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Raman Systems R-2001TM

Operating Instructions Software Version 3.0

Raman Systems, Inc. 108 Water Street

Watertown, MA 02174 (617) 926-2977

(617) 926-7996 (fax)

Raman Systems, Inc.

For the latest information, consult the Raman Systems web site: http://www.ramansystems.com

Or, contact our Technical Service Department by e-mail:

[email protected]

Raman Systems, Inc.

SAFETY PROCEDURES AND WARNINGS

FOR YOUR SAFETY, READ AND UNDERSTAND ALL SAFETY AND OPERATING INSTRUCTIONS BEFORE USING THIS PRODUCT.

Optical Safety The light emerging from the R-2001 fiber optic probe when the shutter is open is from a Class 3b laser. This laser product produces visible and/or invisible laser radiation. It is capable of causing serious eye injury and blindness to anyone who looks directly into the beam. Laser safety eyewear must be worn when the probe’s shutter is open. The SYSTEM ON | OFF switch controls the power to the system. When the system is on, the green System Power Indicator Lamp will be on. Two switches control the operation of the laser.

1. The keyed switch on the front panel of the R-2001 labeled LASER ON/ LASER OFF 2. The pin inserted on the front panel of the R-2001 labeled LASER INTERLOCK

When the keyed switch is in the LASER ON position and the LASER INTERLOCK is connected, the laser and the red Laser Power Indicator Lamp will be on. For additional information on laser safety, refer to the following publications: • American National Standards for the Use of Lasers. American National Standards Institute, 1980. • Performance Standard for Laser Products. FDA, (FR-40) (148): 32252-32265. Department of Health,

Education and Human Service Bureau of Radiological Health, July 31, 1974. • Laser Safety Guide. Laser Institute of America (5th Edition), Toledo, Ohio, 1982. • Safety with Lasers and other Optical Sources. D. Sliney and M. Wolbarsht, Pleum Publishing Company,

New York, NY, 1980.

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Table of Contents

SECTION 1: INTRODUCTION....................................................................................................................................7

1.1 SYSTEM OVERVIEW ............................................................................................................................................... 7 1.2 PARTS INCLUDED................................................................................................................................................... 7 1.3 DAMAGE CLAIMS AND RETURN SHIPMENTS.................................................................................................... 7 1.4 PRODUCT SPECIFICATIONS.................................................................................................................................. 8

SECTION 2: BASIC OPERATING INFORMATION...............................................................................................9

2.1 CONTROL FEATURE DESCRIPTIONS................................................................................................................... 9 Systems Power Switch............................................................................................................................................9 Laser Power Switch................................................................................................................................................9 Laser Interlock Connector....................................................................................................................................9 Laser Power Lamp ..................................................................................................................................................9 Laser Output Port ...................................................................................................................................................9 Spectrometer Input Port ........................................................................................................................................9 USB Interface Port………………………………………………………………………………………………10 The AC Power Cable Input .................................................................................................................................10 Operating Software..............................................................................................................................................10

2.2 FRONT PANEL DIAGRAM.................................................................................................................................... 11 2.3 REAR PANEL DIAGRAM ...................................................................................................................................... 11 2.4 IDENTIFICATION, WARNING, AND DANGER LABELS..................................................................................... 12 2.5 FIBER OPTIC PROBE ............................................................................................................................................ 13

2.6 Sample Holder……………………………………………………………………………………… 14

SECTION 3: SYSTEM SETUP....................................................................................................................................16

3.1 INSTALLING THE RSI R-2001BASE SOFTWARE ............................................................................................... 16 3.2 SPECTROMETER INITIAL SET-UP..................................................................................................................... 18 3.3 CONFIRMING ELECTRICAL POWER................................................................................................................... 18 3.4 INITIAL SOFTWARE SETUP ................................................................................................................................ 19 3.5 CONFIRMING THE CONNECTION TO YOUR COMPUTER............................................................................... 20

SECTION 4: SOFTWARE OVERVIEW ...................................................................................................................21

4.1 MAIN SCREEN LAYOUT ...................................................................................................................................... 21 4.2 BUTTON TOOLBAR.............................................................................................................................................. 22 4.3 CHANNEL SELECTION......................................................................................................................................... 23 4.4 SAMPLE PARAMETER SETTINGS....................................................................................................................... 24 4.5 DISPLAY MODES.................................................................................................................................................. 24 4.6 SPECTRA CHART CONTROLS............................................................................................................................. 25

Chart Cursors........................................................................................................................................................25 Chart Zooming......................................................................................................................................................25

4.7 CALABRATION/VERIFICATION…………………………………………………………………26 4.8 MEASURING DARK CURRENT…………………………………………………………………. 27

4.9 MEASURING SAMPLE SPECTRA......................................................................................................................... 28 4.10 FOCUS MODE MEASUREMENT ........................................................................................................................ 28 4.11 AUTORUN MODE MEASUREMENT ................................................................................................................. 29 4.12 EXPORTING SPECTRA TO GRAMS/32.............................................................................................................. 30 4.13 STATUS BAR ....................................................................................................................................................... 30

SECTION 5: SOFTWARE MENU OPTIONS ..........................................................................................................31

5.1 FILE MENU OPTIONS.......................................................................................................................................... 31

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5.2 VIEW MENU OPTIONS ........................................................................................................................................ 32 5.3 SETUP MENU OPTIONS ...................................................................................................................................... 33

