Apogee PS-100 User manual

1
Spectroradiometer
Owners Manual
Models PS-100 & PS-200

2
Contents
3 Parts list
4 Setup diagram
5 Order of connections
6 Setup instructions
8 USB2 cable installation
9 The two first steps for every measurement
10 Integration time
11 Specifications
12 Taking measurements
14 Three tips for SpectraWiz
15 Spectral modes and applications
19 Detailed control bar descriptions
21 System indicators
22 Menu descriptions
Model PS-100R with carrying case and reflectance wand

3
Parts List
Spectroradiometer
Fiber-optic cable, 2 meters
Cosine-corrected head
Leveling plate
Apogee carrying-case
USB drive containing SpectraWiz
software, calibration files, and man-
uals
Rechargeable 5V output battery
12V output wall mount power supply
for recharging battery
USB2 cable
5 V output wall mount power supply
for spectroradiometer
Reflectance wand

4
5 V output
wall mount
USB2 cable
to computer
2 meter
fiber-optic cable
Leveling plate
Cosine-
corrected
head
Insert fiber-optic
cable here:
Attach fiber-
optic cable here:
Rechargeable
5 V battery
12 V adapter
To recharge
battery
OR
Power the
spectroradiometer with
5 V power supplies only.
The 12 V adapter is for
recharging the battery only.
Spectroradiometer
CAUTION: Do not use
force to bend the fiber
optic cable. It will break.
For use with reflectance wand
attach fiber-optic cable here:
Setup Diagram

5
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Order of Connections

6
Setup Instructions
1. SpectraWiz Installation
Load your CD or USB drive and install the SpectraWiz Software. Different versions of
SpectraWiz are available and are stored in separate folders according to your computer’s
operating system. Choose the “SETUP” application from the appropriate folder. For
Windows XP, select D:\SpectraWiz for Win 2k-NT-XP Ver 4.1, SETUP.
Following the software installation, copy and paste the calibration files, sw.ini and sw1.
icf, into the SpectraWiz folder that has been created on your hard drive: (C:\Programfiles\
StellarNet\SpectraWiz). If you purchased the pre-programmed laptop, software and driver
installations have already been completed, and the calibration files are already found in the
correct directory.
2. Connection to Cosine-Corrected Head
The cosine-corrected head is connected to the spectroradiometer via the fiber optic cable.
The end of the fiber optic cable with the ‘<<-- to spectro’ label connects directly to the
spectroradiometer via the threaded adapter located on the face opposite of the 25-pin port.
The other end of the fiber-optic cable connects to the cosine-corrected head via removing
the top portion of the head, running the fiber optic cable through the slot on the bottom
portion of the head, and connecting to the threaded adapter underneath the white diffusion
disk on top of the head. The leveling plate is designed to connect to the cosine-corrected
head via the bolt through the plate and the threaded hole in the bottom of the head. For
reflectance measurements the fiber optic cable can also be connected to the threaded
adapter on the reflectance wand
3. Connection to PC, USB2 Cable Installation
The spectroradiometer connects to a PC via the USB2 interface cable. The 25-pin male
adapter connects directly to the 25-pin female port on the spectroradiometer. The USB2
adapter connects to a USB port on the PC. The drivers used to communicate with and
operate the spec must be installed on the PC, and are found on the software CD and USB
drive (As noted above, the drivers come pre-installed if a laptop was purchased with the
spectroradiometer.). Before installing the USB2 cable, disconnect any internet connection
to your PC to avoid complications. With the spectroradiometer powered and the USB2
cable fully connected, Windows will bring up the “Found New Hardware Wizard.” Do not
connect to windows update. Windows will automatically find and install the drivers. Detailed
instructions concerning driver installation are found on page 8 “USB2 Cable Installation.

7
4. SpectraWiz Setup
5. Detector Integration Time
Set the Detector Integration Time using the slide bar or the setup menu. Higher integration times are
more ideal, however, if your data over-ranges you should reset for a lower time. Refer to “The First Two
Steps for Every Measurement” on page 9.
6. Dark Scan
Take a dark scan by clicking on the dark light bulb while covering the sensor head. More detailed
instructions are found on “The First Two Steps for Every Measurement” on page 9.
You are now ready to collect data.
Run the SpectraWiz software. The dialogue box
below, “SpectraWiz Spectro Hardware Setup“,
will appear. The correct detector type is “CCD
2048” and the “USB2EPP cable” option should
also be checked. These are the only two options
you should have selected. Exit Setup.
Click on the setup menu and select Unit
Calibration Coefficients. Click OK and enter the
three coefficients listed on the underside of the
spectroradiometer one at a time followed by OK.
Repeat this step to verify.

