InfraSpec VFA-IR IR Spectrometer

TM

Users Guide
Version 2.75 April 2010

InfraSpec is a registered trademark of Wilks Enterprise, Inc. Copyright pyright 2010 Wilks Enterprise, Inc., East orwalk, CT

Table of Content
1 InfraSpec VFA-IR Spectrometer Overview ................................................................................................. 5 1.1 Introduction ............................................................................................................................................. 5 1.2 Basic Measurement Concept ................................................................................................................. 5 1.3 InfraSpec 2.6 Software Program Overview ............................................................................................ 6 2 Getting Started .............................................................................................................................................. 7 2.1 2.2 2.3 2.4 2.5 2.6 Spectrometer Care ................................................................................................................................. 7 Spectrometer Spectral Limits and Serial Number .................................................................................. 7 Supplied and Optional Spectrometer Accessories ................................................................................. 8 Spectrometer Connections .................................................................................................................... 9 Program Installation ................................................................................................................................ 9 Initial Instrument Setup ........................................................................................................................... 9

3 Main Program Panel ................................................................................................................................... 11 3.1 Introduction ........................................................................................................................................... 11 3.2 The InfraSpec Experiment .................................................................................................................... 11 3.3 Control Bar Buttons .............................................................................................................................. 12
3.3.1.1 Background Acquisition ......................................................................................................................... 12 3.3.1.2 Spectrum Acquisition............................................................................................................................. 13

3.3.2 The Experiment Group ................................................................................................................ 14

3.3.2.1 3.3.2.2 3.3.2.3 3.3.2.4 3.3.3.1 3.3.3.2 3.3.3.3 3.3.3.4 Saving Spectra ...................................................................................................................................... 14 Loading Spectra .................................................................................................................................... 15 Starting a New Experiment .................................................................................................................... 15 Experiment Setup .................................................................................................................................. 16 The "Autoscale" Button ......................................................................................................................... 16 The "Set Scale" Button .......................................................................................................................... 16 The "Sel. Traces" Button ....................................................................................................................... 16 The "Abs. Panel"/"Main Panel" Button................................................................................................... 17

3.3.3 The Display Group ...................................................................................................................... 16

3.4 Top Menu Controls ............................................................................................................................... 17 3.4.1 The InfraSpec Menu ................................................................................................................... 17
3.4.1.1 3.4.1.2 3.4.1.3 3.4.1.4 Show Main/Absorbance Panel .............................................................................................................. 17 Open Manual ......................................................................................................................................... 17 Version Info. .......................................................................................................................................... 17 Quit........................................................................................................................................................ 18

3.4.2 The Spectra/Bkgnd. Menu .......................................................................................................... 18

3.4.2.1 Select Spectra ....................................................................................................................................... 18 3.4.2.2 Select Background ................................................................................................................................ 18 3.4.2.3 Load Data From Old VFA Version ......................................................................................................... 18

3.4.3 The Display Menu ....................................................................................................................... 18

3.4.3.1 3.4.3.2 3.4.3.3 3.4.3.4 3.4.3.5 3.4.3.6 3.4.4.1 3.4.4.2 3.4.4.3 3.4.4.4 3.4.4.5 3.4.4.6 3.4.4.7 Autoscale Both Axes ............................................................................................................................. 18 Autoscale X ........................................................................................................................................... 18 Autoscale Y ........................................................................................................................................... 19 Autoscale Y from Zero ........................................................................................................................... 19 Set Scale ............................................................................................................................................... 19 Copy Graph as Picture .......................................................................................................................... 19 Setup Panel ........................................................................................................................................... 19 Start Test Scans .................................................................................................................................... 19 Connect Spectrometer .......................................................................................................................... 19 Show/Hide Igor Menus .......................................................................................................................... 19 Correct Screen Resolution .................................................................................................................... 19 Show Command History Window .......................................................................................................... 19 Restore Factory Default Settings........................................................................................................... 19

3.4.4 The InfraSpec Setup Menu ......................................................................................................... 19

3.5 Cursors ................................................................................................................................................. 20 4 The Absorbance Panel ...............................................................................................................................21 4.1 Introduction ........................................................................................................................................... 21 4.2 The Analyze Heading ........................................................................................................................... 21 4.2.1 Compare ..................................................................................................................................... 21
4.2.1.1 Subtraction Fit ....................................................................................................................................... 22 4.2.1.2 Mean Center Subtraction Fit.................................................................................................................. 22 4.2.1.3 Mean Centered Unit Variance Subtraction Fit ....................................................................................... 23

4.2.2 4.2.3 4.2.4 4.2.5

Baseline Correction ..................................................................................................................... 23 Peak and Area ............................................................................................................................ 24 Difference Spectra ...................................................................................................................... 24 Quantitative Analysis .................................................................................................................. 25

5 The Setup Panel .......................................................................................................................................... 27 5.1 Introduction ........................................................................................................................................... 27 5.2 Bottom Buttons .....................................................................................................................................27 5.2.1 Save For This Session Button .................................................................................................... 27 5.2.2 Save Setup as Default Button ..................................................................................................... 27 5.2.3 Revert to Default Setup ............................................................................................................... 27 5.2.4 Cancel Button............................................................................................................................. 27 5.3 General Tab .......................................................................................................................................... 28 5.3.1 Experiment Setup Heading ......................................................................................................... 28
5.3.1.1 # of Scans ............................................................................................................................................. 28 5.3.1.2 Max Bkgd Age ....................................................................................................................................... 28 5.3.1.3 X Units ................................................................................................................................................... 28 5.3.1.4 Interpolation........................................................................................................................................... 28 5.3.1.5 Crosstalk Correction .............................................................................................................................. 28 5.3.1.6 Ask to Sample ....................................................................................................................................... 29 5.3.1.7 Save Folder ........................................................................................................................................... 29 5.3.1.8 Serial Port.............................................................................................................................................. 29 5.3.1.9 Company .............................................................................................................................................. 29 5.3.1.10 Address .............................................................................................................................................. 29 5.3.1.11 Operator ............................................................................................................................................. 29

5.3.2 Spectrometer Setup Heading ...................................................................................................... 29

5.3.2.1 m at First and Last Pixel ...................................................................................................................... 29 5.3.2.2 Sample Stage ........................................................................................................................................ 29

5.4 The System Tab ................................................................................................................................... 30 5.4.1 Startup Heading .......................................................................................................................... 30

5.4.1.1 Startup Options Panel ........................................................................................................................... 30 5.4.1.2 Password............................................................................................................................................... 30 5.4.1.3 Data Log ................................................................................................................................................ 30

5.5 The Calibration Tab .............................................................................................................................. 31 5.5.1 Current Calibrations, Saving and Loading Calibrations .............................................................. 31 5.5.2 Creating a Calibration ................................................................................................................. 32
5.5.2.1 5.5.2.2 5.5.2.3 5.5.2.4 5.5.2.5 5.5.2.6 5.5.2.7 5.5.2.8 Calibration Wizard Step 1 ...................................................................................................................... 32 Calibration Wizard Step 2 ...................................................................................................................... 32 Calibration Wizard Step 3 (Standard) .................................................................................................... 33 Calibration Wizard Step 4 (Standard) .................................................................................................... 33 Calibration Wizard Step 5 (Standard) .................................................................................................... 34 Calibration Wizard Step 6 (Standard) .................................................................................................... 35 Calibration Wizard Step 7 ...................................................................................................................... 36 Calibration Wizard Step 8 ...................................................................................................................... 37

5.5.3 PLS Calibrations ......................................................................................................................... 37

5.5.3.1 Calibration Wizard Step 3 (PLS)............................................................................................................ 38 5.5.3.2 Calibration Wizard Step 4 (PLS)............................................................................................................ 38

5.6 Simplified Program Tab ........................................................................................................................ 39 5.6.1 Materials Verification Setup ........................................................................................................ 39

5.6.1.1 5.6.1.2 5.6.1.3 5.6.1.4

Largest Acceptable Deviation Value...................................................................................................... 39 Match Method........................................................................................................................................ 40 Range Limits ......................................................................................................................................... 40 No Sample Threshold ............................................................................................................................ 40

5.6.2 Simplified Program Setup: .......................................................................................................... 40

5.6.2.1 Barcode Scanner................................................................................................................................... 40 5.6.2.2 Help Files .............................................................................................................................................. 40

5.7 Verif. Library Tab .................................................................................................................................. 40 5.7.1 Add to Library .............................................................................................................................. 41 5.7.2 Delete Sel. ................................................................................................................................... 42 5.7.3 Load Library ................................................................................................................................ 42 5.7.4 Save Library ................................................................................................................................ 42 6 Simplified Programs for Non-Technical Operators ................................................................................. 43 6.1 Introduction ........................................................................................................................................... 43 6.1.1 Notes on Backgrounds ................................................................................................................ 43 6.2 Quantitative Analysis Simplified Program ............................................................................................ 43 6.2.1 Step 1: Choose A Calibration...................................................................................................... 43 6.2.2 Step 2: Run a Background .......................................................................................................... 44 6.2.3 Step 3: Run a Sample ................................................................................................................. 45
6.2.3.1 Data Logging/Note Option ..................................................................................................................... 46 6.2.3.2 Pass/Fail Option .................................................................................................................................... 46

6.2.4 "Help" and "Exit" buttons ............................................................................................................. 47 6.2.5 "Report Button ........................................................................................................................... 47
6.2.5.1 Single Detail Report .............................................................................................................................. 48 6.2.5.2 Date Range Report ............................................................................................................................... 49

6.3 Materials Verification Simplified Program ............................................................................................. 49 6.3.1 Step 1: Run a Background .......................................................................................................... 49 6.3.2 Step 2: Choose a Material .......................................................................................................... 50 6.3.3 Step 3: Run a Sample ................................................................................................................. 51 7 Spectrometer Specifications ..................................................................................................................... 53 8 Service and Technical Support ................................................................................................................. 54

InfraSpec VFA-IR Spectrometer Overview

The InfraSpec VFA-IR Spectrometer is a new concept in mid infrared instrumentation. It utilizes a patented, cutting-edge design consisting of an electronically modulated source coupled with a linear variable filter (LVF) and multi pixel detector array. The result is a compact infrared spectrometer with no moving parts and no optical path exposed to air. The InfraSpec is capable of gathering infrared data on a vast quantity of materials including liquids, powders, pastes and solids. The InfraSpec is available in Attenuated Total Reflection (ATR) and Transmission models depending on the application, and can be supplied with 3 different filter ranges. The InfraSpec makes quantitative and qualitative measurements quick and easy, and can even be used by untrained personnel.

