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SpectraSuite Installation and Operation Manual

1. 2 Choose where the new graph will be displayed and click Accept 3 Set the desired parameters integration time scans to average and boxcar width The sample below shows a graph with three spectral curves blue pink and orange in the same graph tab 000 20000 300 02 0607 23 5 View Menu Functions Acquisition Toolbar Be Ocean Optics SpectraSuite Fis New eT Oe E Integr ation E Hee eg Ah F gt SVATRI Rz o Le Acquisition rk tere 124ms seg No Pre processor E Graph ay Source USE2GhI42 Wavelength 499 40 Source Box Spectrum Table The Spectrum Table menu selection displays a spectral graph in tabular format Select File Spectrum Table from the menu or click in the Data Display toolbar The spectrum table appears 24 000 20000 300 02 0607 5 View Menu Functions Be Ocean Optics SpectraSuite Fic View Spectrometer Processing Took Window Help deg Average Meed Enable External V trigger Data Sources 4x O raphi x Hi Table B x o A U Wwaneedensgkh nim Intensity counts 178 32 Dm LSK lem 234 00 179 08 2352 00 179 46 282 00 Acquistion 179 84 231 00 Ink dne 12ers A 180 22 2563 00 No Preprotest Iren en 292 00 L5 Graph 180 98 293 00 Int teres Celene d 181 35 Ho Prepi x Ei Graph I91 7 Int time Sias an be te No Pre process bes So Li Graph 62 87 Int tee Gms on 183 25
2. eee eee 21 eic MK 21 000 20000 300 02 0607 Table of Contents KI 21 Curie Fluorescence Measurement nennen nennen nnne nnns nnn nnn nns Error Bookmark not defined OS CLM a 0 MERCREDI A E O E EAEE 22 PS CECI NEE 24 High Speed Acquisition EE 25 Absorbance Measurement EE 32 Transmission Meaeurement nennen enne nhan sna sn sensn seis rsa nnne sns sese rsen 32 Reflection Measurement 32 Relative Irradiance Measurement enne enhn nnne nn nnne nnns 32 Gated Fluorescence Meaeurement nennen nnne nnne nnn nnn nnn 32 Curie Fluorescence Measurement nennen nennen nena nnn nnn nnns nnn nnn 33 Absolute Irradiance Graph eicere terna en satira a ran reve EES neca da SEN 33 New Absolute Irradiance Measurement o nnsosnnoennesnnnennrerresnrrrerrrerrrsrrrrnrrrsnrrerrrerrrenrrrnrrrerrrne 34 New Concentration Meaeurement nennen nennen nnns nnne nn nnn nnns 34 Calor OT EE 35 S LO A U eege 35 SIC EEA I T E T A E ANE sade AE A 38 RE 38 Bue EE 38 Processed Ee ert in TE 38 See tie 7e 16 0 EE 40 Eege 40 DAVES SDe6iIe GOMES CON EE 40 SNe PO o E 40 E 41 bz paces EE 41 mice RN TT Nm 41 en SOS Cll at T EDT 42 SEET O E DNE 42 d m 43 Chapter 5 View Menu Functions ees 44 SUI MNT
3. HCS me d First in Photonics ak SpectraSuite Spectrometer Operating Software Installation and Operation Manual Document Number 000 20000 300 02 0607 DRAFT 06 18 07 Offices E mail Ocean Optics Inc World Headquarters 830 Douglas Ave Dunedin FL USA 34698 Phone 727 733 2447 Fax 727 733 3962 8 a m 8 p m Mon Thu 8 a m 6 p m Fri EST Info OceanOptics com General sales inquiries Orders OceanOptics com Questions about orders TechSupport OceanOptics com Technical support A HALMA GROUP COMPANY Additional OV THREE SES Offices 666 Gubei Road Kirin Tower Suite 601B Changning District Shanghai PRC 200336 Phone 86 21 5206 8686 Fax 86 21 5206 8686 E Mail Sun Ling OceanOptics com Ocean Optics B V Europe Geograaf 24 6921 EW DUIVEN The Netherlands Phone 31 0 26 3190500 Fax 31 0 26 3190505 E Mail Info OceanOpticsB V com Copyright 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 or otherwise circulated without the prior consent of Ocean Optics Inc in any form of binding or cover other th
4. For a range of pixels Select the starting and ending wavelengths Integrate over For the area underneath the trend line Select the starting and ending wavelengths Then select the method for calculating the continuous area underneath the graph curve Rectangular Simpson s or Trapezoid Display Options Select a color for the graph s trend line Scale Trend Value If you would like to adjust your data enter the appropriate information in this field Minimum delay between updates Set the amount of time in milliseconds between data points on the graph ds delay is vedo ide of the integration time The data appears at the slower rate NOTE The longer the time between updates the less computer memory that is used 6 Click Accent J The Strip Chart Options dialog box appears Strip Chart Options lists all of the Strip Charts that you have created along with the options that you have set for each one Use this dialog box to add edit remove or clear trends Note 36 000 20000 300 02 0607 5 View Menu Functions Highlight the desired trend to make the Clear Remove Trend and Edit Trend buttons active Se Strip Chart Options Wavelength tnm Mode Offset 500 27 Value D Remove Trend Edit Trend Add Trend Close 7 Click Accept The strip chart you created appears Note the time scale along the x axis The y axis in this example shows the percentage transmission for the selected pixel s
5. Be Color Measurement Setup wizard 4 of 4 Store Dark Spectrum Dark Spectrum Preview Strobe Lamp Enable LI Oo 200 400 600 800 Wavelength mm Momentarily black the light or uncheck strobellamp and press the button above ta store a dark spectrum Next gt Help Details Graph Shaw details Far Description G 2 degree photopic daylight observer Reflective Observer 2 degree 7 wi Illuminant Reference CIE 15 2 1986 Load Illuminant Creator Provided by Ocean Optics Inc 000 20000 300 02 0607 147 A Experiment Tutorials The fields on this screen are described in the following table zm om Either Emissive or Reflective mode is selected depending on the type of color measurement selected in Step 1 You can change it here Reflective Color measurement of a surface for a selectable CIE defined illuminant Emissive Measurement of the light emitted from an LED ora lamp emission source Observer Specify the observer viewing angle using the drop down list 2 CIE 1931 photopic daylight 10 CIE 1964 scotopic dark adjusted Illuminant If you chose Reflective measurement under Mode select the desired llluminant from the drop down list This illuminant is theoretical and CIE defined it has nothing to do with the actual lamp used in the measurement 9 Your selections are reflected on the right side of the screen Select to view either il
6. Calibration Data Concentration Absorbance Residual id 20 0 0 221923 4 2633E 14 zpo es aaen O OoOo ses mones e214 OO Concentration Ea Absorbance o Use Last Scan Concentration Units Save Calibration Regression Plot Regression Order zero Intercept R z 1 00DOED Order Coefficient 1 2692EU 10 12 14 ige gB 3968E1 Concentration z i 1 9585E0 n3 e 4bsorbance OLD e e 5 Enter options for how the regression is computed in the lower right corner of the window Order Set the regression order to 1 straight line fit or 2 second order polynomial fit Zero Intercept You can force the regression line to pass through the origin that is zero concentration and absorbance by checking this box For a first order fit at least two data points are necessary For a second order fit three points are necessary If Zero Intercept is selected then only one point is required for a first order fit and two points for a second order fit In general more data points result in a better estimation of the concentration of an unknown It is recommended that as many calibration points be sampled in this way as is practical Also allow your reference lamp to stabilize before attempting a calibration with many points as any drift in the lamp s emission will introduce error into these samples The quality of the regression is shown in the lower right as an R 2 value where 1 0 is a perfect fit lo
7. SpectraSuite provides the capability of saving and exporting processed data to a binary or tab delimited file When combined with external triggering this feature can be used to automatically save full spectra timed to one or more external events Procedure 1 Right click on Result in the tree in the Data Sources pane and select Export Result 000 20000 300 02 0607 81 7 Processing Menu Functions Data Sources dl x US62000 Acquisition E Int time 319ms avg 11 boxcar 7 z acessor Scope Mode Right click E Strip Ce 3 Integral 178 32 178 32 nm Click Strip Chart B Strip Chart Processing 4 Wavelength 178 32 nm H Strip Chart E H Strip Chart Processing Properties Serial Number LISB2G6142 Firmware USB2000 2 41 3 Tatal Pixels 2048 Wavelengths 178 3 876 2 nm The dialog box for exporting data appears Save Options File Options File Type OO Binary For z O Save after every scans Between saved scans wait at least T eae sd Save the First available scan every Padding Digits solm Cancel 2 Enter the following information Save options Saves Save every scan Every scan Save after every x scans After every x scans 82 000 20000 300 02 0607 PLICS inc First in PYotonice Between saved scans wait at least Save the first available scan every File options File Type Save to directory Base Filename P
8. SpectraSuite software features one year of free web based automatic upgrades when you buy the software This service requires that you register the first time you connect You can purchase renewals for half the software price per year All customers whether they have a free upgrade plan or not will be able to get free bug fixes The update icon appears on the lower right corner of the SpectraSuite screen when updates are available for your software see Update Available for more information on this icon Click on this icon or select Tools Update Center from the SpectraSuite menu to go to the Update Center Follow the steps in the Update Center wizard to update your SpectraSuite software 4 000 20000 300 02 0607 Chapter 2 Installation Overview The following sections will guide you in installing SpectraSuite on a Windows Macintosh or Linux operating system Note Do NOT connect the spectrometer to the computer until you install the SpectraSuite software Follow the instructions contained in this chapter to properly connect and configure your system Installing SpectraSuite SpectraSuite can be downloaded from the Ocean Optics ftp site or retrieved from the CD that you received with your purchase of the software This section contains instructions for installing SpectraSuite using both methods on each of the following operating systems Microsoft Windows Windows 2000 XP Apple Macintosh OS X version 10 0 or
9. Store Dark Spectrum wizard Absolute Irradiance Setup Wizard 400 300 Wavelength nm Load Dark Spectrum From File Spectrum File Browse New dark spectrum stored Help 000 20000 300 02 0607 B Troubleshooting New Calibration a After selecting New Calibration the Set Acquisition Parameters screen appears Be Absolute Irradiance Setup Set Acquisition Parameters wizard Absolute Irradiance Setup Wizard Integration Time Smoothing Integration he lilien H Scans to time Xl average Strobe Lamp C Boxcar Enable width Last peak value 3352 70 Recommended peak value f 3480 00 Set Automatically Advanced Settings Turn on the light source and set the integration time a0 that the peak value reaches the recommended level n 200 600 1000 Wavelength nm ien Help Next b Set your acquisition parameters for your experiment Then cial Met The Store Reference screen appears Se Absolute Irradiance Setup Store Reference Spectrum wizard Absolute Irradiance Setup Wizard Store Reference Reference Spectrum Previews StrabejLamp Enable a 400 Bn wavelength nm Load Reference Spectrum From File Spectrum File Hew reference spectrum stored 000 20000 300 02 0607 135 A Experiment Tutorials c Turn on your light source then click to store a reference spectr
10. Wavelength tmm Source USB2G6142 Wavelength nm 967 95 111 83 123 54 000 20000 300 02 0607 15 3 Controls and Indicators fs Other Controls Acquisition Controls Much like controls on a VCR the Acquisition Controls allow you to pause and resume continuous spectra acquisition and perform a single acquisition Pause selected acquisition Perform single acquisition Resume selected acquisition A Peak Finding This control located in the bottom right corner of the graph allows you to create a threshold on your spectral graph to isolate peaks Note If this control does not display on your graph click in the graph to make it appear Procedure Click A A threshold line appears on the graph along with more Peak Finding controls The threshold is set high and in most cases should be adjusted 16 000 20000 300 02 0607 a cean ptics Inc Firat in Photonics 3 Controls and Indicators Ge Ocean Optics SpectraSuite File View Spectrometer Processing Tools Window Help Integration em Scans to Boxcar Strobe Lamp Electric dark em SI ai ies time 3120 mliseconds 8 average 15 E width 3 v Enable a correction O FA i b 1 Data Sources 4 x m Graph A x M Haaat T7 SPATRI WH amp esdd E USB2000 2 Acquisition Int time 312ms avg 15 boxcar 5 4000 No Pre processor Scope Mode Result Graph A Properties 3000
11. lw x Z ie sg de nadaa us Eom zi mim S Wenvelenigeh nim Some LSECGADAT w Waeelengthe 178 17 e This table is described below uWatt The calculated power of the sample in microwatts uJoule cm The calculated energy per square centimeter of the sample uWatt cm The calculated power per square centimeter of the sample dBm The decibels referenced to one milliwatt Used to calculate power for lasers The number of photons per square centimeter emitted from the sample each second Photons cm 2 s 76 000 20000 300 02 0607 a cean ptics fine erst in Dreier 7 Processing Menu Functions Total photons The total number of photons calculated Moles of The moles of photons calculated photons New Photometry Measurement This menu selection enables you to take photometry measurements such as lumen lux and candela Phototropic Scotopic values are calculated over a 380 to 780 nm wavelength range Scotopic conditions are defined when the luminance is less than some hundredths of a candela per square meter cd m The difference between this scotopic vision low level condition compared to a photopic high level condition affects the calculations for Lumen Lux and Candela by using the V A spectral luminous efficiency curve instead of the V A curve You must be in Absolute Irradiance mode click I for this menu selection to be active Procedure Create a new graph of spectral data
12. 7 Check the boxes on both sides both Install and Global next to the files modules you want to install If a module is signed you must first view and accept its certificate If the module isn t signed a dialog box appears asking you to confirm that you want to install an unsigned module Then click to install the module s The Restart the IDE dialog box appears asking you whether you want to restart the IDE now or wait until later If you choose to restart now a dialog box appears asking you to confirm that you want to quit the SpectraSuite application Once the IDE is restarted the updates become active 000 20000 300 02 0607 93 8 Tools Menu Functions 94 000 20000 300 02 0607 Chapter 9 Window Menu Functions Overview The Windows menu provides functions for manipulating the SpectraSuite graph windows Close All Documents Use this function to immediately close all the SpectraSuite Documents Select Window Documents to display the Documents dialog box Use this dialog box to switch the SpectraSuite display to one you select close selected document s or save selected document s Se Documents Documents Graph A Switch to Document Strip Chart E Close Documentis Description 000 30000 020 02 0607 95 9 Window Menu Functions Close Window Use this selection to close the currently selected graph window Maximize Restore Window This selection toggles between maximizing t
13. SCC CECR a a Chromaticity Diagram B amp x amp Data views x Graph A x Chromaticiby Diagram E Color Values C Absolute Irradiance D S 000 20000 300 02 0607 149 First in Photonics A Experiment Tutorials Tip To close all three color views Graph Color Values and Chromaticity Diagram at once highlight the color acquisition in the Data Sources pane right click and select Terminate Color Measurement Screen Controls Once you have captured your color data on the Color Measurement screen shown above you can use the following controls in the Color Values section of the screen Edit Color settings Use this control to edit the color settings in your graph See Edit Color Settings for more information Copy Spectral Data to Clipboard Opens a browser for you to select a log file you have created Auto save Saves your color data to a file See below for an example saved in Notepad See Exporting Processed Data for more information E Color CO le Notepad Ele E Format Yew Heb source observer Illuminant Color Mode USe2G6142 2 degree Emissive UsBglq l142 i degree Emissive usB236142 2 degree Emissive UZB2iG6l4Z z degree Emissive us82G6142 2 deagree Emissive USB2G6142 2 degree Emissive usB2G6142 2 de ree Emissive US 2G614 2 2 degree Emissive uSB2G6142 2 degree Emissive 2 degree Emissive 2 degree amiss ive 2 degree Emissive 2 degree gmissive 2 degree Emissive z degree Emissi
14. 51 minimize window 96 MMS Raman spectrometer 60 Module Manager 88 new 21 New Energy Power Photons 74 nonlinearity correction 50 non uniform 66 nonunity correction 51 66 127 0 Open 38 options 87 Output 96 overlay 47 Overlay Menu 65 overlay spectral data 14 000 20000 300 02 0607 p pause acquisition 57 peak finding 16 peaks 46 photometry New Photometry Measurement 77 preprocessing 65 toolbar 51 processed spectrum load stored spectrum 38 Processing mode 67 tools 13 product description 1 Progress Bar 20 Raman 84 shifts 71 Reference 38 41 monitor 66 spectra 107 Reflection measurement 32 mode 70 Reflection Experiments 125 Relative Irradiance Experiments 137 measurement 32 mode 70 remove preprocessor 65 rescan devices 64 restore window 96 resume acquisition 57 S Save Spectra Collection 40 Spectrum 40 scale 44 scale graph height to fill window 11 scale graph to fill window 10 scans to average 49 Scope Minus Dark 69 Scope mode 68 71 screen capture 42 SeaChanger module 51 Set Laser Wavelength 84 000 20000 300 02 0607 show devices 64 small toolbar icons 54 Spectra dark 107 reference 107 spectra collection remove 64 spectrometer features 58 Spectrometer Menu 57 spectrum graph 22 50 IO tools 13 range 48 storage tools 13 table 24 51 status indicators 18 Store 41 strip chart 35 51 controls 104 creating
15. Most spectrometer system operating software does not allow such signal conditioning flexibility With SpectraSuite you can perform time acquisition experiments for kinetics applications As part of the time acquisition function strip charts you can monitor and report up to 6 single wavelengths and up to 2 mathematical combinations of these wavelengths In addition you can perform reference monitoring in a variety of ways single wavelength 1 or 2 channels integrated intensity starting and ending wavelengths for 1 or 2 channels and wavelength by wavelength 2 channels SpectraSuite gives you complete control of setting the parameters for all system functions such as acquiring data designing the graph display and using spectra overlays You can also save and then retrieve all of these system parameters for future experiments SpectraSuite has the benefit of providing various software controlled triggering options for external events such as laser firing or light source pulsing Other advanced features give you several data collection options You can independently store and retrieve dark reference sample and processed spectra All data can be saved to disk using autoincremented filenames You can save data as ASCII files or in the native GRAMS 32 SPC or JCAMP format One feature prints the spectra and another copies spectral data into other software such as Excel and Word 000 20000 300 02 0607 3 1 Introduction Getting Updates
16. Select one spectral source from the table above 4 Select the source of your absorbance measurement and click Net The second page of the wizard appears 000 20000 300 02 0607 109 A Experiment Tutorials K Absorbance Measurement Steps Data Source Acquisition Parameters Reference Spectrum Dark Spectrum Recommended peak value Set Acquisition Parameters wizard 2 of 4 Integration Time Integration Oe Hoo milliseconds ze StrabejLamp Enable d Last peak value 3210 0 3480 Turn on the light source and set the integration time 20 that the peak value reaches the recommended level i cean ptics Inc Fast in PYaforecs Smoothing Scans ka average Boxcar width Preview 4000 S000 2000 1000 0 400 400 600 S Wavelength nm Cancel 5 Turn on your light source and set your acquisition parameters so that the peak value reaches the recommended level Then click Next gt The third page of the wizard appears 110 000 20000 300 02 0607 B Troubleshooting EA Absorbance Measurement wizard 3 of 4 Data Source Acquisition Parameters Reference Spectrum Dark Spectrum Store Reference Spectr Reference Spectrum Preview Strobe Larnp l Enable LI wavelength rm Once the lamp is ready press the button above to store a spectrum Cancel 6 If you have not already done so place a sample of the solvent into a
17. the square root of the number of pixels averaged 000 20000 300 02 0607 49 5 View Menu Functions Strobe Lamp E Enables or disables the spectrometer strobe control function Enable This function toggles the S0 line of the spectrometer Electric dark Enables or disables the correction of the spectral data for correction L electrical dark signal For example if the first 24 pixels in the spectrometer while producing an electrical signal do not respond to light then this option subtracts the average value of these first 24 pixels from the entire spectrum Acquisition Controls Select View Toolbars AcquisitionControls to display hide the tools for pausing and resuming continuous spectra acquisition A control is also available for performing a single acquisition contol Acton Pause selected acquisition Perform single acquisition Resume selected acquisition Correction This toolbar has one tool the nonlinearity correction checkbox This tool enables disables the detector linearity feature The Correction toolbar only displays when you select it with View Toolbars Correction it is absent from the screen by default Data Display The Data Display toolbar contains the icons for the following graph functions Spectrum Graph Displays a new spectrum curve on the current graph with the parameters selected in the Acquisition toolbar Each spectrum curve appears on the graph in a different color The Acquisi
18. 5 Fiber Diameter 1000 micron DUU l C Collection Area Nu Wavelength nm Save To File f Click Ems J The Absolute Irradiance Calibration measurement screen appears Relative Irradiance Relative irradiance is a measurement of light relative to the known color temperature of a blackbody light source Common applications include characterizing the light output of LEDs incandescent lamps and other radiant energy sources such as sunlight Relative irradiance measurements also include fluorescence measurements which measure the energy given off by materials excited by light at shorter wavelengths You must have stored reference and dark spectra before measuring relative irradiance Procedure Place SpectraSuite in Scope mode by clicking the Scope icon in the Experiment mode toolbar or selecting Processing Processing Mode Scope from the menu 2 Ensure that the entire signal is on scale The intensity of the reference signal s peak differs depending on the device being used If necessary adjust the integration time until the intensity is appropriate for your device 000 20000 300 02 0607 137 A Experiment Tutorials 3 Take a reference spectrum using a light source with a black body of a known color temperature such as the LS 1 4 Click the Store Reference Spectrum Y icon on the toolbar or by select File Store Store Reference Spectrum from the menu bar to store the referen