8
USB2 Cable Installation
1. Disconnect the internet connection to your PC (Do not allow windows to connect to Windows Up-
date).
2. Power the spectroradiometer.
3. Connect the USB2 cable to the spectroradiometer and one of the USB ports on your PC. This will
prompt the following wizard:
4. Select “No, not at this time”, and click “Next >”.
5. Select “Install the software automatically”.
6. The driver will usually automatically load and you will be informed that your USB device has been
properly installed. If you need the wizard to “Install from a list or specific location”, the drivers are
located at (D:\EPP_USB2EPP DRIVERS\SWDriver-USB2EPP\Win9x for Windows 95/98/ME or
D:\EPP_USB2EPP DRIVERS\SWDriver-USB2EPP\Win2k for Windows 2000/NT/XP assuming
your CD is drive D).
7. You may verify the cable installation by: right click My Computer Properties Hardware
Device Manager USB Device Stellarnet USB2epp Cable.

9
The First Two Steps For Every Measurement
1. Set Detector Integration Time
The detector integration time is like the shutter speed on a camera. It controls the amount of light
reaching the detector. An integration time that is too high exposes the detector beyond its range and
saturates the readings you will view. A low integration time lacks the exposure to take clear readings.
You must correctly set the integration time before you use the spectroradiometer in a new setting.
1. Set the view to scope mode: View Scope Mode
2. Set the integration time as high as you can without saturating: Setup Detector Integra-
tion Time. This may require experimentation.
Examples of cool white fluorescent (CWF) spectra in scope mode:
IMPORTANT NOTE: The ideal integration time for a given light source must be determined while in
Scope Mode. Changing the mode in the ‘View’ menu resets the integration time to a default value
determined during calibration. If you select the Irradiance (PAR) Mode you must also re-enter the
appropriate integration time.
2. Take Dark Scan
A dark scan is the equivalent of zeroing the instrument. The spectroradiometer must perform a Dark
Scan each time changes are made in the Setup menu, including the Detector Integration Time. This
is done by covering the end of the fiber optic cable or cosine corrected head and clicking on the dark
light bulb near the top of the screen. Another method is to unscrew the fiber-optic cable from the
spectrometer and placing the small black cap on the thread.

10
Integration Time
About the Integration Time
The current integration time is displayed on the status bar at the bottom of the screen (e.g. Time:
100ms). This is the amount of time (in milliseconds) that the spectroradiometer records for a single
measurement. A multi-element array spectroradiometer is like a camera; a short integration time is like
a fast shutter speed. The detectors in the spectroradiometer are like camera film – in low light it is hard
to see details unless the shutter speed is increased to allow more light to reach the film. Bright light
overexposes the film unless the shutter speed is reduced. A long integration time increases sensitivity
in low light, but the detectors over-range with long integration times in high light. The integration time
should be adjusted to obtain the best exposure.
The proper integration time for a given light level will vary depending on the spectrum of the light. 200
µmol from fluorescent lamps will cause a range error at 700 ms but 200 µmol from an incandescent
won’t over range below an integration time of 2000 ms. This is due to the sharp radiation peaks of the
fluorescent lamps at distinct wavelengths (e.g. ~400, 450, and 550 nm).
How To Set The Integration Time
For each given light source you must determine the optimal integration time. The software defaults to
an integration time stored in its calibration files. Changing the integration time in one view mode does
not affect other view modes. The integration time for a given light source must be determined while in
scope mode and re-entered in other modes you use.
1. Set the view to scope mode: View Scope Mode
2. Set the integration time as high as you can without saturating: Setup Detector
Integration Time
3. Cover the sensor head with a black cap and save a dark scan by clicking the dark light bulb icon.
A dark scan should be taken whenever the integration time is changed.
4. If you are using a view mode such as irradiance, you may now return to that mode. Remember
to re-enter the integration time for that mode to override the default.
While in irradiance mode, over-ranging is indicated by a flashing warning message at the bottom of the
screen that says, “RANGE ERR”. When this occurs, take the same steps listed above.

