SpectraSuite Spectrometer Operating Software

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SpectraSuiteSpectrometer Operating SoftwareInstallationInstallation and Operation ManualDocument Number 000-20000-300-02-0307DRAFT 03/16/07Offices:Ocean Optics, Inc. World Headquarters830 Douglas Ave., Dunedin, FL, USA 34698Phone 727.733.2447Fax727.733.39628 a.m.– 8 p.m. (Mon-Thu), 8 a.m.– 6 p.m. (Fri) ESTE-mail:Info@OceanOptics.com(General sales inquiries)Orders@OceanOptics.com(Questions about orders)TechSupport@OceanOptics.com (Technical support)

AdditionalOffices:Ocean Optics Asia666 Gubei Road, Kirin Tower, Suite 601B, Changning District, Shanghai,PRC. 200336Phone 86.21.5206.8686Fax86.21.5206.8686E-Mail Sun.Ling@OceanOptics.comOcean Optics B.V. (Europe)Geograaf 24, 6921 EW DUIVEN, The NetherlandsPhone 31-(0)26-3190500Fax31-(0)26-3190505E-Mail Info@OceanOpticsBV.comCopyright 1999-2007 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, resold, hired out orotherwise circulated without the prior consent of Ocean Optics, Inc. in any form of binding or cover other than that in which it is published.TrademarksAll products and services herein are the trademarks, service marks, registered trademarks or registered service marks of their respective owners.Limit of LiabilityOcean Optics has made every effort to ensure that this manual as complete and as accurate as possible, but no warranty or fitness is implied. Theinformation provided is on an “as is” basis. Ocean Optics, Inc. shall have neither liability nor responsibility to any person or entity with respect toany loss or damages arising from the information contained in this manual.

Table of ContentsAbout This Manual . viiDocument Purpose and Intended Audience. viiWhat’s New . viiDocument Summary. viiProduct-Related Documentation . viiiUpgrades . viiiChapter 1: Introduction .1Product Overview . 1USB Spectrometer and Device Control . 1Features . 2SpectraSuite in the Future. 2Spectroscopic Functions . 3Getting Updates . 4Chapter 2: Installation .5Overview . 5Installing SpectraSuite. 5Retrieving from a CD . 5Downloading from the Ocean Optics ftp Site . 6Chapter 3: Controls and Indicators .9Overview . 9Graph Controls . 9Zoom Tools. 10Spectrum Storage Tools. 13Processing Tools . 13Spectrum IO Tools. 13Layer Tools. 14Other Controls . 16Acquisition Controls. 16Peak Finding . 16Indicators. 18000-20000-300-02-0307i

Table of ContentsStatus. 18Update Available . 19Progress Bar. 20Chapter 4: File Menu Functions.21Overview . 21New . 21Spectrum Graph . 22Spectrum Table . 23High-Speed Acquisition . 24Absorbance Measurement . 31Transmission Measurement . 31Reflection Measurement. 31Relative Irradiance Measurement . 31Absolute Irradiance Graph. 31New Absolute Irradiance Measurement . 32New Gated Fluorescence Measurement. 32New Curie Fluorescence Measurement . 33New Concentration Measurement. 33Color Measurement . 33Strip Chart . 34Open. 37Dark . 37Reference . 37Processed Spectrum . 37Spectrum Collection . 39Save . 39Save Spectra Collection . 39Save Spectrum . 40Store. 40Dark . 41Reference . 41Convert Spectra . 41Screen Capture . 41Exit . 42ii000-20000-300-02-0307