Program Options..................................................................................................................................................33 Communication Parameters...............................................................................................................................34

6.4 RUN MENU OPTIONS .......................................................................................................................................... 35 6.5 HELP MENU OPTIONS ........................................................................................................................................ 35

For additional technical assistance, please contact one of our Applications Scientists or

our Technical Support Department at:

Raman Systems, Inc. 108 Water Street. Suite 2L

Watertown, MA 02472 (617) 926-2977 t (617) 926-7996 (fax)

E-mail: [email protected]

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SECTION 1: INTRODUCTION

1.1 System Overview Thank you for selecting the Raman Systems R-2001. This manual describes the correct operating procedures for the Raman Systems R-2001, a product of joint venture with Ocean Optics, Inc. The Raman Systems R-2001 is a fully integrated, low-cost system for applications involving the sophistication of Raman spectroscopy techniques. Uses for the R-2001 include characterization of highly scattering particulate matter in aqueous solutions, gels, powders, creams, and other media; reaction monitoring; product identification; and remote sensing. The Raman Systems R-2001 is comprised of five basic elements: the diode laser, fiber-optic probe, spectrometer, A/D card, and operating software. The diode laser supplies light through the excitation fiber in the fiber-optic probe. The scattered light from the sample is collected and transmitted to the spectrometer via the collection fiber in the fiber-optic probe. The spectrometer measures the amount of light at each pixel in the sampled spectrum. The A/D card transforms the analog data from the spectrometer into digital information that is passed to a computer. Finally, the operating software converts the digital data from the spectrometer into the Raman spectrum that is pertinent to the user.

1.2 Parts Included Your Raman Systems R-2001 includes the components listed below. Note that once the wavelength of the laser has been chosen (either 785 nm or 532 nm), then the wavelength of the spectrometer, the probe and the safety goggles must match the choice. Optional components, such as Ocean 32 software, can be purchased separately. • Diode laser and miniature fiber optic spectrometer in a 143mm x 104mm x 40mm housing, both tuned to either 785

nm or 532 nm. • Fiber-optic probe (tuned to either 785 nm or 532 nm). • Spectrometer and A/D converter • Operating software, supplied on CD • Laser safety goggles (either tuned to 532 nm for 532 nm system or tuned to 785 nm for 785 nm system) • AC Power Supply and Cord • Operating instructions and accessories price list

1.3 Damage Claims and Return Shipments Thoroughly examine your Raman Systems R-2001 and all accompanying accessories as soon as they are received. Insist that the carrier’s agent verify the inspection and sign the description. Immediately notify the delivering agent in person or by telephone of damage or loss. Carriers are reluctant to make adjustments for damaged merchandise unless it is inspected and reported promptly. Risk of loss of, or damage to merchandise remains with the buyer. It is the buyer’s responsibility to file a claim with the carrier involved. Contact us immediately so that we may assist you. Also, all returned products must have a Return Merchandise Authorization (RMA) number. Please contact an Applications Scientist for specific instructions when returning a product.

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1.4 Product Specifications High-Output Laser *

Output 250-300 mw at probe tip for 785 nm 25 mw at probe tip for 532 nm

Type 785 nm solid state diode (Red laser system) 532 nm solid state diode (Green laser system)

Excitation Delivery Via 90 µm fiber optic probe Numerical Aperture 0.22 Class 3b

Miniature Fiber-optic Spectrometer

Detector 2048 element linear silicon CCD array CCD elements 2048 elements @ 125µm X 200µm per element Well depth (@ 600 nm) 350,000 photons Sensitivity (estimated) 86 photons/count

2.9 X 10-17 joules/count 2.9 X 10-17 watts/count (for 1 second integration)

Integration time 1 second to 4 minutes (need CCD cooling option for > 60 seconds) Grating density 1200 lines/mm Range 785-1000nm or 200-2800cm-1 (Red laser system)

532-690nm or 200-4300cm-1 (Green laser system) Resolution 15 cm-1 Signal-to-Noise 200:1 (observed in measuring benzene)

Collection Optics

Fiber bundle Laser delivery fiber and collection fiber, both labeled Configuration Contact, immersion or stand off

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SECTION 2: BASIC OPERATING INFORMATION

2.1 Control Feature Descriptions The Raman Systems R-2001 is designed to be easy to use. This section will familiarize you with the switches and connections (See Figures 2.1 and 2.2) that will enable you to use the analyzer to its fullest capacity.

Systems Power Switch The system switch, labeled SYSTEM ON | OFF is located on the front panel. It turns the Raman Systems R-2001 on and off. When the System Power Switch is on, the red System Power Lamp is illuminated.

Laser Power Switch The laser power switch, labeled LASER ON | OFF, is located on the front panel. This key type switch must be in the own position before the laser can be turned on.

Laser Interlock Connector The laser interlock connector, labeled Laser Interlock, is located on the front panel. The laser interlock plug must be inserted into the connector before the laser can be turned on.

Laser Power Lamp The red Laser Power Lamp indicates whether or not the laser is on. When the lamp is illuminated, the laser is on.

Laser Output Port The laser output port is located on the front panel. It is equipped with a safety shutter that springs closed when a probe is disconnected.

WARNING: OPERATING THE LASER WITH THE SHUTTER CLOSED CAN CAUSE DAMAGE AND/OR PRODUCT

FAILURE.