19. 99 saving 104 saving data 104 strobe enable 50 strobe gate delay toolbar 54 Template Manager 88 terminate acquisition 57 testing toolbar 54 toggle graph pane 12 Tool menu 87 toolbar 48 acquisition 49 correction 50 customize 55 data display 50 memory 51 preprocessing 51 strobe gate delay 54 testing 54 trigger 54 Transmission Experiments 122 measurement 32 mode 70 trendline 47 trigger toolbar 54 157 Index troubleshooting 151 Window menu 95 Tutorials 105 Windows platform installation 6 uniform 66 X axis units 80 update available 19 7 Update Center 4 89 updates 4 zoom des iid upgrades viii in 11 V out 12 out maximum 10 visible spectrum 47 region 12 set numeric ranges 11 W tools 10 what s new vii 158 000 20000 300 02 0607
20. Collection from the menu bar to permanently save the spectrum to disk 000 20000 300 02 0607 a cean ptics Inc A T Bist in Photonics B Troubleshooting Note If possible do not turn off the light source when taking a dark spectrum If you must turn off your light source to store a dark spectrum allow enough time for the lamp to warm up again before continuing your experiment You must take a dark spectrum before measuring reflection 6 Putthe sample in place and ensure that the light path is clear Then take a reflection measurement by clicking on the Transmission ali icon on the toolbar or selecting Processing Processing Mode Transmission from the menu since the mathematical calculations used to calculate transmission and reflection are identical 7 If you received calibration file with your reference standard click the Non unity Correction icon a on the toolbar The Select Reference File screen appears Sg Select Reference File l Reference Information Wavelength nm 8 Browse to the location where you stored your reflectivity standard files Then click the Apply button The reference information appears on the Select Reference File screen 000 20000 300 02 0607 127 A Experiment Tutorials Se Select Reference File Se File Name al STAN SSH Standard review File Type ODI Ascii Format v i Reference Information Standarcdlnformation versionz1 1 2
21. E Data Views a x EL Graph ay e Relative 138 000 20000 300 02 0607 ne atin Pista B Troubleshooting Fluorescence A fluorescence measurement is a type of relative irradiance measurement in which the energy given off by materials excited by light at shorter wavelengths is measured Advantages of fluorescence include High sensitivity high speed intensity changes on the order of picoseconds and safety nondestructive to sample and no hazardous by products A typical fluorescence set up is shown below Note that the fibers for the lamp and the spectrometer must be at a 90 angle to each other or a CVD DIFFUSE must be used GEB55000 Spectrometer PX2Lamp _ T Computer CUV ALL Cuvette with PN ample Solution A k Fluorescence can be measured in the following modes e Scope mode Scope mode is the preferred mode for configuring your acquisition parameters The signal graphed in Scope mode is the raw voltage coming out of the A D converter This spectral view mode provides complete control of signal processing functions before taking absorbance transmission reflection and relative irradiance measurements This mode reflects the intensity of the light source the reflectivity of the grating and mirrors in the spectrometer the response of the detector and the spectral characteristics of the sample e Relative Irradiance mode Relative Irradiance mode is the preferred mode for fluorescence experiments Rel
22. Far infrared Microwaves and Radiowaves Legend Use this option to add a customizable legend to your graph The legend shows the spectrometer serial number and the name of the file that you loaded the overlay from if applicable Ki Graph i e a T7 SHATRI H p 4 ed amp 7 Intensity counts r2 ex e e USB2G556 USB266142 500 Wavelength tmm Source USB2G6142 Wavelength nm 458 02 E 229 71 188 74 Toolbars This menu item controls which toolbars are visible on the SpectraSuite window Click on the following selections to toggle the toolbar on and off When a toolbar is visible a checkmark appears next to the menu selection 48 000 20000 300 02 0607 i cean tics In Mirgi in rile pL a The toolbars available from this menu item are shown on the SpectraSuite window in the figure below Memory Acquisition Data Display S6 Ocean Optics SpectraSuite Scans to Boxcar Strobe Lamp r1 E f E cs i average E width nable as PE Se db Stray Light External nee X mcm traction correction wiigger Preprocessing Correction BT Testing Acquisition Controls Strobe Gate Delay Acquisition Select View Acquisition to display hide the tools related to the data being acquired and displayed in SpectraSuite Integration opecifies the integration time of the spectrometer which is time analogous to the shutter speed of a camera The higher the integration time t
23. NoPre peoces 183 63 a if Tae 184 01 S Properties 184 38 Saria Humber USE 184 77 Firmware LEE le ve Teck Ad Diale fid iss d amp gt 85 53 185 91 i x Data Virus T rm Graph A 185 67 s BB Table E EEN 187 42 187 50 153 18 183 55 188 54 183 32 High Speed Acquisition Suse this menu selection if you want to capture every scan at a very fast rate 20 ms or faster SpectraSuite performs this high speed data acquisition by capturing raw data without slowing it down by processing it This captured high speed data is called a spectra collection A spectra collection can be viewed in either a graph or table format You can also record the captured data in a 3 dimensional graph and then run other measurements on this captured data It s best to store your reference and dark spectra using the regular graph window before performing a high speed data acquisition The following procedure assumes that you do so High Speed Data Capturing Procedure 1 Save reference spectrum to a file See Reference 2 Savea dark spectrum to a file See Dark 000 20000 300 02 0607 25 5 View Menu Functions Caution To ensure accurate data be sure that you have selected the same parameters integration time scans to average and boxcar width for your high speed acquisition that you used when capturing your dark and reference spectra 3 Select File New High Speed Acquisition If you ha
24. as the LS 1 or LS 1 LL lower right to take a reference spectrum The light to measure lower left accumulates through a CC 3 Cosine Corrector or FOIS integrating sphere into an input fiber which carries the light information to the spectrometer The spectrometer then transmits the information to the computer which compares the measured spectra against the reference spectrum thus removing wavelength dependent instrument response from the measurement Common applications include characterizing the light output of LEDs incandescent lamps and other radiant energy sources such as sunlight Relative irradiance measurements also include fluorescence measurements which measure the energy given off by materials excited by light at shorter wavelengths see Fluorescence Absolute Irradiance Although you have the option to do so you do not need to store reference spectrum first since absolute irradiance is not relative to another measurement However you must store a dark spectrum and have a calibration file before you can measure absolute irradiance Calibration equipment is available from Ocean Optics Contact an Ocean Optics Application Scientist for more information If you select File New Absolute Irradiance Measurement or click I on the Irradiance toolbar the Absolute Irradiance Wizard is activated to guide you through the process If you select File New Absolute Irradiance Graph the Absolute Irradiance graph in Scope mode appear
25. corrector is used define the light collection area as follows If this cosine corrector is used Enter this diameter in um CC 3 or CC 3 UV 3900 SpectraSuite then calculates the collection area from the fiber diameter Calibration You can calibrate your spectrometer in two ways Ocean Optics can calibrate the spectrometer for you and send you the resulting calibration file or You can calibrate the spectrometer yourself using a light source calibration lamp with known spectral output microwatts per square centimeter per nanometer using this menu item Combine Calibration Files This feature allows you to combine two spectrometer calibration files that you have created one file using a calibrated deuterium lamp source UV and the other using a calibrated tungsten lamp source VIS This will result in a spectrometer calibration file that can be used across the entire spectral range Deuterium Calibration Spectrometer Calibration Preview File Mame 060 Irradcal 1E 5 Boundary Wavelength 381 11 Kach m e Koch e Calibration Tungsten Calibration File Name J6VIS IrradCal Browse Sut 900 1300 Wavelength Save Cancel Loaded tungsten calibration Wavelength range 166 24 1097 37 000 20000 300 02 0607 73 7 Processing Menu Functions Procedure 1 Select Processing Absolute Irradiance Combine Calibration Files 2 Enter the file name of the spectrometer
26. dark Nonlinearity wi time ile coo average Width Enable d correction E correction Data Sources Graph By X Graphic x HR ZOO Indigo Carmine Concentration Graph B Graph C Single Update Continuous Update Measurement Setup 4 By default the window will not update on its own Perform a single scan by clicking Ee eo for instance after inserting each cuvette of unknown concentration Click CUI TES if you want the values to update as quickly as possible Note the following on this window e The name of the compound and the units you provided are shown e The numeric value for the concentration appears in black if the calculation was within the bounds of the measurement setup If you calculated the concentration using the Beer Lambert law the concentration appears in black for any positive measured absorbance If you calculated the concentration using known samples the concentration will appear in black only if the measured absorbance is within the range of absorbance sampled by the user If a sample is introduced that falls outside of this range the concentration will appear in red to indicate that it is out of bounds and may not be accurate as shown in the following example 000 20000 300 02 0607 121 A Experiment Tutorials Sg Ocean Optics SpectraSuite File View Spectrometer Processing Tools Window Help Integration E C Scans to Boxcar Strobe Lamp Electric dark Nonlinearity t
27. in Absolute Irradiance mode See Absolute Irradiance in Appendix A Experiment Tutorials for detailed instructions 2 Select Processing Absolute Irradiance New Photometry Measurement to display the Configure Photometry dialog box OR Click i on an Absolute Irradiance graph Be Configure Photometry inurce Observer Information Spectrometers RE tape Details Graph ro cesser Description 2 degree photopic daylight observer r Reference CIE 15 2 1986 Steradians Creator Ocean Optics Inc Date 17 43 38 EDT 2005 Provided by Ocean Optics Inc 000 20000 300 02 0607 77 7 Processing Menu Functions 3 If more than one Absolute Irradiance graph is open select the desired spectrometer by highlighting it under Source 4 Select the Observer from the drop down list 5 Use the default Steradians 1 0 or enter your own value If the steradians value is 1 then candela lumens The right section of the dialog box displays Observer Information in Detail or Graph form Graph form is shown below Detail form is shown on the previous page Be Configure Photometry SOUrCE Observer Information Spectrometers Spectrum Type Details Graph Processed Steradians U0 400 600 Wavelength nm 6 Click Accept The Photometry table appears to the right of the graph You can change these values by clicking the Change icon in the Photometry table 78 000 20000 300 02
28. later Linux Red Hat 9 or later Fedora any version Debian 3 1 Sarge and SUSE 9 0 or later Retrieving from a CD Your SpectraSuite software is shipped to you from Ocean Optics on a CD The software is located either on the main Software and Technical Resources CD or on a separate CD labeled SpectraSuite Spectroscopy Platform Software You will need the password located on the jacket of the CD containing your SpectraSuite software to complete the installation 000 20000 020 02 0607 5 2 Installation gt Procedure l 2 Insert the CD that you received containing your SpectraSuite software into your computer Select the SpectraSuite software for your computer s operating platform via the CD interface Then follow the prompts in the installation wizard Or Browse to the appropriate SpectraSuite set up file for your computer and double click it to start the software installation Set up files are as follows e Windows SpectraSuiteSetup_Windows e Mac SpectraSuiteSetup_Mac dmg e Linux SpectraSuiteSetup Linux Downloading from the Ocean Optics ftp Site Installing on a Windows Platform Total download is approximately 30 MB Procedure l 2 Close all other applications running on the computer Type ftp spectrasuite oceanoptics com into the browser Open FTP Site in Windows Explorer by clicking the Page menu and selecting Open FTP site in Windows Explorer Right click on any white spa
29. one wavelength Then click Next gt The following window appears 116 000 20000 300 02 0607 a cean ptics Inc Fest in Patan B Troubleshooting Be Concentration Measurement Setup wizard Concentration Measurement Setup Wizard Calibration Data Concentration Absorbance Residual Concentration ee Absorbance Use Last Scan Concentration Units mmm Regression Plot Regression Order zero Intercept Bai Coefficient 4bsorbance OD 1 Concentration Cancel d If desired enter the name and concentration units for their compound in the indicated fields this step is optional e To generate a calibration enter a known concentration in the Concentration field and either manually enter the corresponding Absorbance or place the corresponding cuvette into the cuvette holder and click Use Last Scan to measure the absorbance directly Use Notes to enter any comments f Click Add Sample to log the concentration vs absorbance point It will appear on the Regression plot in the bottom of the window and in the table at the top g After entering a few points a regression line will be computed through the concentration points This indicates that sufficient points have been sampled for concentrations to be estimated from unknowns 000 20000 300 02 0607 117 A Experiment Tutorials 118 Be Concentration Measurement Setup wizard Concentration Measurement Setup Wizard
30. strobe lamp scan causes the next single shot acquisition enable etc to take longer than normal because it is really acquiring two scans For the same reason a second external hardware trigger pulse may be required if the Normal free running trigger mode is not being used When preparing to do single shot acquisitions or external triggering it is recommended that all of the acquisition parameters be set in the continuously acquiring free running mode to minimize this effect If SpectraSuite is taking turns acquiring spectra with different acquisition parameters from the same spectrometer it may be doing a stability scan before every sample scan Also as above the number of scans to average is multiplied by the integration time 152 000 20000 300 02 0607 B Troubleshooting Problem Possible Cause s Suggested Solution s Can t access Absolute A spectrometer calibration and a Go to File New New Absolute Irradiance Irradiance mode Dark spectrum have not been Measurement to open a wizard to guide you stored through the process Absolute irradiance requires a spectrometer calibration either loaded from disk or generated using a calibrated lamp and a stored dark spectrum The most typical reason for not being able to access absolute irradiance mode is that you must store a dark spectrum after loading a calibration The graph window On Microsoft Windows systems Right click the desktop choose Properties shows a bro
31. ue 5 e z 2000 Data Views d x E Graph A z 1000 P us s 200 300 400 500 600 700 800 Wavelength nm A SA Pixel Wavelength Center Wavelength v 1 v Show Peak Info A08 Source USB2G6142 Wavelenath 243 91 2j 129 19 PA 2 Click to display the Peak Properties dialog box to set the threshold Se Peak Properties Peak Finding Minimum peak width Baseline Total peaks Found Integration method Fectangular we Close 3 Set the threshold at the level needed to isolate the desired peaks The threshold line moves into the location you selected 4 Use and to move the cursor to the next peak left or right The peak wavelength value appears in the Wavelength field below the graph 5 Check Show Peak Info checkbox to display peak data in the Pixel and Wavelength boxes 000 20000 300 02 0607 17 3 Controls and Indicators Indicators Status SpectraSuite provides you with feedback as to the status of the acquisitions you have graphed The indicators refer to spectra shown on the graph currently displayed as well as spectra on any other graphs that you have open that appear on the graphs accessed from the tabs at the top of the screen The feedback is in the bottom right corner of the screen in the form of different colored circles In the following example two status indicators are shown for both spectral lines on Graph C while a third indicator a
32. which you want to view the time trend from the following This section varies depending on l l the units chosen for the x axis see One wavelength For one pixel used in fluorescence for X axis Units example Select the wavelength Average from For a range of pixels Select the starting and ending wavelengths Integrate over For the area underneath the trend line Select the starting and ending wavelengths Then select the method for calculating the continuous area underneath the graph curve Rectangular Simpson s or Trapezoid 6 Click the Display Options tab 000 20000 300 02 0607 Fast in Fhorongx a cean ptics Inc Ss Chart Trend Settings Spectrometers Spectrum Type 0 USB2G6142 Processed Update Rate Display Options Auto Save Trend Line Color a Select Color Scale Trend Value Multiply by then add o 10 Strip Charts Wawvelength Selection O One wavelength nim STEE to 178 32 i nm Method Rectangular wi Derivative at bi Display Options Select a color for the graph s trend line Scale Trend Value If you would like to adjust your data enter the appropriate information in this field 7 Click the Auto Save tab 000 20000 300 02 0607 101 10 Strip Charts Ze Sg Chart Trend Settings E Spectrometers Spectrum Type 0 USB2G6142 Processed Waveleng
33. 0 Product MamezsT AN SSH Material Al MIST o serial Mumber 00005 Start Wavelength 250 End Wavelength 2500 Data Type R Measurement Type Specular Reflection 600 1700 1 806 2400 wavelength nm 9 Click ze to apply the file data to your graph on the main SpectraSuite screen 10 To permanently save the spectrum to disk click the Save Spectra VW icon on the toolbar or select File Save Save Spectra Collection from the menu bar Note If you change any sampling variable integration time averaging smoothing angle temperature fiber size etc you must store a new reference and dark spectrum Irradiance Experiments Irradiance is the amount of energy at each wavelength emitted from a radiant sample Absolute irradiance is the measure of light in absolute terms Relative irradiance is a comparison of the fraction of energy the sample emits and the energy the sampling system collects from a lamp with a blackbody energy distribution normalized to 1 at the energy maximum SpectraSuite calculates relative irradiance with the following equation S D h B mec 128 000 20000 300 02 0607 B Troubleshooting B Relative energy of the reference calculated from the color temperature at wavelength A S Sample intensity at wavelength A D Dark intensity at wavelength A R Reference intensity at wavelength A Typical relative irradiance setup Use a light source with a known color temperature such
34. 0 20000 300 02 0607 a cean ptics Inc Fest in F uafonw 5 View Men u Functions Be Graph A Layer Options endine Overlay Visible Spectrum Spectrum Range Annotations Cursor Peaks rLaver Properties how annotation laver Hide annotation layer Spectrum Source Selection A Snurce Processing LISB2 3387 Ma Pre pracessor Scope Made 1 USB2G6142 No Pre processor Scope Mode Annotation Properties Mew annotation Edit annotation Delete annotation Fant r Image Apply all annotations oad image Layer Order Annotations The Annotations functionality allows you to add text or an image to a specific location on the graph Annotations are associated with a specific source selectable by you and when the source is removed the annotations associated with it are removed as well A subset of this functionality is also available by right clicking on the graph or clicking A to add an annotation 000 20000 300 02 0607 45 5 View Menu Functions Use Chart to modify the following chart settings on the graph Chart line pattern Chart line width Font size Chart background Number precision for x and y axes Number spacing for x and y axes Tick spacing for x and y axes Grid spacing for x and y axes Grid lines Grid line color Cursor Use the Cursor tab to modify the cursor color Peaks Peaks functionality enables you to perform the following peak monitoring actions Display v
35. 02 0607 cean ptics Inc Fret in Phalonia e e 7 Processing Menu Functions Before you can access Relative Irradiance mode you must take a reference spectrum in Scope mode of a blackbody of known color temperature Additionally you must obtain a dark spectrum by removing the fiber from the reference lamp and preventing light from entering it Relative irradiance spectra are a measure of the intensity of a light source relative to a reference emission source SpectraSuite calculates relative irradiance using the following equation S D Lob ET 2 B Relative energy of the reference calculated from the color temperature Where S Sample intensity at wavelength A D Dark intensity at wavelength A R Reference intensity at wavelength A See Experiment Tutorials for information on conducting an experiment in Relative Irradiance mode Raman Shifts Use this menu item when you are doing Raman spectroscopy This is the distance from the excitation source You must have entered the wavelength of your laser see Set Laser Wavelength to use Raman Shifts Absolute Irradiance Irradiance is the amount of light present on a particular area such as the fiber s cross section at its tip a cosine corrector s surface or the integrating sphere s surface measures the total optical output of a light source inserted into the integrating sphere Scope This menu selection allows you to completely control signa
