Operating Manual and User’s Guide Palm-SPECTM Spectrophotometer Ocean Optics, Inc. 380 Main Street Dunedin, FL 34698 (727) 733-2447 (727) 733-3962 fax For the latest information, consult our web site: www.OceanOptics.com Or, e-mail our Technical Service Department: TechSupport@OceanOptics.
Copyright © 2000 Ocean Optics, Inc. All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted, by any means, electronic, mechanical, photocopying, recording, or otherwise, without written permission from Ocean Optics, Inc. This manual is sold as part of a spectrometer order and subject to the condition that it shall not, by way of trade or otherwise, be lent, re-sold, hired out or otherwise circulated without the prior consent of Ocean Optics, Inc.
Table of Contents Introduction .............................................................................................................. 1 Palm-SPEC Spectrophotometer ............................................................................... 2 Setting Up ........................................................................................................................... 3 Care and Use ............................................................................................................
Method Menu Functions (continued) ............................................................................ 23 Export............................................................................................................................. 23 Open Calibration Curve................................................................................................... 23 View Current Calibration Curve........................................................................................ 23 Exit............
Introduction Ocean Optics miniature fiber optic spectrometers and accessories have revolutionized the analytical instrumentation market by dramatically reducing the size and cost of optical sensing systems. More than 10,000 Ocean Optics spectrometers have been sold worldwide -- striking evidence of the far-reaching impact of low-cost, miniature components for fiber optic spectroscopy.
Palm-SPEC Spectrophotometer The Palm-SPEC Spectrophotometer combines a Palm-size PC with a miniature fiber optic spectrophotometer to create a complete computer-based system with a footprint of just 6" x 4". This system, loaded with touch-screen software, provides the general laboratory with a low-cost, easy-to-use and accurate spectrophotometric instrument. The Palm-SPEC optimizes a 2048-element linear CCD-array detector inside of a miniature cross CzernyTurner optical bench with a 600 lines/mm grating.
Setting Up 1. Read and understand all Compaq literature The following literature can be found in the Compaq packaging. ! Important Safety Information. A Compaq Booklet in 24 languages. ! Audible. A Compaq brochure on the audio capabilities of the Aero. ! Compaq Aero Options Information. A Compaq brochure listing all of the accessories you can purchase from Compaq. ! Battery Safety Information. A warning note from Compaq about the dangers associated with the lithium battery.
4. Install the OOIPSCU Palm-SPEC Conversion Utility Software The OOIPSCU Palm-SPEC Conversion Utility software is designed to retrieve Palm-SPEC files from the Palm-SPEC. With this utility, you can copy or transfer Palm-SPEC files from your Aero to your desktop or laptop PC. Windows CE Services must be installed before installing the OOIPSCU Palm-SPEC Conversion Utility. For complete instruction on installing OOIPSCU, see pages 25-26.
Care and Use " Read and understand all documentation regarding the Aero and Windows CE Services. You can find this Compaq and Microsoft Corporation documentation in the Compaq packaging. " Do not run OOIPSCU Palm-SPEC Conversion Utility software until you have installed Windows CE Services onto your desktop or laptop PC. " Though the main and back-up batteries on the Aero make it possible to use the Aero independently of the Palm-SPEC, keep in mind that both the main and back-up batteries can drain.
Specifications Palm-SPEC Specifications Dimensions: Weight: Power input: Operating temperature: 6" x 4.5" x 7.5" (LWH) 2.52 lb; 1.14 kg 5 V DC 32° to 104°F, 0° to 40° C Detector Specifications Detector: CCD elements: Effective range: 2048-element linear silicon CCD array 2048 elements @ 12.5 µm x 200 µm per element 370-950 nm Optics Specifications Grating: Slit: Optical resolution: Pixel resolution: Stray light: 600 lines/mm, blazed at 400 nm 25 µm width (slit height is 1000 µm) ~2.0 nm FWHM ~0.
OOIPS2000 Spectrometer Operating Software OOIPS2000 Palm-SPEC Spectrometer Operating Software for Windows CE was designed with both the busy lab technician and the lab manager in mind. OOIPS2000 is easy to operate. The Stylus or the touch of a finger is used to navigate through the software. To obtain data, the lab tech places a sample in the holder, and then either selects a previously saved experiment method to receive data or clicks the icons on the screen to take measurements.