Table of ContentsChapter 5: View Menu Functions.43Overview . 43Scale . 43Empty. 43Graph Layer Options . 43Annotations. 44Chart . 45Cursor . 45Peaks. 45Image. 45Draw . 45Trendline. 46Overlay . 46Visible Spectrum. 46Spectrum Range. 47Legend. 47Toolbars . 47Acquisition . 48Acquisition Controls. 49Correction . 49Data Display . 49Memory. 50Preprocessing. 50Testing . 50Trigger . 50Strobe-Gate Delay. 51Small Toolbar Icons. 51Customize. 51Chapter 6: Spectrometer Menu Functions.53Overview . 53Acquisition . 53Pause Acquisition/Resume Acquisition . 53Terminate Acquisition . 53Spectrometer Features. 54MMS Raman Spectrometer . 56Rescan Devices . 60Remove Spectra. 60Show Devices. 60000-20000-300-02-0307iii

Table of ContentsChapter 7: Processing Menu Functions .61Overview . 61Color. 61Edit Color Settings. 61Pre-processing . 61Remove Preprocessor. 61Nonunity Correction. 62Add Reference Monitor. 62Processing Mode. 63Scope. 64Scope Minus Dark . 65Absorbance . 65Transmission . 66Reflection. 66Relative Irradiance. 66Raman Shifts . 67Absolute Irradiance . 67Scope. 67Absolute Irradiance. 67Collection Area . 68Calibration . 69Combine Calibration Files . 69New Energy, Power, Photons . 70New Photometry Measurement. 73X-axis Units . 76Set Color Temperature . 76Exporting Processed Data. 77Set Laser Wavelength . 80Edit Result Colors. 80Chapter 8: Tools Menu Functions .83Overview . 83Options . 83Default Acquisition Settings. 84Template Manager . 84Module Manager . 84Update Center . 85iv000-20000-300-02-0307

Table of ContentsChapter 9: Window Menu Functions .91Overview . 91Close All Documents . 91Documents . 91Close Window . 92Maximize/Restore Window . 92Output. 92Chapter 10: Strip Charts.95Overview . 95Creating Strip Charts . 95Saving Strip Chart Data. 100Strip Chart Controls . 100Appendix A: Experiment Tutorials .101Overview . 101Preparing for Experiments. 101Application Tips . 103Taking Reference and Dark Spectra . 103Absorbance Experiments . 104Concentration Experiments . 109Transmission Experiments . 118Reflection Experiments. 121Irradiance Experiments . 124Absolute Irradiance. 125Relative Irradiance. 133Fluorescence . 135Color Experiments . 137Color Measurement Screen Controls . 146Appendix B: Troubleshooting.147Index.151000-20000-300-02-0307v

Table of Contentsvi000-20000-300-02-0307

About This ManualDocument Purpose and Intended AudienceThis document provides you with an installation and configuration instructions to get your system up andrunning. In addition, user interface for SpectraSuite is provided.What’s NewThis version of the SpectraSuite Spectrometer Operating Software Installation and Operation Manualadds the Layer toolbar and Convert Spectra functions, and a troubleshooting section.Document SummaryChapterDescriptionChapter 1: IntroductionProvides an overview of the SpectraSuite operating software.Chapter 2: InstallationContains instructions for installing and configuring theSpectraSuite software.Chapter 3: Controls and IndicatorsIllustrates options for customizing your graph view. Alsocontains information for peak finding.Chapter 4: File Menu FunctionsContains descriptions of the functions on the File menu.Chapter 5: View Menu FunctionsContains a description of the functions on the View menu.Chapter 6: Spectrometer Menu FunctionsContains descriptions of the functions on the Spectrometermenu.Chapter 7: Processing Menu FunctionsContains descriptions of the functions on the Processingmenu.Chapter 8: Tools Menu FunctionsDiscusses the selections available in the Tools menu.Chapter 9: Window Menu FunctionsContains information for the Window menu functions.Chapter 10: Strip ChartsProvides instructions for using the Strip Charts feature.000-20000-300-02-0307vii

