Ocean Optics OOIBase16 User Manual

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OOIBase Operating Software

Instruction Manual

Version 1.52

Ocean Optics, Inc. 380 Main Street Dunedin, FL 34698 (727) 733-2447 (727) 733-3962 fax

For the latest information and software upgrades consult our web site: www.OceanOptics.com

Or, e-mail our Technical Service Department: TechSupport@OceanOptics.com

070699

Contents

About OOIBase Operating Software

Installing OOIBase Operating Software

Using OOIBase Operating Software

File Menu Functions .........................................................................................3

View Menu Functions .......................................................................................4

Setup Menu Functions......................................................................................6

Toolbar Functions.............................................................................................9

Doing an Experiment

Absorbance Measurement..............................................................................10

Transmission Measurement............................................................................11

...................................................................................10

...........................................................1

.....................................................2

...........................................................3

Relative Irradiance Measurement...................................................................11

Reflection Measurement.................................................................................12

About OOIBase Operating Soft ware

OOIBase is the standard operating software for Ocean Optics spectrometers. OOIBase for Windows is a basic acquisition and display software that provides a real-time interface to a variety of signal-processing functions. OOIBase allows users to perform basic spectroscopic measurements such as absorbance, reflectance and emission, as well as more sophisticated tasks such as the automation of experiments with a time-series acquisition function. OOIBase allows the user to view, in real-time and entirely on one screen, spectral data from up to 8 spectrometer channels.

Absorbance spectrum of cranberry juice

OOIBase offers users considerably more flexibility than they are likely to experience with other spectrometer operating software. The basic concept for the software is that real-time display of data allows users to evaluate the effectiveness of their experimental setup and data processing selections, make changes to these parameters, instantly see their effect, and save the data. OOIBase offers:

! Spectrometer control

• integration time regulation

• multiple triggering options

• channel selection

! Signal Processing including:

• signal averaging

• boxcar pixel smoothing

• electrical dark-signal subtraction

• stray light correction

! Spectral Processing: absorbance, transmission, irradiance ! Time series acquisition for full spectra ! Real time graphical display with zoom, cursor and cosmetic selections ! Multi-window support ! File Export to ASCII format

OOIBase operates with Windows 3.x and Windows 95/98. Windows NT users are easily able to write their own applications using the OOIWinIP Windows or OOILVD La bVIEW drivers.

All Ocean Optics software products comply with Year 2000 requirements.

""""

Installing OOIBase Operating Soft ware

1. Insert the OOIBase floppy disk into a drive.

2. Select

3. Click OK at the “Welcome!” dialog box.

4. Select the

5. In the “Make Backups” dialog box, click

6. After the software installation is complete, you will go back out to your desktop.

7. Start OOIBase by selecting

8. The first time the software starts, the “Interface Setup Parameters” dialog box opens. This box allows

Run

and type

Destination Directory

housed. Clic k OK.

you to specify your Spectrometer, A/D Converter, Base Address (I/O Range), and IRQ (Interrupt Request). Choose the correct parameters for your setup. For the ADC500, ADC1000 or PC2000, choose the same Base Address and IRQ settings as the dip switches on the A/D board. If you left them unchanged, accept the default settings (Base Address of 768 and IRQ of 7). If you have the DAQ-700, you will have to use your computer to find the correct settings of the hardware. For specific instructions on changing the settings for these A/D cards, see the directions that came with your product. If you have the SAD500, ignore the Base Address and IRQ selections. Click OK. You can always go back to this dialog box by selecting

(drive):setup

. Click OK.

. Choose the default destination or type where you want the software

YES

Start | Programs | OOIBase V 1.5 | OOIBase V 1.5

Setup | Configure Hardware

9. If you do not see the “Interface Setup Parameters” dialog box when you start OOIBase, exit OOIBase by selecting open Notepad and allow you to edit the initialization file for our device driver. Find the “Initialized” entry within this file. Make sure this line reads: Initialized=0. Save the OOIDRV.INI file and exit Notepad. Restart OOIBase. You should now see the “Interface Setup Parameters” dialog box allowing you to spec i f y your ha rdware configurat io n.