11
Specifications
PS-100 PS-200
Wavelength range 350 to 1000 nm 300 to 850 nm
Base unit size 15.5 × 9.5 × 4 cm 15.5 × 11 × 8 cm
Base unit mass 500 g 900 g
Detector 2048 pixel, 14 x 200µm microelement array
Linear range 0-2.1 absorbance units (<0.5%)
Exposure Range 4 milliseconds to 60 seconds
(synoptic multi-channel)
Integration time range 4 to 6500 ms
Input power 220-250 mA at + 5 VDC (provided)
Optical cable 2 meters armored cable. Cables are not
interchangeable.
Wavelength accuracy < 0.25 nm
Wavelength repeatability < 0.05 nm
Wavelength stability < 0.001 nm per °C
Dynamic range 1 to 4096 counts (± 0.5%)
Signal to noise ratio Up to 1000:1
Warranty 1 year against defects in materials and workmanship
Power Supplies
The spectroradiometer should never be powered with AC power supplies. Power the spectroradiometer
with 5 VDC. This is a relatively small voltage. Common alarm clocks use a 9 VDC battery. Exceeding
5 V will damage the instrument!
Battery Life
Battery life with continuous scanning is about 5 hours on a full charge (your laptop’s battery may be
less). This power supply uses a sealed, lead acid battery, the same type of battery used in automo-
biles. Lead acid batteries have an exceptionally long life if maintained as close to full charge as pos-
sible. Completely draining this battery (more than six hours of continuous scanning) shortens its life
expectancy, so it should be charged after each use. This differs from the Nickel-Cadmium or Metal Hy-
dride batteries used in laptop computers, which have “memories” and which should be depleted before
recharging. The lead acid battery in this power supply cannot be over-charged and it should be kept
plugged in as much as possible to keep the battery at full charge. When it is unplugged and left in the
on position, there is a slow discharge in the 12-volt battery through the 5-volt converter. An unplugged
battery will deplete completely after about a month of storage.
Fiber Optic Cable
While the fiber optic cable is housed in an armored case it still has a glass core and cannot be bent at
the same acute angles as electrical cable. If the cable is crimped or pinched it can break the glass core
and result in incorrect readings. Never use force of any amount to make bends in the cable.

12
Taking Measurements
This section will very briefly tell how to make basic measurements. See “Spectral Modes and Applica-
tions” on page 15 for more details.
Irradiance / Photon Flux
ap gee
instruments inc.
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1. Determine the integration time and save a dark scan as described above.
2. Make sure temperature compensation is on: Setup Temperature Compensation
3. View Irradiance and select Watts per m-2, μmol m-2 s-1, or lux m-2 as desired.
4. In the view mode you select, re-enter the integration time determined in scope mode.
5. To look at light intensity at a given wavelength: Right-click mouse pointer at the wavelength.
Fine-tune the position of the displayed line using the peak left and right icons .
6. Save scan .

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Reflectance / Transmittance
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1. Determine the integration time and save a dark scan.
2. Save a reference scan using the reflectance standard as shown above left. For reflectance
and transmittance measurements, the sample reading is divided by the reference reading to give
% transmittance (reflectance).
3. View transmittance mode: View Transmittance (re-enter the integration time now).
4. Save scan with the fiber optic cable held or mounted as shown above right.
Absorbance
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1. Determine the integration time and save a dark scan.
2. Save a reference scan as shown above left.
3. View transmittance mode: View Absorbance (re-enter the integration time now).
4. Save scan with the fiber optic cable held or mounted as shown above right.

