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OMNICxi Software Operation

Overview of the Workspace

DXRxi User Guide

Thermo Scientific

General Features and Controls

This section explains the features that are visible in the Acquisition window.

To learn about a feature in the OMNICxi Acquisition window, click its name in the image below.

Figure 63.

OMNICxi Acquisition window, general features and controls

Image Cross Section mode

Show Analysis window

Auto Focus on/off

Video pane

Profile intensity scale

Transparency

Mosaic pane

PV status

Summary of Contents for DXR xi

Page 1: ...DXRxi Instruments and Software DXRxi Raman Imaging Microscope with OMNICxi Raman Imaging Software User Guide 269 300706 Revision A September 2021...

Page 2: ...ical information in this document is for reference purposes only System configurations and specifications in this document supersede all previous information received by the purchaser Thermo Fisher Sc...

Page 3: ...tage Controls 12 Operating the Microscope 13 Indicators 13 Powering the System Up or Down 14 Loading a Sample 14 Available Sample Holders 15 Rotating Stage Holder 17 Sample Holder Breadboard Kit With...

Page 4: ...Infectious Agents 56 Cooling Vents 56 Ventilation 57 Microscope Safety Labels 58 Chapter 3 OMNICxi Software Operation 63 General Workflow 63 Overview of the Workspace 64 OMNICxi Acquisition Window 64...

Page 5: ...ears in the Video Pane or Viewer 173 The Spectrum Has a Sloping Background or a Severe Positive Offset 173 The Spectrum Baseline Is Severely Tilted Curved or Saturating 173 The Video Image is Obscured...

Page 6: ...ent EEPROM 181 No communication 181 Align and Calibration Errors 181 Align calibrate tool not connected 182 Laser output too low 182 No laser at sample 182 Poor quality align calibrate spectra 183 Spe...

Page 7: ...topics About the System The DXRxi Raman Imaging Microscope combines rapid chemical characterization with high end spectral performance It has interchangeable lasers and their associated filters and gr...

Page 8: ...est performance leave the power connected and the instrument powered up even when not in use The DXRxi Quick Reference guide provides a comprehensive overview of the microscope and software If you are...

Page 9: ...e All persons using or in the vicinity of a Class 3B system must wear safety eyewear that exceeds the specifications for the laser in use Do not look directly into a laser even when wearing laser safe...

Page 10: ...Telephone 1 608 273 5017 E mail support madison thermofisher com OMNICxi Raman Imaging Software Descriptions of all software features and controls Troubleshooting Troubleshooting information and desc...

Page 11: ...ed trademarks of Microsoft Corporation in the United States and or other countries MATLAB is either a trademark or a registered trademark of The MathWorks Inc in the United States or other countries A...

Page 12: ...1 Introducing the DXRxi Raman Imaging System Trademarks 6 DXRxi User Guide Thermo Scientific...

Page 13: ...geable lasers and their associated filters and gratings and accommodates polarizers and various optical filters The instrument offers reflected light brightfield sample illumination Optional reflected...

Page 14: ...2 DXRxi Microscope Operation 8 DXRxi User Guide Thermo Scientific...

Page 15: ...optional reflected light brightfield darkfield BF DF illuminator Sample compartment doors lift to open Laser power indicator Power button hold down 3 seconds to power on or off Light path control Eye...

Page 16: ...eld Iris control default all the way in Aperture Iris control default all the way in Neutral density filter control Illumination intensity control Video camera port Video camera Eyepiece Optical filte...

Page 17: ...th reflected light brightfield only illuminator Brightness control for reflected light only Power switch Power indicator Illumination intensity control Video camera cable receptacle Video camera Eyepi...

Page 18: ...s and Controls 10 DXRxi User Guide Thermo Scientific Left Side View Figure 5 Microscope left side view with laser keyswitch Laser keyswitch in locked position laser is disabled Microscope power cord r...

Page 19: ...Microscope Features and Controls Thermo Scientific DXRxi User Guide 11 Inside Sample Compartment Figure 6 Microscope inside sample compartment Single slide holder Objectives Sample stage Nosepiece...

Page 20: ...rols Sample stage Objective Current objective must also be selected in OMNICxi software Nosepiece Single slide holder Joystick fine x and y axis stage control Focus control fine z axis stage control S...

Page 21: ...icator Description Power button and blue indicator LED Hold down power button 3 seconds to power instrument on or off LED lights when instrument is powered on Laser icon and green indicator LED LED li...

Page 22: ...ng a Sample The sample must be held securely to prevent movement during image collection This is commonly done by affixing the sample to a glass slide using double sided adhesive tape or an epoxy We o...

