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 © 2014-2021 Thermo Fisher Scientific Inc. All rights reserved. Microsoft, Windows and Excel are either trademarks or registered 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.
Page 3: Table Of Contents
Contents Chapter 1 Introducing the DXRxi Raman Imaging System......1 About the System ..........1 Getting Started .
Page 4 Contents Using Optical Polarizers ........29 Positioning the Motorized Stage .
Page 5 Contents View Particle Analysis Results ....... . . 149 View Spectrum at Specific Location ......150 Analyze Sample Cross Sections .
Page 6 Contents Alignment/calibration out of date....... 180 Stage firmware out of date ........180 Sample door open .
Page 7: Introducing The Dxrxi Raman Imaging System
Introducing the DXRxi Raman Imaging System Welcome to the Thermo Scientific™ DXR™xi Raman imaging microscope with OMNIC™xi Raman imaging software. This system is intended to be used to analyze the chemical composition of materials using dispersive Raman spectroscopy. This help system will get you started using the microscope and software and demonstrate how to run experiments using a provided sample.
Page 8: Getting Started
Introducing the DXRxi Raman Imaging System Getting Started The instrument includes our OMNICxi Raman imaging software for data collection and analysis. The OMNICxi software comprises two main windows: • the Acquisition window for data collection and on-the-fly analysis • the Analysis window for viewing and processing previously collected image data With automatic feature recognition and real-time optimization of imaging parameters, this imaging system is a powerful tool for component identification that will transform the way you approach materials analysis.
Page 9: About This Help System
Introducing the DXRxi Raman Imaging System About this Help System WARNING Avoid eye injury. The system is a Class 3B laser product emitting visible or invisible laser radiation when using the fiber optic accessory or operating with the microscope cover removed. Exposure to laser radiation could cause permanent eye damage.
Page 10: Conventions
Introducing the DXRxi Raman Imaging System Contacting Us Section Description OMNICxi Raman Descriptions of all software features and controls Imaging Software Troubleshooting Troubleshooting information and descriptions of possible error messages Conventions This help system uses the following conventions for safety and special notices: WARNING Indicates a hazardous situation which, if not avoided, could result in death or serious injury.
Page 11: Trademarks
Introducing the DXRxi Raman Imaging System Trademarks Note Please have the instrument serial number available when you contact us. Trademarks Microsoft, Windows and Excel are either trademarks or registered 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.
Page 12 Introducing the DXRxi Raman Imaging System Trademarks DXRxi User Guide Thermo Scientific...
Page 13: Dxrxi Microscope Operation
DXRxi Microscope Operation The DXRxi Raman Imaging Microscope combines rapid chemical characterization with high-end spectral performance. It has interchangeable lasers and their associated filters and gratings, and accommodates polarizers and various optical filters. The instrument offers reflected light brightfield sample illumination. Optional reflected light brightfield/darkfield and transmission illumination kits are also available.
Page 14 DXRxi Microscope Operation DXRxi User Guide Thermo Scientific...
Page 15: Microscope Features And Controls
Microscope Features and Controls Front View Figure 1. Microscope with optional reflected light brightfield/darkfield (BF/DF) illuminator Power indicator Laser power indicator Light path control Video Sample camera area cover Grating Laser at sample indicator Laser filter Eyepiece Power button (hold down Sample compartment doors Laser 3 seconds to power on or off)
Page 16: Right Side View
Microscope Features and Controls Right Side View Figure 2. Microscope with optional reflected light brightfield/darkfield (BF/DF) illuminator Field Iris control (default all the way in) View path control (default half way in/out) Aperture Iris control (default all the way in) Optical filter slots (2), insert from other side...
Page 17 Microscope Features and Controls Figure 3. Power supply for optional reflected light brightfield/darkfield (BF/DF) illuminator Power indicator Power switch Brightness control (for reflected light only) Figure 4. Microscope with reflected light brightfield only illuminator View path control Optical filter slot (insert from other side) (default half way in/out) Eyepiece...
Page 18: Left Side View
Microscope Features and Controls Left Side View Figure 5. Microscope, left side view with laser keyswitch Grating Microscope power cord receptacle Laser keyswitch in locked position (laser is disabled) DXRxi User Guide Thermo Scientific...
Page 19: Inside Sample Compartment
Microscope Features and Controls Inside Sample Compartment Figure 6. Microscope, inside sample compartment Nosepiece Sample stage Single slide holder Objectives Thermo Scientific DXRxi User Guide...
Page 20: Stage Controls
Microscope Features and Controls Figure 7. Microscope objectives and sample stage (10x objective is included) Current objective must also be selected in OMNICxi software Nosepiece Objective Sample stage Single slide holder Stage Controls Figure 8. Microscope sample stage controls Focus speed control (hold down to speed up focus control, or tap Joystick (fine x and to toggle between slow, medium...
Page 21: Operating The Microscope
Operating the Microscope Indicators Figure 9. Indicators Table 1. Indicator descriptions Indicator 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 lights when laser is powered on. Green indicator LED.
Page 22: Powering The System Up Or Down
Operating the Microscope Powering the System Up or Down  To power up the system 1. Turn on the power strip. 2. Hold down the blue power button on the front of the microscope keypad for three (3) seconds. 3. Ensure stage controller switch is on. 4.
Page 23: Available Sample Holders
Operating the Microscope Available Sample Holders Note This holder is also used to hold the align/calibrate tool for system alignment and calibration. Single Slide Holder Figure 10. Single slide holder Left side Lower right corner Microtiter Well-Plate Holder Figure 11. Microtiter Well-Plate holder Upper left corner Thermo Scientific...
Page 24 Operating the Microscope Dual Slide Holder Figure 12. Dual slide holder set inside Well-Plate holder Upper left corner Dual slide holder Well-Plate holder Acrylic Vacuum Plate Figure 13. 96-acrylic vacuum plate mounted on Well-Plate holder Upper left corner DXRxi User Guide Thermo Scientific...
Page 25: Rotating Stage Holder
Operating the Microscope Capillary Tube Array Holder Figure 14. Capillary tube array holder mounted on Well-Plate holder Capillary tubes Upper left corner Tube retainer Rotating Stage Holder Accepts standard microscope slide, provides manual rotation to any arbitrary position. Holds standard microscope single slide. Figure 15.
Page 26: Sample Holder Breadboard Kit With Clips
Operating the Microscope Sample Holder Breadboard Kit With Clips This sample holder provides maximum flexibility for holding small and uniquely shaped samples without the risk of contamination with adhesives. It is compatible with Ted Pella sample holders. Figure 16. Breadboard kit Thumb- screws Spring...
Page 27: Raman Macro Sampler
Operating the Microscope Raman Macro Sampler Figure 18. Microscope Macro Sampler Adapter To nosepiece Objective Sample holder Mounting plate Adapters Leveling the Sample Holder Figure 19. Screw locations Thumbscrews (3, tall silver) Hold-down screws (3) Thermo Scientific DXRxi User Guide...