Spectrometer Input Port The spectrometer input port is located on the front panel.

USB Interface Port The serial interface port is located on the rear panel. The port is used to link your computer to the Raman Systems R-2001 via an interface cable.

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The AC Power Cable Input The 12/5-volt AC power cord port is located on the rear panel of the Raman Systems R-2001. (See Figure 2.2)

Operating Software The operating software is supplied on a CD. The RSI R-2001Base software performs all the data acquisition and control functions for the spectrometer and provides standard spectroscopy features in a real time data acquisition environment.

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2.2 Front Panel Diagram

2.3 Rear Panel Diagram

I

Figure 2.2

Figure 2.1

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2.4 Identification, Warning, and Danger Labels

Laser Warning Label

Defeatable Interlock Danger Label

DANGER> VISIBILE AND/OR INVISIBLE

LASER RADIATION WITH FIBER

REMOVED. AVOID DIRECT EXPOSURE TO

BEAM

AVOID EXPOSURE> VISIBLE AND/OR INVISIBLE

LASER RADIATION IS EMITTED FROM THIS APERATURE

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2.5 Fiber Optic Probe The laser beam is transmitted to the probe housing and the collected Raman shifted photons are returned to the spectrometer via two fiber optic lines. The laser delivery fiber has a red sheathing, while the collection fiber has a blue sheathing. The optics and the shutter are contained in the Probe Housing. The two fiber optic lines and the two power wires for the shutter are bundled into the Probe Cable, which is sheathed in either PVC or Stainless Steel Monocoil. The laser beam is delivered to the sample and the scattered Raman shifted photons are returned to the Probe Housing via the sample tube. The 4 mm in diameter collimated laser beam the leaves the Probe Housing travels down the sample tube where it passes through a lens that focuses the beam on a 100 micron diameter dot. The probe utilizes three interchangeable Probe Caps marked 1-3 and two interchangeable sample tubes. A six inch sample tube is used for immersion measurements where the tip of the tube is immersed in solvents, while a three inch tube is used with three interchangeable caps: . • Probe Cap 1 – used for verification and calibration, it contains a sample of Teflon on the inside of its cap. • Probe Cap 2 – used for tablets and powders. It is

dimensioned so that the laser beam is focused right at the tip so that, if you press it against a tablet.

• Probe Cap 3 – Used for measuring substances in a transparent container (bottles,

cuvettes, plastic bags, etc.). Probe Cap 3 is dimensioned so that the laser beam is focused approximately 4 mm from the tip of the probe.

Probe Cap

Sample Tube

∼ 4 mm

Sample Tube

Probe Cap

Probe Housing

Probe Cable

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This allows you to press the probe tip against the wall of a container allowing the laser beam to shoot through the container wall and take the measurement of the sample inside the wall at the focal point.

• Probe Cap 4 – Used when the probe is to be inserted into a liquid. The cap contains a Sapphire window that

protects the lenses and optics from the liquid. The cap can be remove and the window cleaned. When reassembling the cap (contains two Teflon washers, one on each side of the sapphire window, and the sapphire window, make sure, that when the cap is reattached to the tube, the seal is water tight. Apply silica grease to the threads and remove the tube from the probe housing to verify the seal is watertight.

2.6 Sample Holder To assist in making measurements through the walls of transparent containers, we supply a sample holder that eliminates any interference from ambient light. To use the Sample Holder first insert the probe’s Sample Tube into the round insertion hole on the side of the Sample Holder.

Next place the sample container into the holder as shown below, positioning it against the Positioner Thumb Screw. Push the Probe’s Sample Tube against the sample container and lock it in place with the Probe Lock Thumb Screw.

Sample Tube

Insertion Hole

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Finally, place the Sample Cover in place

Probe Lock Thumb Screw Positioner

Thumb Screw

Sample Container

Sample Cover

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SECTION 3: System Setup

3.1 Installing the RSI R-2001Base Software Installation with RSI R-2001Base (Windows) A CD containing R2001Base was provided with your R2001. Before installing R2001Base, close all applications that are currently running. Insert the CD into your CD drive. The installation program should automatically start in a few moments. If it does not, follow the procedure below.

1. Under the Start menu select Settings and then select Control Panel. 2. Within the Control Panel window select the Add/Remove Programs option. 3. Within the Add/Remove Programs window click the install button. 4. You will be prompted to insert the installation disks, simply click the next button. 5. box should read D:\setup.exe, unless your CD drive has a different drive letter. If it does click the finish

button, if it does not, enter D:\setup.exe, or the appropriate drive letter, in the Command line for installation program box and then click the finish button.

After searching for a possible previous version of the software on your computer, the installer program’s start screen will appear (see figure 3.1). Press the Next button to start the installation process, or the Cancel button to stop the installation. The next screen of the program installer is where you select the folder on your computer to contain the R2001Base program. (See figure 3.2) If a previous installation was found, the default location will be that folder. You can install to the same folder as the previous version. It will be over-written. To select a different folder press the Browse button. When ready, press the Next button to proceed to the next installation screen.