Page 23: ...ple Holders Single Slide Holder Figure 10 Single slide holder Microtiter Well Plate Holder Figure 11 Microtiter Well Plate holder Note This holder is also used to hold the align calibrate tool for sys...

Page 24: ...ermo Scientific Dual Slide Holder Figure 12 Dual slide holder set inside Well Plate holder Acrylic Vacuum Plate Figure 13 96 acrylic vacuum plate mounted on Well Plate holder Upper left corner Dual sl...

Page 25: ...4 Capillary tube array holder mounted on Well Plate holder Rotating Stage Holder Accepts standard microscope slide provides manual rotation to any arbitrary position Holds standard microscope single s...

Page 26: ...haped samples without the risk of contamination with adhesives It is compatible with Ted Pella sample holders Figure 16 Breadboard kit XPS Sample Holder Permits easy transfer of samples from the Therm...

Page 27: ...DXRxi User Guide 19 Raman Macro Sampler Figure 18 Microscope Macro Sampler Adapter Leveling the Sample Holder Figure 19 Screw locations Objective To nosepiece Adapters Sample holder Mounting plate Ho...

Page 28: ...Use your fingers to push down gently on the back left corner of the slide holder see Figure 19 Then turn the back left thumbscrew clockwise until you feel the bottom of the screw touch the stage 5 Con...

Page 29: ...the top surface of the slide holder at that location into focus 15 Take the new z value and subtract the original z position step 12 Z2 step 15 Z1 step 12 Z for Table 2 Use this number and find the cl...

Page 30: ...ective 18 Bring the top surface of the slide holder at that location into focus Take note of the z position located below mosaic pane for a later calculation 19 Move the stage all the way to the left...

Page 31: ...e is no free space on the microscope nosepiece unscrew one of the installed objectives and gently remove if from the nosepiece 2 If installing a brightfield only objective into a brightfield darkfield...

Page 32: ...illumination is available only if the microscope also has the optional transmitted light illuminator Polarized illumination is available only if you purchased an optional reflected light or transmitt...

Page 33: ...ol When Light Path is set to BF the ND filter is in the light path when Light Path is set to DF the ND filter is not in the light path Reduces glare protects the viewer from sudden changes in illumina...

Page 34: ...figured for reflected light brightfield illumination Use the View Path control to direct light through the microscope eyepiece or to the video camera to produce a video image in the software or both T...

Page 35: ...ondensing optics under the microscope stage The light source is positioned directly under the objective Use the Illumination Intensity control on the microscope to control the brightness of the transm...

Page 36: ...t side of the microscope 2 Hold the filter by the labeled end with the label facing you 3 Gently push the filter all the way into one of the filter insertion slots and then slowly draw it out until yo...

Page 37: ...e sample The configurable polarization analyzer can be used with both of the fixed polarizers reflected light and transmitted light The fixed polarization analyzer works only with the fixed reflected...

Page 38: ...alyzer to capture any change in polarization that is due to the state of the light interacting with the sample Figure 29 Reflected light fixed polarizer The image below shows the location for insertin...

Page 39: ...t polarizer insertion slot 2 Hold the polarizer by the labeled end with the label facing you 3 Gently push the polarizer all the way into the insertion slot and then slowly draw it out until you feel...

Page 40: ...sample beam Click here for more information Figure 32 Attachment for reflected light fixed polarizer Installing the Transmitted Light Fixed Polarizer The fixed polarizer for the optional transmitted...

Page 41: ...cted objective and then move the stage toward the back of the microscope as far as it will go 3 Remove the sample area cover 4 If the handle is not attached to the fixed transmitted light polarizer sc...

Page 42: ...xed polarizers to capture any change in polarization that is due to the sample The configurable polarization analyzer can be used with the fixed reflected light polarizer and the fixed transmitted lig...

Page 43: ...nd then slowly draw it out until you feel the first click and then a second click The two positions are described below 4 When you are finished using the analyzer replace the caps on the analyzer open...

Page 44: ...ed reflected light polarizer includes a small bar and handle that can be used to connect it to the configurable polarization analyzer if one is used This allows the two to be clamped together for easi...

Page 45: ...an image of the polarizer analyzer and bar properly installed Figure 40 Fixed reflected light polarizer and configurable polarization analyzer clamped together for easy operation Positioning the Motor...

Page 46: ...that is useful when examining layered materials or very small samples To make maximum use of your microscope s confocal capability use a 100x objective and select the 25 micrometer confocal pinhole a...

Page 47: ...ire the use of polarization optics should select Depolarized for the Laser Polarization The polarization analyzer can be set to Horizontal X or Vertical Y or any angle from 0 to 180 degrees by specify...

