Indico Pro: User Manual [PDF]

Citation preview

®



Indico Pro User Manual



ASD Document 600235 | Rev. E | December 2011



The ASD Inc. logo, AgriSpec, FieldSpec, Indico, LabSpec, QualitySpec, RxSpec, and TerraSpec are registered trademarks and goLab, HandHeld 2, RS3, and ViewSpec are trademarks of ASD Inc. All other trademarks and registered trademarks are the properties of their respective owners.



Contents



Chapter 1: Indico Pro Software Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 1.1 Computer Requirements for the Indico Pro Software. . . . . . . . . . . . . . . . . . . . . . . . . . . 1 1.2 Instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 1.3 Installing the Indico Pro Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 1.4 Uninstalling . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3



Chapter 2: Running the Indico Pro Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 2.1 Quick Start . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 Starting the Software and Opening a Project. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 Taking a Baseline . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6 Collecting Spectra . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7 2.2 Troubleshooting Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 2.3 Developing Calibration Models . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 Plan Ahead. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 Set Up Instrument for Operation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10 Take a Baseline (White Reference) Spectrum . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10 Collect Spectra from Calibration Samples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10 Obtain Independent Chemical Measurement of Samples . . . . . . . . . . . . . . . . . . . . . . 11 Export Spectral Files to Chemometric Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11 Develop Mathematical Model Using Chemometric Software . . . . . . . . . . . . . . . . . . . 11 Validate Model Using Unknown Samples. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11 The Living Model . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12 2.4 Analyzing Target Materials . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12 Printing Prediction Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12 Reprinting Prediction Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12 2.5 Using ASD Rapid Classifier. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12



Chapter 3: Menus. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16 3.1 File Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17 Projects . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18 View Spectrum File [Alt+F, F] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20 Link File [Alt+F, L] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20 Close File Display [Alt+F, C] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20 Material Report... [Alt+F, M]. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20 Exit [Alt+F, X] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22 3.2 Spectrum Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22 Take a Scan [Alt+S, T] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23 Take a Baseline [Alt+S, B] [Ctrl+R] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24 Indico® Pro User Manual



i



Continuous Collect [Alt+S, U] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25 Sample Count/Average [Alt+S, C] [Ctrl+C] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25 Derivative Gap [Alt+S, G] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26 Dependent Variables [Alt+S, V] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27 Save [Alt+S, A] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28 Save After Collect [Alt+S, O] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28 Display After Save [Alt+S, D] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29 Print Spectrum [Alt+S, P] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29 Print Spectrum Properties [Alt+S, R] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29 Printer Setup [Alt+S, S] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29 Export Spectrum [Alt+S, E] [Ctrl+E] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29 3.3 Project Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31 Properties [Alt+P, P] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32 Instrument Control [Alt+P, I] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35 Start Logging Events [Alt+P, S] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36 Serial Pulse [Alt+P, E]. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36 Prompt Before New Reference [Alt+P, S] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38 3.4 Display Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38 Axes [Alt+D, A] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39 Digital Numbers (DN) [Alt+D, D] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39 Reflectance [Alt+D, R] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40 Transmittance [Alt+D, T] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40 Log 1/R [Alt+D, L] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40 Log 1/T [Alt+D, G] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41 Show Wave Number [Alt+D, W] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41 Show Spectrum Properties [Alt+D, P] [Ctrl+P] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41 Show File List [Alt+D, F] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42 Splice Correction [Alt+D, C] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43 Show Instrument Spectrum [Alt+D, I] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43 Show Chromophores/Overtones [Alt+D, H] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43 3.5 Chemometrics Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46 Working with The Unscrambler X Models . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46 Setup [Alt+C, S] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49 Predict [Alt+C, P] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49 Reload Model Files [Alt+C, M] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54 Predict from File [Alt+C, F] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55 3.6 Run Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55 ASD to SPC Converter [Alt+R, S] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55 ASD to JCAMP Converter [Alt+R, J] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56 ASD to ASCII Converter [Alt+R, A] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57 ASD to U-ASCII Converter [Alt+R, U]. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58 GramsAI. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59 PLSplus/IQ Navigator . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60 3.7 Timers Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61 Reference Timer [Alt+T, R] [Ctrl+B] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61 Auto Collect Timer [Alt+T, A] [Ctrl+A] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62 User Defined Timer [Alt+T, U] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64 3.8 GPS Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65 Setup [Alt+G, S] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66 Activate [Alt+G, A]. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67 ii



Contents



Monitor [Alt+G, M] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3.9 Windows Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3.10 Help Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3.11 Right-Click Menu. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Undo Zoom. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Customize . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . AutoScale . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mark Data Points . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Grid Lines . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Font. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Restore Defaults . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Add Note. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Delete Note. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Take a Scan . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Take a Baseline . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .



67 68 69 70 71 71 72 72 72 72 73 73 73 74 74



Chapter 4: Indico Pro Software Quick Reference . . . . . . . . . . . . . . . . . . . . . . . . 75 Chapter 5: Chemometrics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77 5.1 A Brief Explanation of Principal Component Analysis . . . . . . . . . . . . . . . . . . . . . . . . Case 1: Classification Model . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Case 2: Quantification Model . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5.2 Making an NIR Analyzer Work for You . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sample Characteristics. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Experiment Configuration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5.3 Liquid Samples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5.4 Solid Samples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Data Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5.5 Chemometrics Models . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5.6 Off-the-Shelf Chemometrics Applications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . PLSplus/IQ. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5.7 Quantitative Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5.8 Qualitative Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5.9 Combined Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Unscrambler X Prediction Engine (OLUPX) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Unscrambler X Classification Engine (OLUCX) . . . . . . . . . . . . . . . . . . . . . . . . . . . . .



77 79 80 82 83 83 83 83 84 85 85 86 86 87 87 87 87 88



Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89



Indico® Pro User Manual



iii



Chapter 1: Indico Pro Software Introduction The Indico® Pro software is developed by ASD Inc. Its purpose is to: „



Control the operation of an ASD general-purpose spectrometer.



„



Receive and store the spectral data transmitted from an ASD spectrometer.



„



Make real-time qualitative and quantitative predictions against calibration models.



The following sections provide basic information about the software: „



“1.1 Computer Requirements for the Indico Pro Software” on page 1



„



“1.2 Instrument” on page 2



„



“1.3 Installing the Indico Pro Software” on page 2



„



“1.4 Uninstalling” on page 3



1.1 Computer Requirements for the Indico Pro Software The instrument controller is a computer that manages the instrument, stores data, and processes the results. The minimum requirements for the instrument controller are: „



1.2 GHz Pentium or better notebook or PC with monitor



„



256 MB RAM or more



„



20 GB of free disk space



„



1024 x 768 or better graphics resolution



„



24-bit color or better, 32-bit recommended



„



(Optional) Ethernet wireless (Wi-Fi) adapter: PCMIA, USB, or built-in that is compatible with the 802.11g standard



„



(Optional) Serial communications port (RS-232 COM, Bluetooth®, or USB) (only needed if a GPS is used). Contact ASD for information about using GPS receivers with ASD instruments.



Indico® Pro User Manual



1



The instrument controller requires the following: „



Microsoft® Windows® XP, Windows Vista®, Windows® 7 or previous operating system



„



Microsoft Internet Explorer 6.0 or higher



„



User account that is an Administrator or that has read, write, and execute permissions to the c:\Program Files\ASD folder and subfolders



You should have a basic understanding of the Microsoft Windows operating system, including software installation. International customers using non-English versions of Windows must alter the Regional Settings under Start > Settings > Control Panel. The default language must be set to English (United States) in order for the software to be registered and operate correctly. The numbering format must also be set to English.



1.2 Instrument The Indico Pro software comes standard with some ASD instruments. If you purchased your instrument controller from ASD, the software is already installed. If you purchased your instrument controller from a third party, you can install the software from the USB flash drive that came with your instrument. A single instrument controller can control only one ASD instrument, because the configuration files are calibrated to a specific instrument.



1.3 Installing the Indico Pro Software If you purchased your instrument controller with your instrument, the Indico Pro software is already installed. If you purchased your instrument controller from a third party, you must install the software. To install the Indico Pro software: 1. Insert the USB flash drive that came with the instrument into a USB port on your instrument controller. 2. Do one of the following, depending on which version of Windows. •



Windows 7—Select Start > Computer.



•



Windows XP—Double click My Computer on the Windows desktop.



3. In the Devices with Removable Storage list, double-click the USB flash drive. 4. Find and double-click the setup.exe file in the Indico Pro folder. 5. Follow the installation instructions as you are prompted. •



Select the Typical Install option.



•



If the Indico Pro software does not install correctly, contact ASD Technical Support.



Indico® Pro User Manual



2



1.4 Uninstalling To uninstall the Indico Pro software: „



Windows 7—From the Control Panel, click Uninstall a program.



„



Microsoft Windows XP, Windows Vista—From the Control Panel, use Add or Remove Programs.



Unless you want to keep shared Indico Pro software files for other non-ASD applications, select the Remove All Unused Shared Files option when prompted during the uninstall. Uninstalling the Indico Pro software does not remove your chemometrics project files.



3



Chapter 1: Indico Pro Software Introduction



Chapter 2: Running the Indico Pro Software You use the Indico Pro software to create calibration models for use in qualitative (classification) or quantitative (concentration) analysis. The following sections will help you get started using the Indico Pro software: „



“Quick Start” on page 4



„



“Developing Calibration Models” on page 9



„



“Analyzing Target Materials” on page 12



„



“Using ASD Rapid Classifier” on page 12



2.1 Quick Start This Quick Start section takes you through the primary tasks required to use the software. Although this is specific to one example (analyzing polyester), you can use the basic processes for other near-infrared (NIR) analysis cases. To create a chemometric model for use with the Indico Pro software, you must be proficient in these Quick Start steps. The primary tasks for using the Indico Pro software are: 1. “Starting the Software and Opening a Project” on page 4. 2. “Taking a Baseline” on page 6. 3. “Collecting Spectra” on page 7.



Starting the Software and Opening a Project You work in a project when you collect and save spectra. The project saves all of your collection and other settings. To start the software and open a project: 1. Connect the instrument and the instrument controller. •



Refer to the manual that came with your instrument.



2. Turn on the instrument. 3. If using an accessory light source, turn it on.



Indico® Pro User Manual



4



4. Let the instrument the accessory light source, if any, warm up for at least 15 minutes. •



If you are collecting radiometric spectra, let the instrument warm up for at least one hour before collecting radiance or irradiance data.



5. Turn on the instrument controller. 6. From the instrument controller, select Start > All Programs > ASD Programs > Indico Pro. 7. Verify that the initial splash screen does not display any communication errors. •



If there are errors, you must resolve them before continuing.



8. Click New



.



9. In the New Project window, enter name for the project. 10. If needed, click Change Directory and select where you want to store the project folder. 11. Click OK. 12. In the Add New Project window, enter a Project Description. 13. Click OK. •



The Instrument Display window gives you toolbars for shortcuts to many functions, a a graph of the collected spectra, and a status area.



Toolbars



Spectra graph



Status area



Continue with “Taking a Baseline” on page 6. 5



Chapter 2: Running the Indico Pro Software



Taking a Baseline After you start the software and open a project, you are ready to take a baseline. For additional information about taking a baseline, see “Take a Baseline (White Reference) Spectrum” on page 10. To take a baseline: 1. Start the software and open a project. •



See “Starting the Software and Opening a Project” on page 4.



2. Select Spectrum > Sample Count/Average.



3. Change the Instrument Sample Count as needed for your application. •



Use 25 for this example. The default is 10.



4. Change the Scan Type as needed. •



This option is only for instruments with NIR detectors. The mechanical design allows collection of two different directions: A or B. The default is AB Even. The scan type is used for special applications and/or troubleshooting instrument problems. •



The AB Even option guarantees an equal number of A scans and B scans. For example, if a sample count of 9 is requested, then 10 samples are collected, 5 A and 5 B scans.



•



The A Only option collects only A scans.



•



The B Only option collects only B scans.



•



The A or B option collects a different number of A or B scans. For example, if you set the sample count to 9, then 9 samples are collected in two different combinations: 5 A and 4 B scans or 4 A and 5 B scans.



5. Make sure the light source is on and the probe input end is pointed at the white reference panel. •



Assuming that you are using a contact probe or if your reflectance probe has appropriate spacing or spacers on the end, place the space end against the white reference panel.



Indico® Pro User Manual



6



6. Click Baseline •



.



A message displays confirming that you want to take a new baseline. Leave the Optimize First option selected.



7. Click Yes. •



When optimization and baseline are complete, you should see a straight baseline across the graph at 1.00 (100%).



8. If you saw a saturation alarm, attach the attenuator accessory. •



Sometimes the instrument’s external light source is too bright for the combination of fiber optic cable and dynamic range of the unit. In this case we say that the detectors are saturating. Attenuator



Continue with “Collecting Spectra” on page 7.



Collecting Spectra After you take a baseline, you are ready to collect spectra from the sample. In this example, we are using polyester fabric as the sample. For additional information about collecting spectra, see “Collect Spectra from Calibration Samples” on page 10. 7



Chapter 2: Running the Indico Pro Software



To collect spectra: 1. Place the sample on the white reference panel with the spacer end against the sample. •



This assumes that your reflectance probe has appropriate spacing or spacers on the end. Use the same probe technique that you used to take the baseline.



•



Because light goes through polyester, the we are using the white reference as a background so that additional features are not picked up.



2. Press the space bar. •



When the software finishes recording and averaging the spectra, the graph in the project window updates to show the reflectance spectrum of the sample.



•



The graph shows the spectrum over the spectral region for your instrument. For example, the spectral region for the graph is from using an instrument with the range 1000–2500 nm.



Indico® Pro User Manual



8



2.2 Troubleshooting Options If your output varies significantly while testing samples, try the following troubleshooting options, one at a time: 1. Move the sample a little and take another spectrum. •



A contaminant or physical aberration might be in the sample at the spot measured.



•



Start again from step 2 in “Collecting Spectra” on page 7.



2. Remove the sample and make sure the light source is on. •



You should see a bright spot of light reflecting off the white reference panel.



•



Start again from step 6 in “Taking a Baseline” on page 6.



3. Inspect the white reference panel for possible contamination at the spot you are measuring. •



Start again from step 6 in “Taking a Baseline” on page 6.



