Rev 2.01 10302003 Palm-SPEC Pocket PC-based Spectrophotometer Operating Instructions Including OOIPS2000 Software Instructions Offices: Ocean Optics, Inc. 380 Main Street, Dunedin, Fla., USA Phone 727.733.2447 Fax 727.733.3962 8:30 a.m.-6 p.m. EST Ocean Optics B.V. (Europe) Nieuwgraaf 108 G, 6921 RK DUIVEN, The Netherlands Phone 31-(0)26-3190500 Fax 31-(0)26-3190505 E-mail: Info@OceanOptics.com Info@OceanOpticsBV.com Orders@OceanOptics.com TechSupport@OceanOptics.
Copyright © 2001-2003 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 an 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 1 Palm-SPEC Introduction............................................................................................................... 1 Product Overview ...............................................................................................................................................1 2 Palm-SPEC Specifications ........................................................................................................... 3 How the Palm-SPEC Works ..............................
Palm-SPEC Introduction 1 Palm-SPEC Introduction The following chapter contains introductory information about the Palm-SPEC Pocket PC-based Spectrophotometer, shipment information, and documentation. Product Overview The Palm-SPEC Pocket PC-based Spectrophotometer features a Pocket PC-based handheld computer coupled with an Ocean Optics USB2000 Spectrometer in a customized optical bench to create a spectrophotometer system with a footprint of just 6” x 4.5”.
Palm-SPEC Introduction Wavelength Calibration Data Sheet The bag containing the spectrometer also contains the Wavelength Calibration Data Sheet. The information on both the Wavelength Calibration Data Sheet and in the file on the Spectrometer Configuration Diskette is identical, and this information is unique to each individual spectrometer. Note: Due to the importance of the data contained on the Wavelength Calibration Data Sheet, you should store it for reference after initial use.
Palm-SPEC Specifications 2 Palm-SPEC Specifications This chapter contains an overview of Palm-SPEC operation and component specifications. How the Palm-SPEC Works The Palm-SPEC Spectrophotometer uses a 2048-element linear CCD array detector inside of a miniature cross Czerny-Turner optical bench with a 600 lines/mm grating. This provides a simultaneous display of 2048 wavelengths over the 370-950 nm range.
Palm-SPEC Specifications Optics Specifications Grating: 600 lines/mm blazed at 400 nm Slit: Optical resolution: 25 µm width (slit height at 1000 µm) ~20. nm FWHM Pixel resolution: ~0.3 nm Stray Light: ~0.
Setting Up the Palm-SPEC 3 Setting Up the Palm-SPEC This chapter contains instructions for physically configuring the Palm-SPEC equipment. Connecting the Palm-SPEC Equipment Follow the instructions and diagrams below to connect your Palm-SPEC equipment: Install Microsoft ActiveSync Before connecting and configuring the Palm-SPEC equipment, you must install Microsoft ActiveSync 3.7 (or later) on your desktop or laptop.
Setting Up the Palm-SPEC Compaq Aero The handheld PC seats directly into the cradle mounted on the Palm-SPEC spectrometer. Connect the power supply to the rear of the Spectrometer. The Aero will draw power from the spectrometer and cradle. No additional handheld PC power supply is required. HP Jornada 1. Connect the 1.3 mm adapter connected to the thicker power wire to the rear of the Jornada Cradle. 2. Connect the 1.3 mm adapter attached to the thin black power wire to the rear of the Palm-Spec. 3.
Setting Up the Palm-SPEC • Be wary of the battery life of your handheld PC. If your battery drains, you may lose all installed programs on your handheld PC. This will require you to reinstall OOIPS2000 (and any other previously installed software). • When OOIPS2000 is running, the light source is on. However, you do not need to exit the software when the system is idle in order to lengthen the life of the bulbs in the light source. The light source is designed to last approximately 40,000 hours.
OOIPS2000 4 OOIPS2000 OOIPS2000 Introduction OOIPS2000 Palm-SPEC Spectrometer Operating Software for Pocket PC is designed for ease of use. You can use the stylus to quickly navigate through the software. To obtain data, place a sample in the holder and then either select a previously saved experiment method to receive data or click the icons on the screen to take new measurements. You can access several commonly used OOIPS2000 functions via convenient buttons on the main display screen.
OOIPS2000 OOIPSCU The OOIPSCU Palm-SPEC conversion utility software allows you to convert and transfer any Palm-SPEC file directly to your PC. For more information on OOIPSCU, see page 33. Product Updates OOIPS2000 Palm-SPEC Spectrometer Operating Software is under continuous update and improvement. To obtain free upgrades, visit our web site at http://www.oceanoptics.com/technical/softwaredownloads.asp.
