Thermonicolet Omnic Software User's Guide 6.1 (PDF) - Charles E ...

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Panes A pane is an area of the spectral window used to display a spectrum along with associated information and software features. Here is a pane containing a spectrum: A spectral window can contain one or several panes, as specified by Display Setup and the Window options (available through Options in the Edit menu). You can display spectra in Overlaid or stacked panes, depending on how you want to view the data. See “Setting the display parameters” in the “View” chapter and “Window options” in the “Edit” chapter for information on setting the number of panes. The active spectral window Display colors Only one spectral window can be active (selected) at a time. The active spectral window is the one affected by operations you perform. To make a spectral window active, click anywhere within it or choose its title from the Window menu. The title bar of the active spectral window is displayed in the color you specify using Control Panel. (See your Windows documentation for information on using Control Panel.) You can display several spectra in a spectral window at one time. To help differentiate the spectra, they are displayed in different colors. Eight colors are available and are assigned as spectra are added. When a spectrum is selected, it is displayed in the color specified for selected spectra. A selected spectrum is a spectrum on which you can perform operations. See “Selection tool” for information on selecting spectra. To change the color of the spectra in a spectral window, use Display Setup in the View menu or the Colors button in the View options. See “Setting the display parameters” in the “View” chapter and “Specifying colors for spectra and other features” in the “Edit” chapter for more information. Resizing a spectral window Note To resize a spectral window, drag one of its borders or corners or click the Maximize button or Restore button. (You can also click the Minimize button to shrink the window.) The window’s title box, palette and view finder are scaled proportionately. The panes, spectra and axes are also scaled to fit the window. When a spectral window is maximized, it shares a title bar with the OMNIC window. ▲ 16 Thermo Nicolet
Axes Along the bottom and left side of a pane (or panes) in a spectral window are the axes. The scale and display limits of the X-axis depend on the spectral region you are displaying. If you display a different region by using the view finder or selection tool, the X-axis is automatically adjusted for the new region. See “View finder” and “Selection tool” for an explanation of how to display different regions. For normal FT-IR applications, the most commonly used X-axis units are the wavenumber (cm -1 ) and the micrometer (µm). You can specify the unit by using Display Setup in the View menu. See “Selecting an X-axis format” in the “View” chapter for illustrations of X-axes with these and other units. Note The scale of the X-axis is usually uniform across the spectrum. Sometimes, however, it is easier to see important peaks if a different X-axis scale is used for different regions. Use X-Axis Format in the Display Setup dialog box to split the X-axis into two or three sections, each with a different scale. ▲ The unit used for the Y-axis depends on the final format used when the spectrum was collected and whether you have converted the spectrum to another format. You can set the initial Y-axis unit for collected spectra by using Experiment Setup in the Collect menu (see “Selecting the final format” in the “Collect” chapter for details). The first three commands in the Process menu let you convert the spectra to absorbance, % transmittance, Kubelka-Munk, photoacoustic, % reflectance or log (1/R) units. The “Process” chapter explains how to use these commands. During data collection, the Y-axis unit is the volt, a measure of the interferogram signal. When the interferograms are transformed into a single-beam spectrum, the Y-axis unit used expresses the intensity of the infrared energy versus frequency. Processing interferogram or single-beam data to any other Y-axis units requires a background spectrum. A background spectrum contains information about the instrument and the atmosphere inside the spectrometer or sampling accessory. To remove this information from a sample spectrum, the single-beam sample spectrum is divided by, or ratioed against, the single-beam background spectrum. The resulting spectrum is in % transmittance (or other specified final format) and can be displayed in a spectral window. You can use commands in the Process menu to convert this spectrum to the other Y-axis units, depending on how the sample was measured and the display format you want to use. The “Scale” commands, Display Limits and Roll/Zoom Window in the View menu let you adjust the Y-axis scale. See the “View” chapter for complete information. Note To turn the display of the axes on or off in existing spectral windows, use Display Setup in the View menu. To turn the display of the axes on or off when a new spectral window is created, use the Window options (available through Options in the Edit menu). See “Setting the display parameters” in the “View” chapter or “View options” in the “Edit” chapter for details. ▲ Title box The title box near the top of a spectral window shows the title of the spectrum that was last selected or that is currently selected. A selected spectrum is a spectrum on which you can perform operations. If two spectra are selected, the title in the title box changes to “Two spectra selected.” If more than two spectra are selected, “Multiple spectra selected” appears in the title box. OMNIC User’s <strong>Guide</strong> 17
Page 2 and 3: The information in this publication
Page 4 and 5: Peak area tool.....................
Page 6 and 7: Checking spectrometer performance a
Page 8 and 9: Process............................
Page 10 and 11: Selecting, editing or creating a re
Page 12 and 13: How to use this manual This manual
Page 14 and 15: • If you do not have the DS optio
Page 16 and 17: Note If you have the DS option, you
Page 18 and 19: Digital signature information in a
Page 20 and 21: There are several ways to enter the
Page 22 and 23: Note Some tutorials are available o
Page 24 and 25: Note If you are using Windows 2000
Page 28 and 29: Displaying a list of spectrum title
Page 30 and 31: Displaying a different spectral reg
Page 32 and 33: Copying information to the Clipboar
Page 34 and 35: Note You can select all the display
Page 36 and 37: Next, hold down the Shift key and c
Page 38 and 39: Region tool Some OMNIC commands can
Page 40 and 41: You can position the annotation tex
Page 42 and 43: You can position the annotation by
Page 44 and 45: 2. Click the Annotate button to the
Page 46 and 47: The corrected area is bordered by t
Page 48 and 49: 2. Edit the label text if desired.