10. At this point, OOIBase should be acquiring data from your spectrometer. There should be a dynamic trace responding to light near the bottom of the displayed graph. If your spectrometer is not responding to light (or your computer hangs or crashes), please contact our Technical Support Department.

11. Exit and restart OOIBase. This enables the hardware changes to take effect.

File | Exit

. Then select

Start | Run

, and type C:\windows\ooidrv.ini. This will

Using OOIBase Operating Soft ware

File Menu Functions

New

This command opens a new window and starts acquiring data from the spectrometer. By default, the Master channel is selected and the graph is placed in Scope Mode.

Open

This command opens a dialog box that allows you to reload a saved set of spectra. If you saved the dark or the reference spectra, they are also restored.

This command immediately closes the current graph window. You are current spectrum when this command is chosen.

Store Dark Spectrum

This command stores the current spectrum as the dark spectrum for the channel activated. This spectrum is taken with the light source off or with the light path blocked. (See Saving a dark spectrum is requisite before the software can make the calculations of absorbance, transmission, and relative irradiance spectra.

not

given the opportunity to save the

Doing an Experiment

on page 15.)

Store Reference Spectrum

This command stores the current spectrum as the reference spectrum for the channel activated. This spectrum is taken with the light source on and a blank in the sampling region. (See on page 15.) Saving a reference spectrum is requisite before the software can make the calculations of absorbance, transmission, and reflection spectra.

Doing an Experiment

Save Sample Spectrum

This command opens a dialog box that allows you to save a set of spectra as a binary file. If the dark and reference spectra are saved, they are also saved in the binary file. Data acquisition parameters are also saved.

Export Spectrum

This command opens a dialog box that allows you to export the current spectra (sample, reference, and/or dark) into a comma-delimited ASCII file. You are given the opportunity to specify the filename. The following file extensions are the default:

Spectrum Extension

Reference .REF Dark .DRK Sample

Absorbance .ABS Transmission .TRM Reflection .RFL Scope .SCO

Print Preview

This command opens a window allowing you to view how the current spectrum will look when printed.

This command displays a dialog box allowing you to print the current spectrum. The graph title, grid and cursor are all printed if they are displayed on the screen.

Exit

This command exits OOIBase.

View Menu Functions

Scope Mode

This command switches the current window into Scope Mode. The signal graphed in Scope Mode is the raw voltage c oming out of the A/D converter. Once you open O OIBase and it begins to acquire data, you see the raw voltage from the detector expressed in A/D counts. This spectral view mode is unique to Ocean Optics and allows the user the ability to have complete control of signal processing. Be careful when using this mode, as it represents a combination of several factors: the intensity of the light source, the reflectivity of the grating and the mirrors in the spectrometer, the transmission of the fibers, the response of the detector, and the spectral characteristics of the sample. Scope Mode should only be used to select signal acquisition functions.

Absorbance Mode

This command switches the current window into Absorbance Mode. Before this can occur, both the dark and reference spectra must be stored while in Scope Mode. (See details.) The absorbance of a solution is related to the concentration of species within it. The relationship, known as Beer’s Law, is:

Aλ =

A = absorbance at wavelength λ, ε = extinction coefficient of the absorbing species at wavelength λ, c = the concentration of the absorbing species, and l = the pathlength of the absorption.

Doing an Experimen

on page 15 for

This relationship is used to determine the concentration of a species in solution. Absorb ance is calculated by the following equation. When this equation is evaluated for each pixel of the detector, the absorbance spectrum is produced.

Aλ = - log

= sample intensity of each wavelength,

= reference intensity of each wavelength, λ = each wavelength

(

)

= dark intensity of each wavelength,

Transmission Mode

This command switches the current window into Transmission Mode. Before this can occur, both the dark and reference spectra must be made and stored while in Scope Mode. (See 15 for details.) The transmission of a sample is calculated by the following equation:

%Tλ =

= sample intensity of each wavelength,

= reference intensity of each wavelength, λ = each wavelength

x 100%

= dark intensity of each wavelength,

Doing an Experiment

on page

Irradiance Mode

This comma nd switches the current window into relative Irradiance Mode. The reference spectrum must be made in Scope Mode with a blackbody of known color temperature. A dark spectrum is usually obtained by removing the fiber from the reference lamp and preventing light from entering it. (See

Experiment

source relative to a reference emission source. Relative irradiance is calculated by the following equation:

B S R

on page 15 for details.) Relative irradiance spectra are a measure of the intensity of a light

Iλ =

(

= relative energy of the reference calculated from the color temperature in degrees Kelvin,

= sample intensity of each wavelength,

= reference intensity of each wavelength, λ = each wavelength

)

= dark intensity of each wavelength,

Doing an

Snapshot

This command freezes the data acquisition for the current spectral window and allows you to continue to view a single spectrum.