Page 48: ...ific Figure 43 System with laser being slid into place Figure 44 System with laser slid firmly into place 2 Rotate the handle and lock the laser into place The handle should be point up as shown Figur...

Page 49: ...emove any installed grating Figure 46 Removing a grating 3 Use a clean lint free cotton cloth to wipe the magnets that secure the grating when installed Magnets are located on the bottom of the new gr...

Page 50: ...r button To change the filter 1 Remove the installed filter Figure 49 Removing filter 2 Use a clean lint free cotton cloth to wipe the magnets that secure the filter when installed Magnets are located...

Page 51: ...he laser rotate the laser key to the unlocked vertical position Figure 50 Laser unlocked enabled Optional Class 3B Laser Configuration The DXRxi microscope can be configured as either a Class 1 or Cla...

Page 52: ...look directly into a laser even when wearing laser safety eyewear Set up a laser safety area in the location where a Class 3B system is being used Making adjustments using controls or performing proce...

Page 53: ...connector and rotate the connector and tighten the nut as described above 3 Insert the probe into the probe alignment tool to perform alignment and calibration Rotate the probe into the tool so that t...

Page 54: ...s over the hook installed in the previous step 7 Open the Settings box in the OMNICxi Acquisition window and click Align Calibrate and choose OK to align and calibrate the instrument with the probe Th...

Page 55: ...toward you while you out slide the tool into the detent at the front of the single slide holder and then release the stage clip Make sure the tool is all the way forward in the detent level and secure...

Page 56: ...on and dip it in distilled water 3 Apply low pressure at the center of the glass and make an outward corkscrew motion to clean the glass Do not repeat motion unless step 2 is repeated 4 If there is st...

Page 57: ...vacuum then wiping with a damp cloth CAUTION Avoid shock hazard or system damage Do not allow liquid to run into the power supply or the back of the instrument NOTICE Avoid permanent damage inside the...

Page 58: ...lection in the software to the new objective you will be using Replacing an Illuminator Bulb Time needed Approximately 10 minutes Tools needed A 3 0 mm hex wrench Parts needed Replacement illuminator...

Page 59: ...uminator bulb 1 Turn off the instrument power and unplug the power cable from the power source 2 Use a 3 0 mm hex wrench to loosen but not remove the screw Figure 57 Loosening the screw 3 Lift the cov...

Page 60: ...ays handle a new bulb with a clean tissue or cloth Figure 60 Inserting the bulb 6 Replace the cover Figure 61 Replacing the cover 7 Use a 3 0 mm hex wrench to tighten the screw Do not over tighten Fig...

Page 61: ...ystem read the site and safety manual first WARNING Avoid eye injury The system may be configured as a Class 1 or Class 3B laser product emitting visible or invisible laser radiation Exposure to laser...

Page 62: ...ls for working with and or handling potentially infectious materials Instruments accessories components or other associated materials should not be disposed of and may not be returned to us or other a...

Page 63: ...tallic and optical components in the instrument if seals are not properly maintained or the concentration level of corrosive gases in the air is excessively high due to improper sampling techniques Be...

Page 64: ...Safety Information 58 DXRxi User Guide Thermo Scientific Microscope Safety Labels or...

Page 65: ...Safety Information Thermo Scientific DXRxi User Guide 59...

Page 66: ...Safety Information 60 DXRxi User Guide Thermo Scientific...

Page 67: ...Safety Information Thermo Scientific DXRxi User Guide 61...

Page 68: ...Safety Information 62 DXRxi User Guide Thermo Scientific...

Page 69: ...gh or uneven surfaces A terrain mosaic takes longer to collect than a classic mosaic but results in an image that is completely in focus without special sample preparation Acquire and analyze data Set...

Page 70: ...in depth For the best experience use two monitors to view both windows at once allowing you to view a live image of your sample while you perform your analysis The secondary windows for 3D analysis a...

Page 71: ...rticles This section covers these topics General Features and Controls Video Mode Features and Controls Image Regions Mode Image Cross Section Mode Live Spectrum Mode For an overview of the Acquisitio...

Page 72: ...ion window click its name in the image below Figure 63 OMNICxi Acquisition window general features and controls Video mode Acquisition settings Spectral pane Profile settings Auto Focus settings Setti...

Page 73: ...hemical image data and their associated acquisition settings all applied profiles and their associated profile settings OMNICxi saves the number and type of profiles that were run and the settings tha...

Page 74: ...ified distance from the nearest focus location during collection of a mosaic Spectral auto focus mode and settings Limit spectral range Allows you to limit the frequency range used for spectral auto f...