1.1 Introduction

1.2 Basic Measurement Concept

The InfraSpec can be supplied in two basic sample stage setups: Attenuated Total Reflection or Transmission. In both setups, a multi pixel linear pyroelectric array is coupled with a linear variable filter (LVF) and illuminated by an electronically modulated source. Pyroelectric detectors can be used throughout the entire IR range from visible to the far infrared and provide stable operation without the need for cooling. LVFs are wedge shaped interference filters that gradually change in wavelength transmitted from one end to the other. A LVF typically covers approximately an octave in wavelength (i.e.: 2.5-4.9 microns (400-2041cm-1) or 5.5-10.5 microns (1818-952cm-1)). Figure 1 shows a schematic of the InfraSpecs ATR optical system. The source and detector array are optically connected via an ATR crystal, which is usually made of zinc selenide (ZnSe), zinc sulfide (ZnS) or cubic zirconia (CuZ) depending on the LVF filter range and application. Light emitted from the source reflects down the crystal towards the detector array. En route, the light is absorbed by a sample that is placed in contact with the top of the crystal. The detector array measures the amount of infrared light absorbed from the sample which is separated into different wavelengths by the LVF in order to provide an infrared spectrum. The ATR crystal width accommodates the width of the detector array.

Figure 1: InfraSpec ATR Setup

Figure 2 shows a schematic of the InfraSpec transmission optical system. An electronically modulated source is focused on the pyroelectric detector array such that a sample can be placed between the source and the detector. The detector then measures the amount of infrared light absorbed as it passes through a sample. The sample can be placed in a sealed infrared cell, cuvette or infrared card depending on the application.

Figure 2: InfraSpec Transmission Setup

1.3 InfraSpec 2.7 Software Program Overview

The InfraSpec VFA-IR Spectrometer is operated via dedicated software that was written specifically for the spectrometer. The program provides all of the operating controls and analysis tools needed to use the spectrometer to its full potential. The program allows trained personnel to operate the spectrometer with a full set of analytical tools, and also allows untrained personnel to use the spectrometer via simplified programs for quantitative analysis or materials verification. InfraSpec 2.7 is written within Igor ProTM, which is a program that provides a vast amount of general and spectroscopy tools. An advanced user can take advantage of the InfraSpec 2.7 software and also add on his/her own tools via the Igor programming language.

Getting Started

2.1 Spectrometer Care

The InfraSpec is designed for use in the field or factory, and can handle harsher environments than sensitive lab instruments. Care should be taken, however, not to drop or shock the instrument, especially if the instrument has been calibrated. Excessive shock can damage the instrument, and can also invalidate a calibration or library set. The InfraSpec should be powered and connected to the computer only with the provided connection and power cables. The ATR crystal (if applicable) should be cleaned with hydrocarbon solvents, acetone, alcohol or water with a soft wipe such as a Kimwipe. Do not use caustics, mineral acids, amines or ammonia to clean the crystal. Long exposure to warm water will also degrade zinc selenide or zinc sulfide. Minor scratches may occur as a result of regular use, and will not affect the sample analysis. Note: Wilks Enterprise, Inc. is not responsible for damage to the crystal by the customer (see enclosed warranty). It is recommended to warm up the instrument for one hour before using the instrument for quantitative use. The instrument should be turned off when not in use for extended periods. Do not touch the source or LVF as they are fragile.

2.2 Spectrometer Spectral Limits and Serial Number

The linear array spectral limits are expressed in microns for pixel 1 and 128, and are located on the on the bottom of the instrument along with the serial number.

2.3 Supplied and Optional Spectrometer Accessories

Accessories Supplied With Analyzer:

User's Manual and InfraSpec Program CD Igor Pro Manual and Program CD Universal AC-DC Power Supply AC Power Cord (US version) Polycarbonate Sample Cover USB Cable

Optional Accessories:

Stainless Steel Sample Cover Carrying Case Spare Cables

2.4 Spectrometer Connections

To power on the spectrometer, connect the 12 VDC power supply to the line supply (100 240 VAC) and the 12 VDC output to the female barrel connector on the spectrometer. Connect the USB cable to the instrument and computer. For the initial USB connection, insert the InfraSpec Installation CD in the drive and when the installation wizard asks for where to find the drivers, select the CD-ROM option. Note: It is recommended that the computer be started up before the InfraSpec connection is made. If you do not have a serial port and your InfraSpec does not have a USB connection, install a USB to RS-232 converter following the manufacturer's instructions. A tested and recommended USB to RS232 converter is available as an accessory to the InfraSpec. Using this converter will ensure low noise performance.

2.5 Program Installation

Follow the steps below to install the InfraSpec 2.7 software: 1. Insert the InfraSpec Installer CD. The installer will start automatically. Follow the installer instructions. If this is the first install, be sure to select First Install (Launches Igor Pro Installer), otherwise select Igor Pro Already Installed. 2. If Igor Pro was selected to be installed, the Igor Pro installer will initialize after the InfraSpec software has installed. Follow the Igor Pro instructions to install Igor Pro. The serial number and key are located with the Igor Pro Install CD. Note that the Igor Pro Install CD is not needed for the InfraSpec install since both InfraSpec and Igor Pro are packaged together with the InfraSpec Installer. The Igor Pro CD is provided for backup only. 3. After the Installation is complete, plug in the spectrometer into the wall outlet and then to the computer. If the USB cable is used, a driver must be installed to work properly. The driver can be installed using the Windows New Hardware Wizard. Be sure to select the Installation CD as the location of the driver.

4. The program should now be installed, and can be started from a desktop shortcut or from the programs menu.

2.6 Initial Instrument Setup

Note: In order to get the best performance from the InfraSpec, it is essential to follow these setup instructions before using the InfraSpec for the first time. After the InfraSpec program is started, the Main Panel should show a top bar with buttons and a graph below as shown in Figure 3 (See section 3 for complete Main Panel explanation). The following procedure must be completed before using the InfraSpec for the first time: 1. Click the "Setup" button on the top button bar under the heading "Experiment". A panel as shown in Figure 4 should appear (See Section 5 for more information on the Setup Panel 2. On the right hand side, enter the "m at first pixel", "m at last pixel" and Serial # values, which are located on the bottom of the instrument. This may automatically be completed with newer versions of the InfraSpec 3. Select the "Sample Stage" from the drop down menu according to the type of instrument that is connected, either ATR or Transmission. 4. Enter the company, address and operator in the spaces provided. 5. Click "Save Setup as Default" at the bottom of the panel. This will save these settings so that they will be accessible every time the InfraSpec 2.7 program is opened. Once this process has been completed, the InfraSpec will be ready to use.

Figure 3: InfraSpec Main Panel

Figure 4: InfraSpec Setup Panel

Main Program Panel

When the InfraSpec program starts for the first time, the Main Panel will appear as shown in Figure 5. This panel contains a large graph area for displaying and acquiring spectra, and a top control bar which contains most of the functions needed to operate the InfraSpec. The buttons are separated into 3 headings: "Experiment", "Display" and "Collect". Each of these sets of controls will be explained below. In addition to the button bar, the top of the screen contains menu items, which can be used to access further functions of the InfraSpec 2.7 program. Note that some of these menus are disabled. These are Igor Pro menus, and are used by advanced users and programmers only. The InfraSpec menu items are explained below. Note: Please refer to the Igor Pro manual for information on the Igor menus, or contact Wilks Enterprise, Inc. for more Information

3.1 Introduction

Figure 5: InfraSpec Main Panel

3.2 The InfraSpec Experiment

Every session that spectra are acquired, analyzed or otherwise viewed in the InfraSpec program is called an "experiment". Within an experiment, spectra that have been acquired or loaded will be present, along with their respective background spectra. The spectra can be saved for use in a future

experiment, and can be deleted out of an experiment if they are no longer necessary for the current experiment. Any changes to saved spectra will not be permanent unless the spectra are saved after the changes have been made. For the majority of applications, only the spectra need to be saved in order to use data in the future. For advanced users and programmers, the experiment itself can be saved via the Igor menus, although this is not the recommended way to save data within the InfraSpec program.

