DXR3xi ThermoFisher Scientific Raman Spectroscopy - SOP

This is the standard operational procedure (SOP) for the DXR3xi ThermoFisher Scientific Raman Spectroscopy.

Due to the inactivation of Skedda, Raman booking appointments are now done exclusively via this website: https://management.apcresearch.org/resources/lab/raman. NCI members are expected to adhere to the rules to ensure proper work ethics and safety procedures. Violation of safety rules may result in being reported to the respective user manager and suspended user access to Raman Spectroscopy. Any inquiries can be made by visiting the APC office at room 1B or via email at [e-mail].

PDF version is printable at the following link.

2MB

DXR3xi ThermoFisher Scientific - SOP Raman Spectroscopy - 4th rev.pdf

pdf

Purpose

Users should understand the working principle and able to perform sample measurement using Raman Spectroscopy according to the instrument’s intended use.

Brief overview of the instrument

Figure 1. Front view of the Raman Spectroscopy instrument.

Figure 2. View of the inside of the sample compartment.

Figure 3. Microscope stage controls.

To turn on the Raman spectrometer press the button on the machine (Figure 1). The sample is placed on the stage inside the sample compartment (Figure 2), and to move the stage in X, Y, and Z directions, use the microscope stage controls (Figure 3).

Procedure

Setup/ initialisation

1. Before starting any measurements, please book the Raman machine beforehand through Skedda Website by first registering your email to the Skedda system. Link: https://management.apcresearch.org/resources/lab/raman

2. Before turning on the instrument, please make sure that the AC inside the room is turned on. Check the temperature and relative humidity of the room and make sure the temperature of the room is below the upper limit temperature of 27°C and stays that way throughout the analysis process. (If the temperature of the room reaches 28°C, stop all measurements and remove your sample from the sample compartment and wait until the temperature of the room to stabilize to begin your analysis).

3. Write down the sample details in the logbook, and ensure the water level in the water container of the humidifier is not overloaded or exceeding the marked limit. If the water level exceeds or approaching the marked limit, then please empty the water container before performing an experiment.

4. Before beginning any spectra acquisition, please first measure the SiO2 and HOPG standard reference.

Powering up the instrument

Figure 4. The blue LED is turned on, indicating that the power source of the stage motor is successfully switched on.

1. Turn on the power source for the stage motor by pressing the green button, the cable light will turn blue if the power source for the motor has been turned on successfully (see Figure 4). Wait for 30 minutes.

2. Power up the instrument, hold down the power button for 3 seconds and make sure the power indicator turned blue. Wait for 30 minutes.

3. Turn on the computer.

4. Turn on the laser by turning the laser key on the left side of the instrument to an upright position (Figure 5) and make sure that the laser power indicator is on. Wait for 30 minutes.

Figure 5. Laser key on unlocked position.

5. Turn on the illuminator (Figure 6).

Figure 6. Olympus TH4-200 illuminator.

6. Make sure that there are no samples inside the compartment prior to booting up the software to avoid an error during the stage calibration.

7. Open the OMNICxi application and wait until the boot up process is finished.

8. Wait for 10-15 minutes for the laser to warm up.

9. The instrument is ready to use.

Raman spectra acquisition of samples

1. During the experiment you will spend most of your time in the acquisition screen.

2. For this example, a carbon-based material such as Highly Ordered Pyrolytic Graphite (HOPG) or a silicon wafer can be used as a calibrated standard.

3. To begin spectra analysis, prepare the sample by introducing the sample to an appropriate supporting substrate (silicon wafer or microscope slide) with a double tape or carbon tape to avoid from spilling the sample all over the stage, ideally such substrate should have contrasting color as the basic criterion when probed by Raman instrument.

4. Place your sample inside the stage and make sure that the sample is directly under objective lens using the stage controller (X and Y axis of the stage, see Figure 3). First use the 10x magnification.

5. When the sample is directly under the objective lenses, adjust the focus by turning on the knob on the right side of the controller (Z-axis control of the stage, see Figure 3) whilst paying close attention to the video panel. To speed up the process hold down rectangle button near the knob, if you observe that sample is in close proximity to the objective lens, then gently turn the knob to avoid bumping the sample into the objective lens until reaching the appropriate focus.