36. 0607 S6 Ocean Optics SpectraSuite 7 Processing Menu Functions File View Spectrometer Processing Tools Window Help DATE 1 s v Energy Power Photons D Dr x Integration Scans to Boxcar Strobe Lamp Electric dark time average width Enable correction Data Sources 4 x E Graph A x T Absolute Irradiance B x E D amp eo amp e GEES rIw Ai USB2000 Acquisition 4000 Int time 100ms avg 1 boxcar 0 No Pre processor Scope Mode Graph A Sint time 100ms ava 1 boxcar 0 No Pre processor Scope Mode Absolute Irradiance B Int time 100ms avg 1 boxcar 0 No Pre processor Absolute Irradi 3000 Absolute Irradiance B Properties Serial Number USB2G6142 E Firmware USB2000 2 41 3 Total Pixels 2048 v g lt gt 3 Data Views x i 2000 Graph A amp Absolute Irradiance B E 1000 0 200 300 400 500 600 700 Wavelength nm Source USE2G6142 Wavelength 178 32 21 IO Change Attribute Value Source LISB2G6142 Start 178 32 End 876 19 Method Rectangular uJoule 1 0240E 3 uWatt 1 0000E 2 uJoulejcm 2 1 3038E1 uWatt cm 2 1 2733E2 dBm 5 0000E1 Photons cm 2 s 5 1083E14 Total photons 4 1083E9 Moles of photons 6 8221E 15 EC LISB2G6142 178 32 876 19 Rectangular Photometry F D x Ch
37. 8 To add another trend to this graph click Add Trend S6 Ocean Optics SpectraSuite File View Spectrometer Processing Tools Window Help Integration ues Scans to Boxcar 42 Strobe Lamp Electric dark TE time ee average 20 width T Enable correction HI 1 External mm T Morma trigger Data Sources x C Graph a x EZ Strip Chart C x Gi x EJ D o o gt E Configure HR2000 110 Acquisition Int time 3ms avg 20 boxcar 4 No Pre processor Transmission Mode D Graph A Wavelength 500 27 nm 100 St TS d 90 Properties 80 70 scil Gin a a it Enna I lh A E vg e T g I x9Lb 4 rc a drl st rhH f lt r o 7 v 1 Data Views 4x E ES Graph A E E Strip Chart C 5 Wis E lp we ec Mech MNA og a iT Ae Cite S p E o co e 20 15 12 45 15 12 55 15 13 05 15 13 15 15 13 25 15 13 35 15 13 45 15 13 55 15 14 05 15 14 15 15 14 25 15 14 35 Time 000 20000 300 02 0607 37 5 View Menu Functions Selecting the Open menu option allows you to load previously stored dark spectra reference spectra processed spectra or all stored all spectra files Select the type of spectrum to load then browse to where the file 1s stored Dark A dark spectrum is a spectrum taken with the light path blocked Select File Open Load Dark Spectrum to select and open one or more dark spectra Refere
38. Con I x Cyan Magenta Yellow Extreme Green Measured Color from USB2G26708 v Color Information x 0258 y 0 292 v 0 714 24208 17118 1478 24518 i n 94 995 67 1 57 6 96 1 Custom Color Closest gel from PULETE v L ZN e Si x el ET Permacolor 33650 Woods Glass Siess i in XYZ 0 683 Reference Gel from Al ranges BEE Preview Range Filter Name mM du M d Transmission Graph Light Graph Lee Mallard Green Forest Green Follies Pink Special Rose Pink Plum Chromaticity Diagram B vb Stored Colors Slow Name Configuration Profile CMYG with lenses Illuminant A Z 500 600 700 Store Dark Reference Wavelength nm Force Update Select the serial number of the spectrometer Select a custom color Select All ranges Cinegel Cinelux Roscolux Permacolor or Lee 000 20000 300 02 0607 53 5 View Menu Functions R Color Information x y Y Closest gel from Select All ranges Cinegel Cinelux Roscolux Permacolor or Lee Color difference in XYZ Allows you to preview the Transmission graph and the Light graph The controls in the upper right panel allow you to change the color of the SeaChanger by individually controlling its color wheels Testing The Testing toolbar consists of the speed benchmark This feature allows you to see how fast the
39. JCAMP OOI Binary Format or Tab Delimited The desired directory or browse to the desired directory The name of the files Enter the number of digits to be used when appending to a file enter 3 to save hundreds of files enter 4 to save thousands etc up to 15 for example spectrumfile001 through spectrumfile999 if 3 is selected For future use CRI Ra CRI A 8d EN Go O00 c9 o9 09 00 j E a P i P Li a L a LI a Li a Li a D a L3 3 P D L1 Li u D a D a D a LI a E a D i P i a i a LI a Li a D a i PR ag mo d SD JEJE GOO VA uA WD UD s Es xD D PCI a UC IC ss i CE W I S VUA OCODOOOOOOOOO GOoooooooooooooococococooocooooooooooooooox P a P a LI LU 1 LU r m Li m P a LJ a P a LJ 1 J 1 m Li m Li m v a Lj a P a P a E 1 1 m Li m Li a D a LJ Uc od Wl un P a P a E 1 a T Li LU F a Lj a P a P 1 E 1 L LI m Li v P a P a P a LI 1 La 1 T LU Li F a r a P m m Li E Li T m r a LJ a P a P 1 E E Li Li T a Li a 1 a P a P a P 1 E 1 E T m Y a v a r 83 7 Processing Menu Functions Res Set Laser Wavelength Use this menu item when you are doing Raman spectroscopy Enter the wavelength of the laser you are using You must enter a wavelength before you can access the Raman Shifts menu item See Raman Shifts for more information S Set Laser Wavelength EN Laser Wavelength 785 0 rin Edit Result Colors This function allows you to choose the color in which your data is displayed The color selected will app
40. N 44 e apse eects ean TCI 44 cento T 44 Cae ay Sl KEE ee 44 leie Eden CN 45 Gs EE 46 FS OF eegene ee 46 ii 000 20000 300 02 0607 i cean ptics fine First i eloniex 000 20000 300 02 0607 jM iat Mn g ieren Table of Contents icu eege 46 iM TNT er 46 Bp 46 ihicaelg mMe T TKTT 47 92i 47 Visible SSC MOM ETE TEE TT TEE 47 jeje RET RE E en eee E eee 48 POO ENG PAEA E A E A EE A H 48 MOO ANS EE 48 PAC CANS IO E 49 PC OUINS ION CONTOS t C E 50 GON ECION EE 50 Beteg E 50 MOMO E o1 Wiwel le uu u i o1 SIT ISM EE 51 ToN RMENEIRMEUCUNIT o4 Reg M o4 OS Gae SA NE T oo E TET 54 omal Toolbar COINS RR E 54 Ee TEE 55 Chapter 6 Spectrometer Menu Functions 57 EOW 57 ee IT 57 Pause Acquisition Resume ACQUISITION ccccseeccccsseeeecseececeeeseeecaeeeeeseeeeeeseaseeeeeueeessaeeeeesaeeees 57 Terminals AC OUI SO a EE 57 Spectrometer Features 58 MMS Raman Gpoechomeler nennen ne
41. P format binary format which only SpectraSuite can read or tab delimited format can be opened in an Excel spreadsheet Opens the SpectraSuite Printing dialog box Select what you want to print and to where system printer PDF file You can select to print various layers on your graph zoom in to a section of the graph and add a title if desired You can adjust the font size and display of grid lines The Preview button displays a view of how your printout will look Copy spectral data to clipboard 000 20000 300 02 0607 13 3 Controls and Indicators Overlay spectral data Overlays a previously saved spectrum onto the current graph See o verlay Spectral Data for more information Delete overlay spectra Deletes any spectra that have been overlaid on the current graph E Overlay Spectral Data The Overlay Spectral Data control enables you to display a saved spectrum on the current spectrum Click this control and then browse for the file that you want to overlay on the current graph The overlay shows the spectrometer serial number and the filename that you loaded the overlay from Ee Ocean Optics SpectraSuite File View Spectrometer Processing Tools Window Help Integration nec J Scans to a Boxcar Strobe Lamp Electric dark time gi IR average d width Enable correction c Hi E 1 Data Sources 4x m Graph A x RI De ao e A F SHATI Bdg 2 Acquisition S Int t
42. SpectraSuite application is running how long it takes from the time the data 1s acquired until all the calculations have been performed The Testing toolbar only displays when you select it with View Toolbars Testing it is absent from the screen by default Trigger The External Trigger selection box on the Trigger toolbar enables you to set the following trigger modes of the spectrometer Normal free running Software Integration time is controlled by frequency of triggers External Hardware Hardware fixed or jumpered integration time Strobe Gate Delay This control enables you to set the gating delay in msec Small Toolbar Icons For future use 54 000 20000 300 02 0607 a cean ptics Inc Mirgi in Prolong Customize 5 View Menu Functions This menu selection allows you to customize your toolbars with functions that you choose from the Customize Toolbars dialog box 000 20000 300 02 0607 Ss Customize Toolbars Drag items to or From the toolbars to add or remove them E LC Help M Help E ic System 8 Net Error 9 Previous Error Update Center Print Save 3 Save All E LH view E web Browser a p window E LH SelectDacumentMade New Toolbar small Toolbar Icons 55 5 View Menu Functions 56 000 20000 300 02 0607 Chapter 6 Spectrometer Menu Functions Overview This chapter details the various options and functions available from the Spectrometer menu i
43. adding Digits Preview i H E 3 Click to start the export Color SaveQO000 Notepad Ele Edit Forms Wew Hep source Observer UEB2G6142 USB G14 2 usBla amp sl4 us82G6142 USB2G514 2 us82G61472 UsB2G6142 UzBglgesl4 000 20000 300 02 0607 2 degree z degree 2 degree z degree 2 degree 2 degree 2 degree 2 degree 2 denree 2 degree 2 degree 2 degree 2 degree 2 degree 2 degree 2 de ree z degree degree 2 degree 2 dedgree z degree 2 dedgree 2 degree 2 dedgree 2 degree 2 degree 2 degree 2 degree 2 degree 2 degree 2 degree z degree 2 de gree z degree degree 2 degree 2 degree 2 degree 2 dedgree z degree 2 dedgree 2 degree 2 degree 2 degree 2 degree 2 degree z degree 2 degree Illuminant bbbbhbbbhbbbbbbhbbbhbbbbbhbhbbhbbbbbbhbbhbbbbbbbhbhbbbbbhbbhbbhbEE color Mode Emtissive Bmissive Emissive Emissive Emissive Emissive Emieelvg Emissive missive Emissive Emissive Emissive Emtissive Emissive emissive Emissive Emissive Emlissiwve Emisziuys Emissive Emissivae Emizsive Emissive missive Emissive Emiszive Emissive Emissiue Emissive amissive Emlissiwva Emistive Emissive Emissive Emissive Bmissive Emieelvg Emissive Emissive Emissive emigedve Emissive emissive Emissiyve amiss ive Emissive Emissive Emissive 7 Processing Menu Functions Scans that occur at the interval selected The first scan that occurs after the interval selected Enter Grams SPC
44. adiance Existing acquisition Spectrometer Parameters 2 Select to measure absolute irradiance from either a new or existing acquisition Then click nets The second page of the Absolute Irradiance Setup Wizard appears S amp Absolute Irradiance Setup eg d A f kt Select spectral source wizard Absolute Irradiance Setup Wizard S Hae Preview HRZ gid 185 22 1083 3 nm Select one spectral source from the table above 3 Ifyou have more than one spectrometer highlight the one to be used Then click Net The third page of the Absolute Irradiance Setup Wizard appears 000 20000 300 02 0607 131 A Experiment Tutorials Ce Absolute Irradiance Setup 8 Choose one of the following e Get Irradiance Calibration from File e New Calibration Get Irradiance Calibration from File a After selecting Get Irradiance Calibration from File browse to the desired calibration file Ce Absolute Irradiance Setup sn HR2B1537 D v D HR 281537_111706_OolIrrad My Computer W File name HR2B1537_111706_OOTIrrad cal OOlIIrrad Calibration Files 100 0 L 132 000 20000 300 02 0607 B Troubleshooting wizard Absolute Irradiance Setup Wizard i Use Integrating Sphere C Collection Area cm 2 Fiber Diameter 1000 micron C If you are using an integrating sphere check the Use Integrating Sphere option d If you know the collection area check Collection A
45. alog box do one of the following Select Spectrometer Spectrometer Features from the menu or Right click on the device in the Data Sources pane and select Spectrometer Features Each attached device type has unique features so see the documentation for your particular device to learn more about the available options and their settings The MMS Raman Spectrometer has unique features See MMS Raman Spectrometer for more information The following is an example of the HR4000 Spectrometer Features dialog box EA HR4000 Features Board Temperature Analog In Analog Out Irradiance trabe Trigger Delay Iz SPI GPIO Stray Light Detector Linearity Single Strobe Value 195 70 7410 Let Coefficient 2 66534355E 1 2nd Coefficient 3 6248900E 6 3rd Coefficient 1 7015300E 10 Save to Spectrometer Many of the features listed for the HR4000 Spectrometer are also valid for other spectrometers The table below lists all spectrometer features Check your spectrometer to see which features apply to your model Analog In Set the input voltage and the update interval Analog input can be accessed from the spectrometer s accessory connector Analog Out Analog output can be used for multiple applications such as single pixel intensity analysis or programmable reference dimmer to light sources Set the analog output on this screen 58 000 20000 300 02 0607 a cean ptics Inc Fret in PYatanice 6 Spectrometer Menu Functions Autonu
46. alues on the graph relating to the peak such as peak value center wavelength pixel number centroid etc Set an alarm when a peak is reached You can pause the acquisition save the spectrum and sound a customizable alarm Image This option allows you to add a background image to your graph You can set the size and orientation of the image as well as flipping rotating stretching and skewing it You can also lock the image in place for a given unit range Draw Provides tools for modifying the appearance of the line created by the drawing tool 46 000 20000 300 02 0607 iat es paiana 5 View Menu Functions Trendline This option enables you to change the color and width of the trend line for the selected graph Overlay Use this function to add an overlay to the selected graph Visible Spectrum This option allows you to display the visible spectrum on your graph You can display the spectrum the full height of the chart as a bar on the x axis or beneath the selected trend line as shown in figure below E Graph a x 41 v EHEDaaaqeae FY SHATRI H m Am 7 8 Intensity counts ra e e ea l 500 Wavelength rom Source USB2G6142 s Wavelength nm 733 35 E 113 97 144 08 000 20000 300 02 0607 47 5 View Menu Functions Spectrum Range Spectrum Range allows you to display captions for the following spectrum ranges Gamma X ray UV Visible Near infrared Mid infrared
47. an that in which it is published Trademarks All products and services herein are the trademarks service marks registered trademarks or registered service marks of their respective owners Limit of Liability Ocean Optics has made every effort to ensure that this manual as complete and as accurate as possible but no warranty or fitness is implied The information provided is on an as is basis Ocean Optics Inc shall have neither liability nor responsibility to any person or entity with respect to any loss or damages arising from the information contained in this manual Table of Contents Sinti FIM OGUGHONN sccececcccassccsesescasctatecsansaenpeccducanneaniseseencdiassacmuaness 1 Produ e E 1 USB Spectrometer and Device Control 1 Bt 2 Spec ra SUIS I TNE EE 2 DECI OSCODIC ie Tele 3 Ciis deerit 4 B ileed EET 5 REENEN 5 AS TANG SOC CHA SUNS eebe 5 micceuiions se RE 5 Downloading from the Ocean Optics ftp Gite 6 Chapter 3 Controls and Indicators 9 SUR MMM 9 gc POOTO ETT 9 Zoom ER Ke ie VE 10 Spectrum Storage MOONS ege 13 Processing Ee 13 SS CEM NO Tele 13 EIA SF ONG MN Um 14 KEE EE 16 Acquisition GONE E 16 f FSF CHING m RENE 16 MOC tel ERE TTE T TTE T 18 Eege 18 Uodate Ee TEE 19 meti M 20 Chapter 4 File Menu Functions
48. ange Attribute Value Source LISB2G6142 Observer 2 degree Steradians 1 0000E0 Area m 2 7 8540E 9 Lumen 4 3270E 8 Lux 5 5093E0 Candela 4 3270E 8 9 6281E 17 The Photometry table is described below The absolute irradiance source you selected in Step 3 The type of observer you chose in Step 5 A unit of measurement used to describe the solid angle of a cone from the surface Staradians of a sphere to the center of the sphere It is a solid angular measurement used when calculating illumination The Lumens value is divided by the Steradians value to obtain Candela Area m 2 The light collection area per meter squared Domen The lumen value A lumen is a light watt Lumens are calculated as the absolute spectral response of the human eye x The lux values The lux value is obtained by calculating the lumen per square meter Lux is also called a meter candle The luminous intensity of the sample based on international standards Photosynthetic Active Radiation The number of moles of photons between 400 PAR 700 nm measured by absolute irradiance To vary the 400 700 nm range you can specify the moles of photons range using New Energy Power Photons 000 20000 300 02 0607 79 7 Processing Menu Functions B E X axis Units This menu item allows you to select the units for the x axis on the spectrum graph Choose from Gigahertz Microns Pixels Raman Shifts Nanometers and Wavenumbers The default
49. aph Strip Chart B 1000 200 300 400 500 600 700 300 Wavelength nm Source USE2G6142 w Wavelength 853 72 4 120 00 120 00 AS 3 Youcan save this processed spectrum back out to a file as processed reference or dark spectrum Right click on the Processed Spectrum icon to display the SpectraSuite Save Spectrum dialog box Ge SpectraSuite Save Spectrum Spectrometers Processing 0 CURZG00013 Wo Pre processor Scope Made Desired Spectrum Processed Spectrum File Type OOI Binary Format ae 200 400 600 a00 Wavelength om File name ix required 000 20000 300 02 0607 39 5 View Menu Functions m 4 Enter the file name or browse to a desired file select the desired spectrum processed reference or dark and select the file type binary or tab delimited Tip Save the file as tab delimited if you want to display it in an Excel spreadsheet 5 Click Save Spectrum Collection A spectrum collection is created when you perform a high speed acquisition Select File Open Load Spectrum Collection to browse to and open a spectrum collection from a high speed acquisition Save Save Spectra Collection This menu option allows you to save your spectra collection to a file Select File Save Save Spectra Collection from the menu and enter a file name Also see Exporting Processed Data for information on exporting data to a file Save Spectrum This men
50. ass a 7 S 4 Hem OO Ar pP xx EN 5 FX T j d ee 3 n i alt i E Jj E ep A J ry X i SEO EE EE renintagh fr Sore LORS ap Wasesleegei 04 SEN AR SOUND ORDA ww Wengi ESB ro rd Ug Zoom 1 Zoom2 You can also use the mouse wheel to zoom in on the graph centered around the cursor green vertical line H Zoom Out Use this control to reverse the zoom in process Ed e Zoom to Region This control allows you to select a section of the graph to zoom in on When you click the control a cursor appears on the screen enabling you to box in a region to zoom in on 4 Hgagagga T S4AATRI B amp 4838 Hg eega T SPATRI Rapa Brderete corts n b Ke Ki n O W am SX se 50 me a 60 e e e e 7 Wavelength nen e Toggle Graph Pane Use this control when you have more than one graph and want to switch between graph displays 12 000 20000 300 02 0607 cean ptics me Ine 3 Controls and Indicators Beete oo Tools Store dark mm Store reference spectrum These tools are also available from the File Store menu See Store for more information on these functions Processing Tools LENL O m e These tools can also be accessed from the Processing Processing Mode menu See Processing Mode for more information on these functions Spectrum IO Tools Save Spectra Click to save data in either a Grams SPC format JCAM
51. asurement Selecting your source 2 Setting the data acquisition parameters 32 000 20000 300 02 0607 cean ptics Inc irgi in homage ics 5 View Menu Functions 3 Taking a reference spectrum 4 Taking a dark spectrum 5 Setting your gated delay See Fluorescence for more information on taking a fluorescence measurement Curie Fluorescence Measurement amp The New Curie Fluorescence Measurement menu selection is activated when you are using a Curie UV VIS Emission Spectrofluorometer serial number starts with CUR Note The Curie UV VIS Emission Spectrofluorometer is a discontinued product When you select this menu item a wizard leads you through the steps necessary to take a fluorescence measurement with a Curie spectrofluorometer Absolute Irradiance Graph The Absolute Irradiance Graph menu selection displays the Absolute Irradiance graph With SpectraSuite you can display multiple spectra from multiple devices with independent calibrations You can also calculate integrated intensities watts joules photons and photometric quantities lux lumen candela Select File Absolute Irradiance Graph from the menu The Absolute Irradiance Graph in Scope mode appears See Absolute Irradiance in Appendix A Experiment Tutorials for more information 000 20000 300 02 0607 33 5 View Menu Functions Be Ocean Optics Spectrasujig Pile ew Soectrometer Processing Took Window Help Inbegratio
52. ative irradiance spectra are a measure of the intensity of a light source relative to a reference emission source There are two methods of performing a fluorescence experiment in Relative Irradiance mode run SpectraSuite in Relative Irradiance mode using the calibration files generated during factory calibration or perform your own radiometric calibration using a blackbody of known color temperature See Relative Irradiance for the experiment procedure See the following figures for examples of graphs of relative irradiance in a fluorescence measurement 000 20000 300 02 0607 139 A Experiment Tutorials FVE sample measured with the USB2000 FL spectrometer PX pulsed xenon light source CUV ALL 4 S E m 400 450 500 530 600 650 700 PVE sample measured with the USB2000 FL spectrometer PX2 pulsed xenon light source CUV ALL 4 source used for reference Sample im disposable cuvette 0 3 0 25 Relative Irradiance Ln LA ii 0 05 Wavelength nm 140 000 20000 300 02 0607 niea B Troubleshooting Note If you have a spectrometer with a gated detector such as the USB2000 FLG you can initiate a fluorescence measurement with File New New Gated Fluorescence Measurement If you have a Curie UV VIS Emission Spectrofluorometer serial number starts with CUR you can initiate a fluorescence measurement with File New New Curie Fluorescence Measurement Application Tips Saturates the sp
53. b appears if a USB LS 450 light source is attached to your spectrometer Adjust the analog output current Multi Channel Provider This screen appears for an ADC1000 The Single Strobe signal is a programmable TTL pulse that occurs at Single Strobe a user determined time during each integration period Set the counts for the high and low transition delay SPI The Serial Peripheral Interface is a 3 wire interface that can be used to communicate to multiple slave devices Access the SPI bus communications functions on this screen Stray Light Enter the stray light correction coefficient in this screen TEC For QE65000 spectrometers set the parameters for the TE cooled 000 20000 300 02 0607 9 DIS Est in Photonics 6 Spectrometer Menu Functions Thermoelectric For NIR spectrometers Trigger Delay Same as External Trigger Delay UV VIS ISS UV VIS Enable visible lamp set visible lamp intensity enable UV lamp set UV lamp intensity Wavelength Allows you to enter or change the spectrometer s wavelength calibration coefficients Wavelength coefficients are provided on the Wavelength Calibration Data Sheet that came with the spectrometer MMS Raman Spectrometer The following are features for the MMS Raman Spectrometer Ss MMS Raman Features Raman Exposure Image Wavelength Firmware CCD Temperature CCD Shutter r Intensity Save Brightness sl Contrast Use thi