3.3 Control Bar Buttons

Most of the InfraSpec functions can be accessed via the buttons located on the top control bar. The buttons are separated into groups with headings of Collect", "Experiment" and "Display". Each of these button groups will be explained in detail below.

3.3.1 The Collect Group This heading contains the "Background" and "Sample" buttons. These are the only buttons needed to acquire spectra from samples. In a normal spectrum acquisition, a background scan is obtained with either a clean crystal or in some cases a blank sample. Then, a sample is placed on the instrument and the "Sample" button is pressed to acquire a sample. 3.3.1.1 Background Acquisition 1. Introduction The "Background" button collects and saves a background spectrum. A background spectrum is necessary with the InfraSpec to compensate for variation in individual pixel sensitivity and flattens out the source emission curve. The InfraSpec program ratios sample spectra against the current background that is chosen to get a "transmission" spectrum, which shows the percent of light at a given wavelength absorbed by a sample compared to the background spectrum. In addition, spectra can be displayed in absorbance (see Section 4 for more information on absorbance spectra). The current background can be selected via the background selector (see section 3.4.3.2)
2. Background Collection To run a background spectrum, make sure the sample crystal is clean and dry or that the background sample has been placed on a clean crystal so that the entire crystal is covered. For a transmission instrument, place a blank sample cell/card/cuvette into the spectrometer. Press the "Background" button to begin background spectrum acquisition. Depending on the number of scans chosen (see Section 5.3.1.1) this process should take about 30 seconds to 1 minute. The background is an average every scan acquired so that more scans will result in reduced spectrum noise. While acquiring the background spectrum, the graph will show the resulting background spectrum similar to that shown in Figure 6. Note that the background acquisition can be stopped at any time by pressing the "Stop Scans" button which appears to the right of the "Collect" heading during acquisition. If this button is pressed, no background is saved.

Figure 6: Background Acquisition

3.3.1.2 Check Background XXXXXXXXXX 1. Introduction The Check Bkgnd button checks the background to ensure that the crystal is clean and the background is still adequate.
2. Background Checking To check the background, make sure the sample crystal is clean and dry, and then click the Check Bkgnd button. The instrument will collect three scans and compare them to three scans collected from the first background. A view of the ratio of the checked scans to the current background is displayed in order to help visually determine whether any absorption bands are present that would indicate that either the crystal is not clean or the background is no longer valid. See Figure 7 for an example. In addition to the visual queue of background cleanliness, a number is calculated based on the variance seen. If this number is within +/- 1.0, then the current background is adequate. If the number is greater than 1.0 or less than -1.0, then the sample crystal should be cleaned thoroughly and the background should be re-checked. If the result is still not within +/- 1.0, it is recommended that a new background be run.

Figure 7: Background Checking 3.3.1.3 3.3.1.4 Spectrum Acquisition 1. Introduction The "Sample" button collects and saves a sample spectrum. A background spectrum must be collected first so that a ratio can be calculated.
2. Sample Collection To collect a sample spectrum, make sure a background spectrum has been collected, and then place a sample onto the ATR crystal or into the transmission sample holder. Cover volatile samples with the supplied plastic cover or optional stainless steel cover. Make sure the sample

is covering the whole crystal completely and then press the "Sample" button. In addition, if powders are used with an ATR sample stage, the powders must be finely ground and a weight may need to be used in order to get good crystal contact. Note: Excessive weight or pressure on the ATR crystal can crack or damage the crystal. Contact Wilks Enterprise, Inc. if you are unsure as to how much pressure to apply to the crystal. Wilks Enterprise is not responsible for damage to the crystal by the customer (see enclosed warranty). For the transmission version, fill the sealed cell, cuvette or IR card according to manufacturer's specifications and place into the sample holder. While acquiring a sample spectrum, the graph will show the current average spectrum for the number of scans acquired so far as shown in Figure 7. Note that the sample acquisition can be stopped at any time by pressing the "Stop Scans" button which appears to the right of the "Collect" heading during acquisition. If this button is pressed, no sample is saved. Once sample acquisition has completed, a dialog will allow the entry of a spectrum name. This name must be unique and not contain ; : ' / or + and must have 1-22 characters. After the spectrum name is entered, the spectrum will appear on the graph along with a legend which shows the spectrum name. Spectrum names must always be in quotes in this entry box.

Figure 7: Sample Acquisition 3.3.2 The Experiment Group This heading contains the "Save Spectra", "Load Spectra", "New Exp" and "Setup" buttons. These controls allow you to load InfraSpec spectra into the current experiment, save spectra in a variety of formats, start a new experiment and adjust the settings for the InfraSpec program. 3.3.2.1 Saving Spectra The Save Spectra panel shown in figure 8 below can be accessed by pressing the "Save Spectra" button. There are two basic file types to save a spectrum or group of spectra in the InfraSpec program: InfraSpec type spectra and text spectra. Both will be explained below.

Figure 8: Save Spectra Panel

1. Saving as InfraSpec Saving as InfraSpec is the standard method for saving spectra within the InfraSpec program. This file type saves all of the information that the InfraSpec program needs in order to rebuild spectra in a later experiment. In addition, spectral information can be accessed via a text editor such as WordPad or Notepad. Spectra must be saved in this format to be reloaded into the InfraSpec program at a later date. To save as InfraSpec, select the spectra to be saved using the list of spectra in the Save Spectra Panel. Then choose "Save as InfraSpec". You will then be prompted to enter a name for the group of spectra and a folder to save in. The default folder is InfraSpec_Data. 2. Saving as Text The InfraSpec program also supports saving spectra as a text file to be loaded into other programs for processing or display. Note that if a spectral group is saved as a text file, it cannot be reopened in the InfraSpec program. Therefore it is recommended that a spectral group be saved in both formats if a text file is desired. To save as text, select the spectra to be saved using the list of spectra in the Save Spectra Panel, and then choose "Save as Text". A new panel will appear with checkboxes to select different types of spectral information to save as shown in Figure 9 below. Corrected Reflectance refers to spectral data that has been corrected using Crosstalk Correction (see Section 5.3.1.4 for more information on Crosstalk Correction). Select the types of spectral data to be saved and then press "Save as Text". A dialog will allow you to choose the spectral group name and save location.

Figure 9: Save as Text Panel 3.3.2.2 Loading Spectra Spectra can be loaded into the InfraSpec program if they are in the InfraSpec format. To load spectra, press the "Load Spectra" button and select the file to load. After selecting the file, the spectra within the file will be displayed in the graph area. The loaded spectra will now be part of the current experiment. 3.3.2.3 Starting a New Experiment In order to clear all data, spectra and temporary settings, a New Experiment may be started. This is done by selecting the "New Exp" button. Note: Starting a new experiment will permanently delete all spectra that have not been saved in the current experiment. 3.3.2.4 Experiment Setup Pressing the "Setup" button will access all of the setup options for the spectrometer and program. Please refer to Section 5 for more information on the setup panel. 3.3.3 The Display Group This group of controls contains functions for displaying spectra in various formats and scaling the viewable area of the graph. In addition, the Absorbance Panel can be accessed via these controls (see Section 4 for more information on the Absorbance Panel 3.3.3.1 The "Autoscale" Button The autoscale button scales the spectra in the current top window so that every trace on the graph is entirely visible. This is the default view for the graph window. 3.3.3.2 The "Set Scale" Button The "Set Scale" button sets the x and y scale of the graph using the Axis Scaling Panel, shown in Figure 11 below. After the numbers are entered for the scaling, Press "OK" to set the graph window to the selected scale or "Cancel to return to the previous scale. 3.3.3.3 The "Sel. Traces" Button The "Sel. Traces" button brings up the Select Spectra panel as shown in Figure 10. Several options can be accessed from this panel, including, displaying spectra, displaying spectra as a table, deleting spectra, renaming spectra and restoring processed spectra. Each will be explained below. If a spectrum is clicked in the spectral list box, a spectrum info panel will

appear to the left of the Select Spectra panel. This panel displays information about the current spectrum 1. Displaying Spectra The "Display" button control displays the selected spectra on the current top window (either the Main Panel or the Absorbance Panel). Spectra that are not selected will be removed from the graph window if they were previously displayed. 2. Displaying Spectra as a Table The "Table" button will display the selected spectra in a table format. This table can be copied into spreadsheets or other programs for further processing or displaying. The format of the data is dependent on the current top window and x scaling. For instance, if the Main Panel is displayed and the x scaling is wavelength, the table will display an x column in wavelength and a y column in reflectance/transmittance. 3. Deleting Spectra from the experiment The "Delete" button deletes spectra from the current experiment. Deleting absorbance spectra will delete transmission/reflectance spectra as well and vice versa. Note: Spectra that have not previously been saved will be permanently deleted. 4. Renaming Spectra The "Rename" button renames spectra and their corresponding absorbance and difference spectra will be renamed as well. The new name must be unique and not contain ; : ' / or + and must have 1-22 characters. 5. Adjusting the Spectrum Scale (Main panel only) The "Adj. Scale" button will adjust the wavelength limits of the selected spectra. This is useful in cases where the current scale is not correct or is inaccurate. 6. Restoring Processed Spectra (Absorbance panel only) The "Restore" button will restore any processed spectra in the Absorbance Panel. Note that this button will only appear in the Select Spectra panel if the Absorbance Window is on top. Restoring spectra will permanently remove any baseline corrections that have been done on the spectra. 7. Averaging Spectra (Absorbance panel only) The "Average" button will make an average of any selected absorbance spectra. It is possible to select a 6. Closing the Select Spectra Panel Pressing the "Done" button or the X box in the upper right of the window will close the panel and return the current top window.