Figure 3.1 – Software Installation Start Screen

Figure 3.2 – Software Destination Selection Screen

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The next screen selects the Program Manager Group. This is the location on your Start menu that the program will appear. An icon will also be placed on your desktop. (See figure 3.3) If you’re not sure, just use the default selection by pressing the Next button to continue the installation. The installation program will now give you one last chance to abort the installation. If you select Next, the program will be installed on your system. \ Follow the screen prompts to finish the installation process. A new icon will be added to your desktop screen

Figure 3.4 – Software Installation

Figure 3.3 – Program Manager Group Selection

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3.2 Spectrometer Initial Set-Up Remove and thoroughly examine your Raman Systems R-2001 and all accompanying accessories from the shipping container. If any objects appear damaged in any way DO NOT OPERATE INSTRUMENT. See Section 1 for instructions on how to make a claim for damages. Carefully inspect your goggles. After determining that all components are accounted for and in proper condition, assemble as follows.

Install Fiber-optic Probe Install the fiber-optic probe to spectrometer input port, and laser output port. The excitation fiber installs into the laser output port, and the collection fiber installs into the spectrometer input port. (See Figure 2.1). Be sure you have read and understood all safety procedures prior to use.

Attach AC Power Cord Attach the power cord to the rear panel of the R-2001. Ensure that both the power and laser switches are off prior to installing the AC power cord.

Connect Laser Interlock Connector Insert the Laser Interlock connector into the connector on the front panel labeled Laser Interlock (see Figure 2.1). Unless this connection is made, the laser can not be turned on.

Attach Interface Cable between your computer and the R2001

785 nm Systems and Uncooled CCD 532 nm Systems -- With your computer off, connect the USB cable supplied with your system between your computer and the R2001.

532 nm Systems with CCD Cooling Option – With the 532 nm laser and the electronics for the CCD thermo-electric cooler, we had to move the analog to digital converter (ADC1000) outside the R2001 box. To connect the R2001 to your computer, perform the following steps.

1. First of all, the ADC1000 is in the small box labeled ADC1000. 2. Hook the cable attached to the back of the R2001 to the ADC1000 box. 3. Hook the USB cable between the ADC1000 box and your computer.

Install Operating Software Install operating software. See Section 3.1 for detailed instructions. You are now ready to use your Raman Systems R-2001. Please ensure you have read and understood all the optical safety precautions in this manual prior to use.

3.3 Confirming Electrical Power We first want to make sure that the system has electrical power. You can check whether the system has electrical power by moving the power switch in the upper left-hand corner of the faceplate into the system on position. If the

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system has electrical power then the green system power light next to the power switch on the faceplate will illuminate. If the green system power light does not light up you will need to try one of the following:

• If the green system power light does not come on, but you are able to hear the fan(s) located on the top of the system working, then the bulb for the system power light is simply not working. Please contact [email protected] and we will fix the system at your earliest convenience.

• Make sure the system is connected to an electrical power outlet. If it is not, move the power switch into the system off position and connect the 12V power supply to the back of the R2001 system and then to an electrical power outlet. Repeat the initial procedure to confirm whether your R2001 system has electrical power.

If the R2001 system is properly connected to electrical power and neither the green system power light turns on nor the fan(s) begin to operate then the system will require repair work by a Raman Systems technician. Please contact [email protected] and we will fix the problem immediately.

3.4 Initial Software Setup Before you can measure a sample for the first time you need to configure the R2001Base software. Make sure the spectrometer is energized and the communications cable is properly connected before starting the program. To start, double-click on the desktop icon created during installation, or select the R2001Base program from the Program Group Manager. From the Setup menu, select Communications Parameters to open the communications setup screen. Figure 3.6 shows the setup screen. Make your selections (use selections from the communications sheet we sent with your R2001) and select the OK button to exit. You will then need to close the R2001Base program and restart to enable the new settings. You are almost ready to measure a sample. In the upper-left corner of the program screen is a list of channels available for measurement. The channel box should now have a listing for channel 1.

Figure 3.6 – Communications Setup

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3.5 Confirming the Connection to your Computer We now want to make sure that the R2001 system and your computer are able to communicate. To do this you will need to follow these procedures:

• Connect the probe to the R2001 (See Section 2.5) • Attach Cap #1, the Verification Cap to your Probe’s Sample Tube. • Turn laser power key to the laser on position and make sure the Laser Interlock Connector is plugged in.

• Set the integration time to 10 seconds and press the measurement button.

• If the communication link has been established, you will hear the shutter click open and 10 seconds later you will hear it click shut. While the shutter is open, you will see the red light on the probe housing turn on. When the shutter closes, the light will turn off. If you hear the shutter, proceed on to the next Section.

• If you do not hear the shutter, turn the software and the 2001 off. Turn the R2001 back on and restart the software. Try the Procedure once more. If the problem persists, contact us (617-926-2977).

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Section 4: First Time Software Usage 4.1 Main Screen Layout The main screen of the R2001Base software is shown above in figure 5.1. This is the main operating screen of the software where all sample measurement and analysis is performed. Key components of the screen have been outlined and are explained briefly below.

♦ Channels - Where you enable spectrometer channels for measurement and display. ♦ Sample Parameters – Measurement parameters defined for each channel. ♦ Display Type – Defines how the spectra is displayed on the spectra plot. ♦ Verification/Calibration Button – Button used to calibrate the x and y axes and to verify that the

system is operating properly. ♦ Spectra Chart – The graphic display of the sample spectra. ♦ Toolbar – Buttons for selecting measurement options. ♦ Grams Export – Button to export the current spectra to a running copy of Grams software. ♦ Dark Current Measure – Button used to measure a dark current. ♦ Sample Measure – Button to start all sample measurements. ♦ Status Bar – Information about the current step in a measurement cycle. ♦ Menus - Programs options and parameters are selected here.