54. bsolute irradiance See Experiment Tutorials for information on conducting an experiment in Absolute Irradiance mode Collection Area Select Processing Absolute Irradiance Collection Area to enter the specifications of the collection area 5s Collection Area O Collection Area 1 cm 2 5 Fiber Diameter 1 micron The Collection Area dialog box offers the following options Use Integrating Sphere Enable this option only if you have an integrating sphere and use the LS1 CAL INT calibrated light source In this case the source is inside the sphere and there is no collection area associated normally with a probe When this box is enabled and you are using the integrating sphere to collect light externally source is outside the integrating sphere SpectraSuite assumes the value in the Fiber Diameter field is the diameter of the opening in the integrating sphere Be sure to enter the correct value in microns Collection Area If you know the actual collection area enter it here The default is 1 72 000 20000 300 02 0607 a cean ptics Inc Fret in PYetanice 7 Processing Menu Functions Fiber Diameter If the tip of a fiber is used as the collection probe enter the bare fiber s diameter in microns If an integrating sphere is used to collect light from a surface enter the sphere s opening diameter in microns However if a light source is inserted into the sphere this value is ignored If a cosine
55. calibration file you created with the deuterium lamp source or browse to the desired file 3 Enter the file name of the spectrometer calibration file that you created with a tungsten lamp source or browse to the desired file 4 Inthe Boundary Wavelength field select the wavelength at which point the two files will be joined or go on to Step 5 to just accept the value provided by SpectraSuite 5 Click seve The graph of the combined files appears in the Spectrometer Calibration Preview New Energy Power Photons This feature enables you to measure integrated intensities Radiometric values require that you specify the wavelength range You must be in Absolute Irradiance mode click l for this menu selection to be active Procedure Create a new graph of spectral data in Absolute Irradiance mode See Absolute Irradiance in Appendix A Experiment Tutorials for detailed instructions 2 Select Processing Absolute Irradiance New Energy Power Photons to display the Energy Power Photons dialog box OR Click LA on an Absolute Irradiance graph 74 000 20000 300 02 0607 i cean ptics In D up Firat in Photonics 7 Processing Menu Functions Be Energy Power Photons S5nurce Spectrometers Spectrum Type Processed Integration Options Integrate From 178 32 ta Br 5 18 lt nm Integration Method Rectangular k 3 If more than one Absolute Irradiance graph is open select the
56. ce This command merely stores a reference spectrum in memory You must click the Save Spectra icon on the toolbar or select File Save Save Spectra Collection from the menu bar to permanently save the reference spectrum to disk 5 Ifyou have not already done so store a dark spectrum reading To do this either block the light path to the spectrometer uncheck the Strobe Lamp Enable box in the Acquisition toolbar or turn the light source off Then take a dark spectrum by clicking the Store Dark Spectrum icon on the toolbar or by selecting File Store Store Dark Spectrum from the menu bar This command merely stores a dark spectrum in memory You must click the Save Spectra bal icon on the toolbar Note If possible do not turn off the light source when taking a dark spectrum If you must turn off your light source to store a dark spectrum allow enough time for the lamp to warm up again before continuing your experiment You must take a dark spectrum before measuring relative irradiance 6 Position the fiber at the light source you want to measure Then click L The Relative Irradiance graph appears Be Ocean Optics pectrasulte Die ew mpectromeber Frocessing Toms Winder Heap integ ation Scans ta Bac Strobe Lamp Electric dai time average pecht Enable mi iti T E CN External bigger Date Sources CR L Graph A r H8Hnasgugue I S4AATR CERE Relative Irradiance en Button
57. ce Spectrum Preview Strobe Larnp l Enable LI wavelength rm Once the lamp is ready press the button above to store a spectrum Next gt Finish Help If you are performing an absolute irradiance calibration go on to Step 6 Otherwise continue with Step 5 5 If you have not done so already check the Strobe Lamp Enable box or physically turn on the lamp Once the lamp has warmed up click Y to store a reference spectrum The graph appears in Reference Spectrum Preview 144 000 20000 300 02 0607 a cean i ptics Inc First in Phoronick B Trou bleshooting Be Color Measurement Setup wizard 3 of 4 Store Reference Spectr Reference Spectrum Preview Strobe Lamp a Enable S000 eu 1000 0 200 400 600 s Wavelength mm Once the lamp is ready press the button above ta store a spectrum 6 Click Next The fourth Color Measurement Setup wizard screen appears 000 20000 300 02 0607 145 a cean ptics Inc A Experiment Tutorials i First in Photonics Ge Color Measurement setup wizard 4 of 4 Store Dark Spectrum Dark Spectrum Preview Strobe Lamp l Enable LI Wavelength nm Momentarily block the light or uncheck strobeJamp and press the button above to store a dark spectrum 7 Block the light or uncheck Strobe Lamp Enable Then click T to store a dark reference spectrum The graph appears in Dark Spectrum Preview 146 000 20000 300 02 0607 B Troubleshooting
58. ce in the browser window and select Login As The login and password dialog box appears Enter the following Username username Password password Double click on Installations Drag SpectraSuiteSetup Windows exe to the local computer and execute The default installation directory is Program Files Ocean Optics SpectraSuite The SpectraSuite icon location is Start Programs Ocean Optics SpectraSuite SpectraSuite and the current user s desktop 000 20000 300 02 0607 W cean tics Inc inf in Photenice 2 Installation Installing on a Macintosh Platform You must be logged on as an administrative user to install SpectraSuite on your Mac Total download is less than 15 MB Procedure l 2 Open a terminal window Finder Applications Utilities Terminal Type in your user name and password Paste the following text into this terminal window ftp ftp username password spectrasuite oceanoptics com hash 10000 Icd Desktop cd Installations get SpectraSuiteSetup Mac dmg quit When this command is finished a file named SpectraSuiteSetup Mac dmg appears on the desktop Double click on the SpectraSuiteSetup_Mac dmg file to mount the disk image A new SpectraSuite icon resembling a disk drive appears on your desktop The new icon should open automatically if it doesn t double click it Copy the SpectraSuite 1con to your desktop When the installation is complete drag the SpectraSuite
59. ch spectrometer Using SpectraSuite you can combine data from multiple sources for applications that include upwelling downwelling measurements dual beam referencing and process monitoring SpectraSuite can be used with the following Ocean Optics spectrometers when they are interfacing to a computer through their USB port S2000 Spectrometer with A D Converter USB650 Spectrometer USB2000 Spectrometer USB2000 Spectrometer USB2000 FLG Spectrometer 000 20000 020 02 0607 1 1 Introduction we 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 Spectrometer In 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 be altered or replaced For instance the data acquisition functions the scheduling functions the data processing functions and the rendering functions are all separate modules You can add or delete modules to create a proprietary user interface or functionality create modules to perform calculations automate experiment routines and more You or an Ocean Optics application developer can easily customize SpectraSuite through Java code Platfor
60. creen immediately set a delay time 4 Select to store the captured image as a PNG or JPG file 5 Click Accept l Save 6 You are prompted to choose a name and location to store the captured file then click 999 Exit Caution For Mac operating systems do NOT attempt to exit from the SpectraSuite application by using Quit If you do so the application could hang Should this occur unplug then replug in the spectrometer s before restarting SpectraSuite to make the application work again Select File Exit from the menu to exit the SpectraSuite application A shutdown confirmation dialog box appears Click Yes to exit SpectraSuite Alternately you can click the top right X box of the application s display window Note If your system gets hung after requesting SpectraSuite to shut down press the Escape key twice to exit the application 000 20000 300 02 0607 43 a cean ptics Inc if in Prola f Chapter 5 5 View Menu Functions View Menu Functions Overview This section details the various options and functions available from the View menu in SpectraSuite Scale Empty This menu selection is for future use Graph Layer Options Select View Graph Layer Options right click on the graph and select Graph Layer Options click x or type CTRL ALT L to display the Graph Layer Options dialog box The Graph Layers feature provides more control over the customization of your graph window 44 00
61. cuvette to take a reference spectrum You must take a reference spectrum before measuring absorbance Note Do not put the sample itself in the path when taking a reference spectrum only the solvent 7 Click the Store Reference Spectrum Y icon on the screen This command merely stores a reference spectrum in memory You must click the Save Spectra e icon on the toolbar or select File Save Save Spectra Collection from the menu bar to permanently save the reference spectrum to disk Then click Next gt The fourth page of the wizard appears 000 20000 300 02 0607 111 A Experiment Tutorials n 112 tics Inc irgi in horong Se Absorbance Measurement Steps Dark Spectrum wizard 4 of 4 Data Source Acquisition Parameters Reference Spectrum Dark Spectrum Store Dark Spectrum Dark Spectrum Preview Strobe Larnp 1 Enable LI wavelength rm Momentarily block the light or uncheck strobeJamp and press the button above ta store a dark spectrum Cancel Block the light path to the spectrometer uncheck the Strobe Lamp Enable box or turn the light source off Then take a dark spectrum by clicking You must take a dark spectrum before measuring absorbance This command merely stores a dark spectrum in memory You must click the Save Spectra e icon on the toolbar or select File Save Save Spectra Collection from the menu bar to permanently save the spectrum to disk Note If possible do
62. desired spectrometer by highlighting it under Source 4 Enter the wavelength range to integrate in the Integration Options section 5 Enter the Integration Method either Rectangular Simpson s Rule or Trapezoid 6 Click when finished The Energy Power Photons table appears to the right of the graph You can change these values by clicking the Change icon VO in the Energy Power Photons table 000 20000 300 02 0607 75 5 Dtics inc 7 Processing Menu Functions Ent in Photonics Be Ocean O piks Spectrasue File View Soedromeber Proceeung Took Wink Help Ink er ation S ars t Bim Strobe A se Eed tre dk I ues uer each Foie correctior CATbE S es 4 x E ahi x iL T SL x i CBnergy Power Photeen D P x P ZEE d LA Change 4 Hj Hee amp amp A F uak SIm TEG i Suns LESS 42 Sart 178 x2 an Ered 876 19 d Be tene DOORS avg L boxcar O Perte Eie af gue ha Bi j gr Gees Hose uU kafe lt i NEL 4 Graph fl Ve St S I Ce Bn mec flores Se baocsr 0 i decas ceri ut a I dh si ha Prepona Scope Meade Leth ices EB TE D Abus brackance B re METT int tme 100ms avg L boocar gz e j i Photoreom 2s Be Za No Pre processor Absolute Ira 20 a Tetas peur oer m mene amp chte Lbrmwhanos B Propertuer Teria peices LISBOA 18572 Fees LESRZDOD 2 A1 3 Tatal Pisak MP Moles of photons 1 41671 15 x Data Views Eo geaph rd amp Ate Madarai
63. drive icon to the recycle bin Installing on a Linux Platform Total download is approximately 30 MB Procedure Open a terminal window k 000 20000 300 02 0607 Type in your user name and password Paste the following text into the terminal window ftp ftp username password spectrasuite oceanoptics com hash 10000 Icd Desktop cd Installations get SpectraSuiteSetup Linux bin quit A SpectraSuiteSetup Linux bin file appears on your desktop 2 Installation 2 Start a terminal window and enter the following commands chmod 755 Desktop SpectraSuiteSetup_Linux bin sudo Desktop SpectraSuiteSetup_Linux bin You are prompted for your password which allows you to execute the setup as root Contact your system administrator if you do not have password If the sudo command does not work it may not be set up for your user account then enter the following su enter password for root Desktop SpectraSuiteSetup_Linux bin The Linux version of SpectraSuite requires some libraries that may not be installed by default depending on the Linux distribution The following are libraries are required and are not provided as part of SpectraSuite e libstdc version 5 Some newer systems only install version 6 so a compatibility package may be required In Fedora Core Linux libstdc version 5 is provided by compat libstdc e libXp version 6 earlier versions may work too In Fedora Core 3 and 4 th
64. e Available Version and Installed Version boxes 4 Click to display the SpectraSuite license agreement 000 20000 300 02 0607 91 1 cean ptics Inc 8 Tools Menu Functions i Firat in Photonics Ge License Agreement spectrasSuite is copyright Cl 2005 Ocean Optics Inc http uwww oceanoptics com Portions of this code is copyright by Sun Microsystems Inc Copyright c 2002 Extreme Lab Indiana University Copyright ic 2003 2004 Joe Walnes 5 Click to accept the license agreement and start the download The progress of the download appears on the next screen Ge Update Center Wizard Steps Download Modules 1 Select Location of Modules The Update Center is now downloading modules and or checking digital signatures Select Modules to Install Download Modules and SpectraSuite Color Measurement 1 1 Mewcerfcotesendinsal MM LL MU AN Modules Verified 365 of 365 KBytes 92 000 20000 300 02 0607 Sg Update Center Wizard Steps 1 Select Location of Modules Select Modules to Install Download Modules and Check Digital Signatures iew Certificates and Install Modules 9 Tools Menu Functions iew Certificates and Install Modules Select the modules you wish to install If a module is signed you must view and accept its certificate Modules to Install Include Module Name Global a SpectraSuite Color Measurement version 1 0 0 a Not Signed Save Copy Cancel
65. ected LanBox DMX the SeaChanger DMX Login dialog box appears Enter the Y Seathanger Controls Color Values P bs Ze Bp Log Auo save 96 3 6407 94 6 AOK 96 7 5407X 98 3 S407 92 6 407X 194 1 S407 19 2 407x See 5407 3 2 HOT D ZE AG A Chroenaticity Diagram D Turning on module done 000 20000 300 02 0607 a cean ptics Inc Firg in Prolong 5 View Menu Functions During this time an initialization process occurs in which SpectraSuite automatically does the following for you Turns on the light source Calibrates to the correct integration time Stores a reference spectrum Turns the lamp off to store a dark spectrum Starts a transmission measurement Adds a color measurement for emissive color Starts the SeaChanger s LanBox DMX console and calibrates the measurements until they re stabilized 3 The SeaChanger Console screen appears enabling you to change the parameters listed in the table below lt Ocean Optics SpectraSuite File View Spectrometer Processing Tools Window Help Integration ei _ Scans to oe Boxcar Strobe Lamp Electric dark m x 69 6 78 6MB time 43 397 2 niroseco 3 average Sy eJ width 0 x Enable correction Hi I o P ea en Nonlinearity Stray Light External Normal a Strobe Gate 1 n gt 41S correction ain Ll trigger W Delay Graph D X SeaChanger Console x _ Color Values C SeaChanger
66. ectrometer Decrease the light level Decreasing the integration time or peaks are off the scale on scale in Scope mode Incorporating linear variable filters into your experiment Has too little light Increase the light level on Increasing the integration time or scale in Scope mode Removing linear variable filters from the light path Color Experiments With SpectraSuite you can obtain photopic data in either lumens or lux per unit area based on a CIE standard visibility curve You can also control the parameters for all system and display functions such as data acquisition graph display and cursor configuration In addition you can create a spreadsheet display of lamp output intensity by wavelength providing an easy way to chart and analyze acquired data SpectraSuite will compute all color measurements except RGB gt Procedure To collect color data 1 From the main graph click the Chromaticity icon t on the Processing toolbar OR Select File New Color Measurement The New Color Measurement dialog box appears 000 20000 300 02 0607 141 A Experiment Tutorials Fast in Fhoronax Ss New Color Measurement Select data source For color measurement Q New absolute irradiance processing i New relative irradiance processing Q Existing processing Spectrometers Spectrum Type USB266142 Processed 2 Select the data source for the color measurement and click Accent The first Color Measuremen
67. ensity at wavelength A Typical absorbance setup The light source far right sends light via an input fiber into a cuvette in a cuvette holder bottom center The light interacts with the sample The output fiber carries light from the sample to the spectrometer top center connected to the computer far left Absorbance is also proportional to the concentration of the substance interacting with the light this 1s known as Beer s Law Common absorption applications include the quantification of chemical concentrations in aqueous or gaseous samples Procedure 108 000 20000 300 02 0607 a cean ptics Inc Mirgi in Prolong B Troubleshooting Follow the steps below to take an absorbance measurement using SpectraSuite 1 Place SpectraSuite in Scope mode by clicking the Scope 5 icon in the Experiment mode toolbar or selecting Processing Processing Mode Scope from the menu 2 Ensure that the entire signal is on scale The intensity of the reference signal s peak differs depending on the device being used If necessary adjust the integration time until the intensity is appropriate for your device 3 Select File New Absorbance Measurement from the menu or click A to start the Absorbance Measurement Wizard Be Absorbance Measurement Steps wizard 1 of 4 Data Source Acquisition Parameters Reference Speckrum Dark Spectrum SE Preview 178 32 876 19nm
68. er and SpectraSuite software Appendix B Troubleshooting Provides a table of possible problems and suggested solutions Product Related Documentation External Triggering Options Various USB spectrometer documents such as the USB4000 Spectrometer Installation and Operation Manual ADC1000 USB Operating Instructions SeaChanger 4 Channel Installation and Operation Manual SeaChanger Wash 4 Channel Color Engine Installation and Operation Manual You can access documentation for Ocean Optics products by visiting our website at http www oceanoptics com Select Technical Operating Instructions then choose the appropriate document from the available drop down lists Or use the Search by Model Number field at the bottom of the web page You can also access operating instructions for Ocean Optics products on the Software and Technical Resources CD included with the system Engineering level documentation is located on our website at Technical Engineering Docs Upgrades Occasionally 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 Merchandise Authorization RMA number Please contact Ocean Optics for specific instructions when returning a product viii 000 20000 300 02 0607 Chapter 1 Introduction Product Overview SpectraSuite is a completely modular Java based spectroscopy software platfor
69. es the configuration of the sampling optics for your system Furthermore your choice of reference and data analysis determines how SpectraSuite presents the results Note For each measurement you must first take a reference and dark spectrum before the experiment mode icon A T JE on the toolbar becomes active After you take a reference and a dark spectrum you can take as many measurement scans as needed However if you change any sampling variable integration time averaging smoothing fiber size etc you must store a new reference and dark spectrum 106 000 20000 300 02 0607 L7 Dtics inc i P E Firat in Photonics B Troubleshooting 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 Using a neutral density filter with the correct optical density If the signal you collect has too little light you can increase the light level on scale in scope mode by Increasing the integration time Using a larger diameter fiber Removing any optical filters Taking Reference and Dark Spectra Reference and dark spectra must be stored before collecting experiment data If you pass the cursor over the No preprocessor line in either the Data Sources or Data Views pane a dialog box informs you wh
70. ether reference and or dark spectra have been stored Store Dark Spectrum icon Store Reference Spectrum icon L mE LIES See Rai i HOH Pie Yes Spectrometer Pemi Tom wrek ee bm ai d im p vi Ser o Ep SER TE eid Fer mand w Data Sources pane ame a kreie E ose D H a aunaa r s4ATI Waaa Preprocessor dialog Berg W er LED L2 box Firreana LETUTERI 7 al 3 Total Piste DAE Wanga M eg 2 rin E E De o Vieira Wu ei Data views pane E sss i int Hre ite sen bere 2 S i LED Soe X ounce La d we Wuwmlrwgh A3 5d Wien 8 000 20000 300 02 0607 107 A Experiment Tutorials A reference spectrum is taken when the light source is on and the there is no sample present Click the Store Reference Spectrum icon to take a reference spectrum A dark spectrum is taken in the absence of light Block the light path uncheck the Strobe Lamp Enable option on SpectraSuite s Acquisition toolbar or turn off the lamp and then click the Store Dark Spectrum icon T to take a dark spectrum Absorbance Experiments Absorbance spectra are a measure of how much light a sample absorbs For most samples absorbance relates linearly to the concentration of the substance SpectraSuite calculates absorbance A using the following equation S D A 10 ib n m p Where A Sample intensity at wavelength X D Dark intensity at wavelength A R Reference int
71. he SpectraSuite currently selected SpectraSuite pane to fill the entire SpectraSuite window and redisplaying restoring these panes in the window See the example of a maximized Data Sources pane below Maximize Restore Output Select Window Output to display a list of SpectraSuite status messages in a pane below the SpectraSuite window 96 000 20000 300 02 0607 9 Window Menu Functions cure mu ui mm May 1 2006 8 26 47 AM EDT Hay 1 2006 8 26 47 AM EDT Speed Benchmark module is loading May i 2006 8 26 47 AM EDT Color Measurement module is loading May 1 2006 8 26 47 AM EDT Spectral Correction module is 1oading 000 20000 300 02 0607 97 9 Window Menu Functions 98 000 20000 300 02 0607 Chapter 10 Strip Charts Overview SpectraSuite allows you to use Strip Charts to track processes perform kinetic analyses and monitor spectral events all as a function of time The Strip Chart shows you how the value that you selected appears over time This value can be any of the following One pixel a single wavelength The average of a range of pixels An integral calculated by one of three methods representing the area beneath the graph s trend line You can acquire this data using any processing mode transmission absorbance etc Creating Strip Charts Procedure Place SpectraSuite in Scope mode by clicking the Scope 5 icon in the Experiment mode toolbar or selec