4. Perform a fiber optic check on the external cable, if applicable. •



Refer to the manual that came with your instrument about this process. Not all instruments have an external cable.



•



Start again from step 6 in “Taking a Baseline” on page 6.



5. If these troubleshooting measures are ineffective, shut down your computer, then the instrument and contact ASD Technical Support.



2.3 Developing Calibration Models The goal of calibration development for qualitative models is to use spectral features to classify a target substance as matching one of the models. The goal of calibration development for quantitative models is to identify and characterize the relationship between spectral features and the variable of interest in the product or target substance.



Plan Ahead The spectral feature representing the variable of interest will often be affected by other variables in the product. Therefore, great care must be taken to account for or to exclude these other variables. For example, if the variable of interest is water content and the product also contains varying amounts of salt, sugar, and fat, the sampling scheme in the development of the calibration set must be designed so that the spectral effects of the salt, sugar, and fat do not generate erroneous measurements for water content. One method to accomplish this when developing the calibration set is to allow all the extraneous variables to change in a random fashion from sample to sample. When a sufficient number of samples is collected, the spectral influence of the non-essential variables becomes insignificant.



9



Chapter 2: Running the Indico Pro Software



The manner in which you take your calibration data should use the same method as taking your prediction data later. For a more extensive discussion on calibration or developing a spectral model, refer to the literature supplied with your chemometric software.



Set Up Instrument for Operation Attach the two leads of the fiber optic probe to the port, making sure that no contamination enters the exposed connection port or clings to the end of the fiber optic probe. With reflectance (Chem) probes, the light source lead is distinguishable from the light return lead by the number of fibers. The light source lead contains many more optical fibers than the return lead. (This does not apply to the Reflectance Probe, contact probe, or MugLite.) With immersion probes, (transmittance and transflectance) either lead may be attached to the light source connection. Under noncritical conditions, let the instrument and light source to warm up for at least 15 minutes. This allows the internal light source to stabilize completely which enables the instrument to function with the highest degree of precision. It is not necessary for the instrument controller to be on during the warm-up period.



Take a Baseline (White Reference) Spectrum The first step in data collection is to take a baseline (white reference) spectrum. A white reference spectrum provides the data necessary to eliminate instrument and illumination characteristics from the raw DN spectrum. These characteristics include the spectrum of the light source and fiber optic material, and the characteristics of internal circuitry. Maintain the same instrument configuration and probe technique for all white reference, calibration, and subsequent sample measurements. When using a reflectance-type probe, take a baseline spectrum from a white reference such as Spectralon® or a white ceramic tile. When using a transmittance- or transflectance-type probe, take a baseline using air as the reference medium or a solvent such as carbon tetrachloride or water. The same (uncontaminated) reference material must be used for all white reference spectra in any series of measurements. A transmittance probe may require an attenuator attached to the fiber optic input to prevent saturation. The displayed spectrum becomes a flat line after a white reference is taken. Pressing the space bar will collect a new spectrum that is automatically compared to the white reference as a ratio.



Collect Spectra from Calibration Samples The purpose of this phase is to collect a representative spectrum from each sample in the calibration set. Techniques will vary according to ambient conditions as well as the texture and homogeneity of the material being sampled. When working with solid materials, more than one spectrum may be taken from each sample. „



Use the same probe technique for all samples.



„



Use the same probe for all samples.



„



Use the same white reference throughout.



„



Save each spectrum in the same form, that is, reflectance, transmittance or absorbance.



Indico® Pro User Manual



10



No sample is perfectly uniform throughout. Small physical and chemical differences exist for each point on any sample. A good prediction model requires training data representative of the range of differences. If you only record training sample spectra in one spot on the sample, the resulting prediction model will be too restrictive and will probably not accurately classify the target at other spots.



Obtain Independent Chemical Measurement of Samples Obtaining independent chemical measurements of the samples (or primary data) is a crucial step in the development of any calibration model for quantitative analysis. Spectral characteristics revealed through NIR inspection must be correlated with the known chemical composition in the samples. Therefore, the calibration samples must undergo independent chemical analysis. The results of standard chemical analysis and spectral examination are combined and correlated using chemometric software. For additional information, refer to the literature supplied with your chemometric software.



Export Spectral Files to Chemometric Software Files from the Indico Pro software can be directly imported into Unscrambler 9.2 and higher without any conversions. For earlier versions, use ASD to JCAMP Converter [Alt+R, J] to perform the conversion to JCAMP Files. If GRAMS IQ™ is your choice, use ASD to SPC Converter [Alt+R, S] to convert your ASD spectrum files to Grams SPC files.



Develop Mathematical Model Using Chemometric Software The results of standard chemical analysis and spectral examination are combined and correlated using chemometric software. For information on this process, refer to the literature supplied with your chemometric software or “Chapter 5, A Brief Explanation of Principal Component Analysis” on page 77.



Validate Model Using Unknown Samples Test the accuracy of the mathematical model by using the model to measure a concentration in a sample that was not used to construct the model. Many unknown samples may be used. It is necessary that the concentration of the variable of interest fall within the range upon which the model is based. In situations where the number of calibration samples is limited, the chemist may use the leave-one-out method to validate the model. Here a model is constructed of all but one of the samples. Then the one is analyzed using the model and the accuracy of the model is determined. This process may be carried out repeatedly, selecting a different sample to leave out each time. For additional information on cross validation, refer to the literature supplied with your chemometric software.



11



Chapter 2: Running the Indico Pro Software



The Living Model It is always a good idea not to let a model stagnate. Always be open to adding new information to the model, paying special attention to outliers, anomalies, and endpoints. This is known as a “Living Model.”



2.4 Analyzing Target Materials During routine chemical analysis, it is critical that the product being analyzed is made of the same raw ingredients as the samples that were used to generate the calibration model. Foreign ingredients may introduce bias error into the quantitative result of NIR analysis. It is also important to use the identical fiber optic probe and employ the same probe technique that was used to acquire the spectra for calibration. The same white reference must be used that was used during the development of the calibration model. When measuring solid materials in the field, remember to bring the white reference along. For best results, take new white reference readings every 10 to 15 minutes. To analyze target materials: 1. Start the software and open a project. •



See “Starting the Software and Opening a Project” on page 4.



2. Take a baseline. •



See “Taking a Baseline” on page 6.



3. Collect spectrum from the sample. •



See “Collecting Spectra” on page 7.



4. Execute integrated chemometric processing. 5. Store spectral data.



Printing Prediction Results The Indico Pro software provides the capability to print and preview prediction results in a custom format. See “Predict [Alt+C, P]” on page 49 and “Report Options” on page 51 for more details.



Reprinting Prediction Results Predicted result files may be reprinted. See “Material Report... [Alt+F, M]” on page 20 for more details.



2.5 Using ASD Rapid Classifier This section builds on what was provided in the “Quick Start” on page 4 section by incorporating the ASD Rapid Classifier. ASD Rapid Classifier is a simplified analysis tool that attempts to match a sample with a model stored in its database. Indico® Pro User Manual



12



This section steps you through an example that you can modify and enhance for your specific application. It does not cover use of chemometric models. More advanced chemometric analysis (using other off-the-shelf chemometric software) will follow the same general steps provided here. To use the ASD Rapid Classifier: 1. Start the software and open a project. •



See “Starting the Software and Opening a Project” on page 4.



2. Take a baseline. •



See “Taking a Baseline” on page 6.



3. Select Timers > Auto Collect Timer. •



The auto collect timer lets you automatically store spectrum files with a base name and automatic increment number by pressing space bar.



4. For this example, enter the following and click OK.



13



•



Select the Enable Timer option.



•



Take a Spectrum Every—0 hours, 0 minutes, and 1 second



•



Number of Files to Save—10



•



Starting Sequence Number—1



•



Description—Enter whatever information you would like. This information displays in the Rapid Classifier prediction window. If you leave this blank, the ASD Rapid Classifier has nothing to reference and will not predict anything. ASD Rapid Classifier is a library that requires references, which it gets from the Description field.



•



Base File Name—pe



Chapter 2: Running the Indico Pro Software



•



Spectrum Saving Options—Select the Ask Before Saving a Spectrum option •



This option lets you move the sample slightly between measurements for good coverage of the variation in spectra from one spot to the other. No sample is perfectly uniform throughout. Small physical and chemical differences exist for each point on any sample. A good prediction model requires training data representative of the range of differences.



•



If you only record training sample spectra in one spot on the sample, the resulting prediction model will be too restrictive and will probably not classify the target at other spots accurately.



5. When prompted by the confirmation window, click OK. 6. Be sure you have a good polyester reflectance spectrum showing in the project graph. 7. Place the sample under the probe or into the accessory. •



Use the same probe technique as was used for taking the baseline.



8. Press space bar and click Yes when prompted. •



When using the timer, you are prompted to take a spectrum based on the time that you put in.



•



When the Indico Pro software finishes recording and averaging the spectra, the graph in the project window updates to show the reflectance spectrum of the sample.



9. Move the sample a little so the input end is viewing a different spot on the sample. 10. When prompted to collect spectra, click Yes. •



Each time the measurement is completed, move the sample a little so the fiber optic probe views a different spot on the sample. After you record all 10 spectra, the prompt window will stop appearing.



11. Repeat from steps 3 through 10 for each different type of sample you want to perform a rapid classification on. •



The more spectra that are saved for each sample type, the more accurate the calibration model is.



12. Select Chemometrics > Setup. 13. For this example, select the following and click OK. •



Project Predictors—ASD Rapid Classifier



•



Selected Predictors—ASD Rapid Classifier



•



Selected Model File—If the list does not contain all of the files you want, click Add button to select more files, then click Open. •



Select all of the different spectrum files that you want to include in the ASD Rapid Classifier. (Ctrl+Click or Shift+Click allows you to select more than one.)



•



All of the selected files from the Select Model File window are imported into the the Selected Model Files list.



14. Take a baseline again. •



See “Taking a Baseline” on page 6.



15. Collect spectrum from the sample. •



See “Collecting Spectra” on page 7.



Indico® Pro User Manual



14



16. Click Predict.



15



Chapter 2: Running the Indico Pro Software



Chapter 3: Menus The Indico Pro software has a number of menus, shown in Figure 3.1, which can all be accessed with the mouse or the keyboard: „



“File Menu” on page 17



„



“Spectrum Menu” on page 22



„



“Project Menu” on page 31



„



“Display Menu” on page 38



„



“Chemometrics Menu” on page 46



„



“Run Menu” on page 55



„



“Timers Menu” on page 61



„



“GPS Menu” on page 65



„



“Windows Menu” on page 68



„



“Help Menu” on page 69



„



“Right-Click Menu” on page 70



Figure 3.1: Menus



When using the keyboard, press and hold the Alt key and press the key corresponding to the underlined letter in the menu name, such as: „



Alt+F for File,



„



Alt+S for Spectrum,



„



Alt+P for Project,



„



Alt+D for Display,



„



Alt+C for Chemometrics,



„



Alt+R for Run



„



Alt+T for Timers,



„



Alt+G for GPS,



„



Alt+W for Windows,



„



Alt+H for Help.



Indico® Pro User Manual



16



Once the menu is open, further operations can be launched by pressing the key corresponding to the underlined letter in the desired menu item. In addition, many Indico Pro software operations are available directly through function keys (for example, F1 through F12), other hot-key combinations, and buttons on the toolbar. Menu items typically show the hot-key combination.



Figure 3.2: Indico Pro toolbar



3.1 File Menu The File menu can be reached using the mouse or Alt+F. It includes the items: „



“Projects” on page 18 •



“New Project [Alt+F, N]” on page 18



•



“Open Project [Alt+F, O]” on page 18



•



“Save Project [Alt+F, S]” on page 19



„



“View Spectrum File [Alt+F, F]” on page 20



„



“Link File [Alt+F, L]” on page 20



„



“Close File Display [Alt+F, C]” on page 20



„



“Material Report... [Alt+F, M]” on page 20



„



“Exit [Alt+F, X]” on page 22



Figure 3.3: File menu



17



Chapter 3: Menus



Projects Projects are a way to group prediction equations, models, and spectra together. These files are stored in a directory for the project for better file management on your system. The Indico Pro software maintains the linkage between your project and the associated spectrum, log, and model files, as well as commonly used properties, such as Sample Count/Average [Alt+S, C] [Ctrl+C]. By default, all new spectrum files are placed into the project directory. However, references to spectrum files residing in other directory locations can be added to the project using the View Spectrum File [Alt+F, F] item and then saving the project. Three types of files are associated with a project: „



Spectrum files contain spectral data saved by the Indico Pro software. These files are saved with the .asd file extension. A copy of the reference spectrum is also included with the file.



„



Model files are chemometric model files prepared by GRAMS IQ by Thermo Scientific or The Unscrambler X by CAMO. The Indico Pro software uses the same file extensions for model files used by these software providers.



„



Log files contain logs of Indico Pro software operations. These files are saved with the .asl file extension



New Project [Alt+F, N] The File > New Project item opens a window that allows you to enter a name and destination directory. By default, the destination directory is a subdirectory of the \program files\asd\indicoPro\projects directory. While this project is open, all new spectrum files are stored here.



Figure 3.4: New Project window



Open Project [Alt+F, O] The File > Open Project items opens a window that allows you to select an existing project. As necessary, you can browse for a different directory.



Indico® Pro User Manual



18



The project includes all prediction models as well as a destination subdirectory. Subsequent prediction and save spectrum operations will use the information from this project. You can only have one project open at a time.



Figure 3.5: Open Project



If the project you are opening has been password protected, you are prompted to enter that password. You change the password of a project, by selecting Project > Project Properties.



Figure 3.6: Project Password



Save Project [Alt+F, S] The File > Save Project [Alt+F, S] item updates the current project with prediction equations and models. Saving the project will also store instrument settings, settings for GPS, as well as any spectrum files that are viewed for comparison. If you do not want viewed spectrum files to be added to the project when saved, close them before saving the project. Any spectrum file displayed with a File > View Spectrum File [Alt+F, F] operation will be added to the project automatically in a File > Save Project [Alt+F, S] operation. To remove a spectrum file, use the Display > Show File List [Alt+D, F] item. If you want only the viewed spectrum files saved to the project and not the instrument settings and GPS settings, use the File > Link File [Alt+F, L] item.