Autoscale Y Axis

This command automatically adjusts the vertical scale of a current graph so the selected area fills the graph.

Change Graph Scale

This command opens a dialog box allowing you to manually set both the vertical and horizontal scale of the graph.

Unscale Graph

This command returns the graph to its default scale.

Colors

This command allows the user to choose a color for the frames, background, trace, text, grid, and cursor. It is especially useful if multiple channels are being used. Utilize this function to differentiate one channel’s display from another.

Cursor

This command toggles a vertical cursor on the current graph. The cursor can be moved with either the yellow arrows in the toolbar or via the following keystrokes:

Keystroke Command

Page Up Moves vertical cursor 25 pixels to the right Page Down Moves vertical cursor 25 pixels to the left

(right arrow) Moves vertical cursor 1 pixel to the right

(left arrow) Moves vertical cursor 1 pixel to the left

(up arrow) Moves vertical cursor to beginning pixel

(down arrow) Moves vertical cursor to end pixel

(less than, comma) Moves vertical cursor to next peak

(greater than, period) Moves vertical cursor to previous peak

Grid

This command toggles the display of a vertical and horizontal grid on the graph.

Setup Menu Functions

Configure Hardware

This command opens the “Interface Setup Parameters” dialog box. It allows you to configure the specific type of hardware connecting the spectrometer to the computer. In this box, you specify your

Address

box are usually set only once -- when OOIBase is first installed and the software first starts. (See

Installing OOIBase Operating Software

page 3 for further details.)

Configure Spectrometer

This command opens the “Spectrometer Configuration” dialog box. The number of spectrometer channels in your system is selected. The correct numbers for the

Second Coefficient

been entered from the bottom of the calibration sheet that came with your spectrometer.

Stray light is light detected at a wavelength or wavelengths other than those at which the light should be detected. All spectrometers experience the effects of stray light. The

Enable Stray Light Correction Stray Light Constant

mathematical equation, reduce every pixel’s intensity to compensate for the total amount of stray light in the spectrometer.

Spectrometer, A/D Converter, Base

IRQ

and

. The parameters in this dialog

First Coefficient

Intercept

, and

functions, through a

have already

and the

Time Series Acquisition

This command opens the “Time Series Setup” dialog box. It allows you to specify parameters important to the time series data acquisition of full spectra. You can opt to have up to four

Channels

Enter the

Between Scans

The value entered for Number of Scans will affect the amount of memory (see

Estimated memory

measurements. If these values are too high and require more memory than you have available, your computer may freeze, hang or crash.

The allows you to begin acquiring data at a later time. After entering the time (in

in a time series setup.

Number of Scans

Delay Before First Scan

Spectrometer

Delay

and

you want for your setup .

) required for your

function

seconds), a dialog box opens with a running countdown of the time left before data acquisition begins. At this point during this countdown, you can click “Start Now” to override the delay. Also, when the data acquisition begins, you can always cancel the procedure, which results in a loss of data.

By selecting acquisition may take longer. If you select

Update Graph During Acquisition,

Acquire Data as Fast as Possible

you can see the live spectra being acquired but the

, you will not be able to use

your computer for any other tasks while the time series acquisition is running.

This dialog box also requires that you choose an

Acquisition Mode

. If you choose Absorbance or Transmission, a dialog box opens requiring you to take a reference and dark spectrum – even if you have already done so.

Subtract Dark Spectrum

This command subtracts the current dark spectrum from the spectra being displayed. This command is useful if you are trying to look at a change in an emission spectrum or are trying to eliminate fixed pattern noise from the spectra. The Subtract Dark Spectrum function only acts on the spectra displayed in Scope Mode.