Page 28 Operating the Microscope Figure 20. Using the screwdriver End caps Bit holder Removable double-ended bits Larger Phillips bit Hold-down screw  How to level the sample holder 1. Lower stage and bring to front to make it easier to access single slide holder fasteners. NOTICE Anytime during leveling when moving the stage, the objectives can potentially collide with objects on the sample holder.
Page 29 Operating the Microscope 7. Continue turning the front-left thumbscrew clockwise 1 turn to raise the slide holder in that corner. 8. Repeat step 4 for the right side of the slide holder and the middle-right thumbscrew. 9. Continue turning the middle-right thumbscrew clockwise one-half turn to raise the slide holder on that side.
Page 30 Operating the Microscope Table 2. Amount to rotate thumbscrew μm Revolutions 4/8 (1/2) 2/8 (1/4) Tip Envision pictures of wheels to visualize the rotation amount. Figure 21. Rotation wheels showing fractions of a full revolution 16. Move the stage to position the middle of the slide holder under the objective. 17.
Page 31: Installing Objectives
Operating the Microscope Note If it is critical for the top surface of the sample to be flat, the same leveling technique can be applied to the top of a sample, except Table 1 will no longer be valid. If sample is not very parallel, then leveling the top of the sample will result in the sample holder no longer being level.
Page 32: Configuring Sample Illumination
Operating the Microscope Configuring Sample Illumination This section explains how to set the microscope features that control sample illumination and how to control the brightness for each configuration. It also shows how to install and use the optional filters and polarizers. These topics are covered: Contents •...
Page 33 Operating the Microscope Table 3. Sample illumination controls with the optional BF/DF illuminator Feature Description Available Settings View Path Directs light through the • In (eyepiece only) microscope eyepiece or to the • Middle (eyepiece and video camera (to produce a video video image) image in the software) or both.
Page 34 Operating the Microscope Use the Illumination Intensity control on the illuminator power supply to adjust the brightness. Figure 23. Illumination intensity control for optional BF/DF Illuminator Illuminator power Illuminator power supply supply Illumination intensity control Controlling Illumination with the Optional Reflected Light Brightfield Illuminator If your system has the optional reflected light illuminator, the light path is always configured for reflected light brightfield illumination.
Page 35: Controlling Transmitted Light Illumination
Operating the Microscope Controlling Transmitted Light Illumination If your system has the optional transmitted light illumination kit, you can use transmitted light to observe transparent samples mounted on a transparent slide, or use transmitted and reflected light illumination together to optimize brightness and contrast. Transmitted light observations also require a sample holder that is open in the center.
Page 36 Operating the Microscope The reflected light brightfield/darkfield illuminator has two filter insertion slots (see the image below); the brightfield only illuminator has one. NOTICE Insert optical filters only from the left side of the microscope. Figure 26. Optical filter insertion slots for reflected light BF/DF illuminator Filter insertion slots (2) Insert optical filters from left side only.
Page 37: Using Optical Polarizers
Operating the Microscope Using Optical Polarizers Optional polarizers are available for the reflected light illuminators and the transmitted light illuminator. There are two fixed polarizers that send polarized light to the sample (one for each type of illuminator). polarization analyzers are also available (configurable and fixed).
Page 38 Operating the Microscope Installing the Reflected Light Fixed Polarizer The fixed polarizer for the reflected light illuminators sends polarized light to the sample when reflected light illumination is in use. It can be used with an optional polarization analyzer to capture any change in polarization that is due to the state of the light interacting with the sample.
Page 39 Operating the Microscope  To install the reflected light fixed polarizer 1. Remove the placeholder from the polarizer insertion slot. The placeholder prevents light from entering the opening when the polarizer is not in use. The placeholder looks like this: Figure 31.
Page 40 Operating the Microscope Reflected Light Fixed Polarizer Attachment The reflected light fixed 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 easier positioning into and out of the sample beam.
Page 41 Operating the Microscope The transmitted light fixed polarizer fits in the transmission illumination assembly below the stage platform. Figure 34. Transmitted light fixed polarizer insertion slot on the microscope Insertion slot for fixed polarizer for the transmitted light illuminator  To install the transmitted light fixed polarizer 1.
Page 42 Operating the Microscope  To use the transmitted light fixed polarizer Use the handle to gently push the polarizer all the way back and then slowly draw it forward until you feel the first click, second click and third click. The three positions are described below.
Page 43 Operating the Microscope The image below shows the location for inserting a polarization analyzer into the microscope. NOTICE Insert the polarization analyzer only from the right side of the microscope. Figure 38. Polarization analyzer insertion slot on the microscope Insertion slot for Insertion slot for polarization analyzers polarization analyzers...
Page 44 Operating the Microscope  To install the fixed polarization analyzer 1. Remove the cap from the polarization analyzer opening on the left and right side of the microscope. 2. Hold the analyzer by the labeled end with the label facing up. 3.
Page 45: Positioning The Motorized Stage
Operating the Microscope 5. Use the screw at the end of the polarization analyzer to attach it to the other end of the bar attachment. Here is 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 Handle Configurable polarization analyzer...
Page 46: Using Confocal Operation
Operating the Microscope Feature Description Joystick Moves the motorized stage left and right along the X-axis or forward and back along the Y-axis Focus knob Adjusts the height of the stage along the Z-axis Left button Press to adjust the speed of the XY movement Right button* Press to adjust the focus speed Centering switches...
Page 47: Changing The Laser, Filter, And Grating
Operating the Microscope The microscope employs a 180° degree back-scattering configuration. The z(Y,Y)z, z(X,X)z, z(X,Y)z, and z(Y,X)z polarization states can be measured by selecting the appropriate laser polarization and analyzer polarization. The z(X,X)z is denoted as Horizontal polarization and the z(Y,Y)z is denoted as Vertical polarization. The horizontal axis is across the stage from left to right and the vertical axis goes from front to back.
Page 48 Operating the Microscope 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. Figure 45. System with laser in place and locked Locked position DXRxi User Guide Thermo Scientific...
Page 49 Operating the Microscope  To install a grating 1. Open the grating door. 2. Remove 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 grating and inside the grating compartment on the instrument).
Page 50 Operating the Microscope 5. Open the grating shutter. Figure 48. Grating shutter button Open Closed  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.
Page 51: Installing A 633 Nm Laser
Operating the Microscope Installing a 633 nm Laser If you specifically ordered this laser wavelength with your system, see “Changing the Laser, Filter and Grating.” If you need to add this capability in the future, a service visit is required to ensure optimum alignment and performance.
Page 52: Using A Class 3B Fiber Optic Launcher Accessory
Operating the Microscope WARNING Avoid eye injury. The system is a Class 3B laser product emitting visible or invisible laser radiation. Exposure to laser radiation could cause permanent eye damage. • 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 •...
Page 53 Operating the Microscope Figure 51. Fiber optic launcher installation Fiber optic launcher Laser filter opening CAUTION To ensure safe operation, always connect the collection probe cable to the fiber optic launcher before you connect the excitation probe cable. 2. Connect the fiber optic cables from the probe to the appropriate ports on the fiber optic launcher (see previous image).