14
Three Tips for SpectraWiz
1. How to Set a Photosynthetically Active Radiation (PAR) Range
The SpectraWiz software includes a useful tool for measuring specific spectral regions (e.g. UV only),
but the wavelength range must be set to integrate from 400 to 700 nm to measure Photosynthetically
active radiation (PAR). Click on the ‘View’ drop-down menu. Go to ‘Irradiance’, then ‘Setup Range for
Watt and Rflux measurement’ Choose ‘400’ as the start and ‘700’ for the end of the wavelength range.
This range will remain set until it is changed again, but it should be checked after installing new soft-
ware updates.
2. How to Change the Number of Scans to Average
Under the setup menu, select “number of scans to average” and enter the number of scans you wish
to average.
Increasing the number of scans to average improves the signal-to-noise ratio, but increases the time
required to take each reading. At low integration times averaging several scans can be done quickly.
At higher integration times readings may benefit from an average, but will require more time. Using
an average of three to ten scans is helpful for most applications. An average of three to ten scans
during a dark scan will more accurately zero the instrument.
3. How to Manage Calibration Files for Multiple Spectroradiometers
There are two unique calibration files for each spectroradiometer. They are named sw1.icf and
sw.ini. These files must be in the ‘SpectraWiz’ folder where SpectraWiz was installed. If you use only
one spectroradiometer, leave these files as they were installed.
To connect multiple spectroradiometers to the same computer (such as a UV-PAR and a PAR-
NIR) you will need to manage the calibration files. The software must be prevented from utilizing the
wrong files. Indicate the files to be overlooked by changing their file names. For example, rename
the calibration files for the Spectroradiometer you will not be using to swUV.ini and sw1UV.icf.
Apogee suggests making separate folders (e.g. NIR Cal Files and UV Cal Files) inside the
SpectraWiz folder to help to keep them separate. Change the names of the files but not the exten-
sion. They need to be changed back to sw1.icf and sw.ini when in use or SpectraWiz will not recog-
nize them.
C:\Program Files\StellarNet\SpectraWiz:

15
Spectral Modes And Applications
Reflectance, Transmittance, And Absorbance Measurements
Reflectance and transmittance are measured as percent of the incident incoming radiation and are both
measured using transmission mode: View Transmission. Absorbance is a measure of optical
density and is measured using absorbance mode: View Absorbance.
Side light creates error in these measurements so they should be conducted without the cosine
corrected head, just use the bare end of the optical cable. The optical cable only has a 30˚ angle of
view so it is not influenced by side light when used in close proximity to the sample surface. A high-
reflectivity reference standard is used to eliminate side light error in the measurements of incident
incoming radiation (reference scan) and transmittance.
These measurements also work best with a high input signal. Therefore, set the mode to scope mode
first: View Scope Mode and increase the detector integration time until a reference reading has
a high signal (above 2500 counts) while making a reference scan.
Make a new dark scan whenever you change the integration time.
• Reference scans should be made using a high-reflectivity reflectance standard. This
standard should be held at the same distance from the light source as the canopy or leaf being
measured. Aim the detector directly at the reflectance standard from a distance of about 2
inches. Make sure not to have shadows on the reflectance standard. Record a reference scan
by clicking the yellow light bulb or File Save Reference.
Be careful not to saturate the signal in any region of the spectrum; the region from 500-600 nm is most
sensitive. Saturation of signal is seen as a flat line at the top of the spectrum display and corresponds
with a y-scale of 4000 counts in scope mode. If the signal is saturated, decrease the detector integration
time and take new dark and reference scans.
• Reflectance Measurements should be made by pointing the sensor straight down about 2
inches above the sample. Adjust the distance depending on the view area you want to measure.
The percent of light reflected at each wavelength is shown in transmission mode:
View Transmission.
• Transmittance Measurements are made similar to a reference scan except the end of the
optical cable is covered by a single leaf with the reflectance standard about 2 inches below. The
percent of light at each wavelength transmitted through the leaf is shown in transmission mode:
View Transmission
• Absorbance Measurements are typically used for measuring the absorption spectra of
liquid samples. This feature is similar to the use of a bench top spectrometer for measuring
chemical concentrations in a liquid sample. The output is equal to: –log(Transmittance) and is
shown in absorbance mode: View Absorbance (see page 18 on Chemwiz).