OOIPS2000 Store Reference and Dark Storing a reference and a dark is requisite before the software can calculate absorbance or transmission spectra. The reference is taken with the light source on and a blank in the sampling region. The dark is taken with the light source turned off.
OOIPS2000 Enter the minimum and maximum wavelength X-axis and Y-axis, then click the OK button in the upper right corner when finished. Unscale To reset the scale of a spectrum so that the default scale fills the display area, click the Unscale icon or select Spectra | Scale | Unscale from the menu. Snapshot Mode Before using snapshot mode, you must enable it by selecting Spectra | Snapshot Mode. A check next to this menu option indicates that the mode is already enabled.
OOIPS2000 File Menu Functions File menu functions allow you to manage spectral data, define how OOIPS2000 handles data files, and establish and control user access. Open To open specific file types, select File | Open from the menu and then choose Dark, Reference, Processed or Experiment data files.
OOIPS2000 Save To save specific file types, select File | Save from the menu and then choose Dark, Reference, Sample, Processed, or Experiment. Dark To save a dark spectrum, select File | Save | Dark from the menu. Enter a file name in the Save As dialog box. OOIPS2000 appends the file name with a dark_ps file extension. Reference To save a reference spectrum, select File | Save | Reference from the menu. Enter a file name in the Save As dialog box.
OOIPS2000 Autoincrement Filenames The Autoincrement Filenames option names stored spectra automatically. When you next choose the File | Save | Processed command, the function automatically saves the absorbance, transmission, or scope mode processed spectrum and names the file with a base name and the numerical index you specified when configuring this option. An autoincremented filename of Test00018.
OOIPS2000 Application Log Enable Select File | Application Log | Enable from the menu. This option records all executed software events in a text file, providing an auditing trail for system managers. Configure • Program Events (when tab selected) Program Execution Program Termination User Login • Records the date and time the software was opened, as well as the name of the user who opened it. Records the date and time the software was terminated, as well as the name of the user who terminated it.
OOIPS2000 • Spectra (when tab selected) Storing Reference Spectrum Performing Diagnostics • Documents that a reference spectrum was stored, the sampling parameters (integration time, averaging, boxcar smoothing, etc) used when the spectrum was stored, the name of the user who stored the spectrum, and the date and time it was stored.
OOIPS2000 Data Display Configuration Drift Configuration • Records the scope, absorbance, transmission, and concentration values display precision, the font color and size of the results, and if the results are cursor or concentration values. Only records when these values or functions are altered. Records whether or not drift correction was enabled, the nonabsorbing wavelength, and the bandwidth.
OOIPS2000 • Methods (when tab selected) Executing Method Records the method file name, the date and time of method execution, and the name of the user who executed the method. Storing Method Calibration Point Records the calibration, concentration, and intensity point stored. Saving Method Terminating Method • Records the method file name, the date and time the method was saved, and the name of the user who saved the method.
OOIPS2000 View Current This option allows you to see the current application log file. You must use the scroll bars to view this data in its entirety. This data is stored in memory even if you have not yet specified an application log file name. Select File | Application Log | View Current from the menu to enable this option. View Stored Application Log… This option opens an open dialog box allowing you to choose and view a previously stored application log.
OOIPS2000 Set User’s Rights This option allows you to configure what portions of OOIPS2000 a particular user can access. To set or change the functions available to a particular user, first choose the user's name in the Manage Users screen and then click on the Set User Rights button. A Set User Rights dialog box (illustrated below), containing every function of OOIPS2000, is listed in a tree format. Tap the screen sharply to change the state of the check boxes.
OOIPS2000 Delete User To delete a current user, click the user's name in the Manage Users screen and select the Delete User button. You are prompted to confirm the user deletion. Click the Yes button to delete the user, or click the No button to cancel. Login If security is enabled, users must log into the OOIPS2000 software. You can configure user names, passwords, and options available to each user in the Manage Users | Set User’s Rights screen.
OOIPS2000 Store Reference Only To store a reference spectrum only (without the system automatically storing a dark spectrum and adjusting the integration time) select Spectra | Store Reference Only from the menu. If a long time has passed since storing the last reference spectrum but you don't want to use the Store Reference and Dark function (since that will also turn the light source off to take the dark measurement), select this option.
OOIPS2000 • Wavelength (when tab selected) This screen provides the serial number and the wavelength calibration coefficients of your spectrometer. Do not change these values. • Linearity (when tab selected) This screen allows you to enable or disable the linearity correction, and also provides the linearity correction intercept and coefficients for your spectrometer. Do not change these values.
OOIPS2000 • Stray Light (when tab selected) This screen allows you to enable or disable the stray light correction, and also provides the stray light correction coefficient for your spectrometer. Do not change this value. Note: Stray light is light detected at a wavelength or wavelengths other than those at which the light should be detected. All spectrometers experience stray light.