Display Functions Several OOIPS2000 functions are accessed directly through buttons on the main display screen. From the display screen, you can choose an operation mode, scale the graph, take processed scans and log data. System Diagnostics To perform a diagnostics test, click the System Diagnostics icon or select Spectra | System Diagnostics | Start from the menu. First, you are prompted to name the file for the results of the system diagnostics test. After naming the file, the test begins.
Transmission Mode To view data in transmission mode, click the transmission mode icon or select Spectra | View Mode | Transmission from the menu. Before this can occur, both the dark and reference spectra must be stored. The transmission of a solution is calculated by the following equation: %Tλ = Sλ - Dλ Rλ - Dλ x 100% where S is the sample intensity at wavelength λ, D is the dark intensity at wavelength λ, R is the reference intensity at wavelength λ.
File Menu Functions Open To open specific file types, select File | Open from the menu and then choose Dark, Reference, Processed or Experiment data files. When you open a data file and the acquisition parameters of the file do not match the current settings, a warning box allows you to change the acquisition parameters, ignore the disparity between the parameters, or cancel the opening of the data file.
Sample To save a sample spectrum, select File | Save | Sample from the menu. This command opens a save file dialog box. Whatever name is entered in the File name section, the software adds a sample_ps file extension. Typically, a sample spectrum is made with the sample in the sampling region while in scope, absorbance or transmission mode after taking reference and dark scans. A sample file records the raw spectra used for calculating a processed spectrum.
Application Log Enable Selecting File | Application Log | Enable from the menu records in a text file all executed software events. The log acts as an auditing trail for system managers. Configure • Program Events tab. If selected, -- Program Execution records the date and time the software opened and the user who opened it. -- Program Termination records the date and time the software quit and the user who exited it. -- User Login records the date and time the user logged in and the name of the user.
• Logs tab. If selected, -- Creating Log File records the data log file name; the date and time it was created; and the user who created it. -- Clearing Log File records the data log file name; the date and time it was cleared; and the user who cleared it. -- Saving Log File with New Name records the old data log file name; the new data log file name; the date and time the new data log file name was created; and the user who changed it.
Set Application Log Filename Selecting File | Application Log | Set Application Log Filename from the menu allows you to change the name of the application log file. When you rename this file, all future software events are saved to this new application log file. All past software events are still saved in the old application log file.
Delete User To delete a current user, click the user's name in the Manage Users dialog box and select the Delete User button. When this button is selected, a question appears asking, "Are you sure you want to delete user Fullname Username?" Select either Yes or No and click OK. Login To enter your Username and Password, select File | Login from the menu. This username, password and the commands permitted for a specific user, are selected and configured in the Manage Users dialog box (see page 14).
Spectra Menu Functions Store Reference and Dark To store a reference and a dark spectrum, click the store reference and dark icon or select Spectra | Store Reference and Dark from the menu. Storing a reference and a dark is requisite before the software can calculate absorbance and transmission spectra. This command merely stores a reference and a dark. You must use the File | Save | Reference and File | Save | Dark commands to permanently save the reference and dark spectra.
Absorbance To view data in absorbance mode, click the absorbance mode icon or select Spectra | View Mode | Absorbance from the menu. Before this can occur, both the dark and reference spectra must be stored. Absorbance is calculated by the following equation. When this equation is evaluated for each pixel of the detector, the absorbance spectrum is produced.
Configure Data Acquisition To set data acquisition parameters, select Spectra | Configure | Data Acquisition from the menu. Integration Time (msec) The integration time of the spectrometer is analogous to the shutter speed of a camera. The higher the value specified for the integration time, the longer the detector “looks” at the incoming photons. If your scope mode intensity is too low, increase this value; if too high, decrease the value.
Drift Correction Over time, the detected light from a source fluctuates or drifts. For extended experiments, you achieve the best results if you can take frequent reference spectra. However, for those of you who cannot afford that luxury, you can choose to monitor the light source and OOIPS2000 will correct for any drift that might occur.