Figure 10: Select Spectra Panel 3.3.3.4 The "Abs. Panel"/"Main Panel" Button The "Abs. Panel" button on the top bar of the Main Panel will bring the Absorbance Panel to the top so that spectra can be viewed and processed in absorbance. Similarly, the "Main Panel" button on the top bar of the Absorbance Panel will bring the Main Panel to the top for spectra collection and display in transmittance/reflectance.

3.4 Top Menu Controls

Secondary controls that cannot be accessed via the top bar buttons can be found in the menu controls at the top of the screen. Each active InfraSpec menu function will be explained in detail below. Please refer the Igor Pro manual for more information on the disabled Igor menus.

3.4.1

The InfraSpec Menu

3.4.1.1 Show Main/Absorbance Panel These selections either select the Main Panel or the Absorbance Panel as the top window similar to the button control "Main Panel" and "Abs. Panel". 3.4.1.2 Open Manual This menu selection will open this pdf manual. 3.4.1.3 Version Info This menu selection will open a panel that displays the current version and date along with update information. 3.4.1.4 Quit Quits the InfraSpec Program. Note that any unsaved spectra in the current experiment will be deleted. 3.4.2 Tools Menu

3.4.2.1 Select Spectra Opens the Spectra Selector panel just as the top menu button "Sel. Traces:" does. See Section 3.3.3.3 for more information.

3.4.2.2 Select Background Opens the Background Select Panel as shown in Figure 11 below. This panel allows the option to either display the selected background on the with the "Display" button on the current top graph window, or select a background as the currently active background by using the "Select" button. This will make all subsequent sample collections use this background until another is chosen or a new background is run. This is not necessary under normal circumstances.

Figure 11: Select Background Panel 3.4.2.3 Start Continuous Scanning This menu item begins continuous scans. The display will show a spectrum referenced to the current background, which is updated in real time. This is useful for qualitative analysis of samples that may change in concentration or chemical composition. 3.4.2.4 Start Test Scans Starts instrument test scans. Each raw data scan coming from the spectrometer will be displayed in the graph window of the Main Panel. This is useful for troubleshooting and discerning weak or non-functioning pixels. In addition, this function may be used for qualitative process monitoring. 3.4.3 The Display Menu

3.4.3.1 Autoscale Both Axes Autoscales top graph window to both axes. This is the same function as the "Autoscale" button on the top control bar under the Display heading. 3.4.3.2 Autoscale X Autoscales the X axis only 3.4.3.3 Autoscale Y Autoscales the Y axis only 3.4.3.4 Autoscale Y from Zero Autoscales the Y axis from zero to the maximum of all displayed spectra.

3.4.3.5 Set Scale Opens the Axis Scaling panel for manual scale setting. This is the same function as the "Set Scale" button on the top control bar under the Display heading. 3.4.3.6 Copy Graph as Picture Copies the current top graph as a picture into the clipboard for pasting into other programs. This will only copy the graph portion of the top panel and is useful for presenting data. Note that a graph panel must be currently on top to use this function. 3.4.4 The InfraSpec Setup Menu

3.4.4.1 Setup Panel Opens the Setup Panel. See Section 5 for more information on the Setup Panel 3.4.4.2 Show/Hide Igor Menus Enables or Disables the Igor Menus. By default the Igor menus are disabled. See the Igor Pro manual for more information on these menu items. 3.4.4.3 Correct Screen Resolution After display settings have been changed in the computer running the InfraSpec program, such as after an external monitor is connected to a laptop, it may be necessary to select this function in order to redraw the program windows to the correct size for the new screen resolution. 3.4.4.4 Show Command History Window Shows the Igor Pro command window for manual entry of commands. See the Igor Pro manual for more information. 3.4.4.5 Restore Factory Default Settings Restores the default settings for the InfraSpec program. This should only be used if there are problems with settings, or if a new spectrometer is attached and the settings must be completely reset.

3.5 Cursors
On the bottom of the Main and Absorbance Windows, a white bar contains the two cursors that can be used for identifying points on a spectrum, called the A and B cursors. In order to activate a cursor, use the mouse to drag the circle A cursor or square B cursor onto a trace on the graph. The white bar will give X and Y coordinates as well as information about the distance between the two cursors if relevant. Cursors are also used in the Absorbance window for selecting areas and peaks for spectral processing. See Section 4 for more information about the processing functions that use cursors.

The Absorbance Panel

The Absorbance Panel is similar in many aspects to the Main panel. A top control bar contains most of the same functions as those in the Main Panel, with the exception that the Collect heading is replaced by an Analyze heading. The graph window displays spectra in absorbance rather than the transmission/reflectance spectra displayed in the Main Panel. See Figure 12 below. The Analyze heading contains controls that process and analyze selected spectra in the experiment. Note that absorbance spectra reside separately from the transmission/reflectance spectra, so any spectral processing can be undone by using the "Restore" button in the Select Spectra Panel (see Section 3.3.3.3)

4.1 Introduction

Figure 12: The Absorbance Panel

4.2 The Analyze Heading

This heading is where all spectral processing and analysis takes place. The functions that can be used are Compare, Baseline Correction, Peak and Area, Difference Spectra, Quantitative Analysis. To select a function click the checkbox next to the function name and a panel to the right of the Analyze

4.2.1 Compare Selecting the "Compare" checkbox will open the menu controls shown in Figure 13. This function allows a comparison between a reference and any amount of other spectra as chosen by selecting spectra on the right hand side of the graph. After selecting the spectra and reference to compare, press the "Compare" button to bring up the comparison table shown in Figure 14 below.

Figure 13: Comparison Panel

Figure 14: Comparison Table

The table shown in Figure 13 contains 3 calculations which gauge the closeness of the selected spectrum and the reference spectrum. Each calculation is a subtraction after various preprocessing. Each will be explained below. Note: In the following formulas, A=[a1,a2,...,an] i.e. lower case symbols are scalars, upper case symbols are vectors (spectra). See for example: Chemometrics, Sharaf, Illman and Kiowalski, Wiley, 1986.

4.2.1.1 Subtraction Fit Calculates the point by point subtraction and squares the sum,
F=(R-A)2 Where F is the Subtraction Fit value, R is the Reference spectrum and A is the comparison spectrum.

4.2.1.2 Mean Center Subtraction Fit Calculates the point by point subtraction and squares the sum after the spectra have been mean centered. If the mean of the absorbance spectrum is , then
=1/nai

Where ai is an individual pixel absorbance value and n is the number of data points (pixels). The mean centered spectrum is then defined as A'=A- Where A' is the mean centered comparison spectrum and A is the original comparison spectrum. The resulting Mean Center Subtraction Fit, G, is calculated as G=(R'-A')2

Where R' is the mean centered reference spectrum.

4.2.1.3 Mean Centered Unit Variance Subtraction Fit Calculates the mean centered spectrum similar to 4.2.1.2, and then autoscales this result by dividing the resulting mean centered spectrum by the variance of the spectrum. The variance, s, is defined as
s2=1/n-1(ai-)2 The resulting variance is then divided by the mean centered spectrum as follows: A''=(A- e)/s Where A'' is the mean centered unit variance comparison spectrum. The mean centered unit variance fit, H, can then be calculated as H=(R''-A'')2 Where R'' is the mean centered unit variance reference spectrum. 4.2.2 Baseline Correction Selecting the "Baseline Correction" check box will open the baseline correction tools shown in Figure 15 below. These functions are useful for removing artifacts from spectra.

Figure 15: Baseline Correction Controls

To baseline correct spectra, ensure that the desired spectra are displayed in the absorbance panel graph window. Then, place cursors onto a displayed spectrum and press the "Include" button. The range that has been chosen will be highlighted yellow on the graph panel. Alternatively, a range can be manually entered using the Range entry boxes. To clear all selected regions, press

the "Clear Region" button. To exclude only part of a region, place the cursors on the desired region to exclude and press the "Exclude" button. The excluded region will no longer be highlighted in yellow. Once a desired region has been selected, the "Force Reg. to Zero" or "Baseline Correct" can be pressed to complete the baseline correction. "Force Reg. to Zero" shifts the entire spectrum so that the average value of the selected region is zero. "Baseline Correct" calculates a linear fit across the selected region and then shifts the spectrum so that the calculated fit line has zero slope and intercept.

4.2.3 Peak and Area Selecting the "Peak and Area" checkbox will open the baseline correction panel shown in Figure 16 below. This function calculates the peak location, peak absorbance value and area of a selected region.