16
Overlaying Multiple Spectra
To overlay multiple saved spectral traces:
Open and navigate to the files folder. hold
down the shift key (for contiguous files) or the
control key (for noncontiguous files) to select
multiple files before clicking “open.” Each
spectral trace is graphed in a different color.
Excel is capable of importing files created by
SpectraWiz. The data is delaminated with
spaces.
To overlay traces in real time: (All spectral
traces are graphed the same color.)
View Graph Trace As Overlay
Computing Intensity, Peak Parameters, And Area Under A Trace
The area / centroid icon can be used to pinpoint the light intensity at a specified wavelength, measure
peak parameters (e.g. centroid, peakwave, etc.), or to compute the area under a spectral trace between
user-specified wavelengths.
1. Left-click on the icon to display a solid vertical line with a description in the status panel of the
spectral trace (wavelength, intensity, etc.) where it intersects with the line.
2. Right-click the graph at the desired wavelength to quickly move the line into place. The line will
move to where you click. The line may also be moved by clicking the peak left / right icons, but
this is slow and should be used only for final adjustments.
3. When the line is in place, the peak parameters of the nearest peak can be computed by left-
clicking the area / centroid icon a second time
Computing The Area Between User-specified Wavelengths:
1. Click the area / centroid icon
2. Move the solid line to your first wavelength of interest.
3. Right-click the area / centroid icon. The solid line will change into a dashed line that becomes
the starting-point of your area measurement.
4. Right-click the graph at the desired ending wavelength; a second dashed line will appear where
you click the mouse. This line may then be adjusted by right-clicking or by using the peak left/
right icons.
5. When both lines are in place, right-click on the area / centroid icon again. A dialogue box will
appear and ask if you would like a local baseline based on your starting point. Clicking Yes will
compute the area between the two dashed lines above the intensity at the starting point, and
clicking No will compute the entire area under the curve between the two dashed lines with a
zero baseline.

17
Applications
The Apps menu allows color monitoring, solution concentration predictions, and irradiance and
wavelength calibration.
Cielab
This CIELAB application performs color measurement using the International Commission on
Illumination (CIE) techniques. The application provides a chromaticity diagram for irradiance and a
spectrocolorimeter function for reflectance.
Color Of Irradiant Light
View Irradiance Mode
For irradiance (watts per m2) and for luminosity (lumens), the color of light is displayed using the xy
chromaticity diagram and the related dominant wavelength.
Color Of Reflected Light
View Transmission Mode
The color of reflected light is displayed using the CIELAB circular graph for a* and b*. The L* is the
color lightness and is displayed in a bar graph. The CIELAB Colorimeter function uses the following
routine to calculate color:
1. The colorimeter function derives tristimulus values (proportions of red, green, and blue in
spectrum) from the spectral reading.
2. The CIELAB uniform color space is calculated from the tristimulus values.
a. L* is the lightness from 0 to 100
b. a* and b* are color values
between –60 and +60
3. Tolerancing is used to determine color differences (delta E)
The rectangular coordinates on the chart also relate to the tristimulus values. The application allows
user selection of CIE Standard Illuminants A, B, C, D50, D55, D65, D75 and fluorescent lamps F1
to F12. Selecting the type of illuminant that you are using allows the program to compensate for
the relative spectral power distributions of the light source. The default illuminant is D65 (daylight).
The L* a* b* values are displayed in circular color chart that is updated several times per second,
depending on the user-selected sample rate and sample averaging. If a fiber optic reflection probe
is moved across a spectral color chart, a data cursor can be seen to move in a circle around the
CIELAB color chart.
5. Use the “save standard” function to save a sample that can be loaded at a later time to
compare with other samples. The Delta E* is the square root of the sum of the squares of the L* a*
b*, and is used to determine if another sample is similar. If Delta E* is 3 or greater, then the test
sample is considered a different color than the selected standard.