System Diagnostics This feature monitors the functionality of the system -- such as the performance of the light source, the life of the bulbs, signal-to-noise ratio for the current acquisition parameters, and integration time optimization. Start To perform a diagnostics test, click the System Diagnostics icon or select Spectra | System Diagnostics | Start from the menu. First, you are prompted to name the file for the results of the system diagnostics test. After naming the file, the test begins.
Log Menu Functions Configure Selecting Log | Configure from the menu allows you to set the parameters for what kind of data is logged into a file each time you click the Log button in the main display screen. Every time you change the parameters in this dialog box and click OK, you receive a Log Parameter Change message suggesting that you create a new data log filename.
Save Current Log As Selecting Log | Save Current Log As from the menu allows you to make a copy of the current data log and save it with a new name that you must specify. However, any data logged after you name this current file are written back to the data log file (see below). This command merely takes a snapshot of the current data log file. Set Log Filename Selecting Log | Set Log Filename from the menu allows you to change the name of the data log file.
Method Menu Functions Create Selecting Method | Create from the menu opens a dialog box requiring you to name the experiment method you are about to create. After naming the method, the Edit Method dialog box opens where you must insert the steps for your method. For step-by-step directions on creating a new method, see page 33. Edit Selecting Method | Edit from the menu opens a dialog box listing saved experiment methods.
Help Menu Functions Help Topics Select Help from the menu to access abbreviated OOIPS2000 help files in HTML format. The Contents page lists all help topics according to subject area. The Index page lists all help topics in alphabetical order. By typing a word in the Find page, you are provided with all of the help topics that contain that designated word.
OOIPSCU Conversion Utility The OOIPSCU Palm-SPEC Conversion Utility software is designed to retrieve Palm-SPEC files from the Palm-SPEC. With this utility, you can copy or transfer Palm-SPEC files from your Aero to your desktop or laptop PC. (See " note below.) Before copying or transferring Palm-SPEC files, you can choose how you would like the Palm-SPEC files converted. You can choose to have your Palm-SPEC files converted to tabdelimited, comma-delimited, OOIBase32, or Grams/32 SPC files.
Configure OOIPSCU before converting files. 13. Select File | Connect from the menu (a check mark must be next to Connect in the File menu) or click the Connect icon. The directories and files on your Aero then appear in the left-hand pane. 14. Select Log | Enabled from the menu to enable the Conversion Utility Log function. The Log function is enabled if there is a check mark next to Enabled in the Log menu functions. 15.
File Menu Functions Connect To retrieve Palm-SPEC files from your Aero, you must first connect the Aero to your desktop or laptop PC. 1. Remove the Aero from the Palm-SPEC Spectrophotometer. 2. Find the AC adapter that came with your system. Plug it into the bottom of the Aero and connect the adapter to a power outlet. For added safety, insert the AC adapter into a surge-protected power strip. 3. Find the serial cable that came with your system.
Details To list items and see detailed information about the items, select View | Details from the menu or click the View Details icon. The files are then listed, along with small icons, in alphabetical order. Additional information, such as file type, file size, and the date and time the file was modified, is listed as well. Refresh To update the Palm-SPEC Conversion Utility window to reflect the latest changes, transfers, and deletions, select View | Refresh from the menu or click the Refresh icon.
OOIBase32 To convert Palm-SPEC files into OOIBase32 files, select Conversion | Conversion Format | OOIBase32 from the menu. OOIBase32 is our free advanced data acquisition and display spectrometer operating software for Windows 95/98/2000 and Windows NT. To learn more about OOIBase32, visit our web site at www.OceanOptics.com/ProductSheets/OOIBase32.asp. Grams/32 SPC To convert Palm-SPEC files into Galactic Software GRAMS/32 SPC files, select Conversion | Conversion Format | Grams/32 SPC from the menu.
Set Log Filename To name or rename the Palm-SPEC Conversion Utility Log file, select Log | Set Log Filename from the menu. A dialog box lists the current log filename and provides a place to set the new log filename. View Stored Log To view any saved Palm-SPEC Conversion Utility Log file, select Log | View Stored Log from the menu. When you select a log file, a Notepad file opens with all Palm-SPEC Conversion Utility events listed since the function was enabled or renamed.