Figure 16: Peak and Area Controls

In order to calculate the peak and area values, first display the desired spectra to be analyzed on the absorbance graph window. Then select a region using the cursors at the bottom of the screen or alternatively use the manual range entry boxes. Once the desired region is selected, press the "Include" button. The selected region will be highlighted in yellow. To clear the region, press the "Clear Region" button. Once the desired region has been selected and included, the "Peak and Area of Region" button can be pressed in order to bring up the table shown in Figure 17 below. This table includes the peak location, peak absorbance value and the area of the selected region, along with analysis details. The data from this table can be copied and pasted into another program for further processing.

Figure 17: Peak and Area Table

4.2.4 Difference Spectra Selecting the "Difference Spectra" checkbox will open the difference spectra controls shown in Figure 18. These functions are useful for subtracting one spectrum from another. In order to

difference spectra, first choose a reference spectra, or minuend. This is the spectrum that will be subtracted from the sample spectrum. Next choose the sample spectrum, or subtrahend. Once both spectra have been chosen, the subtraction slider can be used to choose the correct subtraction weight. The subtraction weight is the percent of the reference spectrum that is subtracted from the sample spectrum. As the slider is moved, the resulting difference spectrum is displayed in the graph window. Additionally, the subtraction weight can be entered manually in the entry box, or adjusted with the up and down arrows to the right of the entry box. Note that the original spectra are not affected by generating a difference spectrum. Difference spectra are separate entities and can be displayed in the absorbance window much like absorbance spectra. Difference spectra take the name of the sample spectrum with "_diff" appended at the end of the name.

Figure 18: Difference Spectra Controls 4.2.5 Quantitative Analysis Selecting the "Quantitative Analysis" checkbox opens the controls shown in Figure 19. These functions allow quantitative analysis within the standard program. In order to use these functions, at least one calibration must be created. See Section 5.5 for information on how to generate a calibration. Note that a simplified quantitative analysis program allows for quantitative analysis by untrained personnel. See Section 6.2 for more information on the simplified quantitative analysis program.

Figure 19: Quantitative Analysis Controls

In order to quantitatively analyze spectra in the current experiment, first choose a calibration or calibrations to analyze for. Up to eight calibrations can be analyzed at the same time. Once the desired calibrations are selected, select the spectra to be analyzed using the list box to the right.

All or no spectra can be selected using the "Sel All" and "Sel None" buttons below the list box. Make sure that the spectra to be analyzed are appropriate for the calibration selected to ensure correct quantitative values. After selecting calibrations and spectra to be analyzed, press the "Analyze" button. This will bring up a table similar to that shown in Figure 20. Each spectrum name is displayed and the resulting concentrations for each calibration are shown in the appropriate column. The data from this table can be copied and pasted into another program for further analysis.

Figure 20: Quantitative Analysis Table

The Setup Panel

The setup panel, accessed either from the "Setup" button under the "Experiment" heading in the main and absorbance windows, or from the "Setup Panel' menu item under the "InfraSpec Setup" menu, contains all of the functions for setting up and customizing the InfraSpec program. In addition, Calibrations can be generated and Libraries for Materials Verification can be built. This section describes all of the setup options available. The setup panel contains several tabs with different controls in each, along with a set of buttons at the bottom that are available in every tab. Each tab will be explained separately below.

5.1 Introduction

5.2 Bottom Buttons

The buttons found at the bottom of the setup panel are available in every tab of the setup panel, and are shown in Figure 21 below. These buttons are used for saving the changes that have been made in the setup panel. The changes can be either saved for use only in the current experiment using the "Save For This Session" button, or saved as the default setup so that every experiment will use the current settings with the "Save Setup as Default" button

Figure 21: Bottom Setup Panel Buttons 5.2.1 Save For This Session Button This button allows temporary changes to be made to a current experiment without affecting the default values for subsequent experiments. This option is useful for changing a setting for a specific experiment, such as adjusting the number of scans or changing the x-axis units. When this button is pressed, the setup panel is closed and the values changed in the setup panel will take effect for the current experiment. 5.2.2 Save Setup as Default Button This button allows permanent changes to be made to the setup values. This is useful for the initial setup of the spectrometer, or for changes that will be used many times. When this button is pressed, the setup panel will close and all subsequent experiments will use the settings chosen as default settings. 5.2.3 Revert to Default Setup This button reverts all settings to the default values as chosen the last time the "Save Setup as Default" button was pressed. This is useful to change back many settings made temporarily. In addition, it is useful to revert to the default setting if problems are occurring that may be due to changes in the Setup Panel. 5.2.4 Cancel Button This button closes the Setup Panel and cancels any changes made to the setup panel since it was opened. Note that calibrations are left unchanged by the "Cancel" button.

5.3 General Tab

This tab contains basic setup controls for the spectrometer and experiment. The controls shown in Figure 22 will be displayed when this tab is selected or the Setup Panel is first opened.

Figure 22: General Setup Tab 5.3.1 Experiment Setup Heading This heading contains controls used for the setup of the InfraSpec program and experiment. Each control is explained below. 5.3.1.1 # of Scans This control selects the number of scans that a background and sample spectrum will be averaged from. The higher the number of scans, the lower the resulting spectral noise. Each scan takes approximately 1.5 seconds, so a setting of 40 scans will allow a spectrum to be completed in approximately 1 minute. 40 Scans is recommended for most applications. 5.3.1.2 Max Bkgd Age This option selects the maximum age of a background scan. In the standard program, a warning will pop up once the background has expired, however the user may still run a spectrum using the expired background. In the simplified Quantitative Analysis and Materials Verification programs, the user must run a new background the current background has expired. This setting can be set to "off" as well to never warn that the background has expired. 5.3.1.3 X Units This control selects the units used for the X-axis, either m (microns) or cm-1 (wavenumber). 5.3.1.4 Interpolation This control selects whether the spectra displayed are interpolated. The interpolation is done via a cubic spline algorithm. The number of points in an interpolated spectrum is 1280.

5.3.1.5 Crosstalk Correction Crosstalk correction is a proprietary correction algorithm that attempts to eliminate crosstalk between pixels due to incorrect illumination from imperfectly collimated source light as well as from thermal crosstalk between pixels. The result is an increase in apparent resolution. This should be used for qualitative analysis where the most spectral detail is desired. It is not recommended for quantitative analysis or materials verification. 5.3.1.6 Ask to Sample This option allows the selection of an extra step before sampling or running a background. If this is set to "ON", when the Sample or Background button are pressed, a pop up will ask if the user is ready to run a new spectrum. This prevents an accidental spectrum or background from occurring. When the selection is set to "OFF", a background or sample spectrum will immediately begin after the correct button is pressed. 5.3.1.7 Trace Tags Trace tags will appear on the Main panel and Absorbance panel when a spectrum is clicked in the graph pane. The tag can show the sample name of the spectrum clicked by setting the trace tags option to Notes Only, or it can show details spectrum information by setting the option to Detailed. The tags can also be turned off here. 5.3.1.8 Save Folder This setting selects the default folder to be opened when a spectrum is saved or loaded. If "InfraSpec_Data" is selected, every time the "Save Spectra" or "Load Spectra" button is pressed, the InfraSpec_Data folder will be the start folder in the save/load dialog. If "Last Folder Used" is selected, the folder that was last navigated to on a load or save will be the start folder in the save/load dialog. 5.3.1.9 Company This control sets the company that is using the spectrometer. This name is reported in log files and reports. 5.3.1.10 Address This control sets the company address for the company using the spectrometer. This address is reported in log files and reports. 5.3.1.11 Operator This control sets the company address for the company using the spectrometer. This name is reported in log files and reports. 5.3.2 Spectrometer Setup Heading This heading contains controls used for the setup of the InfraSpec spectrometer hardware. Each control is explained below. 5.3.2.1 m at First and Last Pixel The wavelength values located at the back of the instrument should be entered here. This ensures that the spectra collected will have the correct x-units. 5.3.2.2 Sample Stage This allows the selection of the sample stage type, either ATR or Transmission. This ensures that the y axis contains the correct units and that the crosstalk correction values are appropriate for the sample stage of the selected spectrometer.

5.3.2.3 Serial Port This setting selects the current serial port that the InfraSpec is connected to. If the spectrometer is connected correctly and the program does not recognize the spectrometer, the serial port may be incorrectly set. Use this setting to change the serial port and then use the "Connect Spectrometer" menu item under the "InfraSpec Setup" menu to connect the spectrometer. This can also be used to select between different instruments if multiple spectrometers are connected to the same computer.

5.4 The System Tab

The controls shown in Figure 23 will be displayed when the "System" tab is selected. This tab contains setup controls for program startup and logging.

Figure 23: System Setup Tab 5.4.1 Startup Heading These functions control how the program starts depending on whether the Quantitative Analysis or Materials Verification programs will be used. See Section 6 for more information on the Quantitative Analysis and Materials Verification simplified programs. 5.4.1.1 Startup Options Panel If this control is set to "ON" a startup panel will appear at startup rather than the standard program starting immediately. On this panel there are buttons that allow the user to choose whether to start the program in the standard mode or a simplified mode (quantitative analysis or materials verification). In order to have a selection for a simplified program appear in the startup panel, check the box next to the simplified program desired. When the program is restarted, a button choice will allow the user to start the program in the selected simplified mode. 5.4.1.2 Password If the Sys. Setup control is set to "ON", then a password entry box will appear at the startup panel. This allows an administrator to set up the simplified programs and limit the use of the instrument to the simplified programs unless an administrator password is used. The password

can be set by pressing the "Set/Change Password" button. Note that the default password is blank.