6. After adjusting the focus on the video panel, choose a region of interest (ROI) of sample surface for the spectral analysis using the stage controller.

Figure 7. Choose Region of interest using the stage controller.

7. After choosing an appropriate surface, choose the desired parameters to set up for your sample. Avoid using the laser at high power from the start to avoid burning your sample. For example, start the parameter at 1 mW laser power, 325 Hz exposure time and 10 number of scans. If the spectrum displays a lot of noise, gradually increase the parameter, starting from the number of scans to increase the signal to noise ratio and then the laser power and exposure time.

Figure 8. Set up the desired parameter, you can also set it during live spectrum tab.

8. After setting up the desired parameter, click on the “live spectrum” tab, wait until the live spectra panel shows a live spectrum of the sample.

Figure 9. click live spectrum tab.

9. You can change the parameter if the signal-to-noise ratio is still low by increasing the number of scans and increasing or decreasing the laser power and exposure time, if needed, just be careful not to burn your sample.

10. To save your spectra click the “save spectrum” button and save the .spa spectrum in the appropriate folder path. (Alternatively, you can right-click on the spectra when you’re on the video mode and click “export” into .txt file).

Figure 10. Ways to save spectra.

11. The HOPG sample should have two distinctive Raman bands at around 1580 and 2721 cm-1, corresponding to G and D band. Whereas, a single peak centered at 519 cm-1 is observed for a SiO2 wafer.

12. Take out the sample by first clicking the “Video” tab, after that open the sample compartment and lower the stage using the Z-axis controller. After the sample is far enough from the objective lenses, gently move the stage away using the X, Y axis controller and then take out the sample.

Figure 11. Results of SiO2 wafer and HOPG standard reference.

Raman imaging mode acquisition

Figure 12. Image regions mode and control.

1. For this example we will be using BA2CoCl4 2D perovskite sample as an example.

2. To obtain a Raman image, first load the sample in the stage just like before.

3. Make sure the sample compartment doors are tightly closed.

4. Move the BA2CoCl4 2D perovskite sample to the objective lenses to get the appropriate focus.

5. Obtain the spectra of the sample to be used for imaging (following the same steps in section C or by clicking select stored spectrum and select previously measured sample). Use minimum number of scans (no more than 10) to save imaging time and computer memory!

Figure 13 Obtain spectra or select previously measured spectra from select stored spectrum button

6. After obtaining a clear spectrum, click “zoom to region” button to center and scale the optical image to the mosaic pane.

Figure 14 Click zoom to region butto to center and scale the optical image to mosaic pane

7. Click “START Mosaic” to collect a mosaic. The mosaic is used to get a representative full view of the sample.

Figure 15 Click to start taking mosaic

8. Use the preview box in the mosaic pane to select a region of interest and to obtain the preview chemical image. Center a small region of interest (ROI) in the preview box. If possible, select a region that is representative of all the regions you plan to analyze.

9. click “Apply Displayed Spectrum” above the “Select stored spectrum button”.

10. Select “Image Regions” mode located besides the “Live Spectrum” mode.

Figure 16 Select image regions to start Raman Imaging

11. Click “Collect Preview”.

Figure 17 Click collect preview to obtain preview mapping of ROI (red box)

12. Adjust the image pixel size and Aperture settings, if needed, to optimize the image data if you think the current image data is not sufficient. Keep in mind that the image pixel size and the size of the aperture can affect the imaging time and memory consumption.

13. Make several regions for Raman mapping by clicking “Select Acquisitions Regions Manually” and make several region boxes for imaging.

Figure 18 Click "Select acquisitions Regions Manually" to make regions for Raman mapping

14. When you are ready to collect the image data, click “Collect Regions” located at the top of the mosaic pane.

Figure 19 click "Collect Regions" to start Raman mapping

15. To save the acquired data, right click on the image in the analysis screen and click “Save Current Data”.

Figure 20 Click "Save current data" after finishing Raman Imaging

16. Save the imaging results in this directory path C:\users\public\Documents\Thermo\Omnicxi\Spectra. Name your file properly (Do not use spaces in your file name!) and save it. After confirming that the file has been successfully saved, Please immediately move your file to your folder in Local Disk D, to save computer memory.