72. he longer the detector monitors the incoming photons If your Scope mode intensity is too low increase this value If the intensity is too high decrease this value Adjust the integration time so that the greatest amount of light that you anticipate for your application causes a signal of about 85 of spectrometer s capability for example 3500 for spectrometers with a total of 4096 counts 14000 counts for spectrometers with a total of 16384 counts 50000 for spectrometers with a total of 65535 counts While watching the graph trace adjust the integration time until the signal intensity level is appropriate for the device The integration time specified controls enabled spectrometer channels in the active spectral window Scans to Specifies the number of discrete spectral acquisitions that the average device driver accumulates before SpectraSuite receives a spectrum The higher the value the better the signal to noise ratio S N The S N will improve by the square root of the number of scans averaged Sets the boxcar smoothing width a technique that averages across spectral data This technique averages a group of adjacent detector elements A value of 5 for example averages each data point with 5 points to its left and 5 points to its right The greater this value the smoother the data and the higher the signal to noise ratio If the value entered is too high a loss in spectral resolution will result The S N will improve by
73. her mode Absorbance Transmission etc by clicking on the appropriate icon A T ete Absorbance Measurement A The Absorbance Measurement menu selection launches the Absorbance Measurement Wizard to facilitate taking an absorbance measurement using SpectraSuite The wizard leads you through the steps necessary to take an absorbance measurement 1 Selecting your source 2 Setting the data acquisition parameters 3 Taking a reference spectrum 4 Taking a dark spectrum See Absorbance Experiments for more information on taking an absorbance measurement Transmission Measurement uli The Transmission Measurement menu selection launches the Transmission Measurement wizard to help you through the process of taking a transmission measurement Reflection Measurement R The Reflection Measurement menu selection launches the Reflection Measurement wizard to help you through the process of taking a reflection measurement Relative Irradiance Measurement The Relative Irradiance menu selection launches the Relative Irradiance Measurement wizard to help you take to help you through the process of taking a relative irradiance measurement Gated Fluorescence Measurement amp The New Gated Fluorescence Measurement menu selection is activated when you are using a spectrometer with a gated detector such as the USB2000 FLG When you select this menu item a wizard leads you through the steps necessary to take a gated fluorescence me
74. hese methods of data acquisition Number of Scans Acquire a fixed number of scans fastest method Or Capture Period usec Specify a time period for data capture Show progress Enable this option to show the progress of the acquisition 5 Click Le Your high speed acquisition data appears in the Data Sources pane 000 20000 300 02 0607 27 5 View Menu Functions B Ocean Optics SpectraSuite zi Aoga m nk time eres aeg 13 beta 5 2 Properties High Speed Acquisition Data Wavelengths L78 34376 2 nemi Al Data Views a EL Graph ay H Da amp 8 8 y Electric d ck connection D BAT Goi t StATRI Heda E Wavelength inm 6 Right click on e Spectrum Graph Displays a graph of the spectra Ee Ocean Optics SpectraSuite A menu displays the following selections File View Spectrometer Processing Tools Window Help Integration EE Scans to Boxcar Strobe Lamp Electric dark 7 fh time Tees average width M Enable correction AT Wel External p Mor b trigger N Data Sources a x mm Graph A x TE k RI Dee oe gz SHATRI Rea e 4 Acquisition Int time 20ms avg 1 boxcar 0 No Pre processor Scope Mode Properties Litt e lb zm leen e e lb e be ml ml e ee Q High Speed Acquisition 1 i L 120 E High Speed Acquisition 2 100 4 B High Speed Acquisition 3 5 80 gm i S E Simulated Acqu
75. hooting S amp Concentration Measurement Setup wizard Concentration Measurement Setup Wizard Molar Extinction lic ifcm Path length t cm Wavelength 400 nm Compound Name Sample 1 Concentration Units mol 4 Fill in the fields according to the constants appropriate for your sample The Compound Name and Concentration Units can be set to anything and are simply provided for reference Click Finish See Calibrating from Solutions of Known Concentration a Insert a sample for which the concentration is known into the spectrometer b Select Calibrate from solutions of known concentration insert samples into the spectrometer for which you know the concentration and use that as a basis for computing the concentration of the unknowns Then click Net The following window appears 000 20000 300 02 0607 115 i cean ptics In Fast in Fhorong A Experiment Tutorials Ss Concentration Measurement Setup wizard Concentration Measurement Setup Wizard Wavelength Selection One wavelength Average From C Integrate over 40012 zl Cancel c Choose a single wavelength where the absorbance of your compound is greatest You can also choose an average or integral over a range of wavelengths which may provide a more robust calibration since it is not as reliant on the behavior of the compound at
76. ical to that required for transmission You must first store reference and dark spectra in Scope mode before you can access Transmission mode SpectraSuite calculates the transmission of a solution using the following equation 5 D wT x 100 R D Where S Sample intensity at wavelength A D Dark intensity at wavelength A R Reference intensity at wavelength A See Experiment Tutorials for information on conducting an experiment in Transmission mode Reflection Select Processing Processing Mode Reflection to switch the current window into Reflection mode You can also click R in the graph s toolbar Reflection mode is also the spectral processing mode used for transmission spectroscopy as the math necessary to compute transmission is identical to that required for reflection You must take reference and dark spectra in Scope mode before you can access Reflection mode SpectraSuite calculates the reflection of a solution using the following equation 5 D DT __ x 100 R D Where S Sample intensity at wavelength A D Dark intensity at wavelength A R Reference intensity at wavelength A See Experiment Tutorials for information on conducting an experiment in Reflection mode Relative Irradiance Select Processing Processing Mode Relative Irradiance to switch the current window into Relative Irradiance mode You can also click in the eraph s toolbar 70 000 20000 300
77. ications include measuring the properties of mirrors and coatings Other applications include measuring the visual properties of the color in paints plastics and food products 126 Procedure Perform the following steps to take reflection measurements using SpectraSuite Place SpectraSuite in Scope mode by clicking the Scope 5 icon in the Experiment mode toolbar or selecting Processing Processing Mode Scope from the menu 2 Ensure that the entire signal is on scale 3 Take a reference spectrum with the WS 1 Diffuse Reflectance Standard or the STAN SSH High reflectivity Reference Standard You must take a reference spectrum before measuring reflection 4 Click the Store Reference Spectrum Y icon on the toolbar or by select File Store Store Reference Spectrum from the menu bar to store the reference This command merely stores a reference spectrum in memory You must click the Save Spectra VW icon on the toolbar to permanently save the reference spectrum to disk 5 Either block the light path to the spectrometer uncheck the Strobe Lamp Enable box in the Acquisition toolbar or turn the light source off Then take a dark spectrum by clicking the Store Dark Spectrum Li icon on the toolbar or by selecting File Store Store Dark Spectrum from the menu bar This command merely stores a dark spectrum in memory You must click the Save Spectra icon on the toolbar or select File Save Save Spectra
78. ighest known concentration While going through the wizard when asked to store a reference spectrum put a cuvette full of your solvent in the spectrometer s cuvette holder There are three methods you can use to calculate the concentration of a sample Using Beer s Law see Calculating Concentration Using Beer s Law Calibrating from a solution of known concentration see Calibrating from Solutions of Known Concentration Loading a previously stored calibration from a file see Loading Calibration from an Existing File The Concentration Measurement Setup Wizard allows you to choose one of these three methods 000 20000 300 02 0607 113 A Experiment Tutorials m Before measuring concentration you must first take an absorbance measurement see Absorbance Experiments for instructions Procedure 1 Select File New Concentration Experiment from the menu to open the Concentration Measurement Setup Wizard Be Concentration Measurement Setup wizard Concentration Measurement Setup Wizard Select basis For concentration calculation Calibrate From solutions of known concentration Load calibration From File 2 Select the basis for the concentration calculation Calculating Concentration Using Beer s Law 3 Select Beer Lambert Law to specify the molar extinction constant and a wavelength Then Click vex J The following window appears 114 000 20000 300 02 0607 eg B Troubles
79. ime 307ms avg 5 boxcar 5 No Pre processor Transmission Mode 100 E Graph A Properties Serial Number USB2G09363 op Firmware USB2000 2 41 3 Total Pixels 2048 Wavelengths 179 1 873 1 nm 80 Data Views a x E E Graph a Transmission ce e Spectrum Graph 200 300 400 500 600 700 800 Spectrometer Serial Number Wavelength nm Se Source 582G09363 yw Wavelength 251 83 s 30 775 33 097 e J Layer Tools The Layer tools provide you with functions to write captions and other meaningful data on your graphs Select the tools using the Layer Toolbar AM 79d amp 14 000 20000 300 02 0607 Pol mist in Photonics 3 Controls and Indicators Add New Annotation Displays the New Annotation dialog box to add a new annotation to the selected graph Select and Drag Annotation Allows you to grab an annotation on the graph and drag it to another location Draw Allows you to draw freehand using the mouse on the graph Erase Areas of Drawing Layer Erases selected portions of the drawing created with the Draw tool pencil Clear Drawing Layer Clears the entire drawing made with the Draw tool pencil Graph Layer Options Displays the Graph Layer Options dialog box see Graph Layer Options The following figure shows a graph with an image layer and an annotation circled with the drawing tool lig Graph A Image Intensity counts Cmm cun on
80. ime average width d Enable d correction d correction Data Sources Graph B X th HR2zn Indigo Carmine Concentration fH Graph B amp Graph C single Update Continuous Update Measurement Setup At any time you can click EES to reopen the setup wizard and change the parameters for the concentration measurement Transmission Experiments Transmission is the percentage of energy passing through a sample relative to the amount that passes through the reference Transmission mode can also display the portion of light reflected from a sample since transmission and reflection measurements use the same mathematical calculations We express transmission as a percentage 96T relative to a standard substance such as air SpectraSuite calculates 26 T or 6R with the following equation S Dy x 100 T R D X Where A Sample intensity at wavelength A D Dark intensity at wavelength A R Reference intensity at wavelength A 122 000 20000 300 02 0607 m I First io Photonics B Troubleshooting Typical transmission setup The light source far right sends light via the input leg of a transmission probe into a container bottom center The light interacts with the sample The output leg of the transmission probe carries the information to the spectrometer top center which transmits the information to the computer far left Common transmis
81. in the graph to display its value and wavelength Procedure To create a 3 D graph 1 Right click on the spectrometer in the Data Sources pane and select High Speed Acquisition Or Select File New High Speed Acquisition from the menu The High speed Acquisition dialog box appears 000 20000 300 02 0607 29 5 View Menu Functions Be High speed Acquisition Integration Time usech Scans to Average Baxcar Width Ed External Trigger Mode Electric Dark Correction Strobe Lamp Enable nee 1 j Number of Scans 100 Capture Period usecy 000000 Show progress Done 100 scans book 15 2 ms each 4 2 Enter the parameters and click A The 3 dimensional graph appears Using High speed Acquisition Spectra A spectra collection that you have stored using the high speed acquisition feature has a variety of uses such as the following You can replay the spectra fast forward rewind etc just like any recorded data Strip Chart data can also be replayed see Strip Chart for more information on how to create a Strip Chart You can also conduct further experiments on the recorded data absorbance transmission etc by clicking on the appropriate icon A T R or I Procedure To replay recorded data 1 Right click on the desired spectrum listed under Simulated Acquisition in the Data Sources pane A menu appears 2 Select Spectrum Playback Controls The Spectrum Playbac
82. ine Concentration Units b Select a file that was previously saved with in the Calibrating from Solutions of Known Concentration wizard see Calibrating from Solutions of Known Concentration Step h When an appropriate file is selected the name of the compound and concentration units appear near the bottom of the window c Click Net The resulting window is the same as if you had just entered those values from a known concentration 000 20000 300 02 0607 119 A Experiment Tutorials S amp Concentration Measurement Setup wizard Concentration Measurement Setup Wizard Calibration Data Concentration Absorbance Residual 1 20 0 0 221923 4 2633E 14 z po Wes emm SSCS ses mones e214 Concentration EE Absorbance o Use Last Scan Notes EE Add Sample Compound Mame Concentration Units Save Calibration Regression Plot 0 20 Regression Order zero Intercept R 2 1 0000E0 Order Coefficient 1 2692EU 10 12 14 ige gB 3968E1 Concentration pre 1 9585E0 2 e 4bsorbance OLD When the concentration of the sample has been calculated using one of the three available methods click Ems jJ The Concentration window appears 120 000 20000 300 02 0607 tics Inc D gg Firg in Eotoncs B Trou bleshooting Sg Ocean Optics 5pectraSuite File View Spectrometer Processing Tools Window Help Integration al Scans to Boxcar Strabe Lamp Electric
83. ion 0 3 0 14 FPiaA Firmware FPiaA Firmware version LISB Firmware USB Firmware Version 0 0 0 1 Calibration Source Save exsisting calibration Update Firmware Update Firmware Use this screen to update the firmware You must stop all acquisitions before updating the firmware Se MMS Raman Features CCD Temperature CCD Temperature 100 00 Celsius Update Mow Automatic Update Enable Periodic Update Update Interval CCD Temperature Regulation Enable Temperature Regulation CCD Temperature Set point 25 Celcius v CCD Temp Lock Qut of Set point range 0 1 C Thermistor Faulk status Ok Use this screen to regulate the CCD temperature 000 20000 300 02 0607 6 Spectrometer Menu Functions 63 6 Spectrometer Menu Functions EA MMS Raman Features CCD Shutter CCD shutter is closed Open CCD Shutter This feature allows you to control the CCD shutter Close the shutter to store a dark spectrum Rescan Devices Use this menu selection if you plug in a device after starting the SpectraSuite application SpectraSuite then displays the new device in the Data Sources pane Remove Spectra This menu selection deletes the captured high speed spectra collection data You can also right click on the high speed spectra c
84. is is provided in xorg x11 deprecated libs e libusb version 0 1 10 or newer should be provided in a libusb package or can be downloaded from http libusb sourceforge net download html stable It may be necessary to modify SELinux Security Enhanced Linux restrictions before SpectraSuite will run It is possible to remove SELinux auditing by running setenforce Permissive as root or by customizing your SELinux policies The SpectraSuite installer does not modify system security settings Note The default installation directory is usr local OceanOptics SpectraSuite A symbolic link is put in usr bin so that you can enter spectrasuite on any command line to start the program 3 The SpectraSuite icon A location varies by installation but will be under either Applications or Other under the Application Launcher menu 000 20000 300 02 0607 Chapter 3 Controls and Indicators Overview SpectraSuite consists of a number of visual controls in the form of icons and buttons This chapter describes these controls and how to use them Some menu selections and controls require that some action to be taken before they can be used When unavailable the controls are grayed out Many of these requirements will be lifted so that the software will ask what to do when it is not appropriate to take an action yet but until then the behavior is as follows Acquisition parameters storing dark reference spectra and the Strip Chart require an
85. isition E S Spectrum 100 100 S SEU aa NEE EE 2 No Pre processor Scope Mode E Graph A v Data Views 4x E Graph A 407 20 1 0 200 300 400 500 600 700 800 900 1000 1100 Wavelength nm 28 000 20000 300 02 0607 V PLCS inc First in Diotoos e Spectrum Table Displays spectra data in a table format Wavelength m Intensity counts Wavelength mm 178 32 0 00 178 32 ma aa 178 70 Gem em om oa mun 7946 ma em aa DEER mea em aa e om as i36 9930 O oa wit e e 834 me oO g8eQ 822 is o 182 50 ma mn az DC iM om mm Is en ns mz am an mem an em en am es en em a ma o o o O 8629 ee am ae em om en IA am 187 42 Im e 188 18 Pao Pea Te Pea Pe Po Po or Po Bo r3 Po Po 2 P2 ea Ba Bo Bo co e e ra ra 5 View Menu Functions Intensity counts e Save Spectra Collection Stores the high speed spectra in a file See Creating a 5 D Chart of High Speed Acquisition Spectra for more information about what can be done with stored high speed spectra data e Remove Spectra Collection Deletes the captured high speed spectra collection data You can also select Spectrometer Remove Spectra Collection Creating a 3 D Chart of High Speed Acquisition Spectra You can create a 3 dimensional representation of the data over time in graph form The navigation controls enable you to view the graph from different angles Click on any point
86. isition is the starting ideal state of the lamp Any deviations the lamp makes from that reference spectrum will cause compensation in the sample acquisition For extended experiments you will achieve optimal results if you take frequent reference spectra If this is not possible however you can choose to monitor your light source and instruct SpectraSuite to correct for any drift that might occur There are two types of drift Spectrally uniform and spectrally nonuniform The drift associated with a tungsten lamp is often spectrally uniform but the drift associated with a deuterium lamp is not Reference Monitoring allows you to monitor a reference for variations in spectral intensity based on light source and system drift To monitor a reference the following conditions must be met You are using either multiple spectrometers and spectra overlap in the area to be referenced or one spectrometer with multiple acquisitions and You have stored both a reference and dark spectrum Once these spectra have been stored the Reference Monitoring function is activated is available for use Procedure To perform reference monitoring Start an acquisition on the spectrometer that will monitor the lamp Adjust the acquisition parameters so that the spectrum is on scale 2 Storea reference and dark spectrum for that acquisition 3 Start an acquisition on the spectrometer that will measure the sample 4 Store a dark spectrum for the sam
87. k Controls dialog box appears 30 000 20000 300 02 0607 a cean ptics Inc Mirgi in Prolong 5 View Menu Functions Stop rewind Stop play Click to rewind Slide to rewind Spectrum ZA Delay ms 3 Rewind the recording then press to play the recorded spectrum graph Procedure To do further processing on recorded data 1 Begin playback of recorded data Note that the tree in the Data Sources pane populates with the usual acquisition data 2 If needed load preprocessing data dark and reference spectra by right clicking on No pre processor Scope Mode in the Data Sources pane and selecting Load Reference Spectrum and Load Dark Spectrum Browse to the desired reference and dark files Data Sources AD x Acquisition E Int time 100ms avg 1 boxcar 0 H Ma Pre processor Scope Mode Properties Serial Number USB2G6142 Firmware USB2000 2 31 3 Tatal Pixels 2048 Wavelengths 178 3 876 2 nm Configuration l ol S High Speed Acquisition 1 Click Here Simulated Acquisition Spectrum LOLLO a Pre pracessor Scope Mode Graph 4 El Properties Total Processed Spectra 10 nerFrnmetFer ISR2GR137 T Or you can store reference and dark spectra at any time during playback if you have the necessary data in your collection 000 20000 300 02 0607 31 5 View Menu Functions 3 Once you have loaded the processed spectrum files you can switch to anot
88. ken pattern ATI video cards are known to have then select the Settings tab and click the of dots instead of a problems displaying the graph Advanced button There should be a tab spectrum line properly for the device that allows you to change the hardware acceleration Set the hardware acceleration to about half and press Apply That should immediately correct the problem If not try lowering the acceleration further 000 20000 300 02 0607 153 B Troubleshooting 154 000 20000 300 02 0607 A Absolute Irradiance Experiments 129 graph 33 51 measurement 34 mode 71 Absorbance Experiments 108 measurement 32 mode 69 acquisition 57 controls 16 50 pause 57 terminate 57 toolbar 49 acquisition settings default 88 annotations 45 application tips 141 Beer s Law 69 boxcar width 49 C calibration 73 combine files 73 chart 46 close all documents 95 close window 96 collection area 72 color Experiments 141 measurement 35 settings 65 temperature 80 Concentration Experiments 113 measurement 34 controls acquisition 16 000 20000 300 02 0607 Index graph 9 Convert Spectra 42 correction toolbar 50 Create a new spectral window 22 Curie Fluorescence measurement 22 33 cursor 46 Customize Toolbars 55 D Dark 38 41 dark spectra 107 data display toolbar 50 default acquisition settings 88 device control 1 document audience vii purpose vii su