5.4.1.3 Data Log These functions adjust how the InfraSpec program logs data in the simplified program. By default, every spectrum is logged in the standard InfraSpec format. Data log files can be opened in the standard program just like normal spectra. Information about the log file such as concentration or materials verification data can be accessed in the standard program through the spectra info box that appears when the "Sel. Traces" button is pressed and a spectrum is highlighted in the list.
In addition to setting the Data Logging to "ON" or "OFF", two other options exist. First, the option "ASK" allows the user of the simplified program to decide whether or not to save a log file. "ASK w/ note" also allows the user to decide whether or not to save a log file, and also allows the user to enter notes about the data that was obtained. These notes are accessible thought the spectra info box as described in the previous paragraph. More information on the functions of the data log can be found in Section 6 with regards to their operation within the simplified programs.

5.5 The Calibration Tab

The controls shown in Figure 24 will be displayed when the "Calibration" tab is selected. This tab contains functions which allow the generation of calibrations for use in quantitative analysis. Up to eight different calibrations can be generated separately. There could be, for example, 8 different constituents of the same material to be measured, or 8 separate calibrations of different materials. Quantitative analysis can be done in one of two ways. First, it can be done in a simplified program dedicated to quantitative analysis. See Section 6.2 for more information. Second, it can be done in the absorbance panel under the analysis heading. See Section 4.2.7 for more information. Calibrations are generated using the Calibration Wizard described in Section 5.5.2.

Figure 24 The Calibration Setup Tab

5.5.1 Current Calibrations, Saving and Loading Calibrations The current loaded calibrations are shown in the middle of the Setup Panel in the Calibration tab. These are the calibrations that can be used in the current experiment. Calibrations can be saved and loaded one at a time by using the appropriate button below the current calibrations. This makes it possible to use any number of calibrations for the InfraSpec, although only 8 can be present in the program at any given time. Up to eight calibrations can be loaded into the program; however only 4 can be displayed simultaneously in the simplified program (See Section 6.2 for more information). 5.5.2 Creating a Calibration In order to begin a calibration, press a calibration button at the bottom of the setup panel. Usually if only one calibration is desired, calibration 1 is used. Pressing the calibration button will bring up the Calibration Wizard shown in Figure 25. Clicking "Next" continues to the next step. Clicking "Back" return you to a previous step and "Cancel" will close the wizard without saving any calibration.

Figure 25: Calibration Wizard Step 1 5.5.2.1 Calibration Wizard Step 1 On the first step of the Calibration Wizard, there is a button that allows the user to reset the current calibration. Pressing this button will completely clear the calibration data for the selected calibration. Note that this will permanently delete the selected calibration. Step 1 also asks to choose the type of calibration desired.
A standard calibration uses peak or area measurements in combination with baseline correction to generate a calibration curve. PLS, or Partial Least Squares regression, calibrations use a more complicated mathematical approach to the calibration. This type of calibration can generate better results, especially if the desired measurement peak contains interferences or cannot be calculated well with a typical area measurement. Due to the complicated nature of this type of calibration, please contact Wilks Enterprise, Inc. if a PLS type calibration is desired. The standard calibration steps will be described first, following with the PLS calibration steps. Note that Steps 1 and 2 are the same for both types of calibrations. Click "Next" to continue

5.5.2.2 Calibration Wizard Step 2 The second step of the Calibration Wizard can be found in Figure 26 below. Enter the name of the calibration to be measured, along with the units of the measurement. In addition, specify the precision of the measurement. This is the number of significant digits that the final result will be rounded to.

Figure 26: Calibration Wizard Step 2 5.5.2.3 Calibration Wizard Step 3 (Standard) The third step of the calibration wizard is shown in Figure 27. Enter the type of calibration, either "Area of Region" or "Peak Value". If area of region is used, enter the wavelength range that the area measurement is to be calculated from. If peak value is used, enter the peak value to be used for the calibration.

Figure 27: Calibration Wizard Step 3 (Standard)

5.5.2.4 Calibration Wizard Step 4 (Standard) The fourth step of the Calibration Wizard can be found in Figure 28. In this step, choose the baseline correction, and enter the ranges that the correction will be calculated on. For baseline correction, two ranges are required. For force region to zero, one range is needed. If a single point is desired enter the sample value for start and end values. See Section 4.2.2 for more information on baseline correction. In addition, interpolation and crosstalk correction for the calibration can be selected here. This will select the corrections to be done before a spectrum is analyzed. In most cases, interpolation should be left on, and crosstalk correction should be left off. See Section 5.3.1 for more information on interpolation and crosstalk correction.

Figure 28: Calibration Wizard Step 4 (standard)

5.5.2.5 Calibration Wizard Step 5 (Standard) The fifth step of the Calibration Wizard can be found in Figure 29. In this step, spectra are chosen to use as calibration spectra. To add a calibration spectrum, press the "Add Calibration Spectra" button. A list will appear containing all the spectra in the current experiment. Choose the desired spectra and press the "Select" located below the list. The wizard will prompt you to enter a concentration value for each selection.
Once a concentration values is entered press "Continue". A graph of the chosen spectra corrected using the baseline corrected values entered in step 4 of the wizard will appear. Cursors on the graph denote the area or peak value to be used for the calibration. This graph allows for a final check to make sure the spectrum and area regions are correct. The wizard will ask whether this spectrum is correct. Click "OK" and the area or peak value will be automatically calculated and entered into the table shown on the calibration wizard panel along with the concentration and sample and file name information. In addition a point will be plotted on the graph of concentration vs. area or concentration vs. peak height. Continue adding calibration spectra in this manner until all have been entered. Once this has been completed click "Next" to go to the next step.

If data points are incorrect or need to be removed, highlight the point or points on the table and click "Remove Sel. From Table". The selected points will be removed from the table and the graph to the right.

Figure 29: Calibration Wizard Step 5 (Standard)

5.5.2.6 Calibration Wizard Step 6 (Standard) The sixth step of the calibration wizard can be found in Figure 30. In this step, the calibration curve is specified. This curve will be used to calculate concentration values for this calibration. First, choose the fit type, either "Linear", "Linear w/ Zero Intercept" or "Exponential, Double Exponential, Cubic Spline and 2nd Deg Polynomial.
Once the fit type has been selected, press the "Generate Fit Curve" button. The desired fit will be displayed on the graph, and information about the fit can be found in the lower right section of the graph. "RMSE" stands for Root Mean Squared Error, and is a goodness of fit measure that can be used to compare different calibration fits. If the fit is incorrect, it can be removed with the "Clear Fit Curve" button. Once the desired fit has been placed on the graph, click "Next" to continue. If you are unsure which curve function to use, contact Wilks Enterprise, Inc. for assistance. It is also possible to Cross Validate the fit by pressing the Cross Validate button. In order to use this feature, first select the number of calibration points to leave out. This should be equal to the number of replicates of the same concentration entered in Step 5 previously. When Cross Validate is pressed, the program will leave out each successive concentration level and generate a fit curve without a given concentration level. The fit curve generated will be used to predict the value(s) of the left out calibration points. This allows a more robust prediction of the performance of the calibration curve. It is possible to omit the endpoints in the cross validation by checking the appropriate checkbox. Since curve fitting works best interpolating, the endpoints will include more error as the calibration curve must extrapolate in order to predict these values.

Figure 30: Calibration Wizard Step 6 (Standard) 5.5.2.7 Calibration Wizard Step 7 The next calibration step is shown in Figure 31. In this step, further calibration options are chosen. Pass/fail ranges can be set, and calibrations can be set to only run separate of other calibrations. Options in this step will affect only the Quantitative Analysis Simple Program. See Section 6.2 for more information on this program.
The pass/fail range option allows a calibration to not only print a concentration, but also indicate whether a sample is within preset limits. In order to use the pass fail ranges, first select the pass/fail range to ON or ON with no numeric data. The latter option will display only pass/fail indication and no numeric concentration will be displayed in the Quantitative Analysis Simple Program. After pass/fail range has been turned on, select the concentrations for low failure, low pass, high failure and high pass results. If a sample concentration is below the low failure point or above the high failure point, the result will indicate a failure. If the sample concentration is between the low pass and high pass point, the result will indicate a pass. If the sample concentration lies between the low failure and low pass, or high failure and high pass, a marginal result will be indicated. This will usually mean that the result should be verified with another sample or another method. In addition to the pass/fail range option, this step also contains an option to set the calibration to run separate of other calibrations. This is usually necessary when a special background is required for an analysis. If this option is set to yes, then this calibration will not be allowed to run simultaneously with other calibrations in the Quantitative Analysis Simple Program.

Figure 31: Calibration Wizard Step 7 5.5.2.8 Calibration Wizard Step 8 This is the final calibration step, which is shown in Figure 32 below. This step informs the user that the Calibration is complete. No further action is required. Press the "Save Calibration" button to exit the calibration wizard and save all changes. The calibration will appear in the Calibration Tab as shown in Figure 24.