19



Chapter 3: Menus



View Spectrum File [Alt+F, F] The File > View Spectrum File [Alt+F, F] item opens a window that allows you to select a previously generated spectrum file. This is useful when you want to compare the results from different spectrum captures. Any spectrum files that are opened with View Spectrum File and are still being viewed will become part of the project if the project is saved. Refer to the Display > Show File List [Alt+D, F] item to remove spectrum files from the project. You can open as many spectrum files as you like. They are superimposed on one another for ease in comparison. If the project is not saved on or before the Indico Pro software is terminated, none of the viewed spectrum files will become part of the project the next time it is opened. Whenever the project is saved, all currently viewed spectrum files become part of the project. Any spectrum files that were in the project but are not displayed will remain in the project.



Figure 3.7: Open ASD Spectrum File



Link File [Alt+F, L] The File > Link File [Alt+F, L] item writes to the project all spectrum files that are being displayed for comparison. The Link File [Alt+F, L] item does not save other project settings, unlike the Save Project [Alt+F, S] item.



Close File Display [Alt+F, C] The File > Show File List [Alt+D, F] item will remove a spectrum file from being displayed for comparison. If the file was already in the project, this operation only hides its display and does not remove the spectrum file from the project. This operation is useful when spectrum files were opened for comparison, but when you do not want them added to the project.



Material Report... [Alt+F, M] The File > Material Report item allows you to generate, preview, and print custom reports of the prediction results for the input spectrum files. The input files can be either those used in the most recent prediction or those you explicitly select. The Material Report window has two tabs: List and Report Options.



Indico® Pro User Manual



20



List The List tab shows you a list of spectrum files that are available for the report. If you do not see any spectrum files, use the Browse button to look for them on the system. Select a file or all the files to enable the Print or Preview buttons. Figure 3.9 shows an example of previewing a material report. To edit the prediction result data, select a file and click Edit. Larger projects may have many spectrum files associated with them. You have to select the spectrum files explicitly that are to be use in the material report.



Figure 3.8: Material Report: List tab



Figure 3.9: Preview of Material Report



21



Chapter 3: Menus



Report Options The Report Options tab shows options in the Displayed Fields section for all information that can be included in the report. In this manner, the report can be customized. When the Save as Default option is selected, then those selections are saved for all subsequent prediction sessions.



Figure 3.10: Material Report: Report Options tab



Exit [Alt+F, X] The Exit item closes the Indico Pro software. If the project has been modified, you are prompted whether or not to save the project before closing. Any files opened through the View Spectrum File [Alt+F, F] item will be added to the project if those files are still open when the project is saved. Likewise, any changes to settings will also be saved to the project.



3.2 Spectrum Menu The Spectrum menu can be reached using the mouse or Alt+S. It includes the items: „



“Take a Scan [Alt+S, T]” on page 23



„



“Take a Baseline [Alt+S, B] [Ctrl+R]” on page 24



„



“Continuous Collect [Alt+S, U]” on page 25



„



“Sample Count/Average [Alt+S, C] [Ctrl+C]” on page 25



„



“Derivative Gap [Alt+S, G]” on page 26



„



“Dependent Variables [Alt+S, V]” on page 27



„



“Save [Alt+S, A]” on page 28



Indico® Pro User Manual



22



„



“Save After Collect [Alt+S, O]” on page 28



„



“Display After Save [Alt+S, D]” on page 29



„



“Print Spectrum [Alt+S, P]” on page 29



„



“Print Spectrum Properties [Alt+S, R]” on page 29



„



“Printer Setup [Alt+S, S]” on page 29



„



“Export Spectrum [Alt+S, E] [Ctrl+E]” on page 29



Figure 3.11: Spectrum menu: left side from the Instrument Display window; right side from a Spectrum File Display window



Take a Scan [Alt+S, T] The Spectrum > Take a Scan [Alt+S, T] item the instrument to capture and upload spectral data to the Indico Pro software. Any spectral averaging that is selected as part of the configuration is performed on the instrument before uploading the data. The resulting spectral data are then displayed in the Indico Pro software using the settings selected from the Display menu or buttons. This same Take a Scan [Alt+S, T] operation is also mapped to the space bar key and the external trigger of the instrument, for more convenient collection.



23



Chapter 3: Menus



Figure 3.12: Taking a spectrum



Take a Baseline [Alt+S, B] [Ctrl+R] The Spectrum > Take a Baseline [Alt+S, B] [Ctrl+R] item tells the instrument to capture and upload (baseline) reference data to the Indico Pro software. The baseline (white) reference is required because the instrument only measures the intensity of a light field through a given point in space. Once the baseline (white) reference is available and known, the Indico Pro software can compute the reflectance or transmittance for the material being sampled by the instrument. The Take a Baseline [Alt+S, B] [Ctrl+R] button takes a white reference measurement. This is required to adjust the future measurements to a known standard. A material with approximately 100% reflectance across the entire spectrum is called a white reference panel, usually Spectralon. When doing the Take a Baseline [Alt+S, B] [Ctrl+R] operation, it is important to have a clean white reference available for the instrument to measure. You can initiate a Take a Baseline [Alt+S, B] [Ctrl+R] measurement using: „



Take a Baseline [Alt+S, B] [Ctrl+R] button from the toolbar



„



Spectrum > Take a Baseline [Alt+S, B] [Ctrl+R] menu item



„



Alt+S, B key combination



„



Ctrl+R key combination



A graph will display measurements in reflectance plotted against wavelength with an initial value of 1.00. The data type in the Indico Pro software will specify reflectance. These ratio spectra are calculated in real time with the Indico Pro software.



Indico® Pro User Manual



24



The Indico Pro software optimizes the detector sensitivities for the probe and light source currently being used.The dark offset and white reference will also be measured and saved. Status bars will indicate each process.



Continuous Collect [Alt+S, U] The Spectrum > Continuous Collect item toggles whether the Indico Pro software collects spectrum on its own or waits for an explicit Spectrum > “Take a Scan [Alt+S, T]” on page 23 command. Even though a spectrum might be collected continuously, this does not mean that spectrum files are being saved continuously. This feature only affects what it displayed on the screen. When the Spectrum > Continuous Collect [Alt+S, U] is toggled on at the same time that the Spectrum > Save After Collect [Alt+S, O] is toggled on, the number of files created can become large very quickly.



Sample Count/Average [Alt+S, C] [Ctrl+C] The Spectrum > Sample Count/Average item opens a window to allow you to establish the number of spectra that are averaged together by the instrument to improve the signal-to-noise ratio (S/N). Most users find that a sample average of around 10 to 25 is sufficient. The S/N ratio increases with the square root of the number of samples being averaged together. Thus the S/N ratio would increase threefold by averaging nine samples and fourfold by averaging 16 samples, compared to that of a single measurement. The Indico Pro software also provides spectrum averaging. In the subset section, select the Number of Subsets to Collect option. For example, if the sample count is 4 and subsets are set to 10, the Indico Pro software collects 10 spectra, each one the result of 4 averaged spectra. It then averages the subset of 10 as the final result. The spectrum seen on the screen will change from black to green to represent the full subset has been taken. Scan Type is only for instruments with NIR detectors. The mechanical design allows collection of two different directions: A or B. The default is AB Even. The scan type is used for special applications and/or troubleshooting instrument problems. The AB Even selection guarantees an equal number of A scans and B scans. For example, if a sample count of 9 is requested, then 10 samples are collected, 5 A and 5 B scans. The A only selection collects only A scans. The B only selection collects only B scans. The A or B selection collects a different number of A or B scans. For example, if a sample count of 9 is requested, then 9 samples are collected in two different combinations: 5 A and 4 B scans or 4 A and 5 B scans.



25



Chapter 3: Menus



Figure 3.13: Spectrum Sample Count/Average



Derivative Gap [Alt+S, G] The Spectrum > Derivative Gap [Alt+S, G] item opens a window which allows you to specify the data point distance used in computing the derivative or difference spectrum. The derivative is essentially the slope of the “function” that is represented by the spectral data and requires at least two reference points in order to calculate. Given that the spectral data are a sequence of digital samples, the gap specifies which two digital samples on either side of a point (or wavelength) in the sequence. A gap of 1 means that it uses the digital samples immediately on either side of a point in the sequence. When the spectral features are broad, the gap (or data point distance) can be large. When the spectral features are narrow, the gap has to be smaller in order to include all the spectral information available. A derivative gap of 7 is commonly used.



Figure 3.14: Derivative Gap



Indico® Pro User Manual



26



Dependent Variables [Alt+S, V] Predictions are qualitative or quantitative. Qualitive predictions are used to identify a sample as a match, while quantitative predictions determine the quantity of a constituent, such as moisture in a sample. GRAMS IQ or The Unscrambler X are required for a quantitative model. The preferred method for accomplishing either prediction operation is to use another application (like GRAMS IQ or The Unscrambler X) to define and build the models used in prediction. In this case, the Spectrum > Dependent Variables [Alt+S, V] feature is not needed. The alternative method is to introduce the primary data into GRAMS IQ or the Unscrambler X directly. The Spectrum > Dependent Variables [Alt+S, V] item opens a window which allows you specify model parameters that are later used in prediction. When you set the Number of Dependent Variables to greater than zero, the Current Dependent Variables window changes to allow you to enter a description for those variables (primary data). Then you are expected to establish a model by taking the spectrum of samples for which the item’s quantitative information is known. A qualitative prediction does not use primary data, because it is just an identification mechanism. You can enter up to 100 variants and their constituents as you record each spectrum. During the export step, the headers and values are all exported to the prediction model and linked to the Indico Pro software project. Once the model data are collected, these primary data are passed to another application (such as GRAMS IQ) which builds the model that is later used for prediction.



Figure 3.15: Current Dependent Variables



Figure 3.16: Current Dependent Variables



27



Chapter 3: Menus



Save [Alt+S, A] The Spectrum > Save [Alt+S, A] item opens a window which permits you to save a specific spectrum under a new name and location. Do not confuse the Spectrum > Save [Alt+S, A] with Project > Save Project [Alt+F, S]. A spectrum that is being displayed can be saved anywhere, but it will not be officially part of the project until the project is saved. You can enter a description when saving the spectrum file. This is important if this spectrum file is later used as a model for predictions, such as with the ASD Rapid Classifier.



Figure 3.17: Save Spectrum File



Save After Collect [Alt+S, O] The Spectrum > Save After Collect [Alt+S, O] item is a toggle to automate the storing of spectrum files. Whenever a Spectrum > Take a Scan [Alt+S, T] operation is issued, a spectrum file is saved. This feature is useful in saving files when using the instrument trigger and USB remote trigger. Also, it can be used in an assembly line or other automated situation when external equipment is communicating with the Indico Pro software through the serial interface. Refer to the “Serial Pulse [Alt+P, E]” on page 36. For more convenient collection and saving of spectrum, the Take a Scan [Alt+S, T] operation can also be initiated by the space bar key or the external trigger of the instrument. When the Spectrum > Continuous Collect [Alt+S, U] is toggled on at the same time that the Spectrum > Save After Collect [Alt+S, O] is toggled on, the number of files created can become large very quickly. Indico® Pro User Manual



28



Display After Save [Alt+S, D] The Spectrum > Display After Save [Alt+S, D] item is a toggle to automate the viewing of spectrum files. This is useful when you are manually collecting spectrum and want to observe the differences.



Print Spectrum [Alt+S, P] The Spectrum > Print Spectrum [Alt+S, P] item opens up a window that allows you to specify the destination printer for sending a graphical representation of the active spectrum. The destination printer is highlighted in the Printer drop-down list. The printer properties can be changed using the Setup button (or the Printer Setup [Alt+S, S] item) prior to printing.



Figure 3.18: Printing Project



Print Spectrum Properties [Alt+S, R] The Spectrum > Print Spectrum Properties [Alt+S, R] item opens the spectrum properties window. This can be used to send the spectrum information to the printer configured in the Printer Setup [Alt+S, S]. The spectral data will print out in tabular form.



Printer Setup [Alt+S, S] The Spectrum > Printer Setup [Alt+S, S] item opens up the standard Windows configuration window for specifying the destination printer and its options. This setting remains in effect as the default for the Print Spectrum [Alt+S, P] and Print Spectrum Properties [Alt+S, R] items.



Export Spectrum [Alt+S, E] [Ctrl+E] The Spectrum > Export Spectrum [Alt+S, E] [Ctrl+E] item opens a window with three export options. This is intended for converting the ASD data file format into formats suitable for other post-processing applications. From this window, you can export to: „



29



ASCII - American Standard Code for Information Interchange. File exported into ASCII can be directly imported into many external database, spreadsheet, and word processing applications. This format is independent of computer platform and easily readable and printable. Chapter 3: Menus



„



JCAMP-DX - Joint Committee on Atomic and Molecular Physical Data. Files exported in this format can be imported into several chemometric, data analysis, and charting applications. This format is independent of computer platform. File formats are available from the Web site of the Joint Committee on Atomic and Molecular Physical Data.



„



Unscrambler ASCII - This format is provided to let you transfer dependent variable data to The Unscrambler X software.



You cannot export all output formats in the same operation. Instead, you open the Export Spectrum window, choose the tab of the desired export format, then start the export process. Once this is complete, you have to repeat these steps to also export to other formats.



Figure 3.19: Export Spectrum: ASCII



Indico® Pro User Manual



30



Figure 3.20: Export Spectrum: J-CAMP



Figure 3.21: Export Spectrum: Unscrambler ASCII



3.3 Project Menu The Project menu can be reached using the mouse or Alt+P. It includes the items:



31



„



“Properties [Alt+P, P]” on page 32



„



“Instrument Control [Alt+P, I]” on page 35 Chapter 3: Menus



„



“Start Logging Events [Alt+P, S]” on page 36



„



“Serial Pulse [Alt+P, E]” on page 36



„



“Prompt Before New Reference [Alt+P, S]” on page 38



Figure 3.22: Project menu: The left side from the Instrument Display window; the right side from a Spectrum File Display window



Properties [Alt+P, P] The Project > Properties item opens a window that allows you to see the project name and its location. You can add a description for the project, change the project password, and view files referenced by the project. The Properties item relates to the Projects items from the File menu: „



“New Project [Alt+F, N]” on page 18



„



“Open Project [Alt+F, O]” on page 18



„



“Save Project [Alt+F, S]” on page 19



The Properties item displays the current name, the current path, and the current description. You can also perform the operations: „



“Change Password” on page 33



„



“Project Files” on page 33



Figure 3.23: Project Info



Indico® Pro User Manual



32



Change Password The Indico Pro software can control access to your project if desired. When you create a new password or change the password, you must enter the old password, the new password, and confirmation of the new password. When the project is saved and closed, the password is activated. Be sure to remember your password.