Page 54: Installing The Microscope Alignment And Calibration Tool
Operating the Microscope 4. Connect the power cable for the probe LED. Figure 53. Connect power cable for probe LED 5. Attach the strain relief hook (provided) to the microscope by inserting the two screws (provided) into the two holes at the top of the microscope back panel (behind the laser filter compartment).
Page 55 Operating the Microscope Figure 54. Connecting alignment and calibration tool Connect to microscope Alignment tool  To install the align/calibrate tool 1. Position the tool with the connector extending from the left (see image above). 2. Pull the stage clip 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.
Page 56 Operating the Microscope Cleaning the Glass Window on the Alignment Tool  To clean the glass window on the alignment tool 1. Use a can of dry compressed air or a dust blower to blow off any particles on the surface of the glass.
Page 57: Servicing The Microscope
Servicing the Microscope Cleaning Your Instrument If the outside of the instrument needs cleaning, turn off the power to all components, unplug the power strip from the wall outlet, and wipe the outside of the instrument with a damp (not wet), soft cloth and a mild soap.
Page 58: Replacing The Nosepiece
Servicing the Microscope Replacing the Nosepiece Figure 56. Replacing the nosepiece When installing a nosepiece, make sure to slide it in until it stops, and then tighten the screw until it is just tight. Do not over tighten. When installing a new nosepiece or changing objectives, set the Objective selection in the software to the new objective you will be using.
Page 59 Servicing the Microscope  To replace a brightfield/darkfield illuminator 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.
Page 60 Servicing the Microscope 5. Squeeze the levers, insert the new bulb all the way, and release the levers. To extend bulb life, always handle a new bulb with a clean tissue or cloth. Figure 60. Inserting the bulb 6. Replace the cover. Figure 61.
Page 61: Safety Information
Safety Information NOTICE Be sure that all persons operating this system read the site and safety manual first. Laser Precautions 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 radiation could cause permanent eye damage.
Page 62: Biohazards Or Radioactive Materials And Infectious Agents
Safety Information Biohazards or Radioactive Materials and Infectious Agents Biological samples such as tissues, body fluids, infectious agents, and blood of humans and other animals have the potential to transmit infectious diseases. Wear appropriate protective equipment. Individuals should be trained according to applicable regulatory and organization requirements before working with potentially infectious materials.
Page 63: Ventilation
Safety Information To avoid overheating, do not block the free flow of air around the instrument. There should be at least 2 cm (about 1 in) of clearance behind the instrument and at least 30 cm (about 12 in) of clearance on each side. Ventilation There are no special ventilation requirements for your instrument.
Page 64: Microscope Safety Labels
Safety Information Microscope Safety Labels DXRxi User Guide Thermo Scientific...
Page 65 Safety Information Thermo Scientific DXRxi User Guide...
Page 66 Safety Information DXRxi User Guide Thermo Scientific...
Page 67 Safety Information Thermo Scientific DXRxi User Guide...
Page 68 Safety Information DXRxi User Guide Thermo Scientific...
Page 69: Omnicxi Software Operation
OMNICxi Software Operation Use the OMNICxi Raman imaging software with your DXRxi Raman Imaging Microscope to quickly identify and characterize solids, liquids, or microparticles. Analyze regions of the sample surface, locate and characterize particles, view live spectra, measure how your sample changes over time, or explore 3D visualizations.
Page 70: Overview Of The Workspace
OMNICxi Software Operation Overview of the Workspace Acquire and Analyze Once you have collected a mosaic, set the parameters for your data acquisition and then collect and analyze the data. Your settings and techniques depend on the type of analysis you are performing.
Page 71: General Features And Controls
OMNICxi Software Operation Overview of the Workspace • Create a terrain map to visualize the sample’s surface topography • Locate and characterize particles (see Identify and Analyze Particles) This section covers these topics: • General Features and Controls • Video Mode Features and Controls •...
Page 72 OMNICxi Software Operation Overview of the Workspace 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.
Page 73 OMNICxi Software Operation Overview of the Workspace Table 10. Acquisition window, general features and controls Feature Description New sample Clears all data from the video and mosaic panes in the Acquisition and Analysis windows to prepare the system for collecting data with a new sample.
Page 74 OMNICxi Software Operation Overview of the Workspace Table 10. Acquisition window, general features and controls Feature Description Auto Focus Defines settings for focusing the sample while collecting a mosaic in Settings the Acquisition window, and for applying the focus (Z height) information while collecting data in Live Spectrum mode Image...
Page 75 OMNICxi Software Operation Overview of the Workspace Table 10. Acquisition window, general features and controls Feature Description Auto Focus Turns the Auto Focus settings on and off. The indicator is on when On/Off indicator this option is selected and off when deselected. •...
Page 76 OMNICxi Software Operation Overview of the Workspace Table 10. Acquisition window, general features and controls Feature Description Show Analysis If the system computer is connected to one display monitor (rather window than two), use this button to quickly display the OMNICxi Analysis window.
Page 77 OMNICxi Software Operation Overview of the Workspace Table 10. Acquisition window, general features and controls Feature Description Help Displays Help information for the instrument and software Stage Up/Stage Brings the sample into focus at the current stage location. Drag the Down scroll box up or down for coarse focus.
Page 78 OMNICxi Software Operation Overview of the Workspace Table 10. Acquisition window, general features and controls Feature Description Profile intensity Image Regions mode Image Cross Section mode, defines the scale scale or range and corresponding colors used to create the chemical image.
Page 79 OMNICxi Software Operation Overview of the Workspace To learn about a feature in the spectral pane, click its name in the image below. Figure 64. Spectral pane features and controls Spectrum at current cursor Y-axis data format location in chemical image SAVE Spectrum Spectrum titles View finder...
Page 80 OMNICxi Software Operation Overview of the Workspace Table 11. Spectral pane features and controls Feature Description Save Spectrum Saves the selected spectrum (or spectra) as an OMNIC .SPA (or .SPG) file, which can be opened using the Thermo Scientific OMNIC Workstation for DXRxi Raman Imaging Microscope or OMNIC Specta application for further processing.
Page 81 OMNICxi Software Operation Overview of the Workspace Table 11. Spectral pane features and controls Feature Description Right-click menu • Select all displayed spectra. Selects all the spectra that are options currently displayed in the spectral pane. • Copy displayed spectra as picture. Copies an image of the spectral pane and its contents to the Windows Clipboard.
Page 82 OMNICxi Software Operation Overview of the Workspace Table 11. Spectral pane features and controls Feature Description Right-click menu • Display options (continued) – Full Y scale. Shows all displayed spectra so that they fill the pane vertically. – Common Y scale. Shows all displayed spectra using the same Y-axis scale, making it easy to compare their relative peak heights visually.
Page 83 OMNICxi Software Operation Overview of the Workspace Video Mode Features and Controls Select Video mode in the OMNICxi Acquisition window for the following tasks: • View a live video image of the sample surface. The image is displayed in the video pane. •...