Data Acquisition

This command opens the “Configure Data Acquisition” dialog box (see picture at right). It allows you to specify data acquisition parameters. The choices made in this dialog box control all channels in your system.

Trigger Mode

four modes of operation. The Normal mode is a continuously scanning mode. The Software mode is an external control mode allowing you to signal the spectrometer to take complete data sets. The External Sync mode allows you to control the integration time from an external source, such as a periodic TTL signal. The External Trigger mode is ideal for use with laser and other short-pulse events; however, this mode has a fixed integration time of 55 milliseconds.

allows you to choose between

The first 24 pixels in the spectrometer do not respond to light but they do produce an electrical signal. When you select the

Correct for Electrical Dark Signal

box, this function subtracts the value of these

optical black pixels from the entire signal, reducing the counts of the black pixels to almost zero.

Choosing the

Spectrum

function.

You would only select the

Correct for Electrical Dark Signal

S2000 Strobe Enable

if you were operating an exte rnal strobe source. To

function

does not

replace the

Store Dark

purchase one of our strobe light sources, such as our PX-2 Pulsed Xenon Lamp or our LS-450 Blue LED Pulsed Light Source, contact an Ocean Optics Applications Scientist.

Samples for Static Average

is a signal averaging function that averages x number of spectra before it gets to OOIBase. The value chosen affects all channels in the system. The higher the value, the better the S:N. The S:N will improve by the square root of the number of scans averaged. Samples for Static Average has no limits; thousands of scans can be averaged if you are patient enough. (Another function averages spectra after the scans get to OOIBase. See

Data Analysis

on page 10.)

Integration Time

This command opens the “Integration Time” dialog box (see picture at right). The integration time of the spectrometer is analogous to the shutter speed of a camera. The higher the integration time, the longer the detector “looks” at the incoming photons. If your Scope Mode intensity is too low, increase this value. If the intensity is too high, decrease the value. You should adjust the integration time so that the greatest amount of light that you anticipate for your application causes a signal of about 3500 counts. Whil e watching the graph trace, adjust the integration time until the signal intensity level is approximately 3500 counts. The integration time specified controls all channels i n your system.

Spectrometer Channel

This command opens the “Spectrometer Channel to View” dialog box. It allows you to animate the window for a specific spectrometer channel.

Data Analysis

This command opens the “Configure Data Analysis” dialog box (see picture at right). The functions in this dialog box regulate S:N. The values specified control only the activated window.

Samples to Dynamically Average

averaging function that averages x number of spectra after it gets to OOIBase. The software collects each spectrum and presents the running average of the value entered in this box. The maximum value is 30 scans. The S:N will improve by the square root of the number of scans averaged. (Another function averages spectra before the scans get to OOIBase. Read about this preferred averaging method in

Boxcar Smoothing Pixel Widt h

that averages across spectral data. This technique averages a group of adjacent detector elements. A value of 5, for example, averages each data point with 5 points to its left and 5 points to its right. The greater this value, the smoother the data and the higher the S:N. The maximum value allowed is 50 pixels. However, if the value entered is too high, a loss in spectral resolution will result. The S:N will improve by the square root of the number of pixels averaged.

Choose

Non-Weighted

Data Acquisition

Savitzky-Golay

option.

on page 9.)

if you want the Boxcaring Technique to be weighted; otherwise, choose the

is a signal

is a technique

Set Graph Title

This command opens the “Graph Title” dialog box allowing you to specify the title for the current graph. This title is displayed on the screen and is also printed when you select

File | Print

Toolbar Functions

Many of the Menu functions can also be accessed through your toolbar. All of the toolbar functions, except

New, Data Acquisition, Integration Time

for functions include:

Store Reference Spectrum Subtract Dark Spectrum Set Scale for graph 25 pixels to right Print Transmission Mode Spectrometer Channel 1 pixel to left Open Scope Mode Data Analysis Cursor

New Snapshot Data Acquisition Unscale graph Help Save Absorbance Mode Integration Time 25 pixels to left Store Dark Spectrum Irradiance Mode Autoscale graph 1 pixel to right

, and

Help

, control only the active window. The toolbar

Doing an Experiment

By now, your spectrometer and sapling optics should be set-up for your application. Con firm that the parameters for your setup are satisfactory. Assuming that you have followed the necessary steps and started OOIBase, your spectrometer is already acquiring data. With no light in the spectrometer you should see a fluctuating trace on the bottom of the graph. If you turn on your lamp, you should see the graph trace rise with increasing light intensity.