17. Take out your sample after you are finished obtaining the raman imaging.

18. To begin a new imaging analysis, click “New Sample” on the top left corner and repeat the steps.

Figure 21 Click "New Sample" to begin new analysis

Figure 22. Example of successful Raman imaging of (MA)2CoCl4 2D perovskite sample and (b) crystal structure of (MA)2CoCl4 2D perovskite.

Turning off the instrument

1. To turn off the instrument, close the OMNICxi application.

2. Turn off the computer and make sure it is completely turned off before powering down the instrument.

3. Turn off the illuminator (OLYMPUS TH4-200)

4. Turn the key to a horizontal position to turn off the laser.

5. Press the power button on the instrument for 3 seconds.

6. Turn off the stage motor power source.

Troubleshooting

This section lists the common issue or monitor warning and its solution. Should you encounter new problems, please notify the manager and email them to [e-mail].

General errors

Performance Verification fails

If a PV wavelength accuracy test fails (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

If the spectrum contains excessive instrument noise (spikes), the polystyrene sample may have 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 wavelength accuracy test fails again, contact us.

If the PV image resolution test failed (measured line spacing is outside the specified limits_, open the image map from the most recent PV test (see location above). The map should contain vertical lines as in this example:

If there are no vertical lines in the collected map, check the following and then rerun the PV test:

Make sure the silicon test sample is right side up (the wording on the sample should be right side up when you are looking at the sample through the microscope)

Make sure the 50x objective is fully rotated into the front objectve position

Make sure the correct video calibration for your 50x objective is selected in the OMNICxi Acquisiton window so the scles are synchronized

Make sure the sample is in sharp focus

Make sure the crosshair in the microscope eyepiece is centered on the period in the “0.25” feature on the test sample

If the image resolution test fails again, contact us.

Sample Bands Are Too Large or CCD Overflowed

The Raman signal is too large, which saturates the CCD. You can decrease the signal by doing one or more of the following:

- Decrease the setting of exposure time in the software

- Decrease the aperure size by setting in the software

- Select a pinhole aperture instead of a slit aperture

- Decrease the setting of laser power in the software

- Make sure all doors of the system are tightly closed

If this problem persists, contact our sales or service representative in your area

No Raman Signal Appears in the Live Display or Spectrum Has No Sample Bands

Make sure all doors of the system are tightly closed

If the laser power is off, turn on the laser

Increase the laser power in the software

Make sure the sample is directly under the objectve 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

No Visible Image Appears in the Video Pane or Viewer

If the illuminator is set to low intensity, set it to higher intensity

Change the software to video mode

Make sure the viewer selection control (below the video camera) is in the middle position

Push the ND, FS and AS controls on the illuminator all the way in, if present

If this problem persists, contact our sales or service representative in your area.

The Spectrum Has a Sloping Background or a Severe Positive Offset

The sample may be heating. To account for 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

• Reduce the laser power and collect the sample again

Watch the live display to see if the sample is still heating (Reducing the laser power reduces the Raman signal generated at the sample and terefore the quality of the data. To compensate, try increasing the number of scans or exposure time)

• Reduce the wcposure time and collect the sample again

• Turn on baseline correction in the settings panel

If this problem persists, contact our sales or service representative in your area

The Spectrum Baseline is Severely Tilted, Curved or Saturating

The sample is fluorescing during data collection. To correct this problem, try one or more of the following:

• Turn on baseline correction in the settings panel

• Use a longer wavelenth laser

• Go to live spectrum mode and expose the sample to the laser beam for a period of time before beginning the collection of the sample spectrum. This is known as “Photobleaching”. Photobleaching time can be automatically added t an image collection on the advanced tab of the acquistion 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

The video Image is Obscured or Distorted

• Check the selected objective is in the right position (not eight position), by rotating nse piece and make sure the objective click and centered

• Push the ND, FS and AS controls on the illuminator all the way in, if present

• Make sure the viewer selection control (below the video camera) is in the middle positon

• If the objective is dirty or contaminated, clean it

If this problem persists, contact 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 strip is on

• If the instrument is turned off, turn it on by holding down the blue button on the front of the instrument for five (5) seconds

• Check the cables between the computer and the instrument, If they are disconnected, connect them and restart the software

• Check the cable between the stage and the computer, If the stage is not responding, turn the stage power supply off and on again to regain the control

If this problem persists, contact our sales or service representative in your area.