Page 75: ...performs a spectral auto focus at that location before collecting the data When acquiring image data in a selected region with the Spectral auto focus and Limit spectral range options selected the so...

Page 76: ...her out of date or this laser set has never been validated No PV tests available for current laser set Note Only full range gratings can be verified PV is also unavailable for the fiber probe Also let...

Page 77: ...saic or a terrain mosaic the mosaic appears in the mosaic pane Spectral pane In Video mode if a spectrum was displayed in this pane in Image Regions Image Cross Section or Live Spectrum mode the spect...

Page 78: ...um is quickly searched against the selected libraries To see the search results click SEARCH Displayed Spectrum if available below the spectral pane The results are displayed in a popup window Use the...

Page 79: ...atures and controls Feature Description Y axis data format The Y axis of displayed spectra is always Raman intensity detector counts X axis data format Defined by the Data Format option in the Setting...

Page 80: ...ectral pane If no suitable match is found in the library you can select Unknown and no matching spectrum will be displayed To close the search results window click Search Displayed Spectrum again Afte...

Page 81: ...ing application such as Notepad Send selected spectrum to OMNIC or OMNIC Specta If the computer has the Thermo Scientific OMNIC Workstation for DXRxi Raman Imaging Microscope or OMNIC Specta software...

Page 82: ...ire spectral range Double clicking the spectral pane performs this function as well Auto scale Applies Full Y Scale to all spectra at all times for optimum viewing Stack spectra Stacks multiple displa...

Page 83: ...wheel on the mouse to change the scale in the mosaic pane The mosaic is displayed in the mosaic pane It replaces the optical image Collect a terrain mosaic of an area of the sample surface A terrain m...

Page 84: ...features and controls Feature Description FOCUS Video Brings the sample into focus at the current stage location Objective Allows you to select a video calibration for the objective that is currently...

Page 85: ...trum in the spectral pane Hold down the Shift key while selecting spectra to display multiple spectra Ruler tool In Video mode can be used to measure the length of features in the optical image or mos...

Page 86: ...Image Regions mode or Image Cross Section mode to scan the preview image Scroll boxes Mosaic pane Can be used to zoom or position the optical image or mosaic within the mosaic pane To zoom the optica...

Page 87: ...mple Stage Up Stage Down Brings the sample into focus at the current stage location Drag the scroll box up or down for coarse focus Click directly above or below the scroll box for fine focus or use t...

Page 88: ...regions Locate and select particles for particle analysis Zoom or pan the optical image or mosaic Measure the length of features in the optical image mosaic or chemical image View the spectrum associa...

Page 89: ...learn about a feature click its name in the images below Figure 66 Image Regions mode features and controls Partially collected preview image COLLECT STOP Preview Grab tool Spectrum tool Ruler tool C...

Page 90: ...ler tool COLLECT STOP Regions CLEAR Regions Cursor status Transparency Collect status Spectrum at current cursor location Profile settings for chemical image Partially collected chemical image Region...

Page 91: ...Image pixel size setting before acquiring chemical image data in the final selected regions Preview status Before collecting the preview data this area shows the size of the preview region in pixels...

Page 92: ...pdates the video image in the left pane To resize the preview box drag an edge Restart acquisition of the preview region Click a location in the mosaic during acquisition of the preview image to resta...

Page 93: ...click Collect Regions to acquire a chemical image of each region To delete a drawn region right click the region and choose Delete Selected Region To delete all drawn regions click Clear Regions Manua...

Page 94: ...Auto Regions box zoom the mosaic in or out then click Auto Regions again Exemplar Uses a selected location in the to find similar regions in the displayed optical image or mosaic Use the mouse to clic...

Page 95: ...Load Regions Loads a previously saved region queue REGIONS filename extension and displays its associated regions in the mosaic pane Save Regions Saves the current region queue to a file that can be r...

Page 96: ...tings used to acquire a chemical image of the selected region or regions of the displayed optical image or mosaic Use Collect Preview to acquire a chemical image of the preview region Use Collect Regi...

Page 97: ...lable color combination for all profile types except MCR Select MCR profile colormap Select an available color combination for the MCR profile type Tip Drag the lower limit of the profile intensity sc...

Page 98: ...s file follows the BioFormats format that can be directly imported to image processing applications such as ImageJ and FIJI Export region data as ENVI Exports the selected region of acquired chemical...

Page 99: ...r the peak height peak area and other profile types Click here for details about the features and tools available for the spectral pane Cursor status Shows the X and Y coordinates of the cursor in the...

Page 100: ...l focus before it acquires the spectrum Video Auto Focus mode If the Auto Focus On Off indicator is on and focus type in Auto Focus Settings is set to Video each time you click in the mosaic pane to a...