Page 84 OMNICxi Software Operation Overview of the Workspace Figure 65. Video mode features and controls START/STOP Mosaic Grab tool Mosaic pane CLEAR Mosaic FOCUS Video Spectrum tool START Terrain Mosaic Objective Ruler tool Preview box Scroll box Video scale bar Video pane Zoom To Region Stage status Cursor status...
Page 85 OMNICxi Software Operation Overview of the Workspace Table 13. Video mode features and controls Feature Description Grab tool In Video mode, the Grab tool can be used to: • Drag the video image, chemical image or zoomed in mosaic within their respective panes. (Use the scroll wheel on the mouse or the scroll bars to zoom the mosaic in or out.) •...
Page 86 OMNICxi Software Operation Overview of the Workspace Table 13. Video mode features and controls Feature Description START Terrain Mosaic Opens the Terrain Mosaic Setup dialog to configure the terrain mosaic collection settings. With a classic mosaic, if your sample had a very rough or uneven surface, parts of the sample that were closer or farther than the focal plane may have been out of focus.
Page 87 OMNICxi Software Operation Overview of the Workspace Table 13. Video mode features and controls Feature Description Mosaic pane Before you collect a mosaic video mode, this pane shows a static picture of the sample as it appears when viewed through the microscope eyepiece (one field of view).
Page 88 OMNICxi Software Operation Overview of the Workspace Image Regions Mode Select Image Regions mode in the OMNICxi Acquisition window for the following tasks: • Adjust acquisition and profile settings before acquiring a chemical image • Adjust the size and location of the preview box •...
Page 89 OMNICxi Software Operation Overview of the Workspace This section explains the main features available in the Acquisition window when Image Regions mode is selected. To learn about a feature, click its name in the images below. Figure 66. Image Regions mode features and controls COLLECT/STOP Preview Grab tool Spectrum tool...
Page 90 OMNICxi Software Operation Overview of the Workspace Figure 67. Image Regions mode features and controls Manual Regions Ruler tool COLLECT/STOP Regions Manual Point Spectrum tool Auto Regions Time-Based Collect Scroll box Grab tool CLEAR Regions Settings Region Queue Spectral pane Zoom To Region Acquisition Profile settings...
Page 91 OMNICxi Software Operation Overview of the Workspace Table 14. Image Regions mode features and controls Feature Description Collect/Stop Preview Collects a chemical image of the selected preview region using the current acquisition settings. The preview region is the area inside preview box.
Page 92 OMNICxi Software Operation Overview of the Workspace Table 14. Image Regions mode features and controls Feature Description Collect Status During acquisition of one or more selected regions, this area shows the start time, percent completion and time for each scan and the estimated time to complete all requested scans of each selected region.
Page 93 OMNICxi Software Operation Overview of the Workspace Table 14. Image Regions mode features and controls Feature Description Manual Regions Can be used to manually select the regions that will be used to acquire a chemical image. To select a region, click this option and then use the mouse to draw a box around the region in the mosaic pane.
Page 94 OMNICxi Software Operation Overview of the Workspace Table 14. Image Regions mode features and controls Feature Description Auto Regions Automatically selects regions in the optical image or mosaic using either the Auto Region Selection settings or Particle Selection settings. Settings for Particle Analysis for a description of the Particle Selection settings.
Page 95 OMNICxi Software Operation Overview of the Workspace Table 14. Image Regions mode features and controls Feature Description Region Queue Can be used to manually add to or edit the coordinates of currently selected regions in the optical image or mosaic. These options are available: •...
Page 96 OMNICxi Software Operation Overview of the Workspace Table 14. Image Regions mode features and controls Feature Description Chemical image A scan that contains one spectrum collected at each sampling point in the preview box or a selected region of the mosaic. The number and locations of the spectra that make up the chemical image are defined by the Image pixel size...
Page 97 OMNICxi Software Operation Overview of the Workspace Table 14. Image Regions mode features and controls Feature Description Profile intensity scale Shows the scale and corresponding colors used by the selected profile. Areas of the chemical image that correlate with the profile algorithm are displayed in the colors at the top of the profile intensity scale.
Page 98 OMNICxi Software Operation Overview of the Workspace Table 14. Image Regions mode features and controls Feature Description Right-click menu • Copy region as picture. Copies an image of a region of options (continued) acquired chemical image data to the Windows Clipboard. The copied image can be pasted into any word processing, presentation or other compatible application.
Page 99 OMNICxi Software Operation Overview of the Workspace Table 14. Image Regions mode features and controls Feature Description Spectral pane In Image Regions mode, displays the spectrum collected at the current cursor location in a region of acquired chemical image data. The spectral pane is also used for specifying peak heights and areas for the peak height, peak area, and other profile types.
Page 100 OMNICxi Software Operation Overview of the Workspace The features and tools available in Image Cross Section mode are the same as in Image Regions mode with these exceptions: • COLLECT Regions and CLEAR Regions buttons are unavailable • Manual Regions, Auto Regions, Region Queue, and the Time-Based Collect Setup are not applicable •...
Page 101 OMNICxi Software Operation Overview of the Workspace Note When using Live Spectrum mode to acquire and view spectra, make sure the sample compartment doors are closed and Laser power is greater than 0. The system can collect Raman data only when the laser is directed onto the sample. For your protection, the laser light is blocked when the sample compartment doors are open.
Page 102 OMNICxi Software Operation Overview of the Workspace Table 15. Live Spectrum mode features and controls Feature Description Grab tool In Live spectrum mode, the Grab tool can be used to: • Drag the zoomed in mosaic within its respective pane (use the scroll wheel on the mouse or the scroll bars at the edges of the mosaic pane to zoom the mosaic in or out) •...
Page 103 OMNICxi Software Operation Overview of the Workspace Table 15. Live Spectrum mode features and controls Feature Description View finder Contains an image of the displayed spectrum. Can be used to: • Change the display limits of the spectral pane (drag the vertical limit line at each end of the view finder) View Limit line...
Page 104 OMNICxi Software Operation Overview of the Workspace Table 15. Live Spectrum mode features and controls Feature Description SAVE Spectrum Saves the selected spectrum as an OMNIC SPA file, which can be opened using the Thermo Scientific OMNIC Workstation for DXRxi Raman Imaging Microscope or OMNIC Specta application for further processing.
Page 105: Omnicxi Analysis Window
OMNICxi Software Operation Overview of the Workspace These additional features are available for working with displayed spectra: Table 16. Features for working with displayed spectra If you want to... then... Pan X-axis Use the Grab tool to drag spectra in the spectral pane left and right.
Page 106 OMNICxi Software Operation Overview of the Workspace General Features and Controls All of the features visible in the OMNICxi Analysis window are discussed below. To learn about a feature, click its name in the image below. Figure 69. OMNICxi Analysis window, general features and controls Create/print Open data file Grab tool...
Page 107 OMNICxi Software Operation Overview of the Workspace Table 17. Analysis window, general features and controls Feature Description Open data file Opens an image file that was previously saved. OMNICxi recognizes these file formats: • .MAPX. Can be opened only in OMNICxi software •...