Page 50 and 51: Overlaying spectra lets you see sig
Page 52 and 53: When you hide a stacked spectrum, a
Page 54 and 55: If a pane containing a spectrum is
Page 56 and 57: 46 Thermo Nicolet
Page 58 and 59: File Type Extension Comments Spectr
Page 60 and 61: The settings available in the Y Uni
Page 62 and 63: If Put Opened Spectrum In New Windo
Page 64 and 65: 3. If the Save As dialog box appear
Page 66 and 67: 2. Choose Save Group from the File
Page 68 and 69: 2. Locate and select the desired fi
Page 70 and 71: Save a configuration This procedure
Page 72 and 73: A dialog box appears. 2. Type a use
Page 74 and 75: Note The Enable OMNIC Log-In comman
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Note If a spectrum has been pasted
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Delete files 1. Choose Delete Files
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When you cut a displayed stacked sp
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Pasting duplicate images of spectra
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Note The options you set using Opti
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File Type Initial Spectra Initial E
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Normalize the spectra of standards
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In the upper-left corner of the dia
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Type Annotation Axis Labels Axis Nu
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Specifying how to print axes The op
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Text Type Annotation Axis Labels Ax
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Note If you have turned off Prompt
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Setting Smart Purge The Smart Purge
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Specifying how to list peaks found
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4. Collect a sample spectrum with n
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To specify or do this... The X-axis
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Turn on Display All Annotation if y
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Item Company Name Spectrum Title Da
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Preventing the overwriting of files
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State Enabled Disabled Hidden Descr
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6. If you disabled or hid the Save
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5. Specify the size of the toolbar
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Note You can create an image for a
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The experiment you select also sets
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Note The experiment you select also
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Note If you are studying samples th
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When deciding whether to use this f
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Titling the experiment Bench featur
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The peak-to-peak intensity is the s
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• It helps prevent infrared energ
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Specifying the beamsplitter type If
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The parameter checks appear when yo
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The individual checks are described
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Fringes result when back reflection
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A beamsplitter, detector, source or
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Type the desired minimum peak-to-pe
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Setting Boxcar N-B* Weak N-B* Mediu
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As an example, for a standard DTGS
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If you have installed a Smart Acces
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• Install a 32-bit version of OMN
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• To save the settings in the cur
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The positive settings move your vie
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What happens during collection? The
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3. Choose Collect Sample from the C
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Note To store the spectrum on the h
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Viewing the age of the background D
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If Preview Data Collection is turne
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If at any time the system condition
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Undo a display limit change Choose
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To specify this or do this... The n
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To remove the grid from a spectral
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Note You can display annotations ve
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This format is suitable for high re
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Specifying the sampling information
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Stacked spectra Stacking spectra is
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Full Scale brings the highest data
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Match the Y-axis scale of a spectru
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Display spectra vertically offset 1
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Display spectra full scale automati
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Displaying and using a toolbar Use
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Converting spectra to absorbance Us
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The units are described in the next
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The photoacoustic value (PAS) at a
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Micrometers Select Micrometers to c
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4. Choose OK. • If you selected K
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• To change the final format. You
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What is a baseline? A baseline cons
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Important Be careful not to introdu
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The X and Y values of the point app
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8. When you are finished correcting
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Before searching an ATR spectrum ag
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• A spectrum includes the region
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Replacing a spectral region with a
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Subtracting spectra Use Subtract in
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2. Choose Subtract from the Process
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Subtracting a component or contamin
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Note If negative peaks appear in th
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3. Select the desired number of smo
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Converting spectra to their first o
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Multiplying a spectrum by a number
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Symbol Meaning Examples / Divide. A
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• To change the factor using the
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Here is the normalized spectrum: In
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Normalize the scale of spectra 1. S
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Example libraries The following sec
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Click the Print button in the Find
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6. To display or remove the Y-axis
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3. Choose Average from the Process
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Range of Y values versus X value Pe
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4. If you are not using the search
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Using extended search The Extended
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When you perform the search, the ex
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All the QC libraries and library gr
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Set up a spectral search (The proce
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7. Specify the number of found libr
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5. Specify the spectral regions to
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Search a spectral library 1. Use Li
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If you did not use the search exper
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To print the search expert’s comm
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Color-coded titles of the spectrum
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To print the spectrum and functiona
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You can choose Overlay Spectra from
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Working with libraries Click the Li
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Once a library is created, you can
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3. Click the name of the user libra
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A copy of the spectrum is placed in
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• If you are adding more than one
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3. Click the name of the library. T
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9. Choose Search. The search result
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The kinds of information displayed
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2. Click the Create/Edit Structures
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If you want to print the informatio
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When you are ready to start printin
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You can only add the spectrum to a
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3. If you want to reset the data co
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Follow these general steps to creat
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Type Spectrum Comments Spectrum Cus
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3. Specify the item type by selecti
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5. Choose Preview/Print Report from
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4. If the item type is Spectral Win
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The page number of the currently di
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7. Close the Report Template window
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Adding a report to a notebook Use A
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To view a report notebook, use View
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Searching for text Click the Search
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Express dates on this tab in the fo
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5. To search for reports that conta
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Note When windows are tiled, they m
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atmospheric effects suppressing, 94
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status of, 148 time for, 115, 116,
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detector interface kit, 123 detecto
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finding peaks, 235 fingerprint regi
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special criteria for, 246 spectral
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OMNIC Atlµs default directory, 76
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Process options, 90 Protégé spect
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experiment, 114, 146 default direct
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detector, 127 filter for, 139 for c
Page 350 and 351:
displaying, 14, 20, 39, 95 color fo
Page 352 and 353:
text adding to report template, 297
Page 354:
x X-axis, 14, 17 display limits, 17
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Thermonicolet Omnic Software User's Guide 6.1 (PDF) - Charles E ...

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