89. l processing prior to calibrating the spectral response of your system and taking measurements Use caution when operating in Scope mode since this mode represents a combination of several factors such as the intensity of the light source the reflectivity of the grating and mirrors in the spectrometer the transmission quality of the fibers the response of the detector and the spectral characteristics of the sample Absolute Irradiance Select Processing Absolute Irradiance Absolute Irradiance to create a new graph of spectral data Absolute Irradiance mode You can also click in the Data Display toolbar to use the wizard to create an Absolute Irradiance graph 000 20000 300 02 0607 71 7 Processing Menu Functions Absolute Irradiance Mode calculates the true irradiance of a spectrum displayed in actual nr W cm 2 nm or nu W nm when using an integrating sphere incident on the probe s collection area You do not need to store reference spectrum first since absolute irradiance is not relative to another measurement However you must store a dark spectrum and have a calibration file before you can measure absolute irradiance If your spectrometer was calibrated by Ocean Optics you should have received a CD containing the Radiometric Calibration Files specific to your spectrometer If you do not have these files then you must create your own spectrometer calibration files using calibrated light sources that have lamp files for a
90. le box in the Acquisition toolbar or turn the light source off Then take a dark spectrum by clicking the Store Dark Spectrum T icon on the toolbar or by selecting File Store Store Dark Spectrum from the menu bar This command merely stores a dark spectrum in memory You must click the Save Spectra icon on the toolbar or select File Save Save Spectra Collection from the menu bar to permanently save the spectrum to disk Note If possible do not turn off the light source when taking a dark spectrum If you must turn off your light source to store a dark spectrum allow enough time for the lamp to warm up again before continuing your experiment You must take a dark spectrum before measuring transmission 5 Put the sample in place and ensure that the light path is clear Then take a transmission measurement by clicking on the Transmission TF icon on the toolbar or selecting Processing Processing Mode Transmission from the menu Note the following changes on the screen e The experiment mode listed in the Data Sources and Data Views panes changes to Transmission Mode e The units listed on the Graph pane changes to Transmission 6 To permanently save the spectrum to disk click the Save Spectra VW icon on the toolbar or select File Save Save Spectra Collection from the menu bar 124 000 20000 300 02 0607 i cean tics In AN Mirgi in Gotoruts B Troubleshooting Note If you change an
91. lling Autonulling is an enhanced electrical dark correction Set the autonulling status and value on this screen Board Temperature The HR spectrometers contain a temperature sensor chip on the printed circuit board Use this screen to set the temperature parameters Channel Features For the ADC1000 USB Enable each channel 1 7 by checking box Continuous Strobe Set the continuous strobe delay The Continuous Strobe signal is a programmable frequency pulse train Detector Linearity Use this screen to change the linearity coefficients External Trigger Delay Set the counts for the external hardware trigger GPIO Set the General Purpose Input Output values on this screen Hardware Trigger The spectrometer uses an external rising edge of a TTL signal to begin a single integration cycle Set the delay counts on this screen l2C The Inter Integrated Circuit 2 wire serial bus is widely used in embedded systems applications With IC you can add peripherals to your system without using valuable resources like I O ports The I2C bus communications parameters are set on this screen Irradiance Use this screen to load and save irradiance calibration factors LS 450 This tab appears if a USB LS 450 light source is attached to your spectrometer Check the box for Pulsed LED mode if desired LS 450 Calibration Constants This tab appears if a USB LS 450 light source is attached to your spectrometer LS 450 Current Out This ta
92. luminant or observer details in the Show details for field An example screen with details for the observer is shown below Details Graph Show details Far Observer a Description 2 degree photopic daylight observer Reflective Observer 2 degree hal Illuminant A w Reference CIE 15 2 1986 Creator Ocean Optics Inc Date Provided by Ocean Optics Inc 148 000 20000 300 02 0607 a cean ptics Inc P Mira irs H haofons B Trou bleshooting 10 Select the Graph tab to view a graph reflecting the selections you have chosen An example graph of the illuminant is shown below Details Graph Show graph of Tlluminant wi Mode C Emissive Reflective Load Illuminant ili 200 400 600 Wavelength nm 11 Click Accent Your color data appears on the main SpectraSuite screen as shown below Be Ocean Optics SpectraSuite Ael Die View Spectrometer Processing Took Window Help Integration nar Scans to time average 51 Honlnearity Stray Light External conection correction trigger Data Sources ax Ii Graph A X Absolute Irradiance D X SE Color Values C A EE Ze H Log Auto save E De amp amp e I i 2 Property Value Value AE 3 Acquisition x Int tine beens avg 8 box 3 Ink time Olms avg 1 ba x Int time lems avg 9 box Properties 193 5 16 83 5 20
93. ly to all graphs in which that data appears including Absolute Irradiance and Strip Charts Procedure 1 Select Processing Edit Result Colors to display the Result Color Editor dialog box Sa Result Color Editor Processing 0 USB2G6142 No Pre pracessor Scope Mode 2 Highlight the desired source and click Change Color The Result Color Selection dialog box appears 84 000 20000 300 02 0607 tics Inc irgf in Pralong D Ze Result Color Selection L 1 ee WSL EESEL BEET EEAS eae ae eae WELT SEET WSL BEST TT E E E E E EH E WI EN EEEE SEET ERR EERE a a tt ee A O EESTE PL SEET TL WELT PE WELT Preview D BD D Sample Text Sample Text Sample Text Sample Text le ES L1 Sample Text Sample Text 7 Processing Menu Functions Recent This dialog box provides three methods of selecting color by swatches HSB hue saturation and brightness or RGB red green blue 3 Select the tab corresponding to the color selection method you wish to use 4 Select the desired color The Recent graphic lists any colors that you have recently chosen You can select one of the recent colors instead of creating a new one Once you have selected a color the Preview panel displays an example of the color you have chosen If the color is what you want click the OK b
94. m Independent The SpectraSuite is a platform independent application that provides Graphical and numeric representation of spectra in one window SpectraSuite can operate on a Windows Linux or Macintosh operating system Advanced Data Capture Control SpectraSuite provides the user with advanced control of episodic data capture attributes For instance a user can acquire data for a fixed number of scans or for a specific interval Initiation of each scan can be externally triggered or event driven Captured data is quickly stored into a systems memory at speeds as fast as scan per msec with speeds limited by hardware performance Independent Control of Multiple USB Devices Multiple USB devices can be monitored on the same graph in a single window each of these devices can be controlled independently SpectraSuite in the Future SpectraSuite 1s constantly evolving With the purchase of SpectraSuite you are entitled to one year of free web based automatic upgrades see Getting Updates 2 000 20000 300 02 0607 a cean gt ptics Inc j j atonica 9 T nist in Photonics 1 Introduction Planned future enhancements include the following 21 CFR Part 11 Compliant SpectraSuite will be 21 CFR Part 11 compliant with an encoded binary file This binary data format tracks the complete history of all processing steps that are performed on the data Spectra suite stores and provides data in a variety of other formats includi
95. m that operates on Windows Macintosh and Linux operating systems The software can control any Ocean Optics USB spectrometer and device as well as any other manufacturer s USB instrumentation using the appropriate drivers The SpectraSuite interface looks and feels the same on all operating systems yet retains the familiar 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 and the rendering functions are all separate modules You can add or delete modules to create a proprietary user interface or functionality create modules to perform calculations automate experiment routines and more You or an Ocean Optics application developer can easily customize SpectraSuite through Java code SpectraSuite is the platform for all future Ocean Optics application software development Current software applications including OOISensors and OOILIBS will be migrated to the SpectraSuite platform in the near future USB Spectrometer and Device Control SpectraSuite easily manages multiple USB spectrometers each with different acquisition parameters in multiple windows and provides graphical and numeric representation of spectra from ea
96. meter let you program a newer firmware if necessary 000 30000 020 02 0607 151 B Troubleshooting Possible Cause s Recommended Solution s Some of the menu and Some menu and toolbar items Acquisition parameters storing toolbar items are grayed require some action to be taken reference dark spectra and the Strip out inactive before they can be used Chart require an unambiguous selection of an acquisition If no acquisitions are running try starting one If more than one acquisition is started try clicking on the desired trend in the graph to select the correct target Similarly try expanding the tree under the icon of the spectrometer and see how the controls respond to selecting each item Right click these items or Control click in MacOSX to see additional actions for each Minus dark requires a dark spectrum to be stored A T R and relative irradiance require a reference and dark spectrum to be stored Absolute Irradiance mode I requires a calibration and a stored dark spectrum Photometry and energy power photons measurements require an active absolute irradiance calculation It took longer than The host computer requested opectraSuite discards the next spectrum it expected to get a some change in the spectrometer s acquires after making changes to acquisition spectrum on the graph acquisition parameters integration parameters This extra discarded stability time status of the
97. mmary vii documentation vili Documents 95 draw 46 Edit Menu 44 Edit Result Colors 84 electric dark correction 50 Exit 43 Experiments 40 105 Absolute Irradiance 129 Absorbance 108 Color 141 Concentration 113 Fluorescence 139 Irradiance 128 Preparing 105 Reflection 125 Relative Irradiance 137 Transmission 122 exporting data 81 155 Index features 2 File Menu Functions 21 Configure Export 40 Convert Spectra 42 Exit 43 Open 38 Dark 38 Experiment 40 Reference 38 Save 40 Dark 41 Reference 41 Save Spectrum 40 Stop Export 40 Store 41 Fluorescence measurement 21 22 32 33 Fluorescence Experiments 139 Functions Edit Menu 44 File Menu 21 Overlay Menu 65 Spectrometer Menu 57 spectroscopic 3 Gated Fluorescence measurement 21 32 graph controls 9 Graph Layer options 44 H high speed data acquisition 25 3 D chart 29 capturing data 25 using data 30 image 46 indicators 18 status 18 installation 5 Linux 7 Macintosh 7 via CD 5 156 via ftp 6 Windows 6 integration time 49 Irradiance Experiments 128 L lamp enable 50 layer tools 14 legend 48 Linux platform installation 7 M Macintosh platform installation 7 measurement absorbance 32 color 35 concentration 34 Curie fluorescence 22 33 gated fluorescence 21 32 new absolute irradiance 34 reflection 32 relative irradiance 32 transmission 32 memory toolbar
98. n SpectraSuite Acquisition This menu selection consists of options that control starting and stopping SpectraSuite s acquisition of spectral data If you have more than one acquisition running you must select the desired spectrometer in the Data Sources pane To do this click on the line under the spectrometer that lists the integration time scans to average and boxcar width Pause Acquisition Resume Acquisition These menu selections toggle to pause and restart data acquisition When you start the SpectraSuite application it comes up acquiring spectral data in Scope mode from the attached spectrometers If you are monitoring more than one spectrometer select the desired spectrometer in the Data Sources pane and choose either Spectrometer Acquisition Pause Acquisition to temporarily pause the acquisition Select Spectrometer Acquisition Resume Acquisition to resume the acquisition Terminate Acquisition To completely stop spectral acquisition on a spectrometer select the desired spectrometer in the Data Sources pane if you are monitoring more than one then select Spectrometer Acquisition Terminate Acquisition 000 30000 020 02 0607 57 6 Spectrometer Menu Functions Spectrometer Features This option provides access to additional functionality available with the attached OOI spectrometers You must select a spectrometer in the Data Sources pane to make this menu selection active To display the Features di
99. n a E Scans bo an Boxcar gt Strobsllamp Electric dak E time 3 Autor 3 Lir 20 y vackh 7 e Enable correction LI E Hi I E External na E lrigger mW Data Sources 4x T Zeite iradas i X e 4EDnaagma etfTHuaaasres HeS000 a Ss Aner Std Int tint Sra avg 21 boscar 5 a HaPre proces r Scope Mods Y Abecute rrsdisrce Er ai Drot ties LM MOS 3000 y d V E 1 d E if Ki Data Views 4x l ITI Abschte irrsdisnce II mei y 5 4 j 4 N i Ki box 10007 i NW Ki ke i Ce d i Za d vnm eee ee 200 3x 400 500 Bop HCH BOO WU 1000 LOO Wavelength crum New Absolute Irradiance Measurement The New Absolute Irradiance Measurement menu selection launches the Absolute Irradiance Wizard to facilitate taking an absolute irradiance measurement using SpectraSuite The wizard leads you through the steps necessary to take an absolute irradiance measurement 1 Selecting your source 2 Setting the data acquisition parameters 3 Taking a reference spectrum 4 Taking a dark spectrum 5 Calibrating the spectrometer See Absolute Irradiance for more information on taking an absolute irradiance measurement New Concentration Measurement th Concentration is the amount of a specified substance in a solution Graphs of absorbance vs concentration are known as Beer s Law plots These are prepared by measuring the light absorbed by a series of solutions with different known co
100. n and configuration instructions to get your system up and running In addition user interface for SpectraSuite is provided What s New in this Document This version of the SpectraSuite Spectrometer Operating Software Installation and Operation Manual adds the SeaChanger module Document Summary Chapter 1 ntroduction Provides an overview of the SpectraSuite operating software Chapter 2 nstallation Contains instructions for installing and configuring the SpectraSuite software Chapter 3 Controls and Indicators Illustrates options for customizing your graph view Also contains information for peak finding Chapter 4 File Menu Functions Contains descriptions of the functions on the File menu Chapter 6 Spectrometer Menu Functions Contains descriptions of the functions on the Spectrometer menu Chapter 7 Processing Menu Functions Contains descriptions of the functions on the Processing menu Chapter 8 Tools Menu Functions Discusses the selections available in the Tools menu Chapter 9 Window Menu Functions Contains information for the Window menu functions Chapter 10 Strip Charts Provides instructions for using the Strip Charts feature Chapter 5 View Menu Functions Contains a description of the functions on the View menu 000 20000 300 02 0607 vii About This Manual beer Virgi in Prolong Appendix A Experiment Tutorials Contains instructions for performing sample experiments using an Ocean Optics spectromet
101. nce A reference spectrum is a spectrum taken with the light source on and a blank in the sampling region Select File Open Load Reference Spectrum to select and load one or more reference spectra Processed Spectrum You have the ability to load a previously stored processed spectrum file Procedure 1 Select File Open Load Processed Spectrum from the menu 2 Type the file name or browse to the location of the desired processed spectrum file and open the file The Processed Spectrum icon appears in the Data Sources pane 38 000 20000 300 02 0607 a cean ptics Inc Firat in Photonics 5 View Menu Functions S6 Ocean Optics SpectraSuite File View Spectrometer Processing Tools Window Help Integration al Scans to al Boxcar a StrobesLamp Electric dark TA m SI ai ies time 100 miliseconds M average 1x width Oy Enable O correction O FA H v Ex ci Data Sources 4x CC Graph A x E Strip Chart B x 4 fv Int time 100ms avg 1 boxcar 0 Al I No Pre processor Scope Mode E 4 Result i E D e e Tv S ATRI kl amp Rs d d E mint time 100ms avg 1 boxcar 0 4000 E Simulated Acquisition 3000 4 Properties Processing Mode Intensity Samples Dark Spectrum Not Present Reference Spectrum Spectrometer CLIR2GOO013 Total Pixels 2048 Wavelengths 177 79 877 80 nm Intensity counts c e Len Data Views 40 Gr
102. ncentrations The length of the sample such as the path length of our cuvette holder and the wavelength chosen for monitoring the amount of light absorbed are constants A linear plot from taking scans of these standard solutions with known concentrations is then obtained The plot is then used to determine the unknown concentrations of substances in solutions 34 000 20000 300 02 0607 a cean ptics Inc TN Mirgi in Paton Color Measurement 5 View Menu Functions With SpectraSuite you can calculate and report the Color Rendering Index CRI and Correlated Color Temperature CCT for your samples SpectraSuite will compute all color measurements except RGB You can only perform color measurements on one spectrometer at a time Emissive color measurements Require a spectrometer which has been calibrated to take irradiance readings either relative or absolute SpectraSuite gives you the option of choosing to measure either emissive or reflective color from either absolute or relative irradiance Reflective color measurements Do not require an irradiance calibration but they do require a reference spectrum This reference scan is taken with the same optical configuration except a perfect reflector is placed at the same location as the samples Strip Chart SpectraSuite allows you to use Strip Charts to track processes perform kinetic analyses and monitor spectral events all as a function of time The Strip Chart shows y
103. ng The following table lists common problems and their possible solutions Problem Possible Cause s Recommended Solution s SpectraSuite starts but does 1 The spectrometer is not 1 Plug one end of the USB cable into the not show my spectrometer plugged into the computer spectrometer and the other end into the USB port of your computer 2 The attached spectrometer is 2 See USB Spectrometer and Device not supported by SpectraSuite Control for a list of spectrometers supported by SpectraSuite 3 The device is not detected or 3 Disconnect any lamps or plug ins that identified may be attached to the spectrometer disconnect and reconnect the spectrometer wait 10 seconds and try again If the spectrometer is detected repeat with the lamp or plug in connected This may indicate a problem with an attached device Under Windows and Linux it is also possible that the spectrometer model may be newer than the driver file that informs the operating system about the spectrometer The SpectraSuite update center does not yet update these system files so it may be necessary to reinstall with the latest SpectraSuite installer to get the correct files SpectraSuite s splash window The USB2000 Spectrometer Use the USB Programmer and verify that opens but never finishes has firmware older than 2 41 0 the USB2000 has firmware version 2 41 0 loading when attached to a or newer The USB Programmer will also USB2000 Spectro
104. ng tab delimited ASCII for Excel or other analysis packages Grams SPC and JCAMP Additionally Spectra Suite offers a database module where arbitrary data can be stored in any user selectable format Another benefit of the software s binary data tracking function is that it offers a user process do overs A user can change the values of various parameters in a process and apply those changes to data without having to recreate an entire process Fully Internationalized All of the software s menus dialog boxes prompts messages and files will be able to reflect a native language by simply changing a single file Modules that support Japanese Chinese Korean and Spanish will be available in the near future followed by French German and Italian Spectroscopic Functions SpectraSuite allows you to perform the three basic spectroscopic experiments absorbance reflectance and emission as well as signal processing functions such as electrical dark signal correction stray light correction boxcar pixel smoothing and signal averaging Scope mode the spectrometer operating mode in which raw data signal is acquired by the detector allows you to establish these signal conditioning parameters The basic concept for the software is that real time display of data allows users to evaluate the effectiveness of their experimental setups and data processing selections make changes to these parameters instantly see the effects and save the data
105. nnen nennen nena nnn nnns n naar nnn nnns 60 mic Ne 64 FRC MNO VS DOCU MNT m 64 STEE 64 Chapter 7 Processing Menu Functions 65 e 65 Sor M 65 FGI GONG SOUS ERN QR m 65 micare SING RN mem 65 Remove Preprocessor TE 65 Table of Contents p Nonuniiy COM SCHON EE 66 Adad Reference Re te EE 66 tele 018 1 0 6 EE 67 SCODE 68 CONS IMIS ON dee PH 69 leeden e 69 Buca r 70 SSC Ul OM NR 70 Erd 6 E re 70 EE 71 Absolute ele VE alte TT T 71 Eege 71 league 71 COETIR E 72 EH el pene neem mee ne ene ene ne ee ne ee ene ee eee eee 73 Combine Calibration Files EE 73 New Energy Power Photons cccccsecccceececeesceceeeeeceeeceaeeeceaseeseeessaueessaeeessueessgeeessgeessageeess 74 New Photometry Ieasureligll RE 71 FNS MIS m 80 Set Color Temperature 80 Exp ring Frocessed d Da WEE 81 oerbaser TEE e in E 84 Edit Result Colors ee 84 Chapter 8 Tools Menu Functions eee 87 E TE 87 ee E 87 STAG ACAI SIO SC UNM E 88 Template MANAG CF E 88 Module Manager enne nnne nnns ann nnne nnn nn nnn ses snis a nnne nnns 88 upade AT 89 Chapter 9 Window Menu Function
106. not turn off the light source when taking a dark spectrum If you must turn off your light source to store a dark spectrum allow enough time for the lamp to warm up again before continuing your experiment After the lamp warms up again store a new reference Put the sample in place and ensure that the light path is clear Then click Finish If you have already taken one or more absorbance measurements a dialog box appears asking you to specify whether to display the new data in a new graph or on the existing graph 000 20000 300 02 0607 i cean tics In rii Firat in Pii Shon a B Troubleshooting Show data in existing tab Tab a AXIS Y Axis raph EJ wavelength Absorbance Note the following changes on the screen e The experiment mode listed in the Data Sources and Data Views panes changes to Absorbance Mode e The units listed on the Graph pane changes to Absorbance OD 10 To permanently save the spectrum to disk click the Save Spectra VW icon on the toolbar Note If you change any sampling variable integration time averaging smoothing fiber size etc you must store a new reference and dark spectrum Concentration Experiments To discover the unknown concentration of a substance in a solution you must first take spectral scans of a series of solutions with different known concentrations of the same substance You begin this process by taking an absorbance spectrum of the solution with the h