Figure 3.24: Change Project Password



Project Files The Project Files button opens a window with three tabs for displaying the spectrum files, the model files, and the log files associated with the project. Spectrum files may be removed from the project here. „



Left click to select the file in the list



„



Right click to select the options available for the file.



„



Remove deletes the file from the list, but does not delete it from the file system.



Figure 3.25: Project Files



33



Chapter 3: Menus



Figure 3.26: Project Files



Figure 3.27: Project Files



The Project Files window only displays properties about the project, such as the files in the project. „



To save spectrum files in the project, use the View Spectrum File [Alt+F, F] command to open one or more spectrum files, then use the Save Project [Alt+F, S] command to insert these into the project list.



„



To remove spectrum files from the project, use the Properties [Alt+P, P] command.



Indico® Pro User Manual



34



Instrument Control [Alt+P, I] The Project > Instrument Control item opens a window to let you change the spectral region saved by a full-range instrument that covers the visible (VNIR) and NIR (SWIR1 and SWIR2) ranges. The instrument is still capable of the 350-2500 nm range (or the original spectral range purchased).This feature limits the spectral range saved to the files. Instrument Control [Alt+P, I] will truncate the spectral range. If you want to keep the original spectral range but only want to display certain regions, use the Axes [Alt+D, A] operation. When you select the Display/Save option for a spectral range, the data for the range is included in any spectrum file created with a Save [Alt+S, A] operation. When Display/Save is unselected, the data for that particular range is not included in a saved spectrum file. This feature can be employed when analysis does not require the full range and a smaller spectrum file is sufficient. It can be useful when comparing data that was collected by two instruments with one having a limited spectral range. If you need to collect complete spectrum files but do not need the entire spectrum for the prediction process, see the Region Settings option in the chemometric prediction. You can also use the Instrument Control to truncate ranges from spectrum files. When you perform a View Spectrum File [Alt+F, F] operation followed by a Save [Alt+S, A] operation with settings in the Instrument Control other than full-range, you can remove ranges from the data file. All changes made to the Instrument Control are stored in the project when you perform a Save Project [Alt+F, S] operation. The Instrument Control window permits you to modify the integration time for the VNIR range and the gains and offset for the SWIR1 and SWIR2 ranges. Changes will affect all subsequently saved spectrum files.



Figure 3.28: Instrument Control



35



Chapter 3: Menus



Start Logging Events [Alt+P, S] The Project > Start Logging Events item relates to compliance with the Food and Drug Administration’s (FDA) Code of Federal Regulations (CFR) 21 Part 11. New log files are created for each session with random file names and are never duplicated. Log files are accessible by privileged users only. The Indico Pro software cannot modify or overwrite data files after creation. Log files contain: „



Date and time information



„



User name and ID information



„



Computer name and domain



Once a log file is closed it can't be reopened. It can be viewed by using the viewing project properties. Any number of log files can be created. To start a log file, select Project > Start Logging Events. Log files are automatically given unique random file names all with the .asl extension. The log file will remain open until the project is closed or until you select Project > Stop Logging Events.



Serial Pulse [Alt+P, E] The Project > Serial Pulse [Alt+P, E] item opens a window which allows you to configure the COM port interface needed as it relates to an external trigger and other accessories. The purpose of the serial pulse is allow an instrument with the Indico Pro software to be used with automation. It can be tied in with conveyor belt controls, accessories, external light sources, etc. For example, the control for a conveyor belt can tell the Indico Pro software through input signal that the sample is in position for a spectral measurement. Once the Indico Pro software and the instrument are finished, they can tell the control that the conveyor needs to move a new sample into place. The Indico Pro software can generate a serial pulse (null character or space character) when spectral data are collected. The Indico Pro software can also be triggered to collect a spectrum by an externally generated serial pulse or space character. The Serial Pulse supports an Output Mode and an Input Mode.



Indico® Pro User Manual



36



Figure 3.29: Serial Pulse „



Output Mode—The Indico Pro software instructs the COM port to generate a trigger signal (a serial pulse or character) on every spectrum collection (Take a Scan [Alt+S, T]). It could be used to turn on an external light source. The Generate on “Save Spectrum” Only option allows you to send a trigger signal only when a Take a Scan [Alt+S, T] operation is set up to save the spectrum.



„



Input Mode—The Indico Pro software takes a spectrum when the trigger signal (a serial pulse or character) is received on the internal serial port. This might be used when an accessory, such as an external light source, has an on trigger; as soon as the external accessory is stable, it tells the Indico Pro software that it is okay to perform a Take a Scan [Alt+S, T] operation, which then gets communicated to the instrument. The Save Spectrum after Collection option is used with the Auto Collect Timer [Alt+T, A] [Ctrl+A] to assure that the input trigger also saves the new spectrum with a unique name.



You need to specify the following: „



Serial port



„



Trigger character



„



Bit-rate—A pulse with bit-rate 110 will be approximately 0.09 seconds long. Pulse Width = 1 / Bit-Rate * 10



You might need to use the Windows Device Manager to point the accessory to one port, from COM1 to COM9.



37



Chapter 3: Menus



Prompt Before New Reference [Alt+P, S] The Project > Prompt Before New Reference [Alt+P, S] toggle is a safety feature. When this is active, you are prompted to confirm any Take a Baseline [Alt+S, B] [Ctrl+R] operation before it begins. Its purpose is to prevent changing of the reference information accidently.



3.4 Display Menu The Display menu can be reached using the mouse or Alt+D. It includes the items: „



“Axes [Alt+D, A]” on page 39



„



“Digital Numbers (DN) [Alt+D, D]” on page 39



„



“Reflectance [Alt+D, R]” on page 40



„



“Transmittance [Alt+D, T]” on page 40



„



“Log 1/R [Alt+D, L]” on page 40



„



“Log 1/T [Alt+D, G]” on page 41



„



“Show Wave Number [Alt+D, W]” on page 41



„



“Show Spectrum Properties [Alt+D, P] [Ctrl+P]” on page 41



„



“Show File List [Alt+D, F]” on page 42



„



“Splice Correction [Alt+D, C]” on page 43



„



“Show Instrument Spectrum [Alt+D, I]” on page 43



„



“Show Chromophores/Overtones [Alt+D, H]” on page 43



Figure 3.30: Display menu



Indico® Pro User Manual



38



Axes [Alt+D, A] The Display > Axes item allows you to display different regions of the spectrum in more detail. If the spectrum file has other regions available, use the Display > Axes item to adjust which regions are shown. This setting is for display purposes only. It does not reduce the size of the spectrum file. If you want to truncate a data file from spectral ranges that are not of interest, use the Instrument Control [Alt+P, I] operation.



Figure 3.31: Axes



Digital Numbers (DN) [Alt+D, D] The Display > Digital Number (DN) item changes the display of the spectrum into its raw digital numbers as provided by the instrument’s analog-to-digital converters after dark current has been subtracted. Each 1 nm sample of the spectrum has a 16-bit number associated with it that corresponds to the signal level at that wavelength uncorrected for wavelength-dependent instrument response. All subsequent spectral information, such as reflectance and transmittance, is derived from these raw digital numbers. The raw DN spectrum has not been ratioed against a white reference spectrum, so instrument characteristics such as absorption features in the fiber optic cable have not been eliminated. Raw DN data are a function of the characteristics of the light source used for the measurement, the circuitry and optics within the instrument, and the nature of the target material. Probe characteristics, fiber optic transmission, grating efficiency, and detector sensitivity vary with wavelength. Thus, the shape of raw spectra will often be very different from the shape of corrected spectra, which show characteristics of the sample only.



39



Chapter 3: Menus



Reflectance [Alt+D, R] The Display > Reflectance item changes the display of the spectrum as appropriate for reflectance, whereby the light source and instrument contributions to raw spectra are automatically removed. The Display > Reflectance > Percent item changes the reflectance units to a percentage. Reflectance is a measure of the fraction of incident light reflected from a material. The reflectance spectrum is an inherent property of a material, which means that its characteristic exists independent of the light source. Reflectance is computed by dividing the raw spectrum of the target sample by the white reference spectrum. This operation removes the instrument and illumination characteristics from the spectrum, leaving only the sample characteristics. Reflectance spectra require a baseline reference readings from a white reference. By computing the ratio of the raw, dark current-corrected spectrum of the sample to that of the white reference, the characteristics of the instrument and the illumination source are canceled out. The resultant spectrum reveals characteristics of the sample only. It is important that the physical geometry between a reflectance probe and viewing surface be the same when taking reference readings as when taking sample readings.



Transmittance [Alt+D, T] The Display > Transmittance item changes the display of the spectrum as appropriate for transmittance, whereby the light source and instrument contributions to raw spectra are automatically removed. The Display > Transmittance > Percent item changes the transmittance units to a percentage. Transmittance is a measure of the fraction of incident light passing through a material. The transmittance spectrum is an inherent property of a material, which means that its characteristic exists independent of the light source. Transmittance is computed by dividing the raw spectrum of the target sample by the white reference spectrum. This operation removes the instrument and illumination characteristics from the spectrum, leaving only the sample characteristics. Transmittance spectra require white reference readings that may be taken from various fluids, including pure water or empty air. It is critical that transmittance probes be kept as clean as possible and that the same probe and reference are used for any series of spectra that will be compared. By computing the ratio of the raw, dark current-corrected spectrum of the sample to that of the reference, the characteristics of the instrument and the illumination source are canceled out. The resultant spectrum reveals characteristics of the sample only.



Log 1/R [Alt+D, L] The Display > Log 1/R item changes the display of the spectrum as appropriate for the log of inverse reflectance, whereby the light source and instrument contributions to raw spectra are automatically removed.



Indico® Pro User Manual



40



Log 1/T [Alt+D, G] The Display > Log 1/T item changes the display of the spectrum as appropriate for the log of inverse transmittance, whereby the light source and instrument contributions to raw spectra are automatically removed.



Show Wave Number [Alt+D, W] The Display > Show Wave Number item changes the display of the spectrum to show frequency in units of cm-1.



Show Spectrum Properties [Alt+D, P] [Ctrl+P] The Display > Show Spectrum Properties item displays information associated with the captured spectrum relating to the instrument, such as the number of detectors, their wavelength ranges, and the wavelength increment. The Display > Show Spectrum Properties item also provides access to the material report information, whereby you can print or export header and spectral data in tabular format.



Figure 3.32: Spectrum Properties



41



Chapter 3: Menus



Show File List [Alt+D, F] The Display > Show File List item opens a window that allows you to select which spectrum files are displayed and what colors and properties its display line should have. This item is also used to remove a spectrum file from the project. „



To change how a spectrum file is displayed, highlight it in the Files Currently Displayed section. Select a color and line type from the menus in the Line Settings section. Click Apply.



„



To hide a spectrum file from the combined display graph, highlight it in the Files Currently Displayed section. Select the down arrow to move the file to the Files Available for Display section.



„



To remove a spectrum file from the project, highlight it in the Files Available for Display section and click Remove.



Figure 3.33: Select Files for Display



The legend with the color coding of the spectral samples appears in the upper-right corner of window for the display files, as shown in Figure 3.34. When you are viewing multiple spectrum files, use the Legend button in the upper-right corner of the graph to toggle the legend window.



Figure 3.34: Display Spectrum Legend toggle button



Indico® Pro User Manual



42



Figure 3.35: Display Spectrum Legend window



Splice Correction [Alt+D, C] The Display > Splice Correction item allows you enter a value for the number of spectra used in averaging. Splice correction is for smoothing over the splice points between each instrument (VNIR, SWIR1, and SWIR2). This is called a data smoothing effect. It is usually only used in presentations and does not help the overall data you are interpreting.



Figure 3.36: Splice Correction



Show Instrument Spectrum [Alt+D, I] The Display > Show Instrument Spectrum item superimposes the last spectrum that the Indico Pro software captured on top of the spectra that are displayed from the Show File List [Alt+D, F] operation.



Show Chromophores/Overtones [Alt+D, H] The Display > Show Chromophores/Overtones item plots the data from the spectrum into a format that highlights its relevant chromophores and overtones, which typically are the absorption regions. Figure 3.38 shows the Near-IR absorption bands, while Figure 3.37 shows what the Indico Pro software might output for a sample spectrum.



43



Chapter 3: Menus



Figure 3.37: Chromophores and overtones



Indico® Pro User Manual



44



Figure 3.38: Near-IR absorption bands



45



Chapter 3: Menus



CH H



CH3



700



CH



CH2



ArCH



ArOH



ROH



H20



800



CH



ArOH



CH2



900



CH3



ArCH



RNHR1



H20



ROH



CH



OH H



3rd Overtone



NH NH



1000



RNH2



1110



ArCH



2nd Overtone



3rd Overtone 2nd Overtone



RNH2



3rd Overtone



OH



4th Overtone



THIRD OVERTONE REGION



CH3



1200



CH2



CH



CH



2nd Overtone



1300



1500



CONHR



CH



1400



CH3



CH2



RNH2



CONH2



ArOH



NH



1st Overtone



ROH



H20



CH



1st Overtone Combinations



OH



1st Overtone



SECOND OVERTONE REGION



1600



ArCH



1700



CH3



CH2



CH



SH



CH



1st Overtone



SH S



1st Overtone Overtone



1800



1



1900



2100



2200



CC



CHO



RNH2



H20



Combinations



2300



CH3



2500



Combinations



CH + CC



2400



CH



CH2



Combinations



CH + CH



NH + OH



NH



Combinations



CONH2(R)



ROH



OH



Combinations



2000



CONH2



RCO2R



RCO2H



ROH



H20



C=O



2nd Overtone



FIRST OVERTONE REGION



COMBINATION BANDS REGION



Data sources for Figure 3.38 and the Display > Show Chromophores/Overtones feature: „



Ellis, J.W. (1928) Molecular Absorption Spectra of Liquids Below 3 m, Trans. Faraday Soc. 1928, 25, pp. 888-898.