About This ManualChapterDescriptionAppendix A: Experiment TutorialsContains instructions for performing sample experimentsusing an Ocean Optics spectrometer and SpectraSuitesoftware.Product-Related Documentation External Triggering Options Various USB spectrometer documents such as the USB4000 Spectrometer Installation andOperation Manual. ADC1000-USB Operating InstructionsYou can access documentation for Ocean Optics products by visiting our website athttp://www.oceanoptics.com. Select Technical Operating Instructions, then choose the appropriatedocument from the available drop-down lists. Or, use the Search by Model Number field at the bottomof the web page.You can also access operating instructions for Ocean Optics products on the Software and TechnicalResources CD included with the system.Engineering-level documentation is located on our website at Technical Engineering Docs.UpgradesOccasionally, you may find that you need Ocean Optics to make a change or an upgrade to your system.To facilitate these changes, you must first contact Customer Support and obtain a Return MerchandiseAuthorization (RMA) number. Please contact Ocean Optics for specific instructions when returning aproduct.viii000-20000-300-02-0307

Chapter 1IntroductionProduct OverviewSpectraSuite is a completely modular, Java-based spectroscopy software platform that operates onWindows, Macintosh and Linux operating systems. The software can control any Ocean Optics USBspectrometer and device, as well as any other manufacturer’s USB instrumentation using the appropriatedrivers. The SpectraSuite interface looks and feels the same on all operating systems yet retains thefamiliar appearance of an application native to each OS. Ocean Optics is the first to offer such a flexible,feature-packed application with this level of cross-platform capability.The SpectraSuite Java-based framework is modular and every function in it can be altered or replaced.For instance, the data acquisition functions, the scheduling functions, the data processing functions andthe rendering functions are all separate modules. You can add or delete modules to create a proprietaryuser interface or functionality; create modules to perform calculations; automate experiment routines andmore. You or an Ocean Optics application developer can easily customize SpectraSuite through Javacode.SpectraSuite is the platform for all future Ocean Optics application software development. Currentsoftware applications including OOISensors and OOILIBS will be migrated to the SpectraSuite platformin the near future.USB Spectrometer and Device ControlSpectraSuite easily manages multiple USB spectrometers – each with different acquisition parameters –in multiple windows, and provides graphical and numeric representation of spectra from eachspectrometer. Using SpectraSuite, you can combine data from multiple sources for applications thatinclude upwelling/downwelling measurements, dual-beam referencing and process monitoring.SpectraSuite can be used with the following Ocean Optics spectrometers when they are interfacing to acomputer through their USB port: S2000 Spectrometer (with A/D Converter) USB650 Spectrometer USB2000 Spectrometer USB2000 Spectrometer000-20000-020-02-03071

1: Introduction USB2000-FLG Spectrometer USB4000 Spectrometer HR2000 High-resolution Spectrometer HR2000 High-resolution Spectrometer HR4000 High-resolution Spectrometer QE65000 Scientific-grade Spectrometer NIR-512 Near-IR Spectrometer NIR256-2.1 and NIR256-2.5 Near-IR Spectrometers MMS Raman SpectrometerIn addition, SpectraSuite also supports the following USB devices: ADC1000-USB A/D Converter Spectral Hyper Adapter (SHA-1)Features Modular Framework – The SpectraSuite framework is modular and every function in it can bealtered or replaced. For instance, the data acquisition functions, the scheduling functions, the dataprocessing functions and the rendering functions are all separate modules. You can add or deletemodules to create a proprietary user interface or functionality; create modules to performcalculations; automate experiment routines, and more. You or an Ocean Optics applicationdeveloper can easily customize SpectraSuite through Java code. Platform Independent – The SpectraSuite is a platform-independent application that providesGraphical and numeric representation of spectra in one window. SpectraSuite can operate on aWindows, Linux, or Macintosh operating system. Advanced Data Capture Control – SpectraSuite provides the user with advanced control ofepisodic data capture attributes. For

Ocean Optics is the first to offer such a flexible, . S2000 Spectrometer (with A/D Converter) USB650 Spectrometer USB2000 Spectrometer USB2000 Spectrometer 000-20000-020-0

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