107. ntaining the downloaded files 000 20000 300 02 0607 89 fA cean P 1 Dtics inc 8 Tools Menu Functions i First in Photonics Procedure To download SpectraSuite updates 1 Select Tools Update Center The Update Center Wizard appears Be Update Center Wizard Select Location of Modules Select Update Center s bo connect Update Canter v SpectraSuke Beta Update Center GEI pradtraSua pida Contes To imtiste connection bo the Update Center server dick Next C3 Install Manually Downloaded Modules men Files 2 Click to connect to the update center The second Update Center Wizard screen appears 90 000 20000 300 02 0607 9 Tools Menu Functions Eg Select Modules to Install Avalable Updates and Neve Modules mo spetasute Update Center Digtal Signatures E came 0 Weu Cerbficates ared Install DR SpectraSube Libraries Modules DE coetrasoke 3 Absolute Irradiance Ek d SoectraSute Absolute Trradonce 3 C wp ert o SoectraSute Srip Chat OC CobrMeasurement Dg SpectraSute Color Measurement w Select Modules te Install 3 Download Modules and Check 3 Click to move the all files modules to the Include in Install pane Or Highlight the desired core files and or modules to update and click S to move the selected files modules to the Include in Install pane When you highlight a module or file the size and modification date appear in the lower pane Applicable version levels appear in th
108. nts eun 300 400 500 600 Wavelength nm Source LISB2G6142 Wavelength inm 875 02 sj 3699 34 116 00 Progress Bar tb usg2c6142 10000 msec 20 000 20000 300 02 0607 Chapter 4 File Menu Functions Overview This chapter details the various options and functions available from the File menu in SpectraSuite Where applicable each section contains the associated toolbar icon below the section heading Click on these icons in SpectraSuite to perform the described function New The New menu selection displays the following list of functions that also are available from the Data Display toolbar Spectrum Graph Spectrum Table High Speed Acquisition Absorbance Measurement Transmission Measurement Reflection Measurement Relative Irradiance Measurement Gated Fluorescence Measurement Curie Fluorescence Measurement Gated Fluorescence Measurement amp The New Gated Fluorescence Measurement menu selection is activated when you are using a spectrometer with a gated detector such as the USB2000 FLG When you select this menu item a wizard leads you through the steps necessary to take a gated fluorescence measurement 1 Selecting your source 2 Setting the data acquisition parameters 3 Taking a reference spectrum 000 30000 020 02 0607 21 5 View Menu Functions 4 Taking a dark spectrum 5 Setting your gated delay See Fluorescence for more information on taking a fluorescence measurement Curie Fl
109. o Fill Window This control adjusts the graph display so that the section of the graph relevant to the spectrum line is shown but no more Both the x and y axis are adjusted In this example the graph is zoomed in so that the Y axis Intensity above 3500 no longer appears since the graph line does not extend that far 10 000 20000 300 02 0607 cean ptics Inc Fin in haragcx i ics 3 Controls and Indicators E Graph 4 x e HOQAQQQqae tt SHATRI USnaea 3000 N D Kat e Intensity counts 1000 200 300 400 500 600 700 800 Wavelength nm Source US82G6142 v Wavelength 440 05 4 654 32 AS Scale Graph Height to Fill Window Use this control to zoom in on a graph so that the full height of the spectrum line is shown but no more Unlike the Scale Graph to Fill Window control only the y axis is adjusted Manually Set Numeric Ranges This control enables you to set the exact zoom coordinates When you click on the control the Set Zoom Ranges dialog box appears so that you can enter the desired coordinates Set Zoom Ranges amp Axis Range Minimum 178 32 Maximum Y Axis Range Minimum Maximum e Zoom In Use this control to zoom in on the graph Each time you click this control the display zooms in further 000 20000 300 02 0607 11 Firsf mf otons 3 Controls and Indicators Been mete re rE T e Ee ee 4ATRI Hgaguae2 t S4ATRI H 539 kB D
110. ol enables you to adjust the SeaChanger Color Engine s connected to a CDS LanBox LCE via Ethernet cable You must have a Red Tide USB650 spectrometer with an attached light source to use this SpectraSuite function Procedure 1 Click the SeaChanger control in the toolbar The Choose DMX Source dialog box appears 000 20000 300 02 0607 51 5 View Menu Functions 52 e Choose DMX Source Eg Select None or LanBox DMX for your source then click Accept If you selected None go on to Step 3 a b required information for the Ethernet connection to the LanBox LCE Ze SeaChanger DMX Login Eg Enter information for LanBox DMM interface IP Address 132 168 51 23 Part PPS Base DMM Address d Connect Cancel A graph appears with a message that the lamp is warming up f Ocean Optics SpectraSuite Fie View Spectrometer Processmg Took window Help x Integration Stans to Ke time average Noniinearty P Ciena Forna correction bigger ech dark correction DATUE LECI IA 46 705 2 imeroseen SmbejLamp c oe 7 9uray Ughk Lech Seschanger Console X GahF x Y SHATRI Waka Property Scarce Cerserver D ereved Vve Mode E ABA E e en AU ege dA heres chi a SILT lenin jeni n3 CR 84 RIES CRI RG KRIE ICRIR lena Aa toaa amp 4 SeaChanger W E Waring for lamp to warm up s bb A ptics Inc Eet in Giotoeog If you sel
111. ollection icon in the Data Views pane and select Remove Spectra See High Speed Acquisition for more information Show Devices This feature allows you to redisplay the Data Sources and Data Views panes if they have been closed 64 000 20000 300 02 0607 Chapter 7 Processing Menu Functions Overview This section provides information on the various signal processing functions available under the Processing menu selection Color Edit Color Settings This menu item allows you to make changes to the color settings for color measurements Pre processing Preprocessing functions currently include the following Nonunity correction Add Reference Monitor You can also remove the preprocessing function Remove Preprocessor Select Processing Pre processing Remove Preprocessor to remove the nonunity correction preprocessing function 000 30000 020 02 0607 65 7 Processing Menu Functions Nonunity Correction Select Processing Pre processing Non unity correction for reflection experiments if you need to perform a calculation to compensate for a reflection standard that is not perfectly white You can also access this function with the icon in the Preprocessing toolbar Add Reference Monitor Select Processing Pre processing Add Reference Monitor to adjust the signal to compensate for variations in spectral intensity based on light source and system drift The reference spectrum for the reference acqu
112. ormation Absorbance Select Processing Processing Mode Absorbance to switch the current window into Absorbance mode You can also click A in the graph s toolbar You must first store reference and dark spectra in Scope mode before you can access Absorbance mode SpectraSuite uses an equation to determine the concentration of a species in solution illustrated below The software uses this equation to evaluate each pixel on the detector and produce the absorbance spectrum S D A lo aa A gio R D Where S Sample intensity at wavelength A D Dark intensity at wavelength A R Reference intensity at wavelength A The concentration of a species in a solution directly affects the absorbance of the solution This relationship known as Beer s Law is expressed as A 4 c Where A Absorbance at wavelength A Extinction coefficient of the absorbing species at wavelength A c Concentration of the absorbing species and es the optical path length of the absorption See Experiment Tutorials for information on conducting an experiment in Absorbance mode 000 20000 300 02 0607 69 7 Processing Menu Functions Transmission Select Processing Processing Mode Transmission to switch the current window into Transmission mode You can also click in the graph s toolbar This is also the spectral processing mode used for reflection spectroscopy as the math necessary to compute reflection is ident
113. ou how the value that you selected appears over time This value can be any of the following One pixel a single wavelength The average of a range of pixels An integral calculated by one of three methods representing the area beneath the graph s trend line You can acquire this data using any processing mode transmission absorbance etc Procedure Place SpectraSuite in Scope mode by clicking the Scope icon in the Experiment mode toolbar or selecting Processing Processing Mode Scope from the menu 2 Store a reference spectra and dark spectra 3 Choose the measurement mode absorbance transmission etc 4 Click the Strip Chart button Ex OR Select File New Strip Chart from the menu The Chart Trend Settings dialog box opens 000 20000 300 02 0607 35 5 View Menu Functions Ss Chart Trend Settings Wavelength Selection Spectrometers Spectrum Type D iHR2B1231 Processed One wavelength 188 80 nm O Average from 5550 to ia8s0 Jm Display Options C5 Integrate over agen Trend Line Color m Select Color ta agen zl nm Scale Trend value Minimum delay between updates ms 5 Enter the following data to create your Strip Chart Wavelength Selection Select the type of data for which you want to view the time trend Select from the following One wavelength For one pixel used in fluorescence for example Select the wavelength Average from
114. ow Help Integration Scans to Boxcar Strobe Lam Electric time averane width J n Fnahle dark 41 Nonlinearity Stray Light External T ei fi wi al im tice i trigger Data Sources 4 x mm Graph 4 X HOQQQate f SHATRI Makaa USB4000 USB4000 Data Views Graph A Intensity counts 300 600 Wavelength nm Update Available WWZ3 5 5 A software update is available to be downloaded Go to Tools Update center 000 20000 300 02 0607 19 3 Controls and Indicators iin ae Progress Bar If an acquisition takes longer than one second a progress bar appears at the bottom of the screen A progress bar can appear for each connected spectrometer that is acquiring data Be Ocean Optics SpectraSuite File View Spectrometer Processing Tools Window Help Integration ore Scans to a Boxcar Strobe Lamp Electric dark time CH average width 3 E Enable correction Nonlinearity Stray Light External In Ir zl Mormal v correction a correction a trigger Graph 6 Graphic x 4 HI Deeg ah gi SP ATRI Harada Data Sources AD x US62000 2 Acquisition Int time 100ms avg 1 E Int time 15 avg 10 b No Pre processor E Result Graph C Int time 100ms avg 1 No Pre processor E Result Mm mesnkh ch ae gt Data Views Graph E Graph C Intensity cou
115. p chart you created appears Note the time scale along the x axis The y axis in this example shows the percentage transmission for the selected pixel s 10 To add another trend to this graph click Add Trend S6 Ocean Optics SpectraSuite File View Spectrometer Processing Tools Window Help Integration es Scans to a Boxcar Strobe Lamp Electric dark pm E time Ge E average width Enable correction HI 1 External VC J trigger es Data Sources ax Li Graph A x Eg Strip Chart C x 4 rw i i m x EJ D o o t NM Coporep I Q cea E HD 2000 110 4 Acquisition S Int time 3ms avg 20 boxcar 4 100 No Pre processor Transmission Mode amp j Graph A amp Wavelength 500 27 nm E 90 Properties 80 70 60 Data Views x amp Lad Graph 4 amp Eu Strip Chart C 5 Transmission 56 40 3 20 enken Ken tember Alen OO IS enke kene Der alem Amber Lens Her Aketak dats Alt le Ek een Abee Time 000 20000 300 02 0607 103 10 Strip Charts E Tea Saving Strip Chart Data Note See Creating Strip Charts for information on autosaving gt Procedure To save strip chart data 1 From the Strip Chart graph click WM The Save Trend dialog box appears EA Save Trend Wavelength rm Mode 178 32 value 1 EES 178 32 Wie QD Filename Browse 2 Selec
116. ple acquisition 5 Click on the sample acquisition graph Or In the Data Sources pane select the processing node for the sample acquisition No pre processor etc The reference monitoring action should enable 66 000 20000 300 02 0607 Fast in PYaforeces a cean r ptics In T Processing Menu Functions 6 Click Or Select Processing Preprocessing Add Reference Monitor The Configure Reference Monitoring dialog box appears Be Configure Reference Monitoring Reference Channel Reference Type Processing 0 5BzG5142 Ma Pre pracessor Scope Mode All wavelengths 1 USB263387 No Pre processor Scope Mode C2 Single wavelength DZ C Integrated intensity Processors only appear in this table if they have a dark and reference spectrum stored and if they are different fram the processor far which From oa reference monitoring is being configured ta olg m Cancel 7 Select the desired reference channel 8 Select the Reference Type as follows Requires a minimum of two spectrometer channels in your system both configured for overlapping wavelength ranges Corrects for both uniform and nonuniform drift All wavelengths oingle wavelength Use this selection for pixel by pixel drift correction Integrated intensity Use this selection if the lamp is going to drift uniformly 9 Click Accept Processing Mode Processing mode functions include all of the modes necessary to conduc
117. ppears for the spectral line on Graph B Ge Ocean Optics SpectraSuite File View Spectrometer Processing Tools Window Help Integration il Scans to Boxcar Strobe Lamp Electric dark time average width Enable correction Nonlinearity Stray Light External a iI gt correction correction trigger Data Sources a x Graph B x ml Graph C EIA S ATRI H md d USB2000 Acquisition Int time 100ms avg 1 Int time 16ms avg 1C Int time 100ms avg 1 Properties Serial Number USB2G6 Firmware LISB2000 2 4 Total Pixels 2048 Wavelengths 178 3 8 Copien wie lt gt v Data Views 4 x Graph B Graph C Intensity counts ee 200 300 400 500 600 Wavelength nm v Wavelength nm 467 31 721 87 4011 00 Recent acquisition within normal ranges Saturated signal Acquisition is paused Source USB2G6142 Status Indicators Each circle corresponds to a graphed spectrum If you pass the arrow pointer over a circle it displays the spectrometer to which it refers and the related settings e g USB2G6142 Int time 20 ms avg 10 boxcar 3 Click on a circle to select its associated spectrometer 18 000 20000 300 02 0607 a cean ptics Inc Mirgi in Prolong Update Available 3 Controls and Indicators Ge Ocean Optics SpectraSuite File View Spectrometer Processing Tools Wind
118. rea and enter the value e If you are using a bare fiber or a cosine corrector check Fiber Diameter and enter the value f If you are using an Ocean Optics cosine corrector or a direct attach cosine corrector enter the appropriate value for the Fiber Diameter as follows Cosine Corrector Fiber Diameter CC 3 UV 3900 microns CC 3 DA 7140 microns g Then click Net The Set Acquisition Parameters screen appears 000 20000 300 02 0607 133 A Experiment Tutorials 134 Ce Absolute Irradiance Setup Integration Time Integration Hs he gt niliseconds v Strobe Lamp Enable d Last peak value EE 3352 70 Recommended peak value 3480 00 Set Automatically Advanced Settings Turn on the light source and set the integration time so that the peak value reaches the recommended level Set Acquisition Parameters wizard Absolute Irradiance Setup Wizard Smoothing Scans to average Boxcar width Preview 4000 3000 2000 1000 200 600 1000 Wavelength nm Help Set your acquisition parameters for your experiment using the Integration time and Boxcar width so that the Last peak value is very close to the Recommended peak value Then click Hetz The Dark Spectrum screen appears Ce Absolute Irradiance Setup Strobe Lamp o 160 Enable 120 80 40 0 0 mStore Dark Spectrum Dark Spectrum Preview
119. rmation for each spectrometer listed in this pane consists of the following Acquisition parameters that you set via the integration time scans to average boxcar smoothing Whether reference and or dark spectra have been stored the graph A B C etc associated with this spectrometer that appears in the right pane important if you have installed more than one spectrometer Spectrometer s properties Serial number firmware level number of pixels and wavelengths 000 30000 020 02 0607 105 i cean g k PEICS inc A Experiment Tutorials eee 4 Ucean Optics Speciresute Fie Yew pairalin Procemng Took Wincor Hap Acquisition Die geng er wi Dog p5 Bene ar SmbeRare C Heda a Ire CH ront Erabi Care toolbar End kee 3 bur Dota Sero LN som EDARRA P SAATI DAAA AMA SONCES Experiment mode Anguiehioni TET tane b Ink Grea L ag merece D x I A Mo grec pa Icons TERM rec Fires LECT 7 81 3 Toad Praia 2043 Weteng 178 2 828 2 nim Doc Dust Versa x H x LL mach in P Data Views pane T ES Trace graph W o keggt ed Once you install the hardware and software and establish your sampling system you are ready to take measurements This section details the following types of experiments Absorbance Experiments Concentration Experiments Transmission Experiments Reflection Experiments Irradiance Experiments Fluorescence The type of measurement you will take determin
120. s sse 95 REES 95 close All Reie MI m 95 Wie eU E 95 KEIER 96 Maximize Restore WINGOW EEN 96 iv 000 20000 300 02 0607 a cean ptics Inc First in Pralong CT E 96 Chapter 10 Strip e un CC 99 Sg E 99 Credung Sp ale eege EE 99 Saving Strip Chart BI uz NP 104 EE OT eee eee 104 Appendix A Experiment Tutorials 105 elu UH 105 Preparing Tor EXO TIMIS BT a ANE EANET M 105 APIC ATION UNOS rE E E R E E E E EE E E ERE 107 Taking Reference and Dark Gpecha nnne nnns 107 AD SODANO egen E EE 108 Concentration Experiments lessen eene 113 Transmission Experiments eeessseesssseseeeee eee nennen nennen nnne nnne nnn nnne rna nnns 122 MSC UO ME el T UU T ITI UIT 125 maaa CEE POENE NE Ee 128 Absol te Itt ACN ne 129 Re lativ le Tel ipe EE EDS 137 PUOSC e 139 elle tegen D CC 141 Color Measurement Screen Controls nnne nnns n anna 150 Appendix B Troubleshooting 151 l 155 000 20000 300 02 0607 Table of Contents Table of Contents vi 000 20000 300 02 0607 About This Manual Document Purpose and Intended Audience This document provides you with an installatio
121. s and you must work through the various steps required for an Absolute Irradiance measurement on your own The following procedure assumes that you are using the Absolute Irradiance Wizard 000 20000 300 02 0607 129 Xy cean d ptics Inc Fret in PYatornice A Experiment Tutorials Procedure Perform the following steps to take an absolute irradiance measurement using SpectraSuite 1 Select File New Absolute Irradiance Measurement from the menu or click on the Irradiance toolbar to use the wizard to create the Absolute Irradiance graph Ee Ocean Optics SpectraSuite File view Spectrometer Processing Tools Window Help Integration Scans to Boxcar 5 Strobe Lamp o Electric dark o T b E bos 16 gt mitseconds he time o average width Enable correction 4 Nonlinearity Stray Light External Moral In gt n gt 2x correction Fu O trigger a e Absolute Data Sources ax pm Graph A X Irradiance Button H Dee oe A f SPATRI Negi EY HR2000 4000 3000 w i S 52000 2 pu amp 1000 Data Views ax amp Graph A 0 200 300 400 500 600 700 800 900 1000 Wavelength nm The first page of the Absolute Irradiance Setup Wizard appears 130 000 20000 300 02 0607 B Troubleshooting S amp Absolute Irradiance Setup wizard Absolute Irradiance Setup Wizard Select data source For absolute irr
122. s screen to view the raw data coming from the chip Raman exposure image if your spectral graph looks incorrect The bottom of this screen displays the actual CCD image a 2 dimensional image of the detector Each light stripe is a spectral line The vertical white lines correspond to peaks 60 000 20000 300 02 0607 6 Spectrometer Menu Functions Save Raw Image Processed Image Standard controls to zoom nfout Zoom Standard controls to zoom in out Ss MMS Raman Features Current Laser Current Laser Laser Wavelength Laser Wavelength 784 0 nm Save Co Spectrometer Apply Laser Properties Number of supported lasers 1 Default Laser Use this screen to enter specific information for the laser being used 000 20000 300 02 0607 61 a cean ptics Inc Mirgi in Prolong 6 Spectrometer Menu Functions Sg MMS Raman Features Raman Exposure Image Laser Wavelength Calibration Value 799 7403930 Term Intercept 1st Coefficient 2nd Coefficient 3rd Coefficient Save Co Spectrometer Se MMS Raman Features Raman Exposure Image Laser Wavelength Save Calibration Save to Directory 000000 s Load Calibration Use this screen to save or load calibration files 62 000 20000 300 02 0607 E MMS Raman Features Raman Exposure Image Laser Wavelength Calibration i Firmware i CCD Temperature CCD Shutter errr eee OSF Firmware DSF Firmware Vers
123. sion applications include measuring light through solutions optical filters optical coatings and other optical elements such as lenses and fibers Procedure Perform the following steps to take a transmission measurement using SpectraSuite Place SpectraSuite in Scope mode by clicking the Scope 5 icon in the Experiment mode toolbar or selecting Processing Processing Mode Scope from the menu 2 Ensure that the entire signal is on scale The intensity of the reference signal s peak differs depending on the device being used If necessary adjust the integration time until the intensity is appropriate for your device 3 Ifyou have not already done so place a sample of the solvent into a cuvette and take a reference spectrum You must take a reference spectrum before measuring transmission 000 20000 300 02 0607 123 A Experiment Tutorials Note Do not put the sample itself in the path when taking a reference spectrum only the solvent Click the Store Reference Spectrum Y icon on the toolbar or by select File Store Store Reference Spectrum from the menu bar to store the reference This command merely stores a reference spectrum in memory You must click the Save Spectra icon on the toolbar to permanently save the reference spectrum to disk 4 Ifyou have not already done so store a dark spectrum reading To do this either block the light path to the spectrometer uncheck the Strobe Lamp Enab
124. t Settings E 25 SpectraSuite Settings Default Acquisition Parameters Template Manager Future enhancement Module Manager D Electric Dark Correction EI External Trigger Mode Normal free running Integration Time usec 100000 Mon linearitv Correction Save Last Acquisition Parameters Scans to Average Stray Light Correction Strobe Enable Default Acquisition Parameters The Module Manager displays a list of installed SpectraSuite modules You can select modules to uninstall and or update 88 000 20000 300 02 0607 a cean k ptics In D irgi in horn 9 Tools Menu Functions Sz Module Manager Installed Modules Modules Active version uninstal E ei Infrastructure i TI Uninstall E c Ocean Optics E c Bridges E c Libraries Description Update Center The Update Center contains a link to allow you to connect to Ocean Optic s site to download updated SpectraSuite modules To download upgrades to SpectraSuite you must sign up for a yearly subscription SpectraSuite U Bug fixes are provides free to all SpectraSuite customers Note If the installation computer is not connected to the Internet download the update files on another computer and copy them to the installation computer using a USB flash drive or CD Extract the files to a convenient location then from within the Update Center wizard select Install Manually Downloaded Modules nbm Files and browse to the directory co