„



Goddu, R.F. and Delker, D.A. (1960) Spectra-structure correlations for the Near-Infrared region. Anal. Chem., vol. 32 no. 1, pp. 140-141.



„



Goddu, R.F. (1960) Near-Infrared Spectrophotometry, Advan. Anal. Chem. Instr. Vol. 1, pp. 347-424.



„



Kaye, W. (1954) Near-Infrared Spectroscopy; I. Spectral Identification and analytical applications, Spectrochimica Acta, vol. 6, pp. 257-287.



„



Weyer, L. and Lo, S.C. (2002) Spectra-Structure Correlations in the Near-Infrared, In Handbook of Vibrational Spectroscopy, Vol. 3, Wiley, U.K., pp. 1817-1837.



„



Workman, J. (2000) Handbook of Organic Compounds: NIR, IR, Raman, and UV-VIs Spectra Featuring Polymers and Surfactants, Vol. 1, Academic Press, pp. 77-197.



3.5 Chemometrics Menu The Chemometrics menu can be reached using the mouse or Alt+C. It includes the items: „



“Setup [Alt+C, S]” on page 49



„



“Predict [Alt+C, P]” on page 49



„



“Reload Model Files [Alt+C, M]” on page 54



„



“Predict from File [Alt+C, F]” on page 55



Figure 3.39: Chemometrics menu



The Indico Pro software can work with models from other chemometric software, such as: „



GRAMS IQ



„



The Unscrambler® X



„



ASD Rapid Classifier (included with the Indico Pro software)



Working with The Unscrambler X Models The following sections describe how to work with The Unscrambler X models from CAMO Software: „



“Guidelines for The Unscrambler X Models” on page 47



„



“Using the Unscrambler X Prediction Engine or Unscrambler X Classification Engine Models” on page 47



Indico® Pro User Manual



46



Guidelines for The Unscrambler X Models If you plan to use the Indico Pro software with models created in The Unscrambler X, follow these guidelines when creating or running your models in The Unscrambler X: „



Install the 32-bit versions of the Unscrambler X Prediction Engine (OLUPX) and Unscrambler X Classification Engine (OLUCX), even on a 64-bit computer. The 64-bit versions have not been tested with the Indico Pro software.



„



Start with reflectance or log (1/R) data, then apply pretreatments, if needed.



„



The Indico Pro software uses the first model in a .unsb file. We recommend that you save any model you want to use with the Indico Pro software in a file by itself.



„



If you are using version 10.1 of The Unscrambler X, you cannot use the MSC pretreatment in models that you want to use in the Indico Pro software.



„



The Indico Pro software cannot use password-protected .unsb files.



„



The Indico Pro software has been tested with and supports PLS-1 and PLS-2 prediction models and PCA classification models. Other model types have not been tested and are not officially supported.



„



Models built in The Unscrambler version 9.8 and earlier will not run with Indico Pro version 6.0.6. You must convert earlier models to version 10 format using a file converter available from CAMO.



„



Indico Pro version 6.0.6 supports running multiple prediction models at the same time.



„



For prediction models, save the entire model in The Unscrambler X, not the short model, because the short model does not support the deviation that the Indico Pro software displays.



Using the Unscrambler X Prediction Engine or Unscrambler X Classification Engine Models You can use models created with the Unscrambler X software with the Indico Pro software. For information about how to create models that work with the Indico Pro software, see “Guidelines for The Unscrambler X Models” on page 47. Be sure you know where the engine you want to use is installed. When creating a new project, you must select the .dll file for the engine. To use the Unscrambler X Prediction Engine or Unscrambler X Classification Engine models: 1. Start a new project and give it a name or open an existing model. 2. Select Chemometrics > Setup. 3. In the Chemometrics window, select or enter the options you want.



47



Option



Description



Project Predictors



Select each type of model you plan to use in this project.



Selected Predictors



Select the specific model you want to use now.



Significant Figures



Select the number of digits after the decimal point that you want to display in reports.



Unscrambler X Spectrum Format



Select the type of data used in The Unscrambler X model. The model must use either reflectance or log (1/r) format. Your spectral data must use the same format. Chapter 3: Menus



4. Click Add. 5. Navigate to and select the models you want to use. •



You can select more than one model file.



6. Click Open. 7. Click OK. 8. Navigate to and select the .dll file for the engine you are using. •



You only have to do this when you create a new project. The .dll is in the installation folder with the engine.



•



For the Unscrambler X Prediction Engine, select OLUPX32.dll.



•



For the Unscrambler X Classification Engine, select OLUCX32.dll.



9. Click Open. 10. Take a new baseline. •



See “Taking a Baseline” on page 6.



11. Do one of the following. To use spectra that you are collecting To use spectra saved in a file now 1. Click Reflectance or log (1/r) to set the spectral data to the format that matches the model format 2. Click Predict. • The button stays selected until you click it again. • The software will predict based on the current spectrum and continues to use the model to predict for each new spectrum collected. 3. Click Scan. • If the format of the spectral data matches the format of the model, the Prediction Results window displays with the results. 4. If you receive an error message about the data format, click Reflectance or log (1/r) to set the spectral data to the format that matches the model format. 5. When you are finished using the prediction model, click Predict.



1. Click Predict. • The button stays selected until you click it again. 2. Click Predict From File. • The button stays selected until you click it again. 3. Navigate to and select the spectrum file. 4. Click Open. • If the format of the spectral data matches the format of the model, the Prediction Results window displays with the results. 5. If you receive an error message about the data format, click Reflectance or log (1/r) to set the spectral data to the format that matches the model format. 6. Click Scan and select the spectrum file again. 7. To predict from another file, click Scan and select the spectrum file. 8. When you are finished using the prediction model, click Predict, then click Predict From File.



•



The Prediction Results display with your results in either the Classify or Quantify tab.



•



If you want to generate a report, click the Report Options tab.



•



If you are using the Unscrambler X Classification Engine, you can change the Significance by clicking Scan and either collecting spectrum again or reselecting the spectrum file.



12. Click Close.



Indico® Pro User Manual



48



Setup [Alt+C, S] The Chemometrics > Setup item establishes which chemometrics software package should be used to develop the models for the predictions. The Unscrambler X models will only work if corresponding engine (Prediction or Classification) is installed on the instrument controller. When using the ASD Rapid Classifier, the Significant Figures field specifies how many digits to the right of the decimal point are saved in the spectrum files. This features truncates the values and performs no rounding.



Figure 3.40: Chemometrics window



Predict [Alt+C, P] The Chemometrics > Predict item is used to capture a spectrum from a target sample, apply the chemometric models, and return prediction results. After selecting this item, the software stays in “predict mode” and will apply the prediction to any new spectra collected. To turn this off, select the menu item again or click Predict. The Prediction Results window contains four tabs:



49



„



“Classify” on page 50 tab



„



“Quantify” on page 50 tab



„



“Model Info” on page 50 tab



„



“Report Options” on page 51 tab



„



“Region Settings” on page 53 button, only with ASD Rapid Classifier models Chapter 3: Menus



Classify The Classify tab of the Prediction Results window displays the results of comparing the spectrum of a target sample against the models. A pass/fail designation is provided for all models in the project. The Classify tab is not available when using the quantify models.



Figure 3.41: Prediction Results: Classify



Quantify The Quantify tab of the Prediction Results window displays the results of comparing the spectrum of a target sample against the models. A quantity designation is provided for all models in the project. The Quantify tab is not available when using the classification models.



Model Info The Model Info tab of the Prediction Results window provides more information about the models in the project used for prediction.



Figure 3.42: Prediction Results: Model Info



Indico® Pro User Manual



50



Report Options The Report Options tab of the Prediction Results window displays options for the report information that is stored and printed. The Indico Pro software provides the capability to print and preview prediction results in a custom format. The report output can be customized by selecting the items in the Displayed Fields section. The report configuration can be saved for other prediction sessions by selecting the Save as Default option.



Figure 3.43: Prediction Results: Report Options



The Print button sends the Material Report to a specified printer. The Preview button opens a Preview window allows saving, printing, and navigation of the report.



51



Chapter 3: Menus



Figure 3.44: Prediction Results: Material Report



From the Preview window: „



Select the File > Save item to save the report to text in a comma or tab delimited format.



„



Select the File > Print item to print the report to a specified printer.



„



To navigate the report click the navigate buttons: First page, Previous page, Next page, and Last page. To enhance the viewing of the report use the Zoom In and Zoom Out buttons.



When the prediction is complete, click Material Data and the following data entry form is displayed.



Indico® Pro User Manual



52



Figure 3.45: Prediction Results: Material Data



Use this form to enter a description about the prediction. If the Save as Default option is selected, the description data will be saved and displayed for subsequent predictions. The Save button saves the prediction result data with the spectral data. When the prediction is saved and Auto Save Results is checked, a prediction report in the specified format will be automatically saved to the report subfolder: „



If the format is Text, then the file is the same name as the prediction file with a .txt extension.



„



If the format is Comma Delimited, then the file is the same name as the prediction file with a .csv extension.



„



If the format is Tab Delimited, then the file is the same name as the prediction file with a .tsv extension.



„



If the format is Comma Delimited Log, then the file is the date and time with a .csv extension.



For example: Auto Save Results is selected and the output format is text. A prediction is saved as sample00001.asd and the prediction report is saved automatically in the report subfolder as sample00001.txt. When using the Auto Save Results features of Indico Pro software, files may be overwritten. Be careful not to overwrite files used in building models.



Region Settings The Region Settings button is used only with ASD Rapid Classifier models. It appears in the Prediction Results tabs and opens a subsequent window. Its purpose is to allow you to establish spectral regions for inclusion and exclusion for the prediction process. An example of this could be the transition regions between VNIR and SWIR1 and between SWIR1 and SWIR2, where you might not want a sample’s spectrum compared to the model. Another example could be to exclude wavelength regions that are not of interest for your sample classification. An advantage to doing this here rather than in the Instrument Control [Alt+P, I] is



53



Chapter 3: Menus



that this does not truncate the spectra range of any saved files. The data file can contain the full spectrum for use in other analysis and tests. When establishing regions, always start with the smallest wavelength and make your regions in sequence. Specifically, if your first region happens to be defined at 1300 nm, you will not be able to create a subsequent region anywhere below 1300 nm. Instead, your must redefine your first region to be the lowest wavelength and tweak the other regions accordingly to get them into sequence. The spectral regions cannot overlap.



Figure 3.46: Rapid Classifier Region Settings „



Step—A step of 1 includes all data points. To smooth the data, increase the step to the desired smoothing effect. For example, to smooth the data every 10 nm, change the step to 10.



„



Matches—A match of 1 will display the best match according to the Threshold. To display the top four matches, set the matches to 4. The matches will be sorted from best match to worst match.



„



Threshold—The threshold is the mathematical analysis of the best fit or match to the selected model library. The higher the threshold, the lower the successful matches. The lower the threshold, the higher the successful matches.



When editing the values for threshold, step, and matches, the changes affect the whole column.



Reload Model Files [Alt+C, M] The Chemometrics > Reload Model Files item is available when ASD Rapid Classifier is selected as the predictor from Chemometrics > Setup. This menu item retrieves model information from external chemometric applications. Indico® Pro User Manual



54



This is used when the chemometric application has modified the models for prediction that the Indico Pro software requires. In such an event, you should perform this Reload Model Files operation so that the correct prediction models are in memory.



Predict from File [Alt+C, F] The Chemometrics > Predict from File item lets you run prediction models from existing spectrum files. You need to have spectrum files available whose composition is known. After selecting this item, the software stays in “predict from file mode” and will apply the prediction to any new spectrum file opened. To turn this off, select the menu item again or click Predict From File. The purpose of this tool is to allow testing of the prediction models without requiring real-time data from the instrument. Instead, you use the Predict from File operation to compare spectrum files of known composition to the model to verify that the prediction is accurate. Another use of the Chemometrics > Predict from File item is to test stored spectrum files against other models that analyze different features in the spectral range. Also, it can separate the collection of spectra from the analysis, which might make more efficient use of equipment and personnel.



3.6 Run Menu The Run menu can be reached using the mouse or Alt+R. It includes the items: „



“ASD to SPC Converter [Alt+R, S]” on page 55



„



“ASD to JCAMP Converter [Alt+R, J]” on page 56



„



“ASD to ASCII Converter [Alt+R, A]” on page 57



„



“ASD to U-ASCII Converter [Alt+R, U]” on page 58



Figure 3.47: Run menu



ASD to SPC Converter [Alt+R, S] The Run > ASD to SPC Converter item opens a window to allow conversion of ASD spectral data files to Thermo GRAMS/AI™ SPC data files. SPC files will be created using the ASD file name and the .spc extension.



55



Chapter 3: Menus



Figure 3.48: ASD to SPC



You can convert more than one ASD spectral data file at once. An important ASD to SPC converter feature is the ability to output to a single SPC file. It is important to select Output to Single File or you will be importing one file at a time.



ASD to JCAMP Converter [Alt+R, J] The Run > ASD to JCAMP Converter item opens a window to allow conversion of ASD spectrum data files to JCAMP data files. You can convert more than one ASD spectrum data file at once. JCAMP files will be created using the ASD file name and the .dx extension. Files can also be converted and routed to a single file. You are prompted for a new file name.



Indico® Pro User Manual



56



Figure 3.49: ASD to JCAMP



ASD to ASCII Converter [Alt+R, A] The Run > ASD to ASCII Converter item opens a window to allow conversion of ASD spectrum data files to ASCII files. You can convert more than one ASD spectral data file at once.



57



Chapter 3: Menus



Figure 3.50: ASD To ASCII



ASD to U-ASCII Converter [Alt+R, U] The Run > ASD to U-ASCII Converter item opens a window to allow conversion of ASD spectrum data files to Unscrambler X ASCII data files. Unscrambler X ASCII files will be created using the ASD file name and the .inp extension. Files can also be converted and routed to a single file. You are prompted for a new file name.