Chemical Image Apperars to be Different Than the Video Image

• Check that the objective selected in the software matches up the actua objective focused on the sample

• Check that the video setup has the correct setting and calibration for that objective

• Switch to video mode, mae sure the video image is centered on the area of interest and collect a mosaic to confirm the proper stitching

Chemical Image Does Not Achieve Required Spatial Resolution

• Check if the correct objective is selected and in positon for the spacial resolution selected

• Switch to video mode and make sure the sample is in focus

• Check the sample slide to make sure it is properly seated

• Check the aperture setting, make sure 25 micro pinhole was selected for high spatial resolution imaging

• Lower the image pixel size setting in the software

• Switch to a shorter wavelenth laser

Spatial resolution depends on the wavelenth of the laser

Chemical Image shows Missing Data

• Increase the exposure time in the software

• Increase the number of scans in the software

• Reduce vibrations in the environment

• Use a vibration isolation table

Make sure that the isolation is active (for example, there is air pressure to the table)

X-axis Calibration Fails

The neon bulb used for automatic x-axis calibration may have failed

• Turn off automatic x-axis calibration and run manual calibration, contact our service representative in your area for repair of the automatic x-acis calibration feature.

Error messages

This section lists the common issue or monitor warning and its solution. Should you encounter new problems, please notify the manager and email them to [e-mail].

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. To initialize the stage, from the Acquisition window click Settings > Initialize Stage. If this message appears after the stage is initialized, note the status (colour) of the LED indicator on the front of the stage controller and then contact technical support.

Unknown Stage Location

The OMNICxi software cannot determine the location of the microscope stage. Initialize the stage. To initialize the stage, from the Acquisition window click Settings > Initialize Stage. (before you initialise the sample stage, remove any sample or other items from the stage. Anything that protrudes above the stage may interfere) If this message appears after you initialize the stage, 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. If that doesn’t fix the problem, contact technical support.

Detector too warm

The instrument detector has not cooled to the proper operating temperature. Wait 15 minutes for the detector to cool and then restart data collection . If this message reapperas, check the following:

• Make sure nothing is blocking the vents on the bottom if the instrument (left side)

• Check that the temperature of the room is below the upper limit of the recommended range (below 27°C or 80°F)

• If this message appears after the detector has had sufficient time to cool and the room temperature is within our specifications contact technical support.

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

• The USB cable for the stage controller is securely connected to the computer

• The instrument power supply is connected to a power source and powered on

• Illuminator power supply is connected to a power source and powered on

• Illuminator power supply is connected to a power source and powered on

• The stage controller is connected to a power source and powered on

If this message appears and the instrument is powered on and all three USB cables are connected to the computer, 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 OMNIC xi software. If that doesn’t fix the problem contact technical support.

No filter

The instrument does not have a filter installed. Install a filter with a wavelength range that is compatible with the installed laser or grating.

No grating

The instrument does not have a grating installed, Install a grating with a wavelength range that is compatible with the installed laser and filter or fibre optic launcher.

No laser

The instrument does not have a laser installed. Install a laser that is compatible with the installed grating and filter or fibre optic launcher.

Mismatcher grating

The wavelength of the grating installed in the instrument does not match the wavelength of the installed laser. Install a grating that matches the laser frequency

Mismatcher filter

The wavelength range of the filter installed in the instrument does not match the wavelength of the installed laser. Install a filter that matches the laser frequency.

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. The instrument cannot colllect data until the installed alser set (laser, filter, grating) has been aligned and calibrated

Alignment/calibration out of date

The alignment and calibration for the laser, grating and filter installed in the instrument occured longer ago than the specified interval. The instrument cannot coolect data until the installed laser set (laser, filter, grating) has been aligned and calibrated.

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 data because a sample compartment door is open or a laser interlock override is missing (Class 3B instrument configurations only). Close both sample compartment doors (or install the override), wait for the laser to warm up and restart data collection.

Laser Off

The instrument cannot collect data because the laser setting is off in the software From the OMNICxi Acquisition window, open the settings box select Laser On, close the settings box and restart data collection.