Page 101: ...height area region or baseline information you can use spectra displayed in Live Spectrum mode and the Profile tools to specify these settings Figure 68 Live Spectrum mode features and controls Note...

Page 102: ...cation Shows the most recently clicked location in the mosaic The spectrum acquired at this location is displayed in the spectral pane Cursor status Shows the X and Y coordinates of the current cursor...

Page 103: ...f the view finder Show a different region of the displayed spectrum click the region you want to show in the view finder Expand the X axis to its limits double click between the limit lines in the vie...

Page 104: ...sults window and its spectrum will replace the previous one in the spectral pane If no suitable match is found in the library you can select Unknown and no matching spectrum will be displayed To close...

Page 105: ...ticle analysis results For an overview of the Analysis window and a tutorial on how to open and reanalyze an image file refer to the DXRxi Quick Reference guide A copy of the guide in PDF format is in...

Page 106: ...e click its name in the image below Figure 69 OMNICxi Analysis window general features and controls Show Acquisition window Save current data Select libraries Create print report Grab tool Spectrum to...

Page 107: ...d image data a chemical image of each acquired region also appears in the mosaic pane on top of the mosaic A thumbnail picture of the image data appears at the top of the profiles pane The thumbnail i...

Page 108: ...d their associated profile settings OMNICxi saves the number and type of profiles that were run and the settings that were used The specified profiles are recalculated each time the file is opened Ima...

Page 109: ...ith the instrument To select or deselect a library click its check box in the library list OMNICxi includes features for searching spectra and analysis results against one or more spectral libraries t...

Page 110: ...Hold down the Shift key while selecting spectra to display multiple spectra When collecting time based frames you can extract the spectrum at the selected position from all frames To do this right cl...

Page 111: ...quired regions to the report History details Adds information about operations carried out Page Setup Defines page margins and orientation Print Preview Opens a Print Preview window with additional pa...

Page 112: ...e colors in the chemical image are determined by the profile intensity scale Mosaic An image comprised of static pictures of the sample surface The pictures are stitched together with the edges slight...

Page 113: ...TIFF output will have multiple pages showing each individual frame This file follows the BioFormats format that can be directly imported to image processing applications such as ImageJ and FIJI Expor...

Page 114: ...window displays the spectrum at the current cursor location in a region of acquired chemical image data To show the average of the selected location and the eight adjacent spectra right click in the m...

Page 115: ...h the profile algorithm are displayed in the colors at the top of the profile intensity scale For the MCR profile type shows the color in the chemical image that is associated with each found componen...

Page 116: ...of the sample surface topography 3D Analysis Window General Features and Controls All of the features visible in the OMNICxi 3D Analysis window are discussed below To learn about a feature click its n...

Page 117: ...the region does not have any z slice data the 3D Analysis window opens with a few different tools and features Figure 71 Viewing 2D data in the 3D Analysis window File and Tools menus Spectra pane 3D...

Page 118: ...lick and drag to measure distance on the surface of the volume Rotate mode Click and drag to rotate the 3D volume Drag and move mode Move the 3D volume on the canvas View all Centers the 3D volume on...

Page 119: ...ideo Image Overlays the 2D video image onto the 3D volume Show XYZ Position Diplays the XYZ position of the last point selected with the Select tool Show Outline Box Displays a light border around the...

Page 120: ...rthographic view Restore camera Save camera Perspective view Table 21 Terrain Window features and controls Feature Description File and tools menu File Copy to clipboard Tools Set background color Pic...

Page 121: ...from the Acquisition window It is not available when viewing a chemical region from the Analysis window Once set the smooth strength value is used to collect the chemical region This value is also sa...

Page 122: ...rview of the Workspace 116 DXRxi User Guide Thermo Scientific Instrument Settings To view or change these settings click Settings at the top of the Acquisition window in OMNICxi software Figure 72 Acq...

Page 123: ...When selected and a valid number of minutes greater than 0 is entered automatically turns off the laser after the specified time has elapsed with no data collection activity Recommended to preserve l...

Page 124: ...ed during system installation and do not need further adjustment Initialize Stage Initializes the sample stage on the microscope The stage is initialized automatically after the microscope is powered...

Page 125: ...t Defines the format of Raman data displayed in the spectral pane These options are available Raman shift cm 1 Converts the X axis to Raman shift which is a measure of the difference between the obser...

Page 126: ...nd the sample and can help prevent accidentally bumping the lens into the sample To collect a mosaic you will load a sample and bring it into focus and then collect the mosaic To bring a sample into f...

Page 127: ...s control to bring it into view The video image shows approximately one field of view Click Zoom To Region to center the optical image in the right mosaic pane The optical image shows what you see whe...

