Operating Ocean Optics Spectrometers with
the LoggerPro Interface
Last Update: January 7, 2011
Basic Set Up and Calibration
First, set up the spectrometer and allow it to warm up
here if your spectrometer is a one-piece unit or
here if it consists of multiple parts to read instructions on how to set up
the spectrometer). Start LoggerPro from the desktop shortcut, or from the Start
menu on the lower left-hand side of the screen. If you can't find LoggerPro by
either of these methods, please consult your instructor.
LoggerPro will start and the screen shown in Fig. 1 will
be displayed. If status line displays the message "No device connected," as it
does in Fig. 1, you will need to connect the spectrometer. Do this by selecting
Experiment from the menu bar and then select Connect Interface,
Spectrometer and Scan for Spectrometer.
Figure 1. Starting screen for LoggerPro.
If program finds spectrometer, the “No device connected”
message will be replaced by the spectrometer icon and the message “Absorbance =
x.xxx” where “x.xxx” is some number, as shown in Fig. 2. You will also hear a
click, if you are using one of the one-piece spectrometers.
Figure 2. LoggerPro screen that is displayed once
the Ocean Optics spectrometer has been found by the software.
Once the computer has located the spectrometer, the
software must configured to acquire the data. Click on the spectrometer icon
(or select from menu bar Experiment, Set Up Sensors and select
Spectrometer:1). The Set Up Sensors pop-up shown in Fig. 3 will appear. You
probably won’t have to change anything there. However, if you do change
something and want to return the spectrometer to its factory-default settings,
simply click on the Restore Defaults button. Note that if you change
something in this box after you have taken a background (vide infra), you
will need to reacquire the background. Click
here to read more about each parameter.
Figure 3. Set Up Sensors pop-up box for the Ocean
Before continuing prepare a cuvette containing your
blank. If you are using a spectrometer that has the detector and light
source separated, you must place a thick piece of paper in the sample
holder to block the light beam before proceeding.
In the Set Up Sensors pop-up click on the spectrometer
and a new pop-up will appear. Your options here are Calibrate,
Configure Collection and Current Units (under Current Units,
Absorbance should be selected; do not change). Select Calibrate.
If you have a one-piece spectrometer, it will click and the pop-up shown in Fig.
4 will be displayed. If you have a spectrometer where the detector and source
are separate, you will not hear a click (make sure the light beam is still
Figure 4. Calibrate Spectrometer pop-up immediately
after it has been activated.
After 1 minute the warm-up is complete and the Calibrate
Spectrometer pop-up will look like that shown in Fig. 5. If you are using a
one-piece unit, simply insert the blank into the spectrometer's sample holder.
The light travels across the spectrometer in the long direction, so make sure
the cuvette is arranged so that the light travels through the unfrosted sides of
the cuvette. If you have a spectrometer with separated detector and light
source, first remove the piece of paper that you used to block the beam and then
insert the blank into the sample holder. IMPORTANT! If you don't have a
one-piece spectrometer and did not block the beam, click Cancel and start
the calibration again. Be sure that the unfrosted sides of the cuvette are
pointed toward the fiber optic cables. Once the cuvette is in place click
Finish Calibration to complete the spectrometer calibration. Close the
pop-up by clicking OK when finished.
Figure 5. Calibrate Spectrometer pop-up after warm
up is complete.
Simple Absorbance Measurements
If you have successfully complete all of the steps above,
the Collect button
should now be active and you are ready to acquire absorbance data as a function
of wavelength (the default for the spectrometer). Just click on the Collect
to acquire the spectrum and Stop button
when you are done. If wavelength is not on the x-axis, please check that the
spectrometer is not in the Absorbance vs Wavelength mode, as described below.
Click here to review the function of the other buttons on the LoggerPro tool bar.
Before configuring the spectrometer for a kinetics
experiment, you must first calibrate the spectrometer, as described above.