Laser Key Off

The instrument cannot collect data because the laser keyswitch is off. Set the laser keyswitch to the On position and restart data collection.

Laser Warming Up

The instrument may not produce stable results right now because the laser is warming up. Depending on the type of laser installed, allow 1 to 15 minutes for the laser to warm up and then restart data collection.

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

Cannot read instument EEPROM

The instrument EEPROM has incorrect contents or is corrupted. Contact techincal support

No communications

The software is unable to communivate with the instrement or open the shutter that allows the laser to enter the sample compartement. Cycle the power on the instrument (turn the power switch on the power strip off and back on ad then hold down the instrument power butto for 3 seconds) and then restart the OMNICxi softwaer. If that doesn;t fix the problem, contact techincal support.

Align and calibration errors

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. If the problem persists, contact technical support.

Laser Output too low

The laser output of the instrument is below the minimum specification. Possible causes:

• The laser is not fully seated. (remove and reinstall the laser making sure the latch 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 the problem persists, contact technical support.

No laser at sample

The system is unable to open the shutter that allows the laser to enter the sample compartment. One of the following conditions applies:

• As sample compartment door is open. (close the doors)

• The laser key switch is off. (Set the laser key switch to the On position.)

• The laser is off. (select the Laser on option in the settings box)

• Grating is not fully seated. (Remove the grating, wipe its bottom surface with a clean, lint-free cloth, wipe the magnet inside the grating compartment and then install the grating and secure the compartment door).

• The grating shutter is closed (Open the shutter)

• The filter is not fully seated, (Remove the filter and wipe its bottom surface with a clean, lint-free cloth and then install the filter).

• The 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. 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. If the problem persists, contact technical support (the laser shutter may be broken or its cable has failed)

If the problem persists, contact technical support.

Poor quality align/calibrate spectra

The align/calibrate process is unable to align or calibrate the instrument due to poor quality spectral data. One of the following conditions applies:

• Align/calibrate tool pinhole was not in focus before Align/calibrate was started (Focus the pinhole)

• 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 tool cable is loose. (Check the cable connection at both ends.)

• The objective 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 shutter is closed. (Remove the grating, wipe its bottom surface with a clean, lint-free cloth, wipe the magnet inside the grating compartment, open the shutter and then install the grating and latch the grating door.)

• The 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)

• The laser 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)

• If using the fibre optic probe, check that the fibre optic connection to the system is fully seated and not reversed. Ensure the probe is fully seated in the probe alignment tool.

Check each of these items and then restart Allign/Calibrate. If that doesn’t fix the problem, cycle the power on the computer and the instrument (turn the power witch 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. If the problem persists, contact technical support.

Special 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 pinhole was not in focus before Align/calibrate was started (Focus the pinhole)

• 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 tool cable is loose. (Check the cable connection at both ends.)

• The objective is misaligned. (Make sure the 10x objective is rotated into position and engaged in the detent)

• The sample compartment door is ajar. (Make sure both doors are tightly closed.)

• The grating is not fully seated or the shutter is closed. (Remove the grating, wipe its bottom surface with a clean, lint-free cloth, wipe the magnet inside the grating compartment, open the shutter and then install the grating and latch the grating door.)

• The filter is not fully seated, (Remove the filter,wipe its bottom surface wiht a clean, lint-free cloth, wipe the magnet inside the filter compartment and then install the filter)

• The laser 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)

Check each of these items and then restart Allign/Calibrate. If that doesn’t fix the problem, cycle the power on the computer and the instrument (turn the power witch 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. If the problem persists, contact technical support.

Spectral response too high

The spectral response is too high for the align/calibrate process to continue. One of the following condtions applies:

• Align/calibrate tool pinhole was not in focus before Align/calibrate was started (Focus the pinhole)

• 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 tool cable is loose. (Check the cable connection at both ends.)

• Objective 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 shutter is closed. (Remove the grating, wipe its bottom surface with a clean, lint-free cloth, wipe the magnet inside the grating compartment, open the shutter and then install the grating and latch the grating door.)