Page 108 OMNICxi Software Operation Overview of the Workspace Table 18. Analysis window, general features and controls Feature Description Save current data Saves any newly acquired or updated data in the Acquisition and Analysis windows. The following information is saved: • mosaic, if one was created •...
Page 109 OMNICxi Software Operation Overview of the Workspace Table 19. Analysis window, general features and controls Feature Description Select libraries Click the Select Libraries button to specify regions and to select libraries for the search. Search Setup opens the Search Setup dialog. Use this dialog to specify one or more regions to use for the spectral search.
Page 110 OMNICxi Software Operation Overview of the Workspace Table 19. Analysis window, general features and controls Feature Description Region queue Can be used to view the position, dimensions and acquisition settings for all regions of acquired chemical image data. These options are available: •...
Page 111 OMNICxi Software Operation Overview of the Workspace Table 19. Analysis window, general features and controls Feature Description Create/print report Creates a printable, preformatted report from the data displayed in the Analysis window. When creating a report, the following options are available: •...
Page 112 OMNICxi Software Operation Overview of the Workspace Table 19. Analysis window, general features and controls Feature Description Thumbnail Contains a small picture of the chemical image and its associated analysis and search information for each generated profile (or for each found component for the MCR profile).
Page 113 OMNICxi Software Operation Overview of the Workspace Table 19. Analysis window, general features and controls Feature Description Right-click menu • Copy region as picture. Copies an image of a region of acquired options (continued) chemical image data to the Windows Clipboard. The copied image can be pasted into any word processing, presentation or other compatible application.
Page 114 OMNICxi Software Operation Overview of the Workspace Table 19. Analysis window, general features and controls Feature Description Right-click menu • Show region information. Displays the instrument setup and options (continued) collection parameters for the selected region. This information can be copied to the clipboard for use in other software. •...
Page 115 OMNICxi Software Operation Overview of the Workspace Table 19. Analysis window, general features and controls Feature Description Profile settings Define the mathematical algorithm applied to each spectrum in an acquired region of data to create the chemical image. The algorithm converts each spectrum into a number that is represented by a color in the chemical image.
Page 116: 3D Analysis And Terrain Windows
OMNICxi Software Operation Overview of the Workspace 3D Analysis and Terrain Windows This section covers all features and controls available in the 3D Analysis and Terrain windows. • 3D Analysis window. Used to explore 3D data. • Terrain window. Used to view the terrain map, a 3D visualization of the sample surface topography.
Page 117 OMNICxi Software Operation Overview of the Workspace The OMNICxi Analysis window also allows you to view 2D data in the 3D analysis window. If you right-click a ... and select Analyze Region in 3D but the region does not have any z-slice data, the 3D Analysis window opens with a few different tools and features.
Page 118 OMNICxi Software Operation Overview of the Workspace Table 20. 3D Analysis Window features and controls Feature Description File and Tools Menus Used to copy the image to your clipboard or to change the background color. Select File > Copy to Clipboard to copy an image of the 3D volume as it is currently displayed.
Page 119 OMNICxi Software Operation Overview of the Workspace Table 20. 3D Analysis Window features and controls Feature Description Slice and thresholds • X-, Y-, and Z-Slice slider. Drag slider to view slices along the indicated axis. Select “Bottom to Top” to reverse the direction of slice.
Page 120 OMNICxi Software Operation Overview of the Workspace Terrain Window General Features and Controls All of the features visible in the OMNICxi Terrain window are discussed below. To learn about a feature, click its name in the image below. File and Tools menus Pick mode Rotate mode Drag and move mode...
Page 121 OMNICxi Software Operation Overview of the Workspace Table 21. Terrain Window features and controls Feature Description Restore camera Returns the view to a position previously set with the Save Camera tool. Save camera Set the viewing angle to return to when you click Restore Camera Orthographic view Displays the 3D volume in parallel line orthographic view.
Page 122: Instrument Settings
OMNICxi Software Operation Overview of the Workspace Instrument Settings To view or change these settings, click Settings the Acquisition window in at the top of OMNICxi software. Figure 72. Acquisition window, Settings options DXRxi User Guide Thermo Scientific...
Page 123 OMNICxi Software Operation Overview of the Workspace Table 22. Acquisition window, Settings options Feature Description Default Directory Defines the folder in Windows™ Explorer that OMNICxi software will use to open and save image and spectral data and to load and save the region queue.
Page 124 OMNICxi Software Operation Overview of the Workspace Table 22. Acquisition window, Settings options Feature Description Setup Video Provides tools to: • Calibrate the video image in the OMNICxi software for each installed microscope objective. This lets you retrieve the appropriate video calibration when the objective is changed. To retrieve a video calibration for an objective that was previously calibrated, use the Objective option...
Page 125 OMNICxi Software Operation Overview of the Workspace Table 22. Acquisition window, Settings options Feature Description Alignment/Calibration Shows the date the current laser set (laser, filter and grating) was information last calibrated. These options are available to control the frequency of alignment and calibration: •...
Page 126: Collect A Mosaic
OMNICxi Software Operation Collect a Mosaic Table 22. Acquisition window, Settings options Feature Description Spectral range Use this feature to specify spectral range limits for the installed laser set. Available spectral range shows the full range for the current laser set. To limit the spectral range, for example to eliminate a totally absorbing region at one end, enter Min and Max values in the selected unit (see Data...
Page 127 OMNICxi Software Operation Collect a Mosaic 4. Open the sample compartment doors on the microscope and rotate the desired objective to the front objective position (for easier initial focusing, start with the 10x objective). 5. Select the video calibration for this objective by setting the Objective option in the OMNICxi Acquisition window.
Page 128 OMNICxi Software Operation Collect a Mosaic 10. Click FOCUS Video in the software to bring the sample into sharp focus (adjust brightness as needed). The sample should still be centered under the new objective and focused in the left (video) pane. 11.
Page 129 OMNICxi Software Operation Collect a Mosaic Use the joystick on the stage controller to position the sample under the objective and the focus control to focus the image. Tip For quicker focusing, first watch the stage directly (not through the eyepiece) while using the joystick to position the sample under the spot of white light.
Page 130 OMNICxi Software Operation Collect a Mosaic Figure 73. The Terrain Mosaic Setup dialog NOTICE When adjusting the stage position, be careful not to bump the sample into the microscope objective. The sample will be very close to objective at the highest stage position.
Page 131: Acquire And Analyze Data
OMNICxi Software Operation Acquire and Analyze Data determined by depth of focus of the objective. A higher resolution uses a smaller z increment. The estimated time to collect is displayed in the Terrain Mosaic Setup dialog. The collection time depends on the resolution, total z-range, and collection settings. 20.
Page 132: Analyze Regions
OMNICxi Software Operation Acquire and Analyze Data Analyze Regions Create a chemical image of an area of the sample surface by specifying one or more regions to analyze. To analyze one or more regions, you will select one or more regions to analyze, acquire a preview chemical image, adjust acquisition settings, and collect data.