OOIPS2000 time you store a new reference, OOIPS2000 will automatically adjust the integration time to achieve the best signal. • Spectra to Average This value sets the number of discrete spectral acquisitions that are accumulated before OOIPS2000 receives a spectrum. The larger the value, the better the signal-to-noise ration (S:N). The S:N improves by the square root of the number of spectra averaged.
OOIPS2000 • Concentration Display Precision Select a decimal-place value (from 0 to 6 decimal places) to specify the precision of the result from concentration measurements presented on the display screen and saved in the data files. • Result Font Color Choose from 19 different colors for the color of the data shown in the display screen. • Result Font Size Choose font sizes ranging from 18 to 42 points for the data shown in the display screen.
OOIPS2000 • Configure To set the parameters for correcting drift, select Spectra | Drift Correction | Configure from the menu. Enable Drift Correction Non-absorbing Wavelength (nm) Bandwidth (nm) Enable this function to correct for variations in spectral intensity due to light source and system drift. This function is the same as selecting Spectra | Drift Correction | Enable from the menu. Wavelength that will represent midpoint of your reference area.
OOIPS2000 Graph Colors This option allows you to choose colors for the graph background, the spectral trace, the cursor, and the grid. Choose from one of the 19 colors in the drop-down menu for each option. Select Spectra | Graph Configuration from the menu to access this option. Cursor Configuration This option allows you to configure the cursor’s style, color, and location (wavelength). Select Spectra | Cursor Configuration from the menu to access this option.
OOIPS2000 Log Menu Functions Log menu functions enable you to customize and control how data is logged and how OOIPS2000 handles the log files that you create. Configure Select Log | Configure from the menu to set the log file data parameters. These specifications determine what data is logged each time you click the Log button in the main display screen. Note: When you change the parameters on this screen and click OK, a Log Parameter Change message prompts you to create a new data log filename.
OOIPS2000 Prompt for Description Select this option only if you want to manually enter a description for each log entry after each click of the Log button on the main display screen. The description you type appears only for that one entry. Description Enter a short description that will appear in the data log file each time you click the Log button in the main display screen. Or, if you wish to manually enter description for each logged entry, select the Prompt for Description box.
OOIPS2000 Create Select Method | Create from the menu to start method creation. This command opens a dialog box, where you must enter a name for the experiment method you are about to create. After naming the method, the Edit Method dialog box opens. This is where you can insert the steps for your method. Edit Select Method | Edit to select an existing experiment method to open. After choosing a method file, the Edit Method screen displays all of the steps for your method listed in sequential order.
OOIPS2000 Help Menu Functions Help Topics Select Help from the menu to access the OOIPS2000 help system. The Contents page lists all help topics, organized by to subject. The Index page lists all help topics in alphabetical order. Enter a word in the Find page to search all the help topics for that designated word. About OOIPS2000 The About OOIPS2000 dialog box contains the program version and copyright information. Select Help | About OOIPS2000 to access this information.
OOIPSCU Conversion Utility 5 OOIPSCU Conversion Utility The OOIPSCU Palm-SPEC Conversion Utility (OOIPSCU) software is designed to transfer Palm-SPEC files from the Palm-SPEC to your desktop or laptop computer. OOIPSCU’s flexibility allows you to determine the format (tab-delimited, comma-delimited, OOIBase32, Grams/32 SPC) of exported Palm-SPEC files prior to transferring them to the destination PC.
OOIPSCU Conversion Utility Connect the Handheld PC to the Destination PC OOIPSCU will communicate with the destination computer via the USB connection on your handheld PC. Follow the steps below to connect the handheld and destination PCs: 1. Ensure that the Base of the handheld PC is connected to the USB port of your destination PC and that the power adapter is plugged into a wall outlet. 2. Seat the handheld PC in the base.
OOIPSCU Conversion Utility Selecting an Action to Perform Once your OOIPSCU software is configured, you can perform a variety of actions. The following table details the actions available Action Description Copy Only • The binary files you select on the handheld PC are copied to the Transfer Directory. Copy and Convert • • The original binary files are still saved on the handheld PC. The binary files you select on the handheld PC are copied into the Transfer Directory.
OOIPSCU Conversion Utility Connect To retrieve Palm-SPEC files from your handheld PC, you must first connect the handheld PC to your desktop or laptop PC. See the Connection Instructions for Palm-SPEC Handheld PC Versions section on page 5 for instructions on connecting the handheld PC and the destination PC. Once you connect the equipment: 1. Run OOIPSCU on your desktop or laptop computer. 2. Select File | Connect from the menu or click the Connect icon.
OOIPSCU Conversion Utility Small Icons To display items by using small icons, select View | Small Icons from the menu or click the View Small Icons icon. List To list items, select View | List from the menu or click the View List icon. The files are then listed, along with small icons, in alphabetical order. Details To list and see detailed information about 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.