18
Color Analysis
1. Set the detector integration time to accommodate lighting (see page 9)
2. Change the SETUP parameters as follows:
Number of scans to avg = 4 or higher: Setup Number Of Scans To Average
Pixel smoothing = level 4: Setup Spectral Smoothing Controls
Temperature compensation = ON: Setup Temperature Compensation
3. Save a dark reference and a white reference (using, for example, StellarNet’s RS50
reflectance standard) while in the Scope Mode. Make sure that the bell curve response does
not saturate at the top peak (see page 9). For the best results using a reflectance probe, use a
fixture that holds the tip at the same distance from each sample. Apogee carries such a probe
with a built in light source.
4. Enable the CIELAB Color Monitor application. The New Reference button allows you to take
a “standard white” reference at any time. This should give an L value of 100 in the bar graph.
Most of the SpectroColorimeter buttons are self-explanatory. Save sample allows you to rapidly
record samples into a “colordata.log” file for subsequent viewing or printing.
5. Use the “save standard” function to save a sample that can be loaded at a later time to
compare with other samples. The Delta E* is the square root of the sum of the squares of the
L* a* b*, and is used to determine if another sample is similar. If Delta E* is 3 or greater, then
the test sample is considered a different color than the selected standard.
Chemwiz
ChemWiz allows users to create calibration curves of specific chemical concentrations and to predict
chemical concentrations based on these curves. Because these methods require an accessory
configuration, please contact Apogee for assistance.
Once a method has been configured, it can be opened to operate in real-time. When a method is
opened, SpectraWiz automatically sets all the system parameters required by the specified method
(including detector integration time and all of the setup menu parameters) and begins running. Load
the zero concentration reference in a cuvette and press the Zero Reference button. If a second
spectrometer is not being used for automatic lamp drift correction, perform a Zero Reference as often
as possible. A “ChemData.log” file allows users to quickly save samples for later viewing or printing.

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Detailed Control Bar Descriptions
Move Data Cursor / Seek Peek
When you click on either button, a vertical line appears on the graph of your spectrum. At the bottom of
the screen, the intensity of the spectrum and the wavelength of the vertical line are reported. The line
can be moved to the right or the left by clicking on these buttons. To quickly move the line over a large
distance, right-click the mouse at the wavelength you would like to move to.
Save Sample Spectrum
When you click this icon, the spectrum freezes and you are prompted to save the spectrum. The
spectral mode you are in determines the three-letter suffix. The spectral modes include scope (*.SSM),
absorbance (*.ABS), transmission (*.TRM), irradiance (*.IRR), reference (*.REF), and dark (*.DRK).
When opening files, specify the file type to view the files. Because SpectraWiz is the default directory,
it is easiest to create file folders within the SpectraWiz folder to save spectra, rather than elsewhere in
Windows. The first time you save a file after opening SpectraWiz, you will be prompted to specify the
wavelength range and intervals you would like saved.
Save Dark Scan
The dark scan should be performed with the detector covered using a dark scan sensor cover, before
making measurements. It measures baseline signal (signal that is present even when there is no
incoming light). This should be done every time the integration time is changed. Merely covering
the sensor with your hand still allows some light through and can result in measurement errors. Use
temperature compensation to automatically update the dark scan when making multiple measurements.
Setup Temperature Compensation.
Save Reference Spectrum
A reference scan should be recorded before measuring absorbance, transmission, or reflectance. See
page 15 for a description how to properly perform a reference scan.
Print Graph
Prints directly from SpectraWiz. If print prompts have been entered, you will be prompted to enter
descriptions of the trace you are printing, which will appear on the printout.

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X Zoom Info / Y Zoom Enable
Zooms out to fit the entire wavelength range supported by the spectrometer in use. Holding down the
left mouse button and dragging between the wavelengths of interest will zoom in. This function also fits
the y-scale to the visible spectral trace.
Rescale Y-axis / Unscale Y
Fits the entire spectrum on the screen by adjusting the y-scale to fit the top of the highest peak. This
is useful for zooming out on high-intensity spectral traces that are off-screen, or for zooming in for low-
intensity traces that cannot be seen very well with a large y-scale. If the spectrum still looks chopped off
after you adjust the vertical fit, check to see if signal saturation has occurred (see page 9 for details).
Compute Area & Centroid / Setup Manual Cursors
Can be used to pinpoint the light intensity at a specified wavelength, measure peak parameters (e.g.
centroid, peakwave, etc.), or to compute the area under a spectral trace between user-specified
wavelengths.
• Left-click on the icon to display a solid vertical line with a description in the status panel of the
spectral trace (wavelength, intensity, etc.) where it intersects with the line.
• Right-click the graph at the desired wavelength to quickly move the line into place. The line
will move to where you click. Smaller adjustments may be made by clicking the peak left / right
icons.
• When the line is in place, the parameters of the nearest peak can be computed by left-clicking
the area / centroid icon a second time. For more uses of the area/centroid function, view the
Computing the Intensity, Peak Parameters, and Area Under a Spectral Trace sections.
Set Detector Integration Time
Adjusts detector integration time, which is then displayed in the status bar.