ToolBar

Channels

Sample Parameters

Display Type

Sample Measure

Dark Current Measure

Gramms Export

Spectra Chart

Status Bar

Menus

Figure 4.1 – R2001Base Main Screen

Verification/Calibration Button

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4.2 Button Toolbar The Button Toolbar is a quick method for accessing common program functions. The functions on the toolbar are also available through the menus.

Clear Chart Pressing this button clears ALL spectra from the spectra chart. No warning is given, and all unsaved spectra are lost.

Save Spectra Pressing this button opens a standard Windows file requester. Select a path, and enter a filename, to save the currently displayed spectra to a file. This file can be loaded later using the “Load Spectra” button. The file can also be imported into Grams32 directly for further analysis.

Setup Channel Pressing this button displays the Calibration file setup screen. This option is used to calibrate the spectrometer to increase the accuracy of the Raman shifted peaks.

Toggle Focus Mode Pressing this button toggles the “Focus Mode” of operation on or off. When on, the background of the button is black. Focus mode is a method of rapid and continuous spectral measurement helpful in aligning the sample probe.

Measurement in Process Indicator Indicates the Shutter is open and a measurement is in process. When on, the background of the button is black.

Load Spectra Press this button to load a previously saved spectra file into the chart. A standard Windows file requester will open. Select the desired spectra file. The chart will then display the saved spectra.

Print Spectra Pressing this button will immediately print the currently displayed spectra to the default Windows printer. To select a different printer, select “Printer Setup” from the “File” menu.

Clear Chart

Save Spectra

Setup Communications

Toggle Focus Mode

Measurement in Process Indicator

Load Spectra

Print Spectra

Calibration/Verification

Toggle Autorun Mode

Toggle Dark Current Subtraction

Figure 4.2 – Button Toolbar

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Calibration/Verification Press this button to initiate the Calibration of the x and y axes, and to verify that the system is performing properly.

Toggle Autorun Mode Pressing this button toggles measurement between single spectra measurement, and continous sample measurement. See the Autorun section for additional information. . When on, the background of the button is black.

Toggle Dark Current Subtraction Pressing this button toggles dark current subtraction on or off. When on, the background of the button is black. When dark current subtraction is enabled a dark current measurement is automatically subtracted from the sample spectra to remove the effects of system noise from the spectra. This results in a significant increase in signal-to-noise for the spectra. Refer to the section on Dark Current Subtraction for additional information.

4.3 Channel Selection The channel selection area of the main screen has two main purposes: selection of active channels for measurement, and selection of spectra for display. Note: When the program is used for the first time there are no channels available. This is because channels must be selected using the “Spectrometer Setup” option of the “Setup” menu. Refer to section 3.4 for additional information. Figure 4.3 shows the Channels selector. Up to eight spectrometer channels can be enabled at one time. This box displays a list of channels defined during spectrometer setup. Clicking the box to the left of the channel number enables this channel for measurement. If a channel is listed, but not checked, it will not be measured. If more channels are available than can be displayed, scroll bars appear on the right side of the box to let you scroll up or down in the list. Left clicking on the channel number selects that channel. Selecting a channel displays the last measured spectra in the chart (unless the chart was cleared). The sample parameters setup box will also display the settings for that channel.

Figure 4.3 – Channels Selector

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4.4 Sample Parameter Settings The Sample Parameters section of the main screen is used to select the measurement settings for each spectrum measured. Each channel has a different set of settings.

Integration This is the integration or sampling time in seconds. Increasing the integration time will result in more signal being gathered. Resulting in an increase in the signal-to-noise. The practical limits are that too much signal will saturate the R-2001’s detector. Experimentation with this setting is required determine the proper time for a particular sample. The integration time can be any value between 1 and 480 seconds (8 minutes).

Avg Avg is the abbreviation for average. This is the number of samples to average. For example; if you set this value to 5, then five successive sample spectra will be measured and averaged together. With the resultant averaged spectra being displayed on the chart. The maximum number of spectra that can be averaged is fifteen. The minimum (and default) is one.

Box Box is the abbreviation for Boxcar width. This is a smoothing function that sets the averaging of pixels across the spectrum to smooth the spectrum. A boxcar value of 5 averages each data point with itself, 5 points to its left, and 5 points to its right. The range of values for this function is 0 to 500. Zero disables boxcar smoothing.

4.5 Display Modes There are three modes for displaying data on the chart.

Single This is the default display mode. This displays the current channel spectra full-scale in the chart display. To see other channel spectra, select that channel in the Channels control (see section 5.3).

Stack This display mode displays all channel spectra simultaneously. The individual spectra are stacked vertically, one on top of the other. This allows you to view each spectrum independent of the others.

Overlay This display mode displays all channel spectra simultaneously. The spectra are plotted superimposed over each other at full display. This is helpful to show relative intensity differences on different channels.

Figure 4.4 – Sample Parameters Settings Section

Figure 4.5 – Chart Display Modes

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4.6 Spectra Chart Controls

Chart Cursors Left click on any position on the chart and twin cursors appear. The cursors extend the full height (for the x-axis cursor) and the full width (for the y-axis cursor) of the chart. The values for the selected position are displayed on the axes at the point selected. To turn off the cursors, left clicking anywhere on the gray border of the chart.