Page 133: Settings For Acquiring A Chemical Image
OMNICxi Software Operation Acquire and Analyze Data The software begins creating a chemical image of the preview region. The image is displayed in the left pane (see Figure 66). The chemical image contains an average spectrum collected at each sampling point. The number and locations of the spectra that make up the chemical image are defined by the Image pixel size setting.
Page 134 OMNICxi Software Operation Acquire and Analyze Data Table 23. Acquisition window, standard settings for acquiring a chemical image Feature Description Laser power Laser energy at the sample in milliwatts (0 blocks the laser). Highest available laser power setting depends on the installed laser.
Page 135 OMNICxi Software Operation Acquire and Analyze Data Table 23. Acquisition window, standard settings for acquiring a chemical image Feature Description Preview size Defines the size of the preview region (defined by the preview box in the mosaic pane) in micrometers. Aperture Defines the size of the Raman beam entrance slit or pinhole.
Page 136: Acquire And Analyze A Chemical Image
OMNICxi Software Operation Acquire and Analyze Data Table 24. Acquisition window, Advanced settings for acquiring a chemical image Feature Description Photobleach time Time for each sample point to be exposed to the laser for photobleaching before collection begins. Adding photobleach time may reduce sample fluorescence but will also increase scan time.
Page 137: Profile Settings
OMNICxi Software Operation Acquire and Analyze Data Acquire a preview chemical image and use it to optimize the Image pixel size and Aperture settings. 7. Use one of the following methods to select one or more regions of the sample for analysis. •...
Page 138 OMNICxi Software Operation Acquire and Analyze Data The Analysis window can be used to analyze the same sample using different profile settings in order to compare the results visually. Click here for more information. Use the Spectrum tool to click a point in the acquired (or partially acquired) chemical image. The spectrum collected at that time and location appears in the spectral pane.
Page 139 OMNICxi Software Operation Acquire and Analyze Data Figure 76. Correlation profile settings Table 25. Correlation profile settings Setting Description Apply Displayed Lets you select a spectrum for the correlation reference. To select the Spectrum reference, click the Spectrum tool then click a point in a chemical image (preview image or acquired region) and choose Apply Displayed Spectrum.
Page 140 OMNICxi Software Operation Acquire and Analyze Data Chemigram Profile Settings The Chemigram profile shows the uncorrected area of the specified region for each sample point in the chemical image. The colors in the chemical image represent the relative area under the specified region at each sample point. A higher intensity value (closer to the top of the profile intensity scale) indicates a larger peak area.
Page 141 OMNICxi Software Operation Acquire and Analyze Data Table 27. Peak area profile settings Profile Type Description Area 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.
Page 142 OMNICxi Software Operation Acquire and Analyze Data Table 28. Peak height profile settings Profile Type Description Position Defines the location of the peak of interest. To specify the peak location, select the Spectrum tool then click a point of interest in the chemical image.
Page 143 OMNICxi Software Operation Acquire and Analyze Data Table 29. Peak area ratio profile settings Profile Type Description Intensity Specify a peak area ratio value below which will be reported as 0 (to threshold eliminate peaks below a certain size). Prevents dividing a small peak (or noise 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.
Page 144 OMNICxi Software Operation Acquire and Analyze Data Table 30. Peak height ratio profile settings Profile Type Description Intensity Specify a peak height ratio value below which will be reported as 0 (to threshold eliminate peaks below a certain size). This prevents dividing a small peak (or noise 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.
Page 145 OMNICxi Software Operation Acquire and Analyze Data Table 31. Peak width profile settings Profile Type Description Area 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.
Page 146 OMNICxi Software Operation Acquire and Analyze Data Table 32. Peak position profile settings Profile Type Description Range start/end Defines the location of the region of interest. To specify the region, select the Spectrum tool then click a point of interest in the chemical image.
Page 147 OMNICxi Software Operation Acquire and Analyze Data Table 33. MCR profile settings Profile Type Description Expected Specifies the number of components that will be reported after the MCR components analysis. Enter the number of different components you expect to find in the sample plus one (up to 32 components total).
Page 148 OMNICxi Software Operation Acquire and Analyze Data 3. Select the Spectrum tool, then click a point of interest in a region of acquired chemical image data. The spectrum collected at that location is displayed in the spectral pane. The spectrum is automatically searched against the selected libraries.
Page 149: Reanalyze Image Data
OMNICxi Software Operation Acquire and Analyze Data The match value tells you how well the library spectrum matches the unknown. The closer the value is to 100, the better is the match. Reanalyze Image Data Reanalyze previously collected data to add profile information. ...
Page 150 OMNICxi Software Operation Acquire and Analyze Data Figure 86. Analysis window with two MCR components selected for display Two component check boxes Chemical image with two selected for display MCR components APPLY button To quickly display all found MCR components in the chemical image, select All MCR at the top of the profiles pane.
Page 151: Identify And Analyze Particles
OMNICxi Software Operation Acquire and Analyze Data Identify and Analyze Particles Use the advanced particle analysis tools to locate, characterize, and identify particles. The particle selection tools are available only with the optional Particle Analysis Add-On. Begin particle analysis with either a video image of your sample or with a chemical image. Collecting a chemical image before performing particle analysis allows you more options to analyze your sample but data collection takes longer.
Page 152: Chemical Image-Based Particle Analysis
OMNICxi Software Operation Acquire and Analyze Data Chemical Image-Based Particle Analysis For chemical image-based particle analysis, either open a saved chemical image or collect a region in the Acquisition window and then analyze the chemical image in the Analysis window. ...
Page 153 OMNICxi Software Operation Acquire and Analyze Data  To set up particle analysis 1. Select Auto Regions and navigate to the particle analysis tab. The following particle analysis settings are available: Figure 87. Video-image based particle selection settings These settings are available: Table 34.
Page 154 OMNICxi Software Operation Acquire and Analyze Data Table 34. Particle Analysis settings Setting Description Image Processing Use the Image Processing group to specify how the selection handles particles with holes, touching particles, and partially visible particles. The following tools are available: •...
Page 155: View Particle Analysis Results
OMNICxi Software Operation Acquire and Analyze Data Table 34. Particle Analysis settings Setting Description Number of Particles Use the Number of Particles group to limit the selection based on a maximum count or based on particle size in micrometers. The following tools are available: •...
Page 156: View Spectrum At Specific Location
OMNICxi Software Operation Acquire and Analyze Data When viewing particle analysis data in the Analysis window, the Analysis window will display Particle Analysis mode. The Identification Results table provides Select a color to display this a summary of the analysis component as in the mosaic The Spectra Matches table displays Add or remove property columns...
Page 157 OMNICxi Software Operation Acquire and Analyze Data Acquire Spectra at Selected Sample Locations To compare the spectrum at a specific location to library spectra, you will collect a mosaic, select a spectrum, and search the displayed spectrum.  To acquire spectra at selected sample locations 1.