Figure 32: Calibration Wizard Step 8 5.5.3 PLS Calibrations In addition to the standard calibration, the InfraSpec program allows for a Partial Least Squares (PLS) type of calibration. These calibrations are many times more robust, especially if there are interferences close to the desired measurement region. The InfraSpec software does not support generating PLS calibrations directly within the program. Instead, Wilks Enterprise, Inc. can be contacted to help facilitate this type of calibration. Wilks Enterprise, Inc. can provide the

calibration files needed to complete the PLS calibration wizard. In addition, advanced users can generate calibration files using third party software. Contact Wilks Enterprise, Inc. for more information. Note: Steps 1, 2, 7 and 8 are the same as for the standard calibrations, so they are omitted below. See Section 5.5.2 for information on these steps

5.5.3.1 Calibration Wizard Step 3 (PLS) The PLS Calibration Wizard Step 3 can be found in Figure 33 below. In this step, the Slope Array (denoted B) is loaded. Click "Choose Calibration File" to navigate to the file given by Wilks Enterprise, Inc. or generated on third party software. If the correct file is chosen, the calibration point numbers will appear in the table to the right. The intercept value should also appear the correct location.

Figure 33: Calibration Wizard Step 3 (PLS) 5.5.3.2 Calibration Wizard Step 4 (PLS) The PLS Calibration Wizard Step 4 can be found in Figure 34 below. In this step, choose any pretreatment to be done on the spectra before calculation. Currently only mean centering is supported; however future versions of the program may contain more pretreatment options. Select the pretreatment type if any click "Next" to continue. Note that the final Step 6 is the Same as Step 7 of the standard calibration.

Figure 34: Calibration Wizard Step 5 (PLS)

5.6 Simplified Program Tab

This tab contains settings that affect the Materials Verification Simplified program mode. Figure 35 below shows the setup of this tab.

Figure 35: Simplified Program Setup Tab 5.6.1 Materials Verification Setup This group of controls affects the Materials Verification Simplified Program only. See Section 6.3 for more information on the Materials Verification Simplified Program. 5.6.1.1 Largest Acceptable Deviation Value This control sets the largest deviation allowed that still will result in a pass. This result is directly related to the Match Method below. The deviation value is the value that would be obtained by running a spectral comparison in the standard program. The Compare function is useful in deciding what this value should be set to by comparing spectra from a standard spectrum (See Section 4.2.1 for more information on spectral comparison). This value is set to

70% on the percentage pass/fail scale so that values above this level are failing and values below are passing.

5.6.1.2 Match Method This control sets the method that the materials verification will use to match a data spectrum with the reference. The match methods are described in detail in Section 4.2.1. Note that the match method chosen affects the largest acceptable deviation value since this value will change depending on the match method used. 5.6.1.3 Range Limits If the Range Limits control is set to "ON", entry boxes will appear that allow a start and end range for the verification to work on. This allows for a verification to be done on a part of the spectrum that is of interest instead of the whole spectrum. 5.6.1.4 No Sample Threshold This control, if set to "ON", uses the variance of a data spectrum that has just been acquired to test whether there is a sample placed on the spectrometer. If no sample is detected, a warning will appear and the match calculation will not proceed. This is useful for preventing false verification failures due to a user mistake of not putting sample on.
The Threshold value is the sensitivity. The default value of 100 is roughly a medium sensitivity, but this value may need to be changed depending on the type of materials to be verified. If a false "no sample" report is given in the simplified program, this number should be set to a lower value. If a sample is not placed on the crystal and a "no sample" report is not displayed in the simplified program then this number should be set to a higher value.

5.6.2 Simplified Program Setup: These controls affect the Quantitative Analysis and Materials Verification simplified programs only. Each control is explained below. See Sections 6 and 7 for more information on the simplified programs. 5.6.2.1 Barcode Scanner Setting this control to "ON" makes another step in the simplified programs that asks for a barcode to be scanned in or entered manually. This is useful if samples to be processed contain a barcode as an identifier. The barcode number will be saved in the spectrum note for the log file, which can be accessed in the standard program through the Spectrum Info panel once the log file has been loaded into the experiment. This panel is accessed by pressing the "Sel. Traces" button and clicking on the desired spectrum. 5.6.2.2 Help Files The simplified programs have a "Help" button which can be clicked by the user in order to bring up pertinent information to aid the user in using the instrument. This help file can be any Microsoft Word, text or Adobe pdf file. The default file is this manual, however many applications may require specific instructions. If this is the case, press "Change Help File...". A dialog will allow you to navigate to the correct help file. Once the help file has been selected, the directory to the help file will be displayed below the button.

5.7 Verif. Library Tab

This tab allows the user to create, modify and save different libraries used for materials verification. Figure 36 shows the Verification Library Tab below. The current library is the library that will be used by the Materials Verification simplified program. The window on the left shows the spectra currently

contained in the library. There is no limit to the number of spectra that can be added to the library. Spectra contained in this library are the spectra that a user in the simplified program will have the choice of selecting as the reference material for verification. If only one spectrum is contained in the library, the user of the simplified program will not have to choose a reference material. Libraries can be saved and reloaded as needed, but the current loaded library will be the only active library in the Materials Verification simplified program. Each of the button controls on the tab will be explained below.

Figure 36: Verif. Library Setup Tab 5.7.1 Add to Library Clicking the "Add to Library" button will change the controls to library addition controls shown in Figure 37 below. On the left side there is a list of spectra in the current experiment. To add a spectrum to the current library, select the spectra desired from the list and click the "Add" button. A dialog will ask for a name entry. This allows spectra in the library to have a different name than that of the spectrum used in the current experiment. Once all desired spectra have been added to the library, clicking the "Back" button will return to the normal library controls.

Figure 37: Verif. Library Addition Controls

5.7.2 Delete Sel. This button will delete a spectrum from the library. Select all the spectra to be delete and click this button to permanently delete the spectra from the current library. 5.7.3 Load Library This button will load a saved library into the current library. Note that any spectra in the current library before the load will still reside in the library. In other words, the spectra from the loaded library will be added to the current library. When this button is pressed, a dialog will allow the user to navigate to a library file. 5.7.4 Save Library When this button is pressed, a dialog will appear that allows the entry of a name for saving a library. Note that the saving a library is different than saving the current library. A saved library will not be loaded during the startup of the InfraSpec program. In order to save the current library as the default, press the "Save as Default" bottom button. After this has been done, the current library will be loaded on each InfraSpec program load, including in the simplified program mode.

Simplified Programs for Non-Technical Operators

6.1 Introduction
The InfraSpec program allows for the use of the InfraSpec spectrometer by non-technical operators through the use of simplified programs containing minimal controls and steps. Following the simple steps allows for a fast and easy analysis using the InfraSpec spectrometer. In many cases, these programs are used daily and the standard program is simply used to set up the instrument. In addition, it is possible to have Wilks Enterprise, Inc. set up a simplified program in advance so that no set-up is required before use. Contact Wilks Enterprise, Inc. for more information. The two simplified programs available are Quantitative Analysis, which is used to get a quantitative measure of up to four calibrations in a single run, and materials verification, which allows nontechnical operators to easily test incoming shipments and verify the material is correct. Each will be explained below.

6.1.1 Notes on Backgrounds In both simplified programs, running new backgrounds can be done at any time using the "Background" button. However, the background can also be set to expire after a preset amount of time (see Section 5.3.1.2). Once the background has expired, users of the simplified programs will have to run a new background before continuing. If it is desired that the user run a new background after each sample, then setting the maximum background age to 1 minute and using at least 40 scans will ensure that the user will be prompted to do so.\ In addition, the background quality can be checked with the check background button. See Section 3.3.1.2 for more information on the background checker. In the simplified programs, the check background button will display a number once completed. If the number is greater than 1.0 or less than -1.0 then the sample crystal should be thoroughly cleaned and the background check re-run. If the number is not within +/- 1.0 on the second attempt, it is recommended that a new background be run.

6.2 Quantitative Analysis Simplified Program

The Quantitative analysis program allows for up to four calibrations to be measured in a sample simultaneously by non-technical operators. In order to set up a quantitative analysis simplified program, first a calibration must be generated. See Section 5.5 for more information on setting up a calibration. Next, in order to be able to access the quantitative analysis program, the startup options panel must be selected and set to display the "Quantitative Analysis" button. See Section 5.4.1 for more information. Once InfraSpec program has been set up for the Quantitative Analysis Simplified Program, restart the InfraSpec Program and click the "Quantitative Analysis" program to start. The steps involved in getting a quantitative result will be explained below.

6.2.1 Step 1: Choose a Calibration When the program first starts, the screen shown in Figure 38 will be present. The upper right hand side of the screen will contain information about what steps need to be taken to analyze a sample. Before acquriring spectra, the calibrations to be used for analysis must be chosen. Clicking "Choose Calibration" will make the panel shown in Figure 39 appear. Select at least one and up to four calibrations to analyze and click "OK". Other calibrations can be chosen at any time by selecting the "Choose Calibrations" button on the left side of the screen. Note that while 8 calibrations can be present in memory, only 4 can be chosen to be analyzed and displayed at any given time. Some calibrations may be set to run separately of other calibrations, so these cannot be selected with other calibrations.

