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LabSpec 5 user manual Page

1. Click on Correct in the Intensity Correction section Click OK The Intensity Correction has now been applied to the spectrum Automotive Test Systems Process amp Environmental Medical Semiconductor Scientific Correct Page 45 HORIBA HORIBA an Scientific Note that an intensity correction factor must have been created for the specified laser wavelength 2 SS325i4SE0005 wecinomsainto Reiinen Resse EN 12 532 ane and diffraction grating pair otherwise an error Cx message similar to that shown right will be displayed when an acquisition is started Click on OK or Cancel to clear the message Remember that in this case the spectrum will remain uncorrected The error message will only be shown once during a LabSpec session if LabSpec is closed and then re opened the message will be displayed again if intensity correction is activated when no intensity correction factor has been created 3 5 4 15 Denoise The Denoise function is a unique noise reduction algorithm which can be used to significantly enhance spectrum quality without losing subtle spectral information When Denoise is activated in Acquisition gt Options all data acquired will be processed with the Denoise reduction this includes real time display RTD acquisition ie Ue spectrum acquisition lt a it and multidimensional spectral array acquisition G3 Standard smoothing functions can result in loss of peak
2. Return to first window I Cancel Help Mode Multi windows v Sub pixel number 1 X 100 Min overlap pix Combine data ge w Return to first window Cancel Help Page 53 HORIBA HORIBA al Scientific o Time s in this mode the time in the Extended Range dialog window is specified directly in seconds s In this case the time set in the Control Panel see section 9 9 2 page 235 is ignored Mode Select Single Window Multiwindow or Auto scanning from the Mode drop down box to choose the desired acquisition mode for the extended range measurement See section 3 5 6 1 page 50 for a detailed explanation of these modes Note that if you use Auto scanning it is necessary to set a larger number of accumulations in the Control Panel see section 9 9 3 page 235 Typical values for good results would be between 10 and 50 The larger the number of accumulations the better the averaging will be resulting in a higher spectrum quality signal to noise Sub pixel Number Select the sub pixel number from the drop down box to determine whether data acquisition will be made in the default manner sub pixel 1 or with additional data points to enhance band definition sub pixel gt 1 See section 3 5 6 2 page 52 for a detailed explanation of this function and how it affects the acquired data Min Overlap pix In the Multiwindow acquisition mode each spectral window overlaps with i
3. xe a Ga vy a_i 2r E E E Sources Map Image Reflection ri wv Z Ir Image Help Extra images Image From To Size xe e ve e e 2r E E Sources Reflection Z Image Help Page 64 HORIBA HORIBA a Scientific Click Close to close the Extra Images dialog window Set up the Raman multidimensional spectral array measurement in the normal way using the Map Properties dialog window see section 4 5 5 page 97 Start the Raman multidimensional spectral array measurement in the normal way using the Mapping Acquisition icon G33 amp An additional map image or images will be displayed as the Raman map proceeds 3 5 10 Auto Exposure The Auto Exposure function calculates the necessary acquisition time to acquire a spectrum with a maximum signal level specified by the user It is useful to ensure a good quality spectrum is acquired regardless of the inherent signal strength of the sample The Auto Exposure function initially acquires a test spectrum with a fast test acquisition time and calculates the maximum signal level in the spectrum Based on this data a new final acquisition time is calculated to yield a maximum signal equal to the specified desired intensity and the acquisition is made Minimum and Maximum acquisition times are also set by the user to prevent the software attempting an infinitely short or long measurement Auto exposure
4. With Count ticked the data will be saved as FileName_C xxx where xxx indicates the specified file format Page 48 Explore the future Automotive Test Systems Process amp Environmental Medical Semiconductor Scientific HORIBA HORIBA as Scientific 3 5 5 2 Turning On the Autosave Function In Acquisition gt Autosave tick the box for Save Auto save acquired data Auto repeat Format LabSpec ngs z Folder cA EN M Year M Month T Day File Daa t C P Hou T Mii Count fo Help Cancel 3 5 5 3 Turning Off the Autosave Function In Acquisition gt Autosave untick the box for Save Auto save acquired data Save acquired data DJ Auto repeat Format LabSpec ngs v Folder c data a I Year l Month T Day Data M Hour Mn Ti ve 3 5 6 Extended Range The Extended Range dialog window controls the spectral range which will be analysed during a spectrum acquisition a 1 or multidimensional spectral array acquisition G33 amp When an extended range is specified the software will acquire multiple spectra and seamlessly glue them to give a final spectrum corresponding to the desired extended range Multi windows v Sub pixel number 1 X Min overlap pix 100 Combine data Return to first window Cancel Help Page 49 Explore the future Automotive Test Systems Process amp Environmental Medical Semiconduc
5. Despike as Standard but with an integrated Despike function to remove random spikes also known as cosmic rays o Lite recommended for very noisy spectra with signal to noise lt 20 o Lite Despike as Lite but with an integrated Despike function to remove random spikes also known as cosmic rays Note that this function will be automatically applied to all data acquisition 3 5 4 15 2 Turning Off the Automatic Denoise Function In Acquisition gt Options select Off from the Denoise drop down box 3 5 5 Auto save The autosave function allows data to be saved automatically when a measurement is completed This function is useful to ensure that important data is immediately saved so that there is no risk of loss of data caused by intervention of another user power cut or computer crash Auto save Save acquired data Auto repeat Format LabSpec ngs X Folder c data a l Year M Month T Da Data M Hor F Mn T Co 0 OK Help Cancel ok Note that the autosave function can only be activated for spectrum acquisition W and multidimensional spectral array acquisition 638 amp Real time display RTD data see section 4 5 1 page 95 will not be autosaved even if the autosave function is activated in LabSpec 5 3 5 5 1 Setting the Autosave Function The Autosave function can be configured to automatically save data in a specific format to a specific location Save