Page 128: ...ample onto the microscope stage 2 Configure sample illumination 3 Click the Video button in the software to select video mode 4 Open the sample compartment doors on the microscope and rotate the desir...

Page 129: ...tive if desired Rotate the objective to the front objective position on the microscope and select the video calibration for that objective by setting the Objective option in the Acquisition window 10...

Page 130: ...This will be the highest stage position used to collect the terrain mosaic 18 Select an overshoot percentage The overshoot adds a percent of the total z range to maximum and minimum z position to ens...

Page 131: ...h strength close the window Smooth strength is saved automatically You can now use the terrain mosaic to collect a chemical region or to analyze particles To use the terrain information when collectin...

Page 132: ...focus and collect a mosaic or collect a terrain mosaic 5 Use Live spectrum mode to acquire spectra at several locations of the sample in order to optimize the Laser power Exposure time and Number of s...

Page 133: ...scans You can interrupt and restart the preview scan at any time 10 Adjust the Image pixel size and Aperture settings if needed to optimize the image data for example to sharpen the image or show more...

Page 134: ...tions of a second Also indicates the speed of acquisition in Hz i e number of spectra acquired per second Longer exposure times may increase the height of spectral peaks but will also increase scan ti...

Page 135: ...the spectrum but allows less Raman energy from the sample which may decrease signal intensity Recommended for analyzing samples with fine detail cross sectional analysis and when using a high resolut...

Page 136: ...lection begins Adding photobleach time may reduce sample fluorescence but will also increase scan time EM gain Controls the electron multiplying gain of the detector camera EM gain increases the signa...

Page 137: ...d scans are completed for all selected regions 9 To save the acquired data click Save Current Data select a file format and click Save 10 To collect data from another sample click New Sample After col...

Page 138: ...After you close the search results window the library spectrum disappears from the spectral pane Click here for details about the search results These profile types are available Correlation Profile S...

Page 139: ...ectral pane right click the spectral pane and choose Send selected spectrum to OMNIC or OMNIC Specta Then use the Thermo Scientific OMNIC Workstation for DXRxi Raman Imaging Microscope or OMNIC Specta...

Page 140: ...ical image The colors in the chemical image represent the relative area of the specified peak at each sample point A higher intensity value closer to the top of the profile intensity scale indicates a...

Page 141: ...a start end Defines the location of the peak of interest To specify the peak position select the Spectrum tool then click a point of interest in the chemical image The spectrum collected at that locat...

Page 142: ...atioed areas of the specified peaks A higher intensity value closer to the top of the profile intensity scale indicates a larger peak area ratio Figure 80 Peak area ratio profile settings Table 28 Pea...

Page 143: ...se spike which generates a high response even when the peak of interest is not present in the spectra Numerator Denominator To define the areas of the numerator and denominator peaks select Numerator...

Page 144: ...se spike by an even smaller peak or noise spike which generates a high response even when the peak of interest is not present in the spectra Numerator Denominator To define the heights of the numerato...

Page 145: ...at that location is displayed in the spectral pane Enter X axis start and end locations in their respective boxes or drag the left and right facing triangle tools in the spectral pane to mark the peak...

Page 146: ...sults window and its spectrum is added to the spectral pane After you close the search results window the library spectrum disappears from the spectral pane Click here for details about the search res...

Page 147: ...ty your computer may not be able to calculate more than four or five components We recommend starting with a small number of components and increasing the number in increments of one Limit spectral ra...

Page 148: ...or a found MCR component The name of the best matched library spectrum appears at the top of the search results window and its spectrum is added to the spectral pane You can select another library spe...

Page 149: ...ll profile types except MCR after you enter a value or move one of the selection tools in the spectral pane the software starts calculating the new profile using the new settings Each time you adjust...

Page 150: ...le after you have changed the Expected components setting click APPLY The updated results replace the previous ones in the profiles pane and in the mosaic pane 6 To save the analysis results click Sav...

Page 151: ...using a video image 1 Load the sample onto the microscope stage 2 Configure sample illumination 3 Click the Video button in the software to select video mode 4 Bring the sample into focus and collect...

Page 152: ...b 3 In the Setup tab refine your settings to include particles in the image that you want to analyze and to exclude other areas from the analysis For details see Settings for Particle Analysis 4 When...

Page 153: ...ings are available Table 34 Particle Analysis settings Setting Description Use Defaults Resets all settings to the default values Highlight Regions Select to highlight particles that have been identif...

Page 154: ...ntensity Use the background intensity group to limit the selection based on visual contrast The following tools are available Auto Detect Automatically detects what is a background and what is a parti...