Experiment Tutorial Perform an Absorbance Measurement Absorbance spectra are a measure of how much light is absorbed by a sample. For most samples, absorbance is linearly related to the concentration of the substance. The software calculates absorbance using the following equation: Aλ = - log10 ( Sλ - Dλ Rλ - Dλ ) where S is the sample intensity at wavelength λ, D is the dark intensity at wavelength λ, R is the reference intensity at wavelength λ.
Perform a Transmission Measurement Transmission is the percentage of energy passing through a system relative to the amount that passes through the reference. Transmission is expressed as a percentage (%T) relative to a standard substance (such as air). The software calculates %T by the following equation: %Tλ = Sλ - Dλ Rλ - Dλ x 100% where S is the sample intensity at wavelength λ, D is the dark intensity at wavelength λ, R is the reference intensity at wavelength λ.
Create a New Experiment Method 1. 2. 3. 4. 5. 6. 7. 8. Select Method | Create from the menu. You receive a Create Method dialog box where you must name the method you are about to create. After naming the file, click OK. The method you now create will be saved under this file name. An empty Edit Method dialog box opens. You now need to select and insert the software events you need for your experiment method.
Configure an Experiment Method for Concentration The absorbance of a solution is related to the concentration of the species within it. The relationship, known as Beer’s Law , is: Aλ = ελ c l where A is the absorbance at wavelength λ, ε is the extinction coefficient of the absorbing species at wavelength λ, c is the concentration and l is the optical pathlength. Concentration is the amount of a specified substance in a solution. Graphs of absorbance vs.
5: Initialize method regression Make sure to insert this step. Choose whether you want a First order or Second order regression. The second order regression may provide you with more accurate results, especially if you have several solutions of known concentrations. Next, select the Number of points, or the number of samples of solutions with known concentrations that you are going to be using. Finally, select the Wavelength (nm) for monitoring the concentration of your solutions.
5. When you are ready to execute the concentration method, make sure that you have a blank in the sampling region but that the series of solutions with different known concentrations are at hand, as you will receive prompts to insert these samples into the cuvette holder. 6. Now select Method | Execute from the menu. A dialog box containing method files opens. Select the correct concentration method and click OK. 7.
Appendix A: Method Events List of Available Events +++++ File Menu +++++ Open dark spectrum (D) Open reference spectrum (D) Open processed spectrum (D) Open experiment file (D) Save dark spectrum (D) Save reference spectrum (D) Save sample spectrum (D) Save processed spectrum (D) Save experiment file (D) Enable autoincrement filenames Configure autoincrement filenames (D) Enable application log Configure application log (D) View current application log (D) View stored application log (D) Save application
List of Available Events View data in transmission mode Configure spectrometer (D) Configure data acquisition (D) Configure display (D) Enabled drift correction Configure drift correction (D) Autoscale spectrum Set spectrum scale (D) Reset spectrum scale Perform system diagnostics View system diagnostics results Configure graph (D) Configure cursor (D) Configure grid (D) Enter snapshot mode Event Causes the Following Switches the view mode to absorbance mode.
List of Available Events Set data log filename (D) Clear current data log Save data log as (D) Event Causes the Following Provides a dialog box to change the name of the data log file. When you rename this file, all data logged from this point are saved to this new data log file.
List of Available Events Event Causes the Following Set graph y range +++++ Cursor Commands +++++ Set cursor location Enable cursor +++++ Display Commands +++++ Display method result Display cursor value +++++ Grid Commands +++++ Enable grid on graph Allows you to set the range of the Y axis Set grid ticks +++++ Result Commands +++++ Set display precision Set result font size Set result font color +++++ Snapshot Commands +++++ Take snapshot +++++ Data Acquisition Commands ++ Set acquisition parameters S
List of Available Events Event Causes the Following Write reference spectrum file Write sample spectrum file Write processed spectrum file Write experiment file +++++ File Opening Commands ++++ Open dark spectrum file Open reference spectrum file Open sample spectrum file Open processed spectrum file Open experiment file Empty command Saves a reference spectrum file Saves a sample spectrum file Saves a processed spectrum file Saves an experiment file Opens a dark spectrum Opens a reference spectrum Opens