Now you are ready to take your measurements. There are three basic spectral measurements from which to choose: absorbance, transmission, and relative irradiance. Certain measurements require specific components . Your current setup might not be the best configuration for all measuring functions. Cont act an Ocean Optics Applications Scientist for options.

For each measurement, a reference and dark spectrum must first be made. After taking a reference and a dark spectrum, you may take as many absorbance, transmission, or relative irradiance measurement scans as you want.

Absorbance Measurement

Absorbance spectra are a measure of how much light is absorbed by a sample. Absorbance spectra are formed by radiation that has penetrated a material medium. For most samples, absorbance is linearly related to the concentration of the substance. The software calculates absorbance using the following equation:

Aλ = - log

= sample intensity of each wavelength,

= reference intensity of each wavelength, λ = each wavelength

Absorbance can also be expressed as proportional to the concentration of the substance interacting with the light. Common applications include the quantification of chemical concentrations in aqueous or gaseous samples. To take an absorbance measurement:

1. Make sure you are in Scope Mode, by either clicking the

View | Scope Mode

be about 3500 counts. (See sure nothing is blocking the light path goi ng to your sample . The analyte you want to measur e must be absent while taking a reference spectrum. Take the reference reading by clicking the

Spectrum

2. While still in

your sample. Do not turn off the light source. Take the dark reading by clicking the

Spectrum

3. Begin an absorbance measurement by first making sure the sample is in place and nothing is blocking

the light going to your sample. Then choose the

View | Absorbance Mode Save Sample Spectrum

If at any time any sampling variable changes -- integration time, averaging, smoothing, distance from light source to sample, etc. -- you must store a new reference and dark spectrum.

(

. Make sure the signal is on scale. The peak intensity of the reference signal should

icon on the toolbar or selecting F

Scope Mode

icon on the toolbar or selecting

)

= dark intensity of each wavelength,

Scope Mode

Integration Time

, take a Dark Spectrum by first completely blocking the light path going to

. To save the spectrum, click the

on page 10.) Take a Reference Spectrum by first making

ile | Store Reference Spectrum

File | Store Dark Spectrum

Absorbance Mode

Save

icon on the toolbar, or selecting

Store Reference

Store Dark

icon on the toolbar or select

File |

Transmission Measu rement

Transmission is the percentage of energy passing through a system relative to the amount that passes through the reference. Transmission Mode is also used to show the portion of light reflected from a sample. Transmission and reflection measurements require the same mathematical calculations. The transmission is expressed as a percentage (%T) relative to a standard substance (such as air). The software calculates %T (or %R) by the following equation:

%Tλ =

= sample intensity of each pixel,

= reference intensity of each pixel, λ = each pixel

Common applications include measurement of transmission of light through solutions, optical filters, optical coatings, and other optical elements such as lenses and fibers. To take a transmission measurement:

1. Make sure you are in Scope Mode, by either clicking the

View | Scope Mode

3500 counts. (See nothing is blocking the light path going to your sample. The analyte you want to measure must be absent while taking a reference spectrum. Take the reference reading by clicking the

Spectrum

2. While still in

your sample. Do not turn off the light source. Take the dark reading by clicking the

Spectrum

3. Take a transmission measurement by first making sure the sample is in place and nothing is blocking

the light going to your sample. Then choose the

View | Transmission Mode Save Sample Spectrum

icon on the toolbar or selecting

Scope Mode

icon on the toolbar or selecting

x 100%

= dark intensity of each pixel,

Scope Mode

. Make sure the signal is on scale. The peak intensity of the signal should be about

Integration Time

on page 10.) Take a Reference Spectrum by first making sure

File | Store Reference Spectrum

, take a Dark Spectrum by first completely blocking the light path going to

File | Store Dark Spectrum

Transmission Mode

. To save the spectrum, click the

Save

icon on the toolbar, or selecting

Store Reference

Store Dark

icon on the toolbar or select

File |

If at any time any sampling variable changes -- integration time, averaging, smoothing, distance from light source to sample, etc. -- you must store a new reference and dark spectrum.