Indico® Pro User Manual



58



Figure 3.51: ASD to Unscrambler X ASCII



It is important to select Output to Single File or you will be importing one file at a time.



GramsAI The Run > GramsAI item starts the GRAMS/AI application from Thermo Scientific. The item only appears in the menu when this application has been purchased and installed. GRAMS stands for “Graphic Relational Array Management System,” and AI stands for “Active Interface.” GRAMS/AI is a 32-bit Windows-based suite of software tools for analyzing and processing spectral data. GRAMS/AI's data processing library includes peak-fitting, data smoothing, quantitative analysis, peak picking, and integration, as well as specific routines for FT-IR, NMR, diode-array UV-VIS, NIR, Raman, GC-MS, and chromatography. Refer to the GRAMS/AI documentation for more information.



59



Chapter 3: Menus



Figure 3.52: GramsAI



PLSplus/IQ Navigator The Run > PLSplus/IQ Navigator item starts the application. The item only appears in the menu when this application has been purchased and installed. Refer this application’s user manual for more information.



Indico® Pro User Manual



60



3.7 Timers Menu The Timers menu can be reached using the mouse or Alt+T. It includes the items: „



“Reference Timer [Alt+T, R] [Ctrl+B]” on page 61



„



“Auto Collect Timer [Alt+T, A] [Ctrl+A]” on page 62



„



“User Defined Timer [Alt+T, U]” on page 64



Figure 3.53: Display menu



Reference Timer [Alt+T, R] [Ctrl+B] The Timers > Reference Timer item opens a window that permits setting a reminder for the Take a Baseline [Alt+S, B] [Ctrl+R] operation. The measurements collected by the instrument can be affected by many factors, such as instrument warm-up. A new (white) reference should be established frequently during sampling. 61



Chapter 3: Menus



Figure 3.54: Reference Timer Setup



The Timers > Reference Timer items allows you to establish the time interval between white reference measurements. When the interval is reached, you are prompted with a window.



Figure 3.55: Reference Timer prompt



If the Timers > Reference Timer items was enabled and you later disable it, you are prompted to confirm this selection.



Figure 3.56: Reference Timer disable prompt



Auto Collect Timer [Alt+T, A] [Ctrl+A] The Timers > Auto Collect Timer is a feature for storing the files with a base name and automatic increment number.



Indico® Pro User Manual



62



This save spectrum approach is the simplest way to store a single spectrum file. However, most projects require a sequence of spectrum files. This tool is an efficient way of collecting those spectra with minimal user input.



Figure 3.57: The Auto Save Timer Setup window „



The Take a Spectrum Every field is a timer for automated operation. You can leave these at 30 seconds if you are manually starting the sampling process.



„



The Number of Files to Save field indicates how many files will be saved in this timer session. When the Ask Before Saving Each File option is selected, this setting indicates how many times you will be prompted to save a spectrum.



„



The Description field can contain whatever information you would like. What is typed here is what will show up in the Rapid Classifier prediction window. If you don't fill this out, the ASD Rapid Classifier has nothing to reference and therefore will not predict anything. ASD Rapid Classifier is a library that requires references, which it gets from the description field.



„



The Base File Name field is used in naming all new spectrum files while in the automated operation.



„



The Starting Sequence Number field is used with the Base File Name field to uniquely name each file in the sequence.



„



The Spectrum Saving Options: •



The Automatic Save option is intended for use with the Enable Timer option. Depending upon the time interval, it will regularly save spectrum files. This is intended for automatic operation.



•



The Ask Before Saving a Spectrum option will prompt you before taking the next spectrum. This gives you time to position the probe between samples. •



63



When collecting training sample spectra for a prediction model, do not leave the Ask Before Saving Each File option unselected. In this mode, it is necessary to move the sample slightly between measurements for good coverage of the variation in spectra from one spot to the other. Chapter 3: Menus



„



•



The Don’t Save Spectra option will allow spectra to be collected in an automatic fashion but does not save the files.



•



The Pressing Space Bar Saves Spectrum option will use the Base File Name and Sequence Number, but expects you to press the space bar before a new spectrum is collected and saved to a file. Alternatively, you can use the external trigger instead of pressing the space bar.



The Enable Timer option is used with the Automatic Save option. This is not required with the manual operation modes, such as Pressing Space Bar Saves Spectrum or Ask Before Saving a Spectrum options.



User Defined Timer [Alt+T, U] The Timers > User Defined Timer item opens a window that permits setting a reminder for any operation. You can set up to five different reminders. An example of a typical reminder could be to clean the Spectralon reference panel daily or weekly, depending on instrument usage. When you specify a reminder, you can give it a title as well as a description. The title appears in the blue bar of window that opens when the timer triggers. The description appears within the content area of the window. Figure 3.58 shows the User Defined Timer window with one reminder specified. Figure 3.59 shows the window that appears when that reminder triggers. Reminder settings can be hourly, daily, weekly, monthly, and yearly. The tolerance for the timer is +/- 1 minutes. The timer is dependent on the system clock of the instrument controller. If the Indico Pro software is shutdown for a period of time and then is turned back on, only the first occurrence of user defined timers will trigger. For example, assume you established two user defined timers: „



Reminder #1 notifies you at 10 minutes past every hour.



„



Reminder #2 notifies you every day.



If the Indico Pro software was shutdown at 11 a.m. on Monday and started again at 2 p.m. on Thursday, you would receive at most two notifications: „



Reminder #1 triggers for the past-due event from Monday 11:10 a.m. No other reminder #1 is given. The next reminder #1 occurs at 2:10 p.m. on Thursday.



„



Reminder #2 triggers for the past-due event from Tuesday. No reminder #2 is given for Wednesday. Depending on the time of day for the daily reminder, the next reminder #2 occurs at that time on Thursday or Friday.



Indico® Pro User Manual



64



Figure 3.58: User Defined Timer



Figure 3.59: User Defined Timer that has been triggered



3.8 GPS Menu The Indico Pro software can communicate with an external global positioning system (GPS) which plugs into one of the ports of the instrument controller. You need a National Marine Electronics Association (NMEA) compatible GPS device. The Indico Pro software requires the output of the GPS device to be in the NMEA format. Check your GPS device documentation for output and port settings. The GPS menu can be reached using the mouse or Alt+G. It includes the items:



65



„



“Setup [Alt+G, S]” on page 66



„



“Activate [Alt+G, A]” on page 67 Chapter 3: Menus



„



“Monitor [Alt+G, M]” on page 67



Figure 3.60: GPS menu



When all aspects of the configuration (in the Indico Pro software, the instrument controller, the GPS device, and the cabling between) have been established, the GPS can provide positioning information to the Indico Pro software. The GPS status is located at the bottom of the main window. The status displays the Latitude, Longitude and Elevation of fixed GPS data. When the GPS data are not fixed, these fields will be blank. The GPS information will also be made available to the spectra when it’s saved to a file. The GPS settings are stored to the project file whenever you perform a “Save Project [Alt+F, S]” on page 19 operation.



Setup [Alt+G, S] The GPS > Setup item opens a window that permits setting communication parameters used by the Indico Pro software and the instrument controller to communicate with the external GPS device.



Figure 3.61: GPS Settings



Indico® Pro User Manual



66



To set up a GPS device: 1. In the GPS Settings window, enter communication settings appropriate for your instrument controller’s port intended for use as well as the GPS device. •



Normally, the Baud rate, Data bits, Parity and Stop bits settings will remain the same as what is displayed in the window.



•



The Write to Log File is selected by default. When this field is selected and the GPS fixed data are enabled, an entry will be made to a daily log file (for example, 050302gps.log) when a spectrum is saved.



•



The Indico Pro software settings on the instrument controller and the ports that are used must match the actual port used as well as the settings of the GPS device.



2. Connect an appropriate cable between the instrument controller’s port and the GPS device. •



You may need a serial-USB converter depending upon the instrument controller and GPS device.



3. Enable the GPS functionality in the Indico Pro software by selecting either: •



GPS > Activate menu item



•



Alt+G, A key combination



4. Refer to the manual of your GPS device for further instructions regarding usage and configuration.



Activate [Alt+G, A] The GPS > Activate item is a toggle to turn on and off the GPS communication from the Indico Pro software settings on the instrument controller. It also specifies whether or not: „



GPS data are displayed at the bottom of the main window.



„



GPS data are stored in any saved spectrum files.



Monitor [Alt+G, M] The GPS > Monitor item opens a window with current GPS information from the device. This option is only enabled with a GPS device has been configured and activated.



67



Chapter 3: Menus



Figure 3.62: GPS Monitor



3.9 Windows Menu The Windows menu can be reached using the mouse or Alt+W. It includes the items: „



Cascade - arranges all open spectrum windows such that one is on top of another.



„



Tile Vertical - arranges all open spectrum windows such that are placed next to one another but no window covers another.



„



Tile Horizontal - arranges all open spectrum windows such that they are stacked but with no window covering another.



These are standard features in most Windows compliant applications.



Figure 3.63: Windows menu



Indico Pro software has two main types of windows: the Instrument Display window and the Spectrum File Display window. „



Instrument Display shows whatever spectrum information has come from the last Take a Scan [Alt+S, T] or Continuous Collect [Alt+S, U] operation.



„



Spectrum File Display superimposes all spectra from files opened by the View Spectrum File [Alt+F, F] or Open Project [Alt+F, O] operations. Use the Close File Display [Alt+F, C] operation to remove spectra from being displayed or to remove spectra from the project.



Indico® Pro User Manual



68



When in the Spectrum File Display window, you can superimpose a reading from the instrument with the Show Instrument Spectrum [Alt+D, I] operation.



3.10 Help Menu The Help menu can be reached using the mouse or Alt+H.



Figure 3.64: Help menu



The Help menu contains: „



User Guide [Alt+H, U]: opens a PDF file containing the TerraSpec® Examiner User Manual.



„



Online Documentation [Alt+H, O]: opens your default browser and an HTML page. The page contains hyperlinks to the various ASD references manuals (in PDF format) that have been installed on your system. At minimum, you should have:



„



69



•



The hardware manual for your ASD instrument(s).



•



This TerraSpec® Examiner User Manual



•



The Installation Manual



•



The Accessories Manual



About Indico Pro [Alt+H, A]: opens a window that shows the instrument number and calibration information known to the Indico Pro software. This is the same information that is displayed at Indico Pro software start-up. The Indico Pro software application installed on your system has calibration to match your specific ASD instrument. This window helps you match the installation to the instrument.



Chapter 3: Menus



Figure 3.65: Help > About shows the instrument number and calibration information known to the Indico Pro software



3.11 Right-Click Menu The right-click menu is a context sensitive menu that can change depending upon where the cursor is located when you right-click. Some of the options include: „



“Undo Zoom” on page 71



„



“Customize” on page 71



„



“AutoScale” on page 72



„



“Mark Data Points” on page 72



„



“Grid Lines” on page 72



„



“Font” on page 72



„



“Restore Defaults” on page 73



„



“Add Note” on page 73



„



“Delete Note” on page 73



„



“Take a Scan” on page 74



„



“Take a Baseline” on page 74



Indico® Pro User Manual



70



Figure 3.66: Right-click menu



Undo Zoom The Instrument Display Graph and the File Display Graph can be zoomed to give a better view of spectral features. To enable zoom: 1. Position the cursor over the Instrument Display Graph or the File Display Graph. 2. Click and hold down the left mouse button. 3. Drag the zoom rectangle over the area you would like magnified. •



A magnifying glass icon will appear when the area is sized adequately.



4. Release the button to initiate the zoom mode. The Instrument Display Graph and the File Display Graph can be panned while in the zoom mode to give a better view of spectral features. Panning can be performed by using the mouse and the scroll bars, which appear at the right and below the selected graph. „



Use the up and down controls on the scroll bars to move the displayed waveform up or down.



„



Use the left and right controls on the lower scroll bar to position the waveform left and right.



„



The keyboard up, down, left, and right buttons can also be used to perform the panning operation.



To return to the normal display mode: 1. Position the mouse cursor over the Instrument Display Graph and the File Display Graph. 2. Right-click the mouse. 3. Select Undo Zoom from the menu.



Customize The Customize item from the right-click menu opens a tabbed window that allows you to change in one place many of the settings available through other menus. These include grid lines, fonts, marked data points, colors for spectrum lines, x-y axis extents, and other functionality of the graph object. 71



Chapter 3: Menus



AutoScale The data scaling for the Instrument Display Graph and the File Display Graph are fixed by default. Scaling the data based on the minimum and maximum values of the data (Auto Scaling) can be performed on either display independently. To select the AutoScale mode for the display: 1. Position the mouse cursor over the Instrument Display Graph or the File Display Graph. 2. Right-click the mouse. 3. Select AutoScale from the menu. To return to the normal display mode: 1. Position the mouse cursor over the Instrument Display Graph or the File Display Graph. 2. Right-click the mouse. 3. Select AutoScale from the menu.



Mark Data Points Individual data points can be highlighted in a given spectrum. 1. Position the mouse cursor over Instrument Display Graph or the File Display Graph. 2. Right-click the mouse. 3. Select Mark Data Points from the menu.



Grid Lines Grid lines can be displayed or removed. 1. Position the mouse cursor over Instrument Display Graph or the File Display Graph. 2. Right-click the mouse. 3. Select Grid Lines from the menu. •



Four options are available: •



Horizontal and Vertical



•



Vertical Only



•



Horizontal Only



•



No Grid Lines



4. Select the appropriate.



Font Graph text font can be changed. 1. Position the mouse cursor over Instrument Display Graph or the File Display Graph. 2. Right-click the mouse.



Indico® Pro User Manual



72



3. Select Font from the menu. •



Three options are available: •



Large



•



Medium



•



Small



4. Select the appropriate style.



Restore Defaults If you made any changes to the marking points, grid lines, or fonts, you can quickly return to the default settings with this option. 1. Right-click the mouse. 2. Select Restore Defaults from the menu.



Add Note Graph annotations can be added to the Instrument Display Graph and the File Display Graph. These notes are not saved with the spectrum. The notes are used for the purpose of spectrum comparison and to provide a means of differentiating various points on the display. The annotation points are in reference to the actual data points, so they will change position as the graph is scaled, resized, etc. To add a note: 1. Position the mouse cursor over the Instrument Display Graph or the File Display Graph. 2. Right-click the mouse. 3. Select Add Note from the menu.