• Filter is not fully seated, (Remove the filter,wipe its bottom surface wiht a clean, lint-free cloth, wipe the magnet inside the filter compartment and then install the filter)

• Laser 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)

Check each of these items and then restart Allign/Calibrate. If that doesn’t fix the problem, cycle the power on the computer and the instrument (turn the power witch 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. If the problem persists, contact technical support.

Performace check value(s) out of range

The performance check step of the align/calibrate process was completed but the results indicate the instrument is not performing as expected. Contact technical support.

Misaligned filter or grating

The currently installed grating or filter may be damaged or severely out of alignment. Check the following:

• Align/calibrate tool pinhole was not in focus before Align/calibrate was started (Focus the pinhole)

• 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 tool cable is loose. (Check the cable connection at both ends.)

• The objective is misaligned. (Make sure the 10x objective is rotated into position and engaged in the detent)

• The sample compartment door is ajar. (Make sure both doors are tightly closed.)

• The grating is not fully seated or the shutter is closed. (Remove the grating, wipe its bottom surface with a clean, lint-free cloth, wipe the magnet inside the grating compartment, open the shutter and then install the grating and latch the grating door.)

• The 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)

Check each of these items and then restart Allign/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. If the problem persists, contact technical support.

Unable to read system info

The software is unable to read the instrument EEPROM, laser, grating or filter. Follow these steps:

o Remove the grating , wipe its bottom surface with a lint-free cloth, wipe the magnet inside the grating compartment, make sure the shutter is open and then reinstall the gratng and secure the grating compartment door.

o Remove the filter, wipe its bottom surface with a clean lint-free cloth, wipe the magent inside the filter compartment and then reinstall the filter.

o Remove and reinstall the laser making sure the latch is fully vertical.

Check each of these items and then restart Allign/Calibrate. If that doesn’t fix the problem, cycle the power on the computer and the instrument (turn the power witch 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. If the problem persists, contact technical support.

Unable to collect spectral data

The instrument is unable to collect spectral data during the align/calibrate process. 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. If the problem persists, contact technical support.

Unable to calibrate laser power

The system is unable to calibrate the laser power during the align/calibrate process. Remove and reinstall the laser making sure the latch is fully vertical 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 cak on and then hold down the instrument power button for 3 seconds( and then restart the OMNICxi software and run Align/calibrate. IF the problem persists, contact technical support.

Local troubles

The Sample’s Stage is Unable to Move In Certain Direction

• First, make sure that you initialise the sample stage. TO initialize the stage, from the acquisition window click settings > Initalize stage.

• If that doesn’t work. Cycle the computer power (turn both the PC and Raman instrument off, including the illuminator and sample stage power source and then turn it back on) and restart the OMNICxi application like usual and try moving the stage again.

Instruments off or disconnected

• If you encounter an error status of Instruments off or disconnected, first remove any samples inside the container.

• close the OMNICxi application.

• Restart the computer and leave the machine still turned on.

Video pane not displaying image or error in the video pane.

• If you encounter an error where the video pane displays an error such as distorted images or wrong colour in the video pane, contact the supervisors or superuser in charge of the Raman spectroscopy immediately!

• Remove all samples immediately abort all measurements and turn off the machine completely.

• Prepare clean cotton buds and rubbing alcohol.

• Open the grating filter and carefully remove the filter.

• Swab the filter with the clean cotton buds, do not use the same cotton buds to swab other filters.

• Insert the filter back in.

• Begin the analysis as usual and don’t forget to measure the standard reference first.

Error When Trying to Save the Raman Mapping (.mapx) Files

• Before trying to save any Raman mapping file make sure that you are saving it in the appropriate folder path which is: C:\users\public\Documents\Thermo\Omnicxi\Spectra.

• If that doesn’t work try restarting the OMNICxi application.

Further information

For further information not covered in this SOP guidelines, please refer to the following guide:

5MB

1. ThermoScientific, DXRxi Raman Imaging Microscope with OMNICxi Raman Imaging Software User Guide, 2021, Revision A.pdf

pdf

1MB

2. Raman Quick Reference Guide.pdf

pdf

8MB

3. DXRxi Raman Imaging Microscope - Quick Reference.pdf

pdf

4MB

4. DXR3 Raman Microscope Thermo Scientific.pdf

pdf

7MB

5. Raman Spectroscopy, Microscopy and Imgaing Q&A.pdf

pdf