Page 155: ...elect all detected particles Detect as Points Only available for video image based particle analysis When detecting as points instead of collecting all spectra within the region the spectrum is measur...

Page 156: ...le Click a row in the Spectra Matches table to point to the particle in the mosaic Click a row in the Identification Results table to highlight the component in the mosaic View Spectrum at Specific Lo...

Page 157: ...rum mode 5 Set Laser power greater than 0 6 Use the Grab tool to select a location in the mosaic The large red moves to the selected location The spectrum acquired at that location and the current foc...

Page 158: ...due to signal averaging However increasing number of scans also increases the time required to acquire the data Aperture Defines the size of the Raman beam entrance slit or pinhole The beam passes thr...

Page 159: ...tion EM gain Controls the electron multiplying gain of the detector camera EM gain increases the signal to overcome the readout noise but it also increases other sources of noise The optimal setting f...

Page 160: ...sample into sharp focus 2 Click START Mosaic to collect a mosaic 3 Close the sample compartment doors 4 Click Live Spectrum 5 Set Laser power greater than 0 use an appropriate setting for your sample...

Page 161: ...in as needed to optimize the spectrum Make sure Aperture is set to one of the confocal pinhole options If the spectrum has a curved baseline use Correct baseline in the Settings box to correct it 8 Cl...

Page 162: ...ct a Profile type and adjust the profile settings as needed to create the chemical image For this demonstration we used the MCR profile type with 5 expected components 11 Click Image Cross Section and...

Page 163: ...l image using the MCR profile Each color in the chemical image represents a new layer in the sample Figure 91 MCR cross sectional image of an optically transparent sample 15 Adjust the Image pixel siz...

Page 164: ...able spectral libraries click SEARCH Displayed Spectrum A search results window appears above the button and the best matched library spectrum is temporarily added to the spectral pane Here is an exam...

Page 165: ...layout scanning faxing word processing and other applications Export preview data as ENVI Exports the chemical image as an ENVI file ENVI file name extension which can be opened with the Thermo Scien...

Page 166: ...3 OMNICxi Software Operation Acquire and Analyze Data 160 DXRxi User Guide Thermo Scientific...

Page 167: ...urs for longer collections Trigger Runs multiple frame collection with the start of each frame triggered by an external input Total Intervals Defines the number of frames collected using the trigger T...

Page 168: ...f interest To play through or animate a series of frames select a frame and then use the Play Fast Forward and Stop buttons to start stop and control speed Table 38 Analysis window showing time based...

Page 169: ...ically transparent to the laser wavelength Generally if you can see through the material with your eyes it is a good candidate for this application Acquire 3D Image Data Use the Region Queue to collec...

Page 170: ...llect Regions When collection is complete you can view the data in 3D with the OMNICxi 3D Analysis Window See 3D Analysis Window General Features and Controls for details View 3D Data The 3D Analysis...

Page 171: ...gle slide sample holder is installed on the microscope stage 2 Click the PV status icon and choose Run A message similar to the following is displayed Table 39 PV status available options Icon Meaning...

Page 172: ...compares measured peak locations to known values in wavenumbers When the test is completed a message similar to the following is displayed 7 Place the DXRxi silicon test sample provided with the instr...

Page 173: ...r to the PV troubleshooting information for help 10 When you are finished viewing the results click Close to close the window The software automatically saves the measured PV data polystyrene spectrum...

Page 174: ...additional features are available in the PV results window Table 40 PV results window available features Feature Description Print Prints a report of the displayed PV results including instrument ID...

Page 175: ...sets were aligned and calibrated We recommend aligning and calibrating once a week You have just moved the instrument You see an error message related to the detector signal intensity no signal or sig...

Page 176: ...holder is installed on the microscope stage 3 Install the alignment and calibration tool on the single slide sample holder Make sure the tool is in the detent level and secured by the stage clip and b...

Page 177: ...alignment tool through the eyepiece The pinhole is located on a substrate mounted inside the alignment tool The substrate is visible through the opening as shown below Figure 94 Alignment tool opening...

Page 178: ...ol to bring the pinhole into sharp focus adjusting the brightness as needed to optimize the image contrast Figure 95 Backlit pinhole in focus but not centered 9 Position the focused pinhole exactly in...

Page 179: ...r a red X appears instead One of the following conditions may apply Grating door is open close the grating door Grating shutter is closed open the shutter Grating is not fully seated Remove the gratin...

Page 180: ...g to recalibrate the video image To retrieve a video calibration for an objective that was previously calibrated use the Objective list box in the OMNICxi Acquisition window If you have a new objectiv...