Figure 3.67: Add Note to Spectrum Graph



4. Enter the note text in the text box. •



The note color is visible to the right of the Note Color Button.



5. Click Note Color to change the color of the displayed note.



Delete Note 1. Position the mouse cursor over display graph. 2. Right-click. 3. Select Delete Note from the menu. • 73



The Note is deleted from the graph. Chapter 3: Menus



Take a Scan The Take a Scan item from the right-click menu is the same as the Spectrum > Take a Scan [Alt+S, T] item.



Take a Baseline The Take a Baseline item from the right-click menu is the same as the Spectrum > Take a Baseline [Alt+S, B] [Ctrl+R] item.



Indico® Pro User Manual



74



Chapter 4: Indico Pro Software Quick Reference To use the shortcuts: „



Alt key shortcuts—Press and hold the Alt key and press the letter key.



„



Ctrl key shortcuts—Press and release the Ctrl key, then press the letter key.



Table 4.1: Indico Pro software shortcut quick reference Function



Shortcut key



New Project



Alt+F, N



Open Project



Alt+F, O



Save Project



Alt+F, S



View Spectrum File



Alt+F, F



Link File



Alt+F, L



Material Report



Alt+F, M



Exit



Alt+F, X



Take a Scan



Alt+S, T



Take a Baseline



Alt+S, B Ctrl+R



Continuous Collect



Alt+S, U



Sample Count/Average



Alt+S, C Ctrl+C



Derivative Gap



Alt+S, G



Dependent Variables



Alt+S, V



Save



Alt+S, V



Print Spectrum



Alt+S, P



Print Spectrum Properties



Alt+S, R



Printer Setup



Alt+S, S



Export Spectrum



Alt+S, E Ctrl+E



(Project) Properties



Alt+P, P



Indico® Pro User Manual



75



Table 4.1: Indico Pro software shortcut quick reference Function



Shortcut key



Start Logging Events



Alt+P, S



Serial Pulse



Alt+P, E



Prompt Before New Reference



Alt+P, B



Axes



Alt+D, A



Digital Numbers (DN)



[Alt+D, N



Reflectance



Alt+D, R



Transmittance



Alt+D, T



Log 1/R



Alt+D, L



Log 1/T



Alt+D,G



Show Wave Number



Alt+D, W



Show Spectrum Properties



Alt+D, P Ctrl+P



Show Splice Correction



Alt+D, C



Show Chromophores/Overtones



Alt+D, H



(Chemometrics) Setup



Alt+C, S



(Chemometrics) Predict



Alt+C, P



Reload Model Files



Alt+C, M



Predict From File



Alt+C, F



(GPS) Setup



Alt+G, S



(GPS) Activate



Alt+G, A



(GPS) Monitor



Alt+G, M



User Defined Timer



Alt+T, U



Reference Timer



Alt+T, R Ctrl+B



Auto Collect Timer



Alt+T, A Ctrl+A



Indico® Pro User Manual



76



Chapter 5: Chemometrics The Indico Pro software bridges the spectral information about a sample collected by an ASD spectrometer with the chemometrics applications that can perform qualitative analysis (classification) and quantitative analysis (concentration and an amount associated with the spectrum). The purpose of this chapter is to provide background on chemometrics and describe how this combination of chemistry and mathematics relates to the NIR analysis. It is divided into the following sections: „



“A Brief Explanation of Principal Component Analysis” on page 77



„



“Making an NIR Analyzer Work for You” on page 82



„



“Chemometrics Models” on page 85



„



“Off-the-Shelf Chemometrics Applications” on page 86



5.1 A Brief Explanation of Principal Component Analysis By David C. Hatchell, ASD Qualitative (classification) and quantitative (concentration) measurements can be made with visible and near infrared spectrometry through the use of regression methods with statistics, which is sometimes referred to as chemometrics. Many steps and methods may be used in chemometrics, depending upon the nature of the data and how well one step or method works over the other. One of the steps that is commonly used and often misunderstood is known as Principal Component Analysis (PCA). Many excellent texts cover this subject thoroughly, and you are encouraged to explore them. This section is intended to be a brief introduction of PCA in terms of how it relates to visible and near infrared spectrometry.



Indico® Pro User Manual



77



The LabSpec spectrometer (350-2500 nm) has thousands of wavelength channels. For simplicity, let’s assume that we are using a spectrometer that has only three wavelength channels.



Figure 5.1: Wavelength channels on a spectrometer



Figure 5.1 is basically what we would see on the screen for this three-channel spectrometer. A different way of viewing this data would be like Figure 5.2, where each wavelength channel is re-drawn with its own vertical axis rather than using a common vertical axis for all three.



Figure 5.2: Wavelength channels each on their own vertical axis



Still another way of viewing this data would be to join the vertices of the independent axis in an orthogonal, or non-correlating, manner as shown in Figure 5.3.



Figure 5.3: Orthogonal wavelength axis



Indico® Pro User Manual



78



We can find the intersection of the data points in this new three dimension space by drawing the box shown Figure 5.4, and that intersection is the circle at the corner of the box.



Figure 5.4: Intersection in the new three dimension space



In other words, we have created a new coordinate system, where all three data points are represented by one point at the circle with coordinates,



Case 1: Classification Model Suppose we are interested in developing the simplest of models, that is a classification model that will tell us if the material viewed by the spectrometer is material O or not. So, far we have only collected one spectrum that consists of the three data points mentioned above. Of course there is no such thing as a material that is perfectly homogeneous in terms of its physical structure and chemical distribution. So, spectral measurements for this material should be made at several locations. For each measurement, the data point will be located in a slightly different position in our three-channel-three-dimensional space. Let’s assume that the material produces a distribution of data points similar to the circles shown in Figure 5.5.



Figure 5.5: Distribution of data points



79



Chapter 5: Chemometrics



The line that is that explains most of the variance in the data are called the first principal component (PC1), or factor. After PC1 has been defined, the next best orthogonal line that helps define the second direction of maximum spread in the remaining part of the space is PC2. The next orthogonal line would be PC3, and then PC4 and so on, until the distribution of points was covered to our required accuracy threshold. For simplicity, however, let’s assume that we are satisfied with the threshold limits as indicated by PC1. By the way, these points used to build the PC’s are known as training data and the samples used for these points are called training samples. Now, we take spectra of unknown materials samples and see if the points fall within our defined threshold limits around PC1. If the fit is good such as the point indicated with the gray-filled circle, then the material is material O. If the fit is bad, such the point indicated by the X, then the material is not material O. A model for classifying many different materials, such as material O, material †, and material U, can also be created by finding the PC’s for each in this three-channel, three-dimensional space as shown in Figure 5.6.



Figure 5.6: PC’s for each of three channels



Case 2: Quantification Model Instead of classifying materials, suppose we want to predict the concentration of a different material O, †, and U evenly distributed throughout a sample. In this case, samples with different known concentrations of each material will be used for generating the training data. As with the reflectance spectral data, we can also create a three-dimension space for the concentrations of each material in each sample as Figure 5.7.



Figure 5.7: Different material O, †, and U space



Indico® Pro User Manual



80



The concentration coordinates of the point represented by the + symbol are then,



In our three-channel-three dimension space, the data points indicated by the symbols will be the result of the spectra mixture of all three materials in each sample as shown in Figure 5.8.



Figure 5.8: Spectra mixture of three materials



For example, the data point farthest to the right might be from a sample with a high concentration of material O, while the one farthest left could be from a sample with a low concentration of material O. As with the classification model, more than one point could be also collected on different positions of each sample to account for any variability in homogeneity. Again, the line that explains most of the variance in the data are the PC1 for Reflectance. If we continue graphing this concentration training data we’ll eventually create a distribution of data points as shown in Figure 5.9. The line that explains most of the variance in the data are the PC1 for concentration. Again, more PC’s can better define the distribution, but for simplicity, we’ll just use the first PC.



Figure 5.9: Distribution of data points from concentration training



Now, each reflectance data point corresponds to a concentration data point, +. So, we can create a new set of orthogonal coordinate axis comprised of the concentration PC versus 81



Chapter 5: Chemometrics



reflectance PC. However, optimally we would like to graph only those PC’s that show a strong relationship or correlation between the concentration PC’s and the reflectance PC’s. In other words, we only want those PC’s for which:



A PCA method known as Partial Least Squares Projection to Latent Structures, or PLS Regression, calculates and recalculates the PC’s until the optimal set is found, and then generates the regression model as shown below.



Figure 5.10: The regression model



The final regression line represents spectral reflectance versus concentration, and that line is the Model. Concentrations of an unknown sample can now be predicted by projecting its reflectance data point up to the model line, and over to the concentration line. It is important to note that in this brief introductory explanation of PCA methods, the numbers of wavelength channels, materials, and PC’s were limited to three dimensions for simplicity. Any number of dimensions is possible in mathematics. This is fortunate, because the 350-2500 nm version of LabSpec spectrometer has thousands of wavelength channels that can be used and because the Indico Pro software allows for recording the concentrations of up to one hundred different material components. It is also fortunate that current computers can keep track of them all.



5.2 Making an NIR Analyzer Work for You In recent years, NIR analysis has steadily grown in popularity because of its ability to quickly provide qualitative and quantitative information on many products, especially raw materials. To determine if NIR spectroscopy is a reasonable alternative to more traditional methods, many factors must be considered. These factors include: „



“Sample Characteristics” on page 83



„



“Experiment Configuration” on page 83



„



“Data Analysis” on page 84



Indico® Pro User Manual



82



Sample Characteristics The chemical constituents and physical phenomena of interest should have direct or indirect absorbance in the NIR region. Virtually all organic compounds do, particularly those with functional groups like hydroxyl, carboxyl, amine, and carbon-hydrogen. A good reference for researching near infrared spectra is The Atlas of Near Infrared Spectra, Bio-Rad Sadtler Division, Philadelphia, Pennsylvania. For calibration samples, the amount of analyte in the sample set should be above the detection limit and have sufficient variability. Some analytes are reportedly detectable at the ppm level. For most analytes, the nominal detection limit will be 1% or above. The analytical chemist must have an accurate independent method for measurement of the properties and must know the level of error in the reference methods. Errors in NIR prediction most often arise from errors in the reference methods, instability of the NIR spectrometer, and inappropriate choice of the calibration model. The samples used in the development of calibration sets must be representative. All the variations in the future unknown samples should be covered in the “training” calibration sets, for example, sample composition and particle size, homogeneity, and temperature variation at the working environment. As a rule of thumb, the more samples you have for the training set, the more reliable the calibration model.



Experiment Configuration When using an NIR analyzer, instrument characteristics such as sensitivity, resolution, and signal-to-noise ratio parameters need to be evaluated. The quality of these values is a function of the light source stability, optics throughput, dispersion/filter element accuracy, and detector sensitivity in the instrument. The choice of accessories is application dependent.



5.3 Liquid Samples For liquid samples, transmission and transflectance modes are commonly employed using fiber optic probes or cuvettes. The path length is sample dependent, usually ranging from 0.1 to 1 cm. The advantage of using a fiber-optic probe is that sample preparation is significantly reduced and noninvasive or nondestructive measurements become possible.



5.4 Solid Samples For solid samples, diffuse-reflectance spectra collected by a reflectance probe will provide information for analytes. Diffuse reflectance should be measured without interference from specular reflectance. The setup configuration, such as the angle of incident light and the distance of light illumination / collection ought to be consistent through all the measurements, including those taken in developing the calibration set and for predicting the future unknowns. For solid samples, the sample should be rotated and measurements done on different spots of the sample to average out the sampling error. A group of spectra may be averaged to increase the 83



Chapter 5: Chemometrics



signal-to-noise ratio. Random noise is reduced by the square root of the number of spectra averaged. For ASD’s NIR spectrometer, it takes 0.1 seconds to acquire one spectrum. Therefore, a 10 second measurement reduces the random noise by a factor of 10.



Data Analysis NIR spectroscopy is an extremely rapid method of measurement, capable of performing an analysis within a minute. The time-consuming part of NIR work is the data analysis phase, where chemists try to find the correlation between near-infrared spectral characteristics and the property, or properties, of interest as measured by more traditional methods. There are several commercially available software packages for doing this task. Data analysis involves the following: „



“Data Preprocessing” on page 84



„



“Outlier Detection” on page 84



„



“Building a Good Calibration Model” on page 84



„



“Validation” on page 85



„



“Prediction” on page 85



Data Preprocessing When the spectral data plots are presented, first determine if there is any baseline drift or slope in the spectra, which often occurs in diffuse-reflectance measurements. Baseline subtraction, first derivative and second derivative transformations may be performed to reduce these effects if necessary. There is a trade-off though, each successive degree of derivative that is taken introduces more noise into the spectral data.



Outlier Detection An outlier is a data point that falls well outside of the main population. Outliers result from lab measurement errors, samples from different categories, and instrument error. It is important to check for and remove outliers in both the training set and the set of unknowns that the calibration is to be tested on (see “validation” and “prediction”).



Building a Good Calibration Model This is one of the most important steps in NIR analysis. Developing a calibration model involves calculating the regression equation based on the NIR spectra and the known analyte information. The model is then used to predict the future unknowns. Multiple Linear Regression (MLR), Principal Component Regression (PCR) and Partial Least Squares (PLS) are commonly used linear calibration methods, along with Locally Weighted Regression (LWR) for nonlinear models. In developing a calibration model, several parameters are evaluated: factors (or primary components), loadings, and scores. When choosing the number of factors, avoid under-fitting, i.e. too few factors, and over-fitting, i.e. too many factors. If an insufficient number of factors are chosen, the prediction is not reliable because useful information has been left out. If too many factors are chosen, however, more uncertainty is included in the calibration set which will result in errors in prediction. Scores are used to check the sample homogeneity and possible clusters, while loadings are used to interpret how the variables are weighted in principal component space.



Indico® Pro User Manual



84



Validation The validity of the model must be tested. Usually the way this is done is to split the whole sample set into two sets; one set for calibration and the other for validation. If there are not enough samples, “leave-one-out” cross validation can be performed. This means leaving one sample out, using the rest of the samples to build a calibration model and then using the model to predict the one that was left out. The advantage of doing cross validation is that, unlike calibration with a full data set, the sample being predicted is not included in the calibration model. Thus, the model can be tested independently.