Relative Irradian c e Measurement

Irradiance is the amount of energy at each wavelength from a radiant sample. In relative terms, it is the fraction of energy from the sample compared to the energy collected from a lamp with a blackbody energy distribution, normalized to 1 at the energy maximum. Relative irradiance is calculated by the following equation:

Iλ =

(

= relative energy of the reference calculated from the color temperature in Kelvin,

= sample intensity of each wavelength,

= reference intensity of each wavelength, λ = each wavelength

Common applications include characterizing the light output of LEDs, incandescent lamps and other radiant energy sources such as sunlight. Also included in irradiance measurements is fluorescence, in which case the spectrometer measures the energy given off by materials that have been excited by light at a different wavelength. To take a relative irradiance measurement:

)

= dark intensity of each wavelength,

1. Make sure you are in Scope Mode, by either clicking the

selecting should be about 3500 counts. (See

View | Scope Mode

. Make sure the signal is on scale. The peak intensity of the signal

Integration Time

Scope Mode

icon on the toolbar, or

on page 10.) Take a Reference Spectrum by first making sure nothing is blocking the light path. The light source must be a blackbody of known color temperature. Take the reference reading by clicking the toolbar or selecting

2. While still in clicking the

Store Dark Spectrum

File | Store Reference Spectrum

Scope Mode

, take a Dark Spectrum by blocking the light. Take the dark reading by

icon on the toolbar or selecting

Store Reference Spectrum

File | Store Dark Spectrum

icon on the

3. Take a relative irradiance measurement by first positioning the fiber at the light source you wish to measure. Then choose the

Irradiance Mode

icon on the toolbar or select

View | Irradiance Mode

dialog box opens requiring the light source’s color temperature in Kelvin. Enter the color temperature and click OK. To save the spectrum, click the

Spectrum

If at any time any sampling variable changes -- integration time, averaging, smoothing, distance from light source to sample, etc. -- you must store a new reference and dark spectrum.

Save

icon on the toolbar or select

File | Save Sample

Reflection Measurement

Reflection is the return of radiation by a surface, without change in wavelength. The reflection may be specular, from a smooth surface; diffuse, from a rough surface or from within the specimen; or total, a combination of the two. Reflection is expressed as a percentage (%R) relative to the reflection from a standard substance (such as our WS-1 white reference material for a diffuse reflection measurement):

. A

%Rλ =

= sample intensity of each wavelength,

= reference intensity of each wavelength, λ = each wavelength

x 100%

= dark intensity of each wavelength,

Common applications include measuring the reflection properties of mirrors, anti-reflection coatings, and measuring the visual properties of the color in paints, graphics arts, plastics, and food products. To take a reflection measurement:

1. Make sure you are in Scope Mode, by either clicking the

View | Scope Mode

. Take a Refer ence Spectrum by first making sure nothing is blocking the light

Scope Mode

icon on the toolbar, or selecting

path going to your reference. (For diffuse reflection measurements, place the reflection probe over a diffuse white standard. For specular reflection measurements, place the reflection probe over a firstsurface mirror.) The analyte you want to measure must be absent while taking a reference spectrum. Take the reference reading by clicking the

File | Store Reference Spectrum

2. While still in

Scope Mode

, take a Dark Spectrum by first completely blocking the light path going to

your sample. Do not turn off the light source. Take the dark reading by clicking the

Spectrum

icon on the toolbar or selecting

Store Reference Spectrum

File | Store Dark Spectrum

icon on the toolbar or selecting

Store Dark

3. Take a reflection measurement by first making sure the sample is in place and nothing is blocking the light going to your sample. Then choose the

Transmission Mode

. The Transmission Mode uses the same mathematical formula for both

Transmission Mode

icon on the toolbar or select

View |

transmission and reflection measurements (%R is calculated in the same wa y as %T). To save the spectrum, click the

If at any time any sampling variable changes -- integration time, averaging, smoothing, distance from light source to sample, etc. -- you must store a new reference and dark spectrum.

Save

icon on the toolbar or select

File | Save Sample Spectrum

Ocean Optics OOIBase16 User Manual

Specifications and Main Features

Frequently Asked Questions

User Manual