Chart Zooming To zoom into a region of the chart to observe greater detail, left click on the chart and hold down the left mouse button. While holding down the button, drag the mouse down and to the right. This will draw a box around a region of the chart. The portion of the chart that lies within this box will be enlarged to full chart scale. As you can see in figure 4.7, there are eight black control boxes on the zoom box. Four on the sides, and four on the corners.

Placing the mouse over one of the boxes changes the cursor to double arrows. Click and drag any control box to resize the zoom box.

Placing the cursor on one of the four edges of the zoom box changes the cursor to a four-arrow cursor. Left click and drag to move the position of the zoom box around the chart

display area.

Placing the cursor anywhere inside the zoom box changes the cursor to a key symbol. Left click when this symbol is displayed and the zoom will occur.

To scroll the chart, move the cursor over any portion of the spectra line. The cursor will change to a hand. Click and drag the spectra around to position it wherever you desire.

To abort the zoom process and remove the zoom box, left-click anywhere on the chart border. To return the chart to full scale, right-click anywhere on the chart border.

Figure 4.7 – Chart Zooming Cursor

Figure 4.6 – Chart Cursors

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4.7 Calibration/Verification The R2001 has the capability to automatically calibrate the x and y axes, thus removing discrepancies resulting from laser variations and the nonlinearities of the CCD. In the process, the R2001 determines whether or not it is functioning properly.

• Click on the Verification/Calibration Button (See Figure 4.1) on the Computer Display to start the Verification/Calibration Process.

• The following window will appear on your screen. Attach the Verification Cap to the Probe’s Sample Tube (see Section 2.5) and select OK.

• After you have installed the software, the first time you run the Calibration/Verification procedure you will be prompted for the wavelength of your laser. Select the wavelength and press OK.

The verification/calibration process will take about a minute. During that time, a window will first appear on your computer display showing that the Dark Current is being measured. Next a window will show that a spectrum is being taken. Finally, if the calibrations and verification were successful, the following window will appear on your screen.

Replace the verification cap with the measurement cap you are using and you are ready to collect Spectra. If the Verification fails, make sure the Verification Cap is securely attached and repeat the procedure. If the failure persists, contact us (617-926-2977).

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4.8 Measuring Dark Current Dark current is the inherent noise present in the system. This undesirable portion of the measurement sample needs to be removed to separate actual spectral peaks from the noise. To remove this noise you need to measure a dark current and subtract it from the sampled spectra.

To measure a new dark current, press the “Dark” button. If the laser is currently on, it will be temporarily shutdown until the dark current measurement is complete. (Refer to Program Options to adjust the time the laser is allowed to warm-up or shutdown between measurements.)

During a dark current measurement the chart border will change color as a visual indicator that a dark current measurement is in progress. A progress bar will appear in the center of the screen to countdown the integration time during the dark current measurement. The parameter settings for the dark current must be the same as the parameter settings used for sample measurement. (See section 4.4) When the dark current measurement is complete, the dark current spectra will be displayed in the chart window. A message box will appear asking you if the dark current is correct. You have three options to choose from. Yes – The dark current is correct. Save and use the current dark current. No – The dark current is incorrect. Measure another dark current. Cancel – Exit the dark current measurement without saving the current dark current. Important Note: Dark current measurements are not saved when the software is shutdown. You need to take new dark current measurements at the start of a new program session.

To use the dark current measurement you need to select the Dark Current Subtraction button on the button toolbar. Dark current subtraction must be “on” prior to taking a sample measurement. Figure 4.10 illustrates the difference in sample spectra when dark current subtraction is used.

Figure 4.9 – Dark Current Measurement

Dark Current Subtraction ON

Dark Current Subtraction OFF

Figure 4.10 – Dark Current Subtraction Example

Figure 4.8 – Dark Current Integration Progress Bar

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4.9 Measuring Sample Spectra

Note: Follow all optical safety precautions stated in this manual. The following are all the steps necessary for a sample measurement. Many of these steps need only be performed once. 1. Connect the probe to the R2001 (See Section 2.5) 2. Turn the System Power Switch and the Laser Power Switch on,

and make sure the Laser Interlock Connector is inserted. (See Sections 2.2)

3. Start the software. 4. Verify that the R2001 is working properly (See Section 4.7) 5. Prepare your sample for measurement (See Sections 2.5 and 2.6) 6. Adjust the sample parameters. (See section (4.4) 7. Record a Dark Current and turn on dark current subtraction. (See Section 4.8) 8. Press the Sample Measure button to record a Spectrum.

The measure button looks like a traffic light. When the program is ready to measure the traffic light is green. During measurement it is red. Press the measure button to start the measurement process. The measurement progress bar will appear on the screen to countdown the integration time.

The measure button is used to start all measurement modes (except dark current). In some measuring modes (Autorun and Focus modes) the measure button is pressed again to stop measurement.

4.9 Focus Mode Measurement Focus mode measurement is a special measurement mode available to help you adjust your fiber probe for maximum signal.