Page 158 OMNICxi Software Operation Acquire and Analyze Data Table 35. Acquisition window, standard acquisition settings in Live Spectrum mode Feature Description Laser power Laser energy at the sample in milliwatts (0 blocks the laser). Highest available laser power settings depends on the installed laser.
Page 159: Analyze Sample Cross Sections
OMNICxi Software Operation Acquire and Analyze Data Figure 89. Live Spectrum mode, advanced acquisition settings Table 36. Acquisition window, advanced acquisition settings in Live Spectrum mode Feature Description 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.
Page 160 OMNICxi Software Operation Acquire and Analyze Data  To acquire a cross sectional chemical image of a layered sample: 1. Select Video mode and use the available tools to locate, zoom and bring the surface layer of the sample into sharp focus. 2.
Page 161 OMNICxi Software Operation Acquire and Analyze Data Figure 90. Live Spectrum mode used to explore the layers in an optically transparent sample Grab tool Live Spectrum mode Current cursor location Laser power Spectral pane Stage status SEARCH Displayed Spectrum Spectrum at current cursor location in mosaic 7.
Page 162 OMNICxi Software Operation Acquire and Analyze Data NOTICE Be careful not to bump the sample against the objective during this step or you may damage the objective or the sample. Use the Focus control on the stage controller to slowly move the sample toward the objective approximately 10 to 20 μm to change the focal (Z) depth.
Page 163 OMNICxi Software Operation Acquire and Analyze Data 14. Click COLLECT Cross Section to collect the chemical image. The image appears in the left pane. The cross sectional chemical image shows depth (Y-, Z-axis) information rather than the normal surface (X-, Y-axis) information acquired Image Regions mode.
Page 164 OMNICxi Software Operation Acquire and Analyze Data 17. Select the Spectrum tool and then click each colored layer in the chemical image to display the spectrum acquired at that focal plane in the sample and its associated (calculated) pure component spectrum in the spectral pane. 18.
Page 165: Measure Change Over Time
OMNICxi Software Operation Acquire and Analyze Data 19. To save the selected spectrum as an OMNIC format .SPA file, click SAVE Spectrum. To select a spectrum, click its title in the spectral pane. To select additional spectra, hold down the Shift key while you click another spectrum title.
Page 166 OMNICxi Software Operation Acquire and Analyze Data DXRxi User Guide Thermo Scientific...
Page 167 OMNICxi Software Operation Acquire and Analyze Data These settings are available: Table 37. Time-Based Collect settings Setting Description Mode Available settings: • None. Runs standard collection. • Time. Runs time-based collection with frames collected at fixed time intervals. – Total Time. Defines the total length of the experiment from the start of the first frame to the start of the last frame.
Page 168: View Time-Based Data
OMNICxi Software Operation Acquire and Analyze Data View Time-Based Data You can view individual frames of time-based data in the Analysis window, or animate a series of frames. Many of the features available in the OMNICxi Analysis window also function with time-based data.
Page 169: Measure And View 3D Volumes
OMNICxi Software Operation Acquire and Analyze Data Figure 93. Time-based data collection Frame selection bar Play (or fast forward) (for time-based data only) animation Stop animation Measure and View 3D Volumes Acquire 3D image data to view in the 3D Analysis window. To collect 3D image data, the sample must be optically transparent to the laser wavelength.
Page 170: View 3D Data
OMNICxi Software Operation Verify Instrument Performance 3. Click the Video button in the software to select video mode. Bring the sample into focus and collect a mosaic. 5. Use Live spectrum mode to acquire spectra at several locations of the sample in order to optimize the Laser power,...
Page 171 OMNICxi Software Operation Verify Instrument Performance PV status icon Table 39. PV status, available options Icon Meaning PV information for current laser set is valid (all tests passed) and up-to-date PV information for current laser set is invalid (one or more tests failed during last PV run) PV information for current laser set is either out-of-date or this laser set has never been validated...
Page 172 OMNICxi Software Operation Verify Instrument Performance 3. Place the polystyrene sample provided with the instrument on the slide holder. 4. Rotate the 10x objective into the front objective position. (The software automatically selects the video calibration for the 10x objective in the Acquisition window.) 5.
Page 173 OMNICxi Software Operation Verify Instrument Performance If all the test results show “Passed” as in the example above, the instrument passed the PV test. If one or more tests show a “fail” result, refer to the PV troubleshooting information for help. 10.
Page 174 OMNICxi Software Operation Verify Instrument Performance Laser, filter, grating sets that have PV information available PV results for selected laser set All known laser sets for this instrument are listed in the top pane. An asterisk (*) appears to the left of the installed laser set. The selected laser set appears in bold. To show the most recent PV test results for a different laser set, select the laser set in the top pane.
Page 175: System Tools
System Tools Use these tools to align and calibrate a laser set (laser, filter, and grating) or to create or edit the video calibrations for your microscope objectives. Contents • Aligning and Calibrating Laser Sets • Creating a New Video Calibration Aligning and Calibrating Laser Sets Use the Align/Calibrate feature in the OMNICxi software to align the installed laser, filter and grating and to calibrate the laser wavelength.
Page 176 System Tools The instrument should be powered up and running for at least one hour before you align and calibrate a laser set. OMNICxi software should be running and the status indicator in the upper right corner should show a green check mark. Wait at least 5 minutes after changing the installed grating before you align and calibrate a laser set.
Page 177 System Tools Turn up the brightness as far as it will go. When you look at the alignment tool directly (not through the eyepiece), you should see a pool of white light from the illuminator on the surface of the tool. Continue looking at the alignment tool directly while using the joystick on the stage controller to roughly position the opening in the surface of the alignment tool under the white light.
Page 178 System Tools 8. Locate the pinhole in the substrate. Turn the brightness control most of the way down (the pinhole is backlit). Adjust the X and Y position of the stage until the substrate fills the field of view. Then look for the pinhole.
Page 179 System Tools 10. When the pinhole is in focus and perfectly centered, close the sample compartment doors and then click OK in the software to start the align/calibrate process. The software aligns the spectrograph to maximize the signal, calibrates the laser wavelength and then checks system performance.
Page 180: Creating A New Video Calibration
System Tools Creating a New Video Calibration The video image in OMNICxi software is directly related to the stage position and the magnification of the selected objective. When you change the objective on the microscope, the dimensions of the video system’s field of view change. Calibrating the video image defines the new size, in micrometers, of the video system’s field of view so the image data accurately describes the sample.
Page 181 System Tools The slide has a scale in the center that can be used to calibrate the video image. The image below shows the distance between major division lines. The distance between the minor division lines is 10 micrometers. Figure 99. Calibration slide micrometer scale The instrument should be powered up and running for at least one hour before you create or update a video calibration.
Page 182 System Tools 6. From the OMNICxi Acquisition window, click Settings and then click The Setup Video window is displayed with an area for the video image and features for calibrating it. Figure 100. Setup Video window 7. In the Setup Video window, set Current calibrations to the correct calibration for the 10x objective.