Open the Set Up Sensors pop-up box again, click on
and select Configure Collection or click on the Configure Spectrometer
icon on the tool bar. The window shown in Fig. 6 will open. Set the data
collection mode to Abs(orbance) vs Time (for kinetics experiments) or
Abs(orbance) vs Wavelength (used to obtain a spectrum). When Absorbance
vs Time is selected, the check boxes under Full Spectrum are
activated and you can choose which wavelength, or wavelengths, to follow as a
function of time. When you check the Absorbance vs Time box, the program
will automatically select a wavelength to monitor. If you used the Examine
the software will default to the wavelength that the cursor was last set to,
otherwise the software automatically selects the first point in the list. With
Absorbance vs Time selected, you will be able to use the check boxes
under the Full Spectrum heading to select the wavelength or wavelengths
that you wish to monitor. Click OK when finished to close this window.
Figure 6. Configure Spectrometer Data
Upon closing the Configure Spectrometer Data
Collection window, the main LoggerPro page should now have absorbance on the y
axis and time on the x axis, as shown in Fig. 7. The current absorbance at the
wavelength(s) that you specified will be displayed in the lower left-hand
portion of the screen.
Figure 7. LoggerPro screen after the data
collection mode has been set to absorbance as a function of time.
Now set the data acquisition parameters by clicking the
Data Collection button
on the tool bar (or from the menu bar by selecting Experiment, Data
Collection). If you have successfully switched the spectrometer to
time-based measurement mode, then the window shown in Fig. 8 will open. If not,
then the data collection window for an absorbance as a function of wavelength
measurement will appear (Fig. 9) and you will need to reset the collection
mode. Note that if you try to change between a time-based measurement and a
wavelength-based measurement without changing the data collection mode as
described above, then you will see an error message and things will not work
Figure 8. Data Collection window for time-based
Figure 9. Data Collection window for
In the Data Collection window for a time-based
measurement, you need to set four parameters. First, select the Length
of the experiment (enter the number in the first box and the units in the
second). Check the Sample at Time Zero check box if you want the
computer to measure the absorbance immediately at the start of the experiment (a
good idea in most cases). Select Sampling Rate either using the slide bar
or by typing a number into one of the boxes below the slide bar. Some important
things to know about the sampling rate: 1) the units on the sampling rate are
the same as those you selected in the Length of the experiment, 2) when
you type a value in one the sampling rate boxes, the computer automatically
calculates the other and 3) if you select a sampling rate that is faster than
the spectrometer can actually do, a message will be displayed and you will not
be allowed to proceed.
To have the spectrometer wait before it begins to record
data (i. e., set a delay), select the Triggering tab and the window
should now look like that shown in Fig. 10. Click on the Triggering check box
to activate triggering and select either the On Keyboard or On Sensor
Value options. On Keyboard means that the computer will wait until
you press a key on the keyboard (the Enter key is a good choice) before
it starts taking data, while On Sensor Value means that the computer will
wait until the reading from the sensor is a particular value before beginning.
Of the two On Keyboard is usually more useful.
Figure 10. Triggering control window.
If you enter "0" in the Collect ___ Samples before
Trigger box, the software will start acquiring data only after you have
started the run (see below) and hit a key on the keyboard. If you enter any
other number in the Collect ___ Samples before Trigger box, the software
behaves somewhat differently. Once you have started the run, you cannot start
acquisition until the number of points that you specified have been acquired.
Then and only then can you hit a key to initiate acquiring the rest of the data.
When you finish setting up the collection and triggering
parameters for your experiment, click Done. You should now be ready to
make a run. To initiate the run, push the Collect button
If you selected the On Keyboard trigger then the message "Waiting for
keyboard trigger . . ." will be displayed in the center of the graph. If you
selected to acquire no data before the trigger, simply press a key on the
keyboard to start acquisition. If you elected to acquire samples before the
trigger, you will have to wait the amount of time required to obtain these data
before pressing a key on the keyboard. Once acquisition has been triggered, the
"Waiting for keyboard trigger . . ." message will go away and the first data
point will be displayed.
To stop data acquisition simply click the Stop button