Page 181: ...re should be running and the status indicator in the upper right corner should show a green check mark To create a new video calibration or update an existing one 1 Open the sample compartment doors 2...

Page 182: ...m the illuminator Turn up the brightness to optimize the contrast When you look at the calibration slide directly not through the eyepiece you should see a pool of white light from the illuminator on...

Page 183: ...e into sharp focus clockwise knob rotation moves the stage up Bringing the aperture into focus also focuses on the calibration slide Figure 101 Calibration scale in focus at 10x magnification When the...

Page 184: ...uggest using the magnification of the objective followed by its numerical aperture for example 10x 0 25 or the model name Objectives are typically labeled with this information After you complete the...

Page 185: ...e joystick to move the stage Line up one of the vertical division lines on the calibration slide with the vertical cross hair in the eyepiece Use the diopter ring on the right lens if necessary to str...

Page 186: ...tive 13 Maximize the Setup Video window to enlarge the video pane Turn down the brightness until a video image appears in the video pane Tip It can be helpful to place the vertical cross hair at the l...

Page 187: ...image To adjust the cropping box grab an edge Figure 105 Cropping box adjusted to cover half of available area for two different objectives 15 Use the mouse to place the centering yellow marker in th...

Page 188: ...video image To adjust the size and shape of the cropping box drag its border To move the cropping box drag its center to the desired location Figure 108 Cropping box correctly sized and positioned for...

Page 189: ...xisting video calibration 1 Rotate the objective you are recalibrating to the front objective position 2 From the OMNICxi Acquisition window click Settings and then click 3 In the Setup Video window s...

Page 190: ...MNICxi software follow the steps to reset the box or move markers in Creating a New Video Calibration 5 Click Save To delete a saved calibration 1 From the OMNICxi Acquisition window click Settings an...

Page 191: ...ave been out of focus Rerun the PV test making sure the focus is correct If a wavelength accuracy test fails again align and calibrate the installed laser set and then rerun the PV test If a wavelengt...

Page 192: ...he software Select a slit instead of a pinhole aperture Increase the setting of laser power in the software If this problem persists contact our sales or service representative in your area Sample Ban...

Page 193: ...r this condition try one or more of the following Use a different laser shorter wavelengths heat samples less If the sample looks burned replace it or move it so the laser will strike a fresh area Red...

Page 194: ...our sales or service representative in your area The Computer Cannot Communicate with the Instrument If the front panel indicators are not on make sure the instrument is plugged in and the power stri...

Page 195: ...pixel size setting in the software Switch to a shorter wavelength laser Spatial resolution depends on the wavelength of the laser Chemical Image Shows Missing Data Increase the exposure time in the s...

Page 196: ...location Detector too warm Detector disconnected No filter No grating No laser Mismatched grating Mismatched filter Invalid fiber probe configuration Uncalibrated laser grating filter set Alignment c...

Page 197: ...wer strip off and back on and then hold down the instrument power button for 3 seconds and then restart the OMNICxi software If that doesn t fix the problem contact technical support Video camera disc...

Page 198: ...the instrument power button for 3 seconds and then restart the OMNICxi software If that doesn t fix the problem contact technical support Detector too warm The instrument detector has not cooled to t...

Page 199: ...n the instrument power button for 3 seconds and then restart the OMNICxi software If that doesn t fix the problem contact technical support No filter The instrument does not have a filter installed In...

Page 200: ...Aligning and Calibrating Laser Sets Stage firmware out of date A newer version of firmware for the stage controller is required Contact technical support Sample door open The instrument cannot collect...

Page 201: ...unable to communicate with the instrument or open the shutter that allows the laser to enter the sample compartment Cycle the power on the instrument turn the power switch on the power strip off and...

Page 202: ...h is fully vertical Filter is not fully seated Remove the filter and wipe its bottom surface with a clean lint free cloth wipe the magnet inside the filter compartment and then reinstall the filter If...

Page 203: ...is misaligned Make sure the 10x objective is rotated into position and engaged in the detent Sample compartment door is ajar Make sure both doors are tightly closed Grating is not fully seated or the...

Page 204: ...fully seated Remove and reinstall the laser making sure the latch is fully vertical Check each of these items and then restart Align Calibrate If that doesn t fix the problem cycle the power on the co...

Page 205: ...nt Check the following Align calibrate tool is dirty Clean the glass window on the tool Align calibrate tool is misaligned Make sure the tool lays flat and is secured by the stage clip Align calibrate...

Page 206: ...nstrument power button for 3 seconds and then restart the OMNICxi software and run Align Calibrate If the problem persists contact technical support Unable to collect spectral data The instrument is u...

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ThermoFisher Scientific DXR xi, User Manual

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