Figure 38: Quantitative Analysis Startup Screen

Figure 39: Choose Calibrations Panel 6.2.2 Step 2: Run a Background After choosing calibrations, a background must be run in order to continue. The sample button will not be active until a valid background has been acquired. Press the "Background" button to run a background. See Section 3.3.1.1 for more information on backgrounds. A graphical display will show the background acquisition progress as shown in Figure 40. Pressing the "Stop Scans" button will reset back to Figure 38 without finishing the background acquisition. Once the background has completed, the default screen will return as shown in Figure 38 except that the "Run Sample" button will now be active.

Figure 40: Background Acquisition 6.2.3 Step 3: Run a Sample Once a background has been acquired, place a sample on the spectrometer fully covering the crystal, or place a sealed cell, cuvette or IR card into a transmission model. See section 3.3.1.2 for more information on placing a sample on the spectrometer. Cover the sample with the supplied plastic cover or optional stainless steel cover. Once the sample has been placed on the spectrometer, press the "Run Sample" button to begin sample acquisition. If the barcode scanner option is selected, the user will be prompted to scan a barcode or enter the barcode/sample ID number. Otherwise the acquisition will begin, and a screen similar to Figure 40 will appear as the acquisition proceeds. Once the spectrum has been acquired, a screen similar to Figure 41 will appear. All selected calibrations (up to four) will be displayed in grey boxes with the calibration name and concentration.

Figure 41: Sample Concentration Display 6.2.3.1 Data Logging/Note Option If "ASK" is selected in the Data Log setup found in Section 5.4.1.3, the "Accept Results" button will be present at the bottom of the screen. The log file for the current sample will not be saved

until this button is pressed. This allows the user to disregard data that was taken erroneously. Note that if the "Accept Results" button is not pressed, no log file will be saved. If the data log setup is set to "ASK w/Note" (see Section 5.4.1.3), The note entry box will be displayed as well. This allows for entry of explanations, sample names/concentrations or other comments to be appended to the data log file. To retrieve the notes, open a log file in the standard program and press the "Sel. Traces" button. Select the log spectrum that contains the desired note and the Spectrum Info. box will appear. This box will contain the notes entered in the Simplified Programs. If the "Run Sample" or "Run Background" button is pressed before accepting the current results, a warning will appear asking the user whether they really want to run a new sample/background without accepting the current results. Once the "Accept Results" button has been pressed, it will become disabled and the notes entry box will disappear.

6.2.3.2 Pass/Fail Option In addition to displaying the concentration, it is also possible to display pass/fail/marginal data. See Section 5.5.2.7 for more information on setting the pass/fail limits. If this option is set, the result will be displayed as red (fail), yellow (marginal) or green (pass) as shown in Figure 42 below. In addition, the pass/fail result will be displayed. The concentration may or may not be displayed along with the pass/fail result depending on the options set. Example results with this option set are shown in Figure 42

Figure 42: Pass/Fail Display Examples

6.2.4 "Help" and "Exit" buttons Pressing the "Help" button will open the help file, either a pdf or text document as chosen in the Simple Program setup (see Section 5.6.2.2). The default help file is this manual. The ability to choose a help file allows administrators to provide specific information for the analysis that the user will be running.
Pressing the "Exit" button will return the user to the startup screen.

6.2.5 "Report Button A report button is provided to allow a user to print or save reports that include detailed data from the current sample or general data from any number of past samples. When the button is pressed, the window shown in Figure 43 will appear. Pressing the "Print Report" button will print the selected report automatically, using the default printer for the computer. Pressing "Save Report" button will save the report a file

Figure 43: Generate Report Window 6.2.5.1 Single Detail Report If a single report of the current sample is desired, select "Single Detail Report". This report will contain the information shown in Figure 44 below. If the report is saved with the "Save Report" button, this file will be saved as an Adobe Acrobat .pdf file.

Figure 44: Detail Report Example 6.2.5.2 Date Range Report If a report of past samples is required, select the "Date Range Report" option. Selection menus will appear that allow the selection of the date range specified. Any log files located in the current log folder that were created within the selected date range will be included in the report. An example of a date range report can be found in Figure 45. If the Date Range Report is selected to be saved, it will be saved as a comma separated value file that can be opened with Microsoft Excel or any other spreadsheet program.

Figure 45: Date Range Report Example

6.3 Materials Verification Simplified Program

The Materials Verification simplified program can be used to verify that the correct material has been received from a shipping depot or lab. Any application where a known sample must be verified to be the correct material can utilize this simplified program. In order to use this simplified program, a materials library of a least one sample spectrum must be created first. See Section 5.7 for more information. In addition other setup parameters must be entered. See Section 5 for more details on the setup parameters used for the Materials Verification Simplified Program. The steps involved in verifying a material can be found below.

6.3.1 Step 1: Run a Background When the program first starts, the screen shown in Figure 46 will be present. The user will be prompted to run a background. All buttons except the "Run Background" button will be disabled. Click the "Run Background" button to acquire a background. The background will begin a graph will denote the background progress as shown in Figure 47. Pressing "Stop Scans" will halt the acquisition and no background will be saved.

Figure 46: Materials Verification Startup Screen

Figure 47: Materials Verification Background Acquisition

6.3.2 Step 2: Choose a Material After a background has been acquired, press the "Choose Material" button to bring up the screen shown in Figure 48. Select the material type from the library list and then press "Select". A screen will display the material to be verified as shown in Figure 49.

Figure 48: Choose Material Screen

Figure 49: Ready to Verify Screen

6.3.3 Step 3: Run a Sample After a selecting the material to verify, place a sample on the spectrometer and click "Run Sample". Sample acquisition will begin and a graph will display progress. Once the sample has been acquired and verified, a screen similar to either Figure 50 or Figure 51 depending on whether the sample was verified or not will appear.
The green or red box will state whether the material was verified and in addition will give details about the spectral match. The Match Method is the method that was used to verify the material, either subtraction, mean centered subtraction or mean centered unit variance subtraction.

The Largest Acceptable Deviation Value is the highest deviation value that will still give a verified result. This is set by the administrator in the setup panel (see Section 5.6.1). The Percent Match is a closeness of fit parameter based on the deviation value and largest acceptable deviation value. The largest acceptable deviation value is set to a percent match of 70 percent, and a deviation value of zero (perfect fit) is set to 100%. This makes any value below the largest acceptable deviation value have a "passing" grade of 70% or above. Values above the largest acceptable deviation value will have a "failing" grade below 70%. In addition to this scale, the actual deviation value found is printed as well. Depending on the settings chosen for data logging, the "Accept Results" button may be present. If so, this button must be pressed in order to save a log file. This prevents undesired results stemming from operator mistakes, etc. from being saved as a log file. In addition, a notes area may be present that allows the entry of notes about the sample. Once the "Accept Results" button has been pressed, it will become disabled and the note entry box will disappear.

Figure 50: Material Verified Screen

Figure 51: Material Not Verified Screen

Spectrometer Specifications
2.75 x 6.0 x 6.5, 7 cm x 15.25 cm x 16.5 cm 3.0 lbs., 1.4 kg ( total with standard ATR plate ) RS-232 or USB 12V DC, 2.0 amps Universal AC/DC converter type (supplied as standard) 1.5-108 (cm.Hz)0.5/W 15oC - 60oC 0 98% relative humidity (non-condensing) 128 Pixel linear pyroelectric array 2.5-5 m (2000-400 cm-1), 5.3-10.8 m (1890-925 cm-1)) 7-14 m (1430-710 cm-1)) 25 cm-1 Cubic Zirconia, Zinc Selenide, or Zinc Sulfide 50 x 16 mm 10

Dimensions Weight P.C. Interface Power Requirements Power Supply Detectivity D* @ 10 Hz Suggested Temp. Operating Range Humidity Detector Array Standard Spectral Ranges Resolution ATR Crystal Material ATR Surface Size # of Reflections

Service and Technical Support

Your InfraSpec VFA-IR Spectrometer may have been purchased either directly from Wilks Enterprise or from a local dealer or representative. In cases of any difficulties or problems associated with operation you are recommended to contact your local representative or dealer first. If the analyzer was purchased direct, or if there are problems that are unanswered by the local representative, or you have a technical question relative to the operation of the instrument or relative to the analysis, please contact Wilks Enterprise at the contact address provided below: Customer Services Department Wilks Enterprise Inc. 25 Van Zant Street Suite 8F East Norwalk, CT 06855 Telephone: (203) 855-9136 FAX: (203) 838-9868 E-mail: tech@WilksIR.com

Service and Repair:

During the warranty period, Wilks Enterprise, Inc. offers free factory service for all failures that occur from normal instrument usage. The user is only required to cover the cost of shipping the instrument to the factory. After the warranty period, the user is required to cover the factorys cost of servicing plus all shipping charges. Normal one week turnaround is offered for all InfraSpec instruments that are returned to the factory for service. For users requiring faster service times, Wilks Enterprise also offers an advance replacement program that can respond to a users needs with instrument replacement typically in less than 24 hours. For extended service contracts, advanced replacement programs, factory service charges, please contact Wilks Enterprise, Inc. for details.

Please note:
As we get feedback from our customers, we will upgrade the software and the manual and send updates. Your comments and suggestions will be greatly appreciated. For comments, software updates or manual updates please send your email information to info@wilksIR.com and note that you want to be put on the InfraSpec Customer list.