125. t Setup wizard screen appears Ge Color Measurement Setup wizard 1 of 4 Dara Preview 178 32 875 1 9nm Select one spectral source from the table above 3 Highlight the desired spectral source to select it Then click Next gt The second Color Measurement Setup wizard screen appears 142 000 20000 300 02 0607 Fest in PYatorict a cean i ptics Inc Be Color Measurement Setup Integration Time wizard 7 of 4 Integration milliseconds time Strobe Lamp Enable LI Last peak value 3363 8 Recommended peak value 3480 Set Automatically Advanced Settings Turn on the light source and set the integration time sa that the peak value reaches the recommended level B Troubleshooting 4 r5maathing Scans to average Boxcar width Preview 4000 3000 2000 1000 U e00 400 600 Wavelength mm 4 Turn on your light source Adjust the Integration time Scans to average and Boxcar width so that the Last peak value is within the proper range near the Recommended peak value When this happens the Last peak value reading changes from pink to black Then click Net The third Color Measurement Setup wizard screen appears 000 20000 300 02 0607 143 A Experiment Tutorials Be Color Measurement Setup wizard 3 of 4 Store Reference Spectr Referen
126. t experiments These modes are also available from the toolbar above the graph See Experiment Tutorials for more information about how to conduct experiments using the processing modes 000 20000 300 02 0607 67 7 Processing Menu Functions Scope Select Processing Processing Mode Scope to switch the current spectral window into Scope mode You can also click in the graph s toolbar 68 000 20000 300 02 0607 cean e ptics Inc Fret in Phalonia e e 7 Processing Menu Functions The signal graphed in Scope mode is the raw voltage coming out of the A D converter This spectral view mode provides complete control of signal processing functions before taking absorbance transmission reflection and relative irradiance measurements This mode reflects the intensity of the light source the reflectivity of the grating and mirrors in the spectrometer the transmission efficiency of the fibers the response of the detector and the spectral characteristics of the sample Use Scope mode when configuring your setup adjusting the integration time and taking a reference and a dark scan Scope Minus Dark Select Processing Processing Mode Scope Minus Dark to switch the current spectral window into Scope mode and subtract the stored dark spectra from each spectrometer channel before SpectraSuite displays it You can also click in the graph s toolbar See the description of Scope mode Scope for more inf
127. t the trend to save and enter a file name Then click save Strip Chart Controls Use the following controls to adjust the display of your strip chart Resumes any strip chart trends you have paused Pauses all strip chart trends Restarts any strip chart trends with a fixed length or duration see Creating Strip Charts Clears all strip chart trends Automatically scrolls the strip chart graph to the newest data 104 000 20000 300 02 0607 Appendix A Experiment Tutorials Overview The following sections contain information on conducting sample experiments using a USB2000 Spectrometer and SpectraSuite For information on experiments with Ocean Optics spectrometers other than the USB2000 consult the operating instructions for your particular spectrometer model Preparing for Experiments Verify that you have correctly installed SpectraSuite installed the spectrometer and configured the light source and other sampling optics If you followed the previous steps and started SpectraSuite the spectrometer is already acquiring data in Scope mode Even with no light in the spectrometer SpectraSuite should display a dynamic trace in the bottom of the graph window If you allow light into the spectrometer the graph trace should rise with increasing light intensity This indicates that you correctly installed the software and hardware Note the spectrometer s that you have installed are listed in the Data Sources pane Info
128. th Selection One wavelength aam i nim W Update Rate Display Options Auta Save Enable Trend Auto Save Average from 178 32 Si Save Co Directory DS ta 178 32 nim Padding Digits 5is Method Rectangular wi 7 32 Clm Auto Save Enable Trend Auto Save Enables the auto save option Save to Directory Enter the directory where you want to save the files Base Filename Enter the filename to be used Padding Digits Enter the number of digits to be used when appending to a file enter 3 to save hundreds of files enter 4 to save thousands etc up to 15 for example spectrumfile001 through spectrumfile999 if 3 is selected Preview For future use Save after every Enter the time interval for the save If set to 0 every scan is saved Clear Trend from Memory After Flushes the data from memory after each autosave to Save conserve memory usage 8 Click Accept The Strip Chart Options dialog box appears Strip Chart Options lists all of the Strip Charts that you have created along with the options that you have set for each one Use this dialog box to add edit remove or clear trends Note Highlight the desired trend to make the Clear Remove Trend and Edit Trend buttons active 102 000 20000 300 02 0607 Fast in PYafoarnice a cean ptics Inc 10 Strip Charts Ge Strip Chart Options Wavelength nm Mode Offset Ak TS 2 1 YS Se T al DU USB2G6142 178 32 vue 9 Click dese J The stri
129. ting Processing Processing Mode Scope from the menu 2 Store a reference spectrum and a dark spectrum 3 Choose the measurement mode absorbance transmission etc 4 Click the Strip Chart button OR Select File New Strip Chart from the menu The Chart Trend Settings dialog box opens with the Update Rate tab shown 000 30000 020 02 0607 99 10 Strip Charts 100 Ss Chart Trend Settings Source Spectrometers Spectrum Type D USb2G6142 Processed Update Rate Display Options Auto Save Update after every scan Range Selection O Update after every 100 scans One Wavelength 178 32 2 nm 5 Between updates wait at least Lack zen EE C5 Update with the first available scan every to ona nm ss sec v Q Integrate ONSE 178 32 a inte v io i amp 32 glam Pause until started by user NEE Rectangular v Stop after this many scans moi Compute Derivative Stop after this amount of time Ei Select the source of the Strip Chart Update Rate tab Updates the strip chart Update after every scan After every scan Update after every x scans After the number of scans selected Between updates wait at least After the interval selected between updates Update with the first scan every After the first scan then at the interval selected Start at the beginning of the next At the beginning of each new selected interval Range Selection Select the type of data for
130. tion parameters for each curve are listed in the Data Sources pane 50 000 20000 300 02 0607 ae pestle Paeonia 5 View Menu Functions Spectrum Table Displays the data acquisition in a table format A tab for the table appears at the top pf the graph pane See Spectrum Table for more information Absolute Irradiance Graph Displays a graph of absolute irradiance data This graph appears on its own page with a tab at the top of the graph pane It is also listed in the Data Views section Color Measurement Launches the Color Measurement wizard See Color Measurement for more information Strip Chart Allows you to track processes perform kinetic analyses and monitor spectral events all as a function of time See Strip Charts for more information Memory The Memory toolbar consists of a display of the memory being used by the SpectraSuite application 7 1 22 6MB l E l Click this icon to force SpectraSuite to clean unneeded data from memory The Memory toolbar only appears when you select it with View Toolbars Memory it is absent from the screen by default Preprocessing The Preprocessing toolbar contains icons for the following functions Nonunity correction Performs a calculation to compensate for a reflection standard that is not perfectly white Add Reference Monitor Adjusts the signal to compensate for variations in spectral intensity based on light source and system drift SeaChanger This contr
131. u options displays the Save Spectrum dialog box Use this box to configure how you want to save your spectra After you set the options and click Accept choosing File Save Save Spectrum or typing CTRL S exports the spectrum according to your settings in this dialog box To change these settings select File Save Configure Export To cancel the export of the spectra select File Save Stop Export 40 000 20000 300 02 0607 a cean ptics Inc First ars Protons 5 View Menu Functions Sd Save Spectrum Spectrum Source Processing 0 USb266142 No Pre processor Subtract Dark Spec 1 USB2G3387 Mo Pre pracessor Scope Mode Save Options File Options Save every scan Save after every moo scans O Between saved scans wait at least sol v File Type QOI Binary Format k 2 Save the first available scan every Save to Directory EE m inue v Padding Digits h Pause until started by user SE aaa Stop after this many scans 1004 Stop after this amount of time 00 s fmsec After setting Up a valid save configuration clicking CTRL S or File Saye Save Spectrum again will Start restart or repeat the export as configured above To change the configuration choose File Save gt Configure Export To cancel the export choose File Save Stop Export Cancel Store Use this menu selection to store reference and dark spectra before running
132. um The Dark Spectrum screen appears S amp Absolute Irradiance Setup Store Dark Spectrum wizard Absolute Irradiance Setup Wizard Store Dark Spectrum Dark Spectrum Preview Strobe Lamp 160 Enable 12n DU 400 300 Wavelength nim Load Dark Spectrum From File Spectrum File Mew dark spectrum stored d Block the light path or uncheck the Strobe Lamp Enable box then click to take a dark spectrum The graph appears on the right side of the screen Click Next gt The Lamp File wizard screen appears Be Absolute Irradiance Setup Lamp File wizard Absolute Irradiance Setup Wizard fern Fie 110306 VIS FIE LMP Lamp Intensity Preview Wavelength mm Intensity uien z inmi 300 0 2142E z Sa james Sau Lige O Lamp calibration loaded Value Cie PAPAE RIPACTETICICT cun cikurceuri Rep 400 an Wavelength tmm e 136 000 20000 300 02 0607 D a cean ptics Inc H IST m oons B Troubleshooting e Enter the name of the lamp file or browse to the desired file to use The final screen of the calibration wizard appears Note in the Spectrometer Calibration Preview that the lamp file curve in yellow is overlayed on the spectrometer s curve red Once you apply this calibration the curves should be exactly the same Be Absolute Irradiance Setup Final Calbration wizard Absolute Irradiance Setup Wizard Collection Area d LIsing Integrating Sphere
133. unambiguous selection of an acquisition If no acquisitions are running try starting one If more than one acquisition is started try clicking on the desired trend in the graph to select the correct target Similarly try expanding the tree under the icon of the spectrometer and see how the controls respond to selecting each item Right click these items or Control click in MacOS X to see additional actions for each Minus dark requires a dark spectrum to be stored A T R and I relative irradiance require a dark and reference to be stored Absolute Irradiance mode I requires a calibration and a stored dark spectrum Photometry and energy power photons measurements require an active absolute irradiance calculation Graph Controls The heart of the SpectraSuite application is the spectrum graph SpectraSuite provides you with a wide variety of options to customize and monitor your graph views Controls are organized into the following toolbars that can be displayed or hidden using the Down Arrow button T 000 30000 020 02 0607 9 3 Controls and Indicators be Zoom Tools Zoom Out to Maximum This control zooms out to display a full view of the spectrum graph HETAQAAHt PY SPATRI WH amp mag 4000 3000 2000 Intensity counts 1000 200 300 400 500 600 700 300 Wavelength nm Source USB2G6142 Wavelength 856 70 4 Wij 517 90 ANS HI Scale Graph t
134. uorescence Measurement amp The New Curie Fluorescence Measurement menu selection is activated when you are using a Curie UV VIS Emission Spectrofluorometer serial number starts with CUR Note The Curie UV VIS Emission Spectrofluorometer is a discontinued product When you select this menu item a wizard leads you through the steps necessary to take a fluorescence measurement with a Curie spectrofluorometer Absolute Irradiance Graph New Absolute Irradiance Measurement New Concentration Measurement Color Measurement Strip Chart Spectrum Graph m The Spectrum Graph menu option displays a new curve of spectral data on the open graph based on the parameters set in the Acquisition toolbar Each new curve you create appears as a different color in the graph Graphs appear in scope mode by default If you click on a curve its corresponding parameters appear in the Acquisition toolbar The data source spectrometer is listed in the Source box Procedure To display a spectral graph follow the steps below 1 Select File New Spectrum Graph Or Im Click L in the Data Display toolbar A dialog box appears asking if you want to display the new graph in the current graph tab or start a new graph tab 22 000 20000 300 02 0607 a cean ptics Inc iret i horno 5 View Menu Functions Show data in existing tab Tab a AXIS Y Axis Graph A Wavelength Intensity
135. utton If you wish to reselect the original color click the Reset button then click OK 5 The screen returns to the Result Color Editor dialog box Click Close The graph now displays in the selected color 000 20000 300 02 0607 85 7 Processing Menu Functions 86 000 20000 300 02 0607 Chapter 8 Tools Menu Functions Overview The tools menu provides the functionality to access the update center select NetBeans settings for SpectraSuite modules and to control the SpectraSuite parameters Options Options is a powerful tool that enables you to specify the defaults for SpectraSuite parameters all in one location Ze Options Took Provides access bo the mena configuracion 000 30000 020 02 0607 87 8 Tools Menu Functions Default Acquisition Settings You can set acquisition settings for your spectrometer s to persist through shutdown and restart using Tools Options SpectraSuite Settings Default Acquisition Parameters Ss Options Options Server and External Tool Settings E ic System E EN Modules S Infrastructure S Ocean Optics S Libraries E a Object Types amp Links Fixed Action Instances Fixed ET NBM Objects Folders Fixed sML Configuration Files Fixed Action Instances Fixed amp Unrecognized Objects Fixed System Settings E Ca Autoupdate Types Ga Spectrasuite Beta Update Center Ca SpectraSuite Update Center Update Center sagt Prin
136. value is Wavelength nm Set Color Temperature Setting the color temperature is useful if you have a lamp and you know what its temperature is You can use the lamp color temperature that you set here when doing a color measurement see Fluorescence gt Procedure 1 Select Processing Select Color Temperature to display the Configure Photometry dialog box Color Temperature kelvin 2 Set the desired color temperature in Kelvin and click Amet The color value that you set here appears in the Color Values pane of the Color Measurement window 80 000 20000 300 02 0607 fA cean 5 Dptics inc P E _ m T First in Photonics 7 Processing Menu Functions Be Ocean Optics Spoctrasuite Hie Yew Spectrometer Processing Zoch Window Hep Integr ato Scan to Boxcar Strobe Lame Electric dark m EI La ere FNF path Erestia connection z T gt Jin es al x Graph A x iE Color Values E GE z Color Setting RHAQaghe 17 SHATRI beet aha 2 71 11 6561 58 Acisi r4 7 71 3 e 4000 m Ini teme Here a D boca O pL J NoPre processor Scope Mode ul 0 4386 a Graph A H pus amp Priati fl Ra SARL MA G IE 7 SE 3 Dec ake CCT LE x0 S 0 2794 o 0 5445 ud 0 1701 Lg Faces ane D T degrees ae saturation D C Derinant Wave Xe 4 rem Daba Wees LE zu Graph L i 1000 Ire zu XN AO Kal Em Bod Woseelengrh rim Jar Uis p wo W e iece h 205 37 S611 Xen Exporting Processed Data
137. ve 2 degree Emissive z degree Emissive 2 deagree Emissive z degree usB236142 2 degree USB2G6l4Z z degree UuSB2G6142 2 degree UsSB2o6142 2 degree uSe2G6142 2 degree 2 degree 2 degree 2 degree 2 degree 2 degree RI d CRI Ra CRI ron NH FP HN P WP LUI Ken a FE Sal Sch ELE i ed e Gd Emissiwe missive Emissie Emissive Emissiva emissive Emissive Emniss ive Emissiva amiss ive emissive amiss ive emissive Emissiwe Emissive Bmissive emissive Emissive Emissiva Emissive Emissiva Emissiva emissive Emissive Emissive Emissiva Emissivg Emissive amissive Emissiva EM Lab a wj E T d zl dun um d d a a a LI a Rd Loi iai P deqree degree i degree 2 degree z degree 2 degree 2 degree 2 degree 2 degree USB2G6142 2 de ree US6266142 2 degree use2G6142 2 degree UsB2G614 2 2 degree 2 degree 2 degree 2 degree d h Ex te P Da n P Kn Dao Hx th ah Oh de oe de Hi BIO M OOOOuudqd d qp A I wu be a s paa pa ea ea pn a n euh usen us i degree degree degree him oie fe ZS Da be P oS es ie Deleg Rl U5B2G6142 use oe14 2 bbbbbbhbhbbbhbbbhbbbbbhbbbhbbbEbbbEbEbbbbbbbbbbhbbbhbbbbhhbhbiEERE ai UJ Let RAO ai IU LU GAP UU ME A Kd Ud GU Ld Ai Wel LO Ld UO Lat OE CAPIO a GU ad UJ GU RO el d ai Wi Lef and GAP UO ME GU ad ME Uu Ku usd Fal Sall Sal Sal al Fal Eg zb Sd E ES kt cn un id ud ER 150 000 20000 300 02 0607 Appendix B Troubleshooti
138. ve other acquisitions running a warning message appears telling you that all other acquisitions will be stopped when you are acquiring high speed data Either stop all your other acquisitions or click OK on this message and SpectraSuite will temporarily stop them The High speed Acquisition dialog box appears Be High speed Acquisition Integration Time usec Scans to Average Boxcar Width RENE a LIU External Trigger Made Electric Dark Correction Strobe Lamp Enable me i Number of Scans 100 5 Capture Period usech 000000 Select one Show pragress Done 100 scans took 15 2 ms each Acquisition BEREREREEEEEEREERRRRREREEEERRRERR 4 pi Le cos Click The top third of the form lists the parameters selected in the main graph window 26 000 20000 300 02 0607 a cean ptics Inc irgf mm eit FT mist in Photonics 5 View Menu Functions 4 Enter the following information Integration Time usec Specify the integration time in usec Scans to Average Enter the number of scans to average Boxcar Width Enter the boxcar width External Trigger Mode Select the external trigger mode Normal Software Synchronization External Hardware Electric Dark Correction Enable this option for electric dark correction otrobe Lamp Enable Enable this option to turn on the lamp Filename Enter the name or browse to the file where you want to store data in a tab delimited format Choose one of t
139. wer numbers indicate a poorer fit The residual value for each point is also shown in the table at the top of the window this indicates the difference between the known concentration for a sampled absorbance and the estimated concentration using the regression In the ideal case this value will approach zero Note that very small values on the order of 10 12 or smaller are normal even for a good fit this is due to a rounding error and should have no discernable effect on solution quality 000 20000 300 02 0607 a cean ptics Inc Firgi in Ear B Troubleshooting 6 At any time you can select a sample from the table at the top of the window and click Remove Sample to discard the point Once enough points exist to compute a regression the will be enabled to allow the current set of samples to be saved to disk for later retrieval 7 Click when you have entered enough points to generate a regression line Loading Calibration from an Existing File a Select Load calibration from file to recall a calibration from known solutions that was performed previously The following window appears the example below is in Windows XP format Be Concentration Measurement Setup wizard Concentration Measurement Setup Wizard 2 cma My Recent Documents My Documents Ja My Computer KI My Network Places File name indigoCarmine concentration Files of type concentration calibration files v Compound Indigo Carm
140. y sampling variable integration time averaging smoothing fiber size etc you must store a new reference and dark spectrum Reflection Experiments Reflection is the return of radiation by a surface without a change in wavelength Reflection can be Specular the angle of incidence is equal to the angle of reflection Diffuse the angle of incidence is not equal to the angle of reflection Every surface returns both specular and diffuse reflections Some surfaces may return mostly specular reflection while others may return mostly diffuse reflection Specular reflection increases proportionately with the amount of gloss on a surface Reflection is expressed as a percentage R relative to the reflection from a standard reference substance Sa D X1 PR pn 00 Where A the sample intensity at wavelength A D the dark intensity at wavelength A R the reference intensity at wavelength A The following figure shows a typical reflection setup A light source sends light via the input leg of a reflection probe onto a sample A reflection probe holder holds the probe in either a 90 or 45 degree angle from the surface The output leg of the reflection probe carries light from the sample to the spectrometer which is connected to the computer 000 20000 300 02 0607 125 A Experiment Tutorials Deg Light Source Peflection Probe a 4 Sample Typical Reflection Setup Common reflection appl
141. your experiment Dark A dark spectrum is a spectrum taken with the light path blocked Select File Store Store Dark Spectrum from the menu to save a dark spectrum to a file You can also click in the graph toolbar Reference A reference spectrum is a spectrum taken with the light source on and a blank in the sampling region 000 20000 300 02 0607 41 5 View Menu Functions Select File Store Store Reference Spectrum to store a reference spectrum file You can also click Y in the graph toolbar Convert Spectra This function enables you to convert between file types Select File Convert Spectra The File Converter dialog box appears Use this dialog box to select the file s to convert and to specify the file type desired M File Converter Convert File From Number af Files bo Convert g Convert File Ta Screen Capture This function takes a snapshot of the current SpectraSuite window or the entire computer screen and stores it in the format and location that you specify Procedure 1 Select File Screen Capture The Screen Capture Config dialog box appears 42 000 20000 300 02 0607 5 View Menu Functions Be Screen Capture Config EA Capture Spectrasuite window Capture entire screen Delay before capture 54 seconds Image Format 2 Select to capture either the just SpectraSuite window or the entire computer screen 3 If you don t want to capture the s

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