regulation up to approximately 8 slave units is 0.4%.

Since the linear array uses virtually no power, no heat is internally generated (except in the
system by the power supply). Thus, the spectrometer system is sensitive to only ambient
temperature variations. Output "tilt" observed on many linear arrays due to differential
dissipation is not observed in the S1000.

Signal Averaging A 12 bit ADC is accurate to +/- the value of the least significant bit. This
translates into a dynamic range of 4096, or for a 10 volt output system a smallest resolvable
voltage of 2.4 mV. Although this range matches well with saturation to s/n=1 range of most
optical sensors, the S1000 system is capable of better resolution.. One strategy is to use a 14 or
16 bit ADC. This is advisable if one plans to cool the array and implement long integration
times. An attractive alternative is to signal average the data. Provided that noise exceeds +/- one
digit of the LSB, and is truly stochastic, we can use signal averaging to define an output to
approximately +/- 0.24 mV. This is equivalent to a 15 bit ADC. (see O'Malley and O'Mongan,
"Charge-coupled devices: frame adding as an alternative to long integration times and cooling,"
Optical Engineering,
March 1992, Vol.31, No. 3). We have included signal averaging in all our software. Since S/N
improves as the root of the number of samples, 100 samples is "usually" adequate. Remember
that signal averaging only works with stationary signal sources.

Filtering There are situations, for example visual matching of spectra using an oscilloscope,
where small amounts of noise can detract from performance. A space has been left on the S1000
circuit board (and slaves) to place a capacitor across a 5k resistor. The resulting pole is at 1/RC.
This is noted on the board as CT1 for surface mount and CT2 for lead through. Excess filtering
also affects the spectral structure in the output and should be used with caution.

Control Pin outputs D9 connector

Pin Signal Purpose
1.00 Ground
5.00 TTL + Fires strobe at most expedient time under
software control

S1000 to Computer Interface

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Interface Pins - D25 INPUT/OUTPUT to DAS-16 or equivalent D37 PC socket
Interconnection cable: D25 - male; D37 - female

S1000 DAS-16 Signal Purpose

D25 D37
1.00 20.00 CR2 out clock from DAS-16 to S1000
2.00 3.00 enable read enables ADC triggers when
ready
3.00 25.00 ADC triggers supplies ADC triggers to DAS-
16
7.00 7.00 ground power ground (shield around
D25 - 1,2,3,9,20,22)
9.00 1.00 +5 VDC power supply
11.00 36.00 Video (slave) Slave video out
12.00 29.00 LLGND Signal Ground (shield around
D25 - 11,13)
13.00 37.00 Video (master) Master video out
20.00 23.00 TTL + Strobe enable (not fire)

All drive signals are buffered through the S1000 system. Do not couple them directly to the
illumination without a buffer/driver unless they have an internal buffer. The maximum available
drive current is 25 ma, HIGH or LOW. The signal ground LLGND and power ground are single
point on the S1000 master board.

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