OOIPSCU Conversion Utility Conversion Format Select Conversion | Conversion Format | to select the type of file format you wish to export to the destination PC. See page ASOIGO for a description of available file formats. Prompt Before Overwriting Output File This option enables a prompt that warns you if you are about to overwrite an existing file. Select Conversion | Prompt Before Overwriting Output File to enable this option.
OOIPSCU Conversion Utility 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.
Sample Experiments 6 Sample Experiments The following sections contain information on conducting sample experiments using the Palm-SPEC Spectrophotometer and OOIPS2000. Preparing for Experiments Follow the steps below to configure the Palm-SPEC Spectrophotometer and OOIPS2000 for experiments: 1. Double-check that you have correctly installed the Palm-SPEC Spectrophotometer, installed OOIPS2000 on the handheld PC, and configured the light source and other sampling optics. 2.
Sample Experiments Application Tips If the signal you collect is saturating the spectrometer (intensity greater than 4000 counts), you can decrease the light level on scale in scope mode by: • Decreasing the integration time • Attenuating the light going into the spectrometer • Using a smaller diameter fiber (when using an external light source) • Using a neutral density filter with the correct optical density (when using an external light source) If the signal you collect has too little light, you
Sample Experiments Absorbance Experiments Absorbance spectra are a measure of how much light a sample absorbs. For most samples, absorbance is linearly related to the concentration of the substance. OOIPS2000 calculates absorbance (Aλ) using the following equation… Aλ = - log10 Sλ - Dλ ( R -D ) λ λ …where Sλ is the sample intensity at wavelength λ, Dλ is the dark intensity at wavelength λ, Rλ is the reference intensity at wavelength λ.
Sample Experiments Transmission Experiments Transmission is the percentage of energy passing through a sample relative to the amount that passes through the reference. Transmission Mode also displays the portion of light reflected from a sample, since transmission and reflection measurements use the same mathematical calculations. The transmission is expressed as a percentage (%Tλ) relative to a standard substance (such as air).
Index Index A A/D Converter, 4 About OOIPS2000, 35 About OOIPSCU, 46 Absorbance, 25 Absorbance Mode, 11 Absorbance Mode Display Precision, 28 ActiveSync, 5 Administration Tab, 21 Adobe Acrobat Reader, 2 Aero, 6 Application Log, 18 Administration Tab, 21 Clear Current Application Log, 22 Configuration Tab, 19 Enable, 18 Files Tab, 18 Logs Tab, 20 Methods Tab, 21 Program Events Tab, 18 Save Current Application Log As, 22 Set Application Log Filename, 22 Spectra Tab, 19 View Current, 22 View Stored, 22 Autoin
Index Display Functions, 10 Absorbance Mode, 11 Autoscale, 11 Cursor Placement, 12 Log Values, 12 Scope Mode, 11 Set Scale, 12 Snapshot Mode, 12 Store Reference and Dark, 11 System Diagnostics, 10 Transmission Mode, 11 Unscale, 12 Drift Configuration, 20 Drift Correction, 29 Configure, 30 Enable, 29 E Edit, 34 Enable, 16, 18, 29 Enable Drift Correction, 30 Enabled, 44 Execute, 34 Executing Method, 21 Exit, 24, 34 Exit - OOIPSCU, 40 Experiment, 14, 15 Experiments, 47 Absorbance, 49 Transmission, 50 Export, 3
Index Set User’s Rights, 23 Method Menu Functions, 33 Create, 34 Edit, 34 Execute, 34 Exit, 34 Export, 34 Open Calibration Curve, 34 View Current Calibration Curve, 34 Methods Tab, 21 Move and Convert, 38 Move Only, 38 N Non-absorbing Wavelength (nm), 30 O OOIPS2000, 9 About, 35 Features, 9 OOIPSCU, 5, 10, 36 About, 46 Clear, 46 Configure, 37 Connect, 40 Connect Hardware, 37 Conversion Format, 44 Conversion Menu Functions, 42 Convert Local Files, 44 Convert Only, 38 Convert Selected Files, 44 Copy and Conve
Index Scope Mode Display Precision, 28 Select an Action, 38 Set Application Log Filename, 22 Set Log Filename, 33 Set Log Filename - OOIPSCU, 46 Set Scale, 12, 30 Set Transfer Directory - OOIPSCU, 42 Set User’s Rights, 23 Setup, 5 Shipment Components, 1 Small Icons - OOIPSCU, 42 Snapshot Mode, 12, 31 Software and Resources Library CD, 2 Specifications, 3 A/D Converter, 4 Detector, 3 Handheld PC, 3 Optics, 4 Sampling Component, 4 System, 3 Spectra Menu Functions, 24 Configure, 25 Configure Data Display, 28 C