Pressing the Focus Mode button before starting measurement places the program in Focus mode. A very short integration time is used, and no dark current

subtraction is used during measurement. The shutter is open for 20 seconds, then closed for 10 seconds. During the 20 seconds that the shutter is open, the raw spectra are plotted as rapidly as possible to the chart. During the 10 seconds that the shutter is closed, plots are made, but the laser is not illuminating the sample. Figure 4.12 shows an example of the Focus mode in operation. Note the large amount of noise on the signal. This is actually due to the extremely small amounts of energy recorded. The chart is scaled full scale by default on the first scan only. Auto scaling of the chart is disable for all subsequent scans. You can increase the signal levels but adjusting the parameters for the focus mode. To adjust the focus mode parameters press the “Pause” key on your computer’s keyboard. The sampling cycle will pause and the Focus Mode Setup window will appear. (See figure 4.13)

Figure 4.11 – Sample Measurement Progress Bar

Figure 4.12 – Focus Mode Measurement

Raman Systems, Inc.

In the center of this window is a field that contains the current integration time for the Focus mode (default is 0.1 seconds). Increase this value to increase the signal level, at the cost of speed of signal update. A horizontal and vertical red line represents the axes on the chart. Two fields on each display the current minimum and maximum values for those axes. You can type in new values to zoom into a specific area of the chart during focus mode measurement. When you are finished, press the “Resume” button to return to the Focus mode measurement cycle using the new settings. To rescale the chart to full signal, right-click on the charts border. To exit Focus mode, press the measure button a second time.

4.10 Autorun Mode Measurement Autorun mode is a measurement mode used if you want to take multiple sample spectra. It is a free-running mode in that you cannot select the number of measurements, instead the program continuously measures spectra until the measure button is pressed a second time to stop measurement. It is similar to Focus mode, except that all measurement parameters are used for each measurement, as well as dark current subtraction. In addition, sample spectra can be saved to a file.

To engage the Autorun mode, press the “Auto” button. A window will open that prompts you for the amount of delay time between each measurement. (Figure 4.14)

Enter a delay time in minutes and/or seconds. This is the delay between subsequent measurements. A checkbox called “Free Running Mode” is used to indicate that you don’t wish to save sample spectra. If left unchecked (the default), a Windows file requester will appear when you select the “Done” button. Select a storage path and a base filename to save the spectra. The storage filename is the base filename you select, appended with the channel number and an incremental number. For example, if you enter “Test” as a base filename, the first spectra measured on channel one would have the filename “TestCH1_0000.spc”, the second “TestCH1_0001.spc”, etc. To exit Autorun mode, either press the Autorun button again (if you have not started measuring), or press the measure button to stop measurement. The Autorun mode is reset after completing a measurement cycle. You will need to reselect the Autorun button if you want to measure in this mode again.

Figure 4.13 – Focus Mode Parameters

Figure 4.14 – Autorun Delay Interval

Raman Systems, Inc.

4.11 Exporting Spectra to Grams/32

Once a sample spectrum has been acquired and displayed in the chart window, the data can be automatically transferred to Grams/32* for further analysis if desired.

For this function to operate properly, Grams must already be running in the background. The data is transferred to Grams, and Grams is automatically brought to the front of the display. If Grams is not already running, then pressing the “To Grams” button will have no effect. This function has been tested on versions 5, 6, and 7 of Grams/32. (*Grams/32 is a registered trademark of Galactix Industries Co rporation. All rights reserved)

4.12 Status Bar

The status bar at the bottom of the program screen displays informational messages during the program usage. Refer to the status bar to determine which task is currently underway during a measurement cycle. In addition, that status bar displays the current date and time.

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Section 5: Software Menu Options

5.1 File Menu Options Figure 5.1 shows the File Menu. It is primarily used for importing/exporting data and printing spectra. Each option is described below.

Open … This option is for importing saved spectra for display in the chart window. A Windows file requester is displayed when selected. Browse and locate a previously saved spectra file. The spectra will be plotted to the chart window. This option is also available from the button toolbar.

Clear Chart Selecting this option immediately clears all spectra displayed on the chart window. This includes spectra not visible from other channels. This action is permanent. This option is also available from the button toolbar.

Save This option saves the currently selected channel’s spectra to a disk file. The default extension for spectra files is “.spc”. This format can be directly read into Grams/32 if desired. . This option is also available from the button toolbar.

Printer Setup … Select this option to select a printer other than the Windows default printer. A printer setup dialog box is displayed. You can also adjust the printer and paper options. These settings are not saved when the program is closed.

Print… This immediately prints the spectra of the currently selected channel to the default Windows printer.

Export File… Selecting this option lets you save the data for the currently selected channel as a comma-delimited text file, suitable for direct importation into a spreadsheet program. The default extension is “.csv”.

Exit Exits the program. Any unsaved spectra are lost. No dark currents are saved as part of the shutdown, however channel parameter settings are saved. You can also close the program by clicking the “X” button on the far right side of the title bar.

Figure 5.1 – File Menu Options

Raman Systems, Inc.

5.2 View Menu Options The view menu contains options pertaining to the display of data in the chart window. Each option is explained below.

AutoScale Plot Selecting this option places a checkmark beside it. When checked, the chart window is automatically scaled to show the entire spectra each time a new spectrum is acquired. When unchecked, the X and Y axis scaling remains the same for every successive scan. This is useful to zoom to a specific region that you wish to concentrate on during measurement.

Toggle Peak Pick Selecting this option places a checkmark beside it. When checked, a peak pick algorithm selects the major peaks on the spectra and displays the value at that peak. This is useful when creating a new calibration file.