Page 183 System Tools 9. Bring the scale in the center of the calibration slide into focus. Close the sample compartment doors. If you have the optional reflected light brightfield/darkfield illuminator, pull out the field iris (FS) control. Then look through the eyepiece while using the focus knob on the stage controller to bring the edge of the field iris aperture into sharp focus (clockwise knob rotation moves the stage up).
Page 184 System Tools 10. Rotate the objective you are calibrating (or recalibrating) to the front objective position and then look through the eyepiece while you use the fine focus control to bring the scale (or a portion of it) into sharp focus. Here is the calibration slide in focus using a 100x objective.
Page 185 System Tools 12. Line up the scale on the calibration slide with the cross hairs in the microscope eyepiece. Look through the right eyepiece on the microscope and use the 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.
Page 186 System Tools Figure 104. Calibration scale properly aligned with cross hairs for 100x objective Tip It can be helpful to place the vertical cross hair at the left or right edge of the division line on the calibration slide, especially for high magnification objectives (see the image above).
Page 187 System Tools 14. Adjust the edges of the light colored rectangular area in the center of the video image so the area covers about half the screen. We will refer to this light colored area as the “cropping” box. It contains a centering marker and two distance markers that are used to calibrate the video image.
Page 188 System Tools 16. Use the cropping box to define the size of the video image in the OMNICxi Acquisition window. Expand the size of the cropping box to the full extent of the screen, and then bring the edges in to eliminate areas where the illumination is not ideal. Only this area will appear in the video pane of the OMNICxi Acquisition window and be used for capturing video images.
Page 189 System Tools Here are some examples showing the calibration markers correctly placed for two different objectives. Tip If you lined up the vertical cross hair at the left or right edge of a division line, place the other two markers at the same edge of their respective division lines for greater accuracy.
Page 190 System Tools If you want to move the markers or adjust the size, shape and location of the cropping box to change the video image in OMNICxi software, follow the steps to reset the box or move markers in Creating a New Video Calibration.
Page 191: Chapter 4 Troubleshooting
Troubleshooting • Problems and Solutions • Error Messages Problems and Solutions Performance Verification fails • If a PV wavelength accuracy test failed (peak location is outside the specified limits), use OMNIC software to open the spectral (.SPA) file from the most recent PV test. The most recent PV test files (polystyrene spectrum and image map) are located here: Thermo/OMNICxi/Spectra/PV Data –...
Page 192: Sample Bands Are Too Small
Troubleshooting Problems and Solutions – Make sure the 50x objective is fully rotated into the front objective position – Make sure the correct video calibration for your 50x objective is selected in the OMNICxi Acquisition window so the scales are synchronized. –...
Page 193: No Visible Image Appears In The Video Pane Or Viewer
Troubleshooting Problems and Solutions • Make sure the sample is directly under the objective and in focus • Make sure the shutter door on the grating is open • The sample may not be Raman active; test the system by using a known good sample If this problem persists, contact our sales or service representative in your area.
Page 194: The Video Image Is Obscured Or Distorted
Troubleshooting Problems and Solutions This is known as “photobleaching.” Photobleaching time can be automatically added to an image collection on the advanced tab of the acquisition settings. • Make sure the slide, coverslip, or other sample properties are not responsible for the fluorescence If this problem persists, contact our sales or service representative in your area.
Page 195: Chemical Image Does Not Achieve Required Spatial Resolution
Troubleshooting Problems and Solutions Chemical Image Does Not Achieve Required Spatial Resolution • Check if the correct objective is selected and in position for the spacial resolution selected • Switch to video mode and make sure the sample is in focus •...
Page 196: Error Messages
Troubleshooting Error Messages Error Messages Contents • General Errors • Align and Calibration Errors General Errors • Instrument off or disconnected • Video camera disconnected • Stage controller off or disconnected • Stage controller failed • Unknown stage location • Detector too warm •...
Page 197: Video Camera Disconnected
Troubleshooting Error Messages Instrument off or disconnected The instrument is powered off or a cable is disconnected. Check the following: • Both instrument USB cables are securely connected to the instrument and to USB 2.0 connectors on the system computer •...
Page 198: Stage Controller Failed
Troubleshooting Error Messages Stage controller failed The OMNICxi software can detect the sample stage but not control its position. Turn off the stage controller, wait 5 seconds and then turn it back on. Then initialize the sample stage. NOTICE Before you initialize the sample stage, remove any sample or other items from the stage.
Page 199: Detector Disconnected
Troubleshooting Error Messages Detector disconnected The instrument cannot communicate with the detector. Check the following: • Both instrument USB cables are securely connected to the instrument and to a USB 2.0 connector on the system computer • USB cable for the stage controller is securely connected to the computer •...
Page 200: Invalid Fiber Probe Configuration
Troubleshooting Error Messages Invalid fiber probe configuration The installed fiber probe is not compatible with the current laser set (laser or grating). Install a compatible laser set. Uncalibrated laser, grating, filter set The laser, grating, and filter set installed in the instrument has not been aligned and calibrated.
Page 201: Sample Signal Too High
Troubleshooting Error Messages Sample signal too high The sample signal is saturating the instrument detector. Change one or more of the following settings and measure the sample again: • Reduce the laser power • Reduce the exposure time • Select an aperture that has a smaller opening If the problem persists, contact technical support.
Page 202: Align/Calibrate Tool Not Connected
Troubleshooting Error Messages Align/calibrate tool not connected The align/calibrate tool is not connected to the instrument. Before you start the align/calibrate process, install the align/calibrate tool on the microscope stage and plug in the cable. If this message appears when the align/calibrate tool is installed and connected to the instrument, cycle the power on the computer and the instrument (turn the power switch on the power strip off and back on and then hold down the instrument power button for 3 seconds) and then restart the OMNICxi software and run Align/Calibrate.
Page 203: Poor Quality Align/Calibrate Spectra
Troubleshooting Error Messages Check each of these items and then restart Align/Calibrate. If that doesn’t fix the problem, cycle the power on the computer and the instrument (turn the power switch on the power strip off and back on and then hold down the instrument power button for 3 seconds) and then restart the OMNICxi software and run Align/Calibrate.
Page 204: Spectral Response Too Low
Troubleshooting Error Messages Spectral response too low The spectral response is too low for the align/calibrate process to continue. One of the following conditions applies: • 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.)
Page 205: Performance Check Value(S) Out Of Range
Troubleshooting Error Messages • Filter is not fully seated. (Remove the filter, wipe its bottom surface with a clean, lint-free cloth, wipe the magnet inside the filter compartment, and then install the filter.) • Laser is not fully seated. (Remove and reinstall the laser making sure the latch is fully vertical.) Check each of these items and then restart Align/Calibrate.
Page 206: Unable To Read System Info
Troubleshooting Error Messages Unable to read system info The software is unable to read the instrument EEPROM, laser, grating or filter. Follow these steps: • Remove the grating, wipe its bottom surface with a clean, lint-free cloth, wipe the magnet inside the grating compartment, make sure the shutter is open and then reinstall the...

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