Prediction Finally, the calibration can be used to predict future unknowns, assuming that the unknowns are in the same sample population as those used in the calibration set. Whether the unknown is an outlier needs to be tested.



Summary Applying an NIR analyzer to a particular application requires the development of a reliable calibration model. The most important steps involve a thorough consideration of experimental design and multivariate calibration. Once this is established, one can enjoy the advantages of the NIR analysis. The speed of the analysis will save time and avoid many mistakes instantaneously. The speed advantage is so valuable to engineers involved with on-line process monitoring that instruments are routinely installed in the process line with feedback loops. With a NIR analyzer, such samples can be non-invasively analyzed on-the-spot, which can dramatically reduce costly and time-consuming laboratory analysis. The low absorptivity in the NIR region allows measurements to be taken on raw materials without elaborate sample preparation. NIR analysis finds a wide range of applications in food, agriculture, pharmaceutical, polymer, cosmetics, environmental, textile, and medical fields.



5.5 Chemometrics Models In order for any NIR analyzer to make quantitative measurements or qualitative discriminations, the instrument controller must have access to one or more chemometrics models, which represent the type of material being tested. The model is a mathematical construct that had been developed using samples of the same product or class of products. The instrument controller applies the model(s) to the target spectrum and returns a model result. A chemometrics model is developed by collecting spectral readings from a group of samples that display:



85



„



the maximum variability of the characteristic of interest, and



„



non-correlating or random variability in all other characteristics.



Chapter 5: Chemometrics



The same samples are submitted for independent testing to measure the characteristic of interest by a standard analytical method. The spectral data and independent test data are then analyzed using commercially available chemometrics software (see “Off-the-Shelf Chemometrics Applications” on page 86). The statistical processes used in quantitative spectral analysis include: „



multiple linear regression



„



classical least squares



„



inverse least squares



„



principal component regression



The statistical processes used in qualitative spectral analysis include: „



K-nearest neighbors



„



SIMCA



„



and others



When a sufficient number of samples has been collected and properly analyzed, a mathematical model is constructed that describes the relationship between specific spectral features and the sample characteristic of interest. Thereafter, a chemist or technician may quickly measure that same characteristic in a new target sample by applying the chemometrics model to the spectrum of the target sample. An NIR analyzer is also able to identify an unknown target sample if its spectral signature matches any of the models already developed.



5.6 Off-the-Shelf Chemometrics Applications The Indico Pro software has been designed with an integrated version of: „



Thermo PLSplus/IQ.



„



Unscrambler X Classification Engine (OLUCX).



„



Unscrambler X Prediction Engine (OLUPX).



They add powerful multivariate analysis tools for building quantitative calibrations as well as qualitative models for discriminant analysis. Qualitative and quantitative methods can be linked together to provide a complete spectroscopic model of your samples.



PLSplus/IQ PLSplus/IQ is a recent concept in multivariant software. PLSplus/IQ was designed to build robust calibration models and distribute these applications to the real world. While PLSplus/IQ contains a wealth of tools suitable for exploratory data analysis by the statistician, its focus is in assisting the analyst in solving problems using multivariant methods. PLSplus/IQ incorporates both quantitative and qualitative methods both alone and in combination to provide the appropriate solution to the analyst’s problems. PLSplus/IQ supports the popular and powerful multivariant algorithms: „



Partial Least Squares Type 1 (PLS-1) and Type 2 (PLS-2)



Indico® Pro User Manual



86



„



Principal Component Regression analysis (PCR), and



„



Thermo’s own field proven PCA-R discriminate analysis.



PLS and PCR have been proven to be superior to such methods as peak area or height as well as the related multivariant techniques known as Classic Least Squares (CLS) and Inverse Least Squares (ILS) for many quantitative applications. PCA-R discriminate analysis is based on similar methodology but is applicable to qualitative problems involving classification or identification. All of these techniques are typically full spectrum techniques where the data are fit to many data points thereby improving sensitivity. In addition, they are mathematically robust and can provide optimal solutions to quantitative applications.



5.7 Quantitative Methods The most popular multivariate algorithms (PLS-1, PLS-2 and PCR) are all available. These multivariate full spectrum calibration methods have been proven to provide robust solutions for difficult and complex samples



5.8 Qualitative Methods In many situations, primary calibration data are just not available, are too difficult to obtain, or the costs involved are prohibitive. However, this does not rule out using spectroscopy and chemometrics for quality control and assurance. PLSplus/IQ includes PCA for performing simple data exploration and visualization. Coupling this with Thermo's field proven algorithm for Principal Component Analysis / Mahalanobis Distance with Residual weighting (PCA/MDR) provides the ability to construct complete models of the spectra without any calibration information at all. This type of chemometric model can be used for sample identification and screening as well as sample grading and purity testing.



5.9 Combined Methods Because spectral data are required by both methods, qualitative tests can be performed using quantitative models as if the calibrations were designed for that purpose. Using Discriminant Analysis as a pre-filter before applying the quantitative calculations allows GRAMS IQ to select the calibration that best matches the sample spectrum (which in some cases might be “None!”). In addition, outlier samples can be quickly and easily determined during sample prediction giving you the utmost assurance of the results. A portion of the preceding text was extracted from documents shown on the Thermo website.



Unscrambler X Prediction Engine (OLUPX) The Indico Pro software has been designed with an integrated version of the Unscrambler X Prediction Engine (OLUPX). You can execute predictions using sophisticated models. You get not only the predictions, but also additional results to ensure that the predictions are correct. 87



Chapter 5: Chemometrics



OLUPX has been integrated using API calls for the fast operation. Contact CAMO ASA for more information about The Unscrambler X software.



Unscrambler X Classification Engine (OLUCX) The Indico Pro software has been designed with an integrated version of The Unscrambler X Classification Engine (OLUCX). It has the same concept as OLUPX, but for qualitative prediction. The Unscrambler X software must be installed on the instrument controller to create real-time predictions against The Unscrambler X models. Copy the model file to the instrument controller, then use Indico Pro to run the model (which uses either OLUPX or OLUCX). You can assess quality from multi-channel measurements or the combination of many different measurements. This often gives more accurate control. It is also used to speed up measurements used for feedback or monitoring. You estimate quality from other parameters that are easy to obtain. The same concept is used to replace costly measurements with inexpensive ones. Sometimes you can estimate process output from process input or process measurements, even if there is a time lag in the process. Multivariate regression models can be used to quantitatively predict properties of new samples, or qualitatively classify (or identify) new samples. Contact CAMO ASA for more information about The Unscrambler X software.



Indico® Pro User Manual



88



Index A activate GPS 67 Alt+C, F Predict from File 55 Alt+C, F Reload Model Files 54 Alt+C, P Predict 49 Alt+C, S Setup 49 Alt+D, A Axes 39 Alt+D, C Splice Correction 43 Alt+D, D Digital Numbers (DN) 39 Alt+D, F Show File List 42 Alt+D, G Log 1/T 41 Alt+D, H Chromophores/Overtones 43 Alt+D, I Show Instrument Spectrum 43 Alt+D, L Log 1/R 40 Alt+D, P Show Spectrum Properties 41 Alt+D, R Reflectance 40 Alt+D, T Transmittance 40 Alt+D, W Show Wave Number 41 Alt+F, C Close File Display 20 Alt+F, F View Spectrum File 20 Alt+F, L Link File 20 Alt+F, M Material Report 20 Alt+F, N New Project 18 Alt+F, O Open Project 18 Alt+F, S Save Project 19 Alt+F, X Exit 22 Alt+G, A GPS activate 67 Alt+G, M GPS Monitor 67 Alt+G, S GPS Setup 66 Alt+H, A About 69 Alt+H, O Online Documentation 69 Alt+H, U User Guide 69 Alt+P, B Prompt Before New Reference 38 Alt+P, E Serial Pulse 36 Alt+P, I Instrument Control 35 Alt+P, P Properties 32 Alt+P, S Start Logging Events 36 Alt+R, A ASD to ASCII Converter 57 Alt+R, J ASD to JCAMP Converter 56 Alt+R, S ASD to SPC Converter 55 Alt+R, U ASD to U-ASCII Converter 58 Alt+S, A Save 28



Indico® Pro User Manual



Alt+S, B Take a Baseline 24 Alt+S, C Sample Count/Average 25 Alt+S, D Display After Save 29 Alt+S, E Export Spectrum 29 Alt+S, G Derivative Gap 26 Alt+S, O Save After Collect 28 Alt+S, P Print Spectrum 29 Alt+S, R Print Spectrum Data 29 Alt+S, S Printer Setup 29 Alt+S, T Take a Scan 23 Alt+S, U Continuous Collect 25 Alt+S, V Dependent Variables 27 Alt+T, A Auto Collect Timer 62 Alt+T, R Reference Timer 61 Alt+T, U User Defined Timer 64 analyzing target materials 12 annotation add 73 delete 73 ASCII 29 ASCII conversion 57 ASD Rapid Classifier 12 auto collect timer 62 average sample 25 axes 39



B baseline reference 10 C calibration acquire spectra 10 calibration model 9 CFR 36 changing graph font 72 chemometric export to 11 mathematic model 11 chemometric software 12 Chemometrics Predict 49 Predict from File 55 pull-down menu 46



89



Reload Model Files 54 Setup 49 chemometrics 77 chemometrics models 85 chromophores 43 classification model 79 close file display 20 collect, continuous 25 collection timer 62 computer requirement 1 continuous collect 25 conversion ASCII 57 JCAMP 56 SPC 55 U-ASCII 58 Ctrl+A Auto Collect Timer 62 Ctrl+B Reference Timer 61 Ctrl+C Sample Count/Average 25 Ctrl+E Export Spectrum 29 Ctrl+P Show Spectrum Properties 41 Ctrl+R Take a Baseline 24



D data point mark 72 data scaling 72 dependent variables 27 derivative gap 26 digital numbers 39 Display Axes 39 Digital Numbers (DN) 39 Log 1/R 40 Log 1/T 41 pull-down menu 38 Reflectance 40 Show Chromophores/Overtones 43 Show File List 42 Show Instrument Spectrum 43 Show Spectrum Properties 41 Show Wave Number 41 Splice Correction 43 Transmittance 40 Display After Save 29 E exit 22 export spectrum 29 export spectrum files 11 F File Close File Display 20 Exit 22 Link File 20



TerraSpec Users Guide



Material Report... 20 New Project 18 Open Project 18 Projects 18 pull-down menu 17 Save Project 19 View Spectrum File 20 file predict from 55 file extension ASD 18 ASL 18 Grams 18 Unscrambler 18 files log 18 model 18 spectrum 18 font of graph 72



G GPS Activate 67 Monitor 67 Setup 66 Grams AI 55, 59 graph font 72 grid lines 72 H Help pull-down menu 69 I installation Indico Pro 2 uninstall 3 instrument control 35 instrument controller 1 Instrument Display 68 instrument spectrum 43 J JCAMP 29 JCAMP conversion 56 L language settings, Windows 2 link file 20 log 1/R 40 log 1/T 41 log events 36 log files 18



90



M marking data points 72 material report 20 menu Chemometrics pull-down 46 Display 38 File 17 help 69 Project 31 Run pull-down 55 Spectrum 22 Timers pull-down 61 Windows pull-down 65, 68 model calibration 9 chemometric 11, 85 classification 79 quantification 80 reload files 54 model files 18 monitor GPS 67 N new project 18 note add 73 delete 73 O OLUCX 88 OLUPX 87 open project 18 overtones 43 P pan 71 PLSplus/IQ 86 PLSplus/IQ Navigator 60 predict from file 55 prediction 49 print results 12 printing results 12 print prediction results 12 setup 29 spectrum 29 spectrum data 29 Project Instrument Control 35 Prompt Before New Reference 38 Properties 32 pull-down menu 31 Serial Pulse 36 Start Logging Events 36



91



project new 18 open 18 properties 32 save 19 show file list 42 properties show spectrum 41



Q quantification model 80 quick start 4 ASD Rapid Classifier 12 R reference baseline 10, 24, 38 timer 61 white 10, 24 reflectance 40 reload model files 54 restore defaults 73 Run ASD to ASCII Converter 57 ASD to JCAMP Converter 56 ASD to SPC Converter 55 ASD to U-ASCII Converter 58 GramsAI 59 PLSplus/IQ Navigator 60 pull-down menu 55 S sample count average 25 sample count/average 25 save after collect 28 spectrum 28, 29 save project 19 scan take a new spectrum 23 Scan Type 25 selecting grid lines 72 serial pulse 36 setup GPS 66 setup chemometrics 49 show file list 42 show wave number 41 software requirement 1 SPC conversion 55 spectrometer 2 Spectrum Continuous Collect 25 Dependent Variables 27 Derivative Gap 26



Index



Display After Save 29 Export Spectrum 29 Print Spectrum 29 Print Spectrum Data 29 Printer Setup 29 pull-down menu 22 Sample Count/Average 25 Save 28 Save After Collect 28 Take a Baseline 24 Take a Scan 23 spectrum new 23 save after collect 28 show file list 42 show properties 41 truncate 35 Spectrum File Display 68 spectrum files 18 spectrum save 28, 29 spectrum, continuous collect 25 splice correction 43 subset 25



Z zoom 71 undo 71



T take a baseline 24 take a scan 23 Timers Auto Collect Timer 62 pull-down menu 61 Reference Timer 61 User Defined Timer 64 transmittance 40 U U-ASCII conversion 58 undo zoom 71 Unscrambler 58 Unscrambler ASCII 30 Unscrambler Online Classifier 88 Unscrambler Online Predictor 87 user defined timer 64 V view spectrum file 20 W wave number show 41 white reference 10 Windows pull-down menu 65, 68 Windows language settings 2



TerraSpec Users Guide



92



2555 55th Street, Suite 100 Boulder, CO 80301 Phone: 303.444.6522 Fax: 303.444.6825 [email protected] www.asdi.com



Indico® Pro User Manual ASD Document 600235 |Rev. E | December 2011 To obtain a copy of this instruction manual online, visit our website at http://support.asdi.com



© 2011 ASD Inc. All rights reserved.