Raman Shift Selecting this option places a checkmark beside it. When checked, the x-axis of the chart window displays values in Raman shifted wavenumbers. This change takes effect on the next sample measurement. “Raman Shift” and “Pixel” and mutually exclusive options. This is the default setting.

Pixels Selecting this option places a checkmark beside it. When checked, the x-axis of the chart window displays values in raw pixel numbers. There are 2048 pixels measured by the detector in the R-2001. This change takes effect on the next sample measurement. “Raman Shift” and “Pixel” and mutually exclusive options.

Figure 5.2 – View Menu Options

Figure 5.3 – Spectra with Peak Pick Enabled

Raman Systems, Inc.

5.3 Setup Menu Options The Setup menu contains options pertaining to the setup parameters for program operation. Each operation opens a separate window with controls and fields to configure that section of the program. Verify – Triggers the Automatic Calibration/Verification algorithm. Laser Select – Allows you to specify your laser wavelength. Program Options – This option lets you customize certain actions in the program. Communications Parameters – Used to select communication settings for the spectrometer used.

Program Options The program options screen contains additional options available to the program. Future options will be added to this screen. Presently there are two sections: General Settings, Auto Dark Current.

General Settings There are two general settings, both pertain to the laser. Laser Warm-up Delay: The amount of time, in seconds, that the laser is allowed to stabilize before measurement is allowed. A progress meter appears on the main screen below the measure button to countdown the warm-up time. Laser Shutdown Delay: The amount of time, in seconds, that the laser is allowed to cool down before a measurement is made (typically a dark current measurement).

Auto Dark Current When enabled, the Auto Dark Current feature allows for an automatic measurement of a new dark current measurement, on all enabled channels, after a specified time interval. This is only used during Autorun and Production modes of operation. Enable Auto Dark Current: Check this box to enable the Auto Dark Current feature. Uncheck to disable. Measure Delay: The amount of delay before a new dark current is automatically measured. Laser Warm-up Delay: A special warm-up delay used when Auto Dark Current is enabled. This supersedes the general Laser Warm-up Delay. This allows for a longer warm-up delay to ensure a stable laser signal before continuing measurement.

Figure 5.5 – Program Options Screen

Figure 5.4 – Setup Menu Options

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Communications Parameters This window is typically only used once after the program is initially installed. Settings are saved and available even if the R2001Base program is removed from the computer, and re-installed. Figure 6.8 shows the setup screen with typical settings for the R-2001 spectrometer. Unless specified otherwise by Raman Systems, these are the settings you should use for your R-2001 system. Spectrometer Type: This is a list of supported Ocean Optics spectrometers. The default spectrometer in the R-2001 is the USB2000. Select the appropriate spectrometer if you are using a different model. A/D Converter Type: This field specifies the type of onboard Analog to Digital converter used. The R-2001 uses a serial communications system. Some units have been equipped with a Universal Serial Bus (USB) system. Select the appropriate method for your system. The following options may not all be available if you select a different spectrometer or A/D type than the those specified. Serial Port: This is the serial port (Com Port) on your computer that you have connected the communications cable to. If port #1 is unavailable, and you have another free port, select that port number here. Baud Rate: This is the communications data speed. The typical settings is 57600. Values higher than these have typically proven unreliable. If you are having problems communicating with the R-2001, try setting this field to a lower rate. ADC1000 Pixel Resolution: Leave this value at 1. Higher numbers will reduce the quality of your sampled spectra. Compress Data: Check this option to realize a small speed increase in sampling time. Data sent from the spectrometer is compressed before transmission when checked.

Figure 5.6 – R-2001 Communications Setup

Raman Systems, Inc.

5.4 Run Menu Options The Run Menu allows an alternate method of selecting most of the measurement-related options that are selected using the button toolbar. The exception is the last option “Calculate Concentration”. Select this option when a spectrum is displayed in the chart window. This allows you to calculate the concentration and Mahalanobis Distance values of this spectra using a selected PLS calibration file. 1. Measure a new sample spectrum, or load a saved spectrum. 2. Select “Calculate Concentration”. 3. A Windows file requester opens, prompting you to select a PLS calibration file. Select one appropriate for this

spectrum. 4. The results of the calculation are shown in a message box on the screen. (See figure 5.8) If the PLS file does not match the sample spectra, an error message is displayed “Source data does not match data information stored in the calibration file.”.

5.5 Help Menu Options The Help menu has three options.

Password This option is to activate to optional Production Mode section of the R2001Base program. Selecting this option opens a message box that prompts you for the password to enable the Production mode. Production mode is the Process Control section of the program that allows real-time strip chart recording of data from multiple channels overtime. Data can be optional recorded to disk, and/or sent to an external controller via Modbus or 4-20mA communications. Refer to the Production mode section for additional information. When a valid password has been entered, this menu option will disappear Once the proper password has been entered, a new “Mode” menu is available that lets you toggle between the standard “User” mode of operation, and the “Production” mode of operation.

Figure 5.7 – Run Menu Options

Figure 5.8 – Calculated Concentration Results Example

Figure 5.9 – Help Menu Options

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R2001Base Manual Loads and displays the portable document format (PDF) version of this file. You must have the Adobe Acrobat viewer installed on your computer to view it.

About Displays contact information for Raman Systems, Inc.

Figure 5.10 – Program About Screen

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