6. HORIBA Scientific 3 7 Setup The Setup menu provides access to some specific functions for hardware control Instrument Calibration Instrument Init ICS Filters 3 7 1 Instrument Calibration The Instrument Calibration dialog window allows the user to perform a manual calibration of the spectrometer and provides additional useful information and control for general maintenance of the system Instrument Calibration Calibration Options Reference 20027 50 Counts 2nd Spectrum e045 3rd Spectrum l 4th Spectrum Pixel Calibration I Set Unit to Pixel Show Diode Show Central Pix I Open Shutter Motor Calibration Motor Spectro X Position lt 654360 inci Grating 1800 Zero 8000 Koeff 0 002526 Cancel Help Apply 3 7 1 1 Calibration Options The Calibration Options section displays the maximum signal level of the active spectrum and the relative intensity of the next three spectra displayed in the spectrum window In the example shown right the active spectrum Calibration Options has a maximum intensity of 20027 50 counts 20 000 Reference 20027 50 Counts whilst the second spectrum has a maximum iso Zndigpectum 60 45 8 o 8 3rd Spectrum intensity of 12105 90 counts which is 60 45 of Foo x the active spectrum intensity E j 5 000 a 500 600 Raman Shift cm 3 7 1 2 Pixel Tick the Set Unit to Pixel to
7. displayed when an acquisition is started Click on OK or Cancel to clear the message and start the acquisition Remember that in this case the spectrum will be uncorrected The error message will only be shown once during a LabSpec session if LabSpec is closed and then re opened the message will be displayed again if intensity correction is activated when no intensity correction factor has been created LabSpec 5 user manual Could nat load correction file lt c program files horibajy ngslabspec plugins acquisition Respanses Respanse_EM_32_532_300 ngs gt 3 5 4 14 3 Turning Off the Automatic Intensity Correction In Acquisition gt Options select Off from the Intensity Correction drop down box Click OK Intensity Correction is now inactive The Intensity Correction indicator icon is no longer displayed in the Status Bar 3 5 4 14 4 Applying Post acquisition Intensity Correction Ensure that the correct laser wavelength and diffraction grating pair are selected in the Control Panel If multiple injection rejection or photoluminescence PL filters have been set up for a single laser wavelength ensure the correct filter is selected from the ICS Filters dialog window by clicking on Setup gt ICS Filters Select the spectrum which is to have the Intensity Correction applied post acquisition In Acquisition gt Options select HORIBA ICS from the Intensity Correction drop down box
8. Range 1500 1600 T cm Exposure 0 3 sec IV Profile Zone T xy i um l Time sec Help Cancel Page 60 Explore the future Automotive Test Systems Process amp Environmental Medical Semiconductor Scientific HORIBA HORIBA Scientific Z parameters Select the motor type from the Device drop down box Depending on the instrumentation configuration there may only be one motor available The typical devices which are used are as follows o Motorized this uses the Z motor connected to the fine focus wheel of the microscope o Pifoc this uses the piezo Z axis motor attached to a specific objective Select the scan type from the adjacent drop down box There are two types of autofocus scans which can be used o Continuous the motor will make a continuous sweep through the Z axis whilst reading out the signal o Step by step the motor will move to a set position then read out the signal then move to the next position etc Set the Z scan Range and Step The range must be set sufficiently large to ensure that the sample s roughness can be countered using Autofocus however the range must not be set so large that the objective would be driven into the sample With the Motorized Z motor device the range is only limited by the microscope focus mechanism and the available space between the objective and the sample With the Pifoc piezo motor the range is limited by the pie
9. acquired data If the Save acquired data box is ticked the Autosave function is active and data will be automatically saved Page 47 Explore the future Automotive Test Systems Process amp Environmental Medical Semiconductor Scientific HORIBA HORIBA oes Scientific Auto repeat If the Auto repeat box is ticked a spectrum acquisition lt i it will be continuously repeated until the STOP icon D is clicked Each spectrum displayed on the screen will be replaced by the next spectrum If the Save acquired data box is also ticked each individual spectrum will be automatically saved Format Select the file format from the drop down box which will be used to save the data Please see section 3 1 1 1 page 10 for full details about available file formats o LabSpec ngs data will be saved in its inherent LabSpec 5 format Spectra will be saved as ngs and multidimensional spectral arrays including time profiles Z depth profiles temperature profiles XY maps XZ and YZ slices and XYZ datacubes will be saved as ngc Dilor ms0 data will be saved a legacy file format for Dilor Raman instruments o Grams spc data will be saved in a Grams SpectraCalc spectrum file format compatible with many common spectroscopy software packages o LabSpec tsf data will be saved in the previous generation LabSpec 4 format Spectra will be saved as tsf and multidimensional spec
10. be achieved because the final acquisition time required to reach this intensity would need to exceed the Maximum exposure time In this the Maximum exposure time is used 3 5 10 1 Turning the Auto Exposure Function On and Off The Auto Exposure function is turned on and off using the Autoexposure drop down box in Acquisition gt Options see section 3 5 4 12 page 42 When Auto Exposure is active the Acquisition Acquisition Time section in the Control Panel is set to Auto lt gt f and greyed out Auto D 2 3 5 11 Heat Detector For peltier cooled liquid nitrogen free detectors the Heat Detector function will switch off the peltier cooling and allow the detector to warm up to room temperature Cooling can be restarted either by setting the temperature in Acquisition gt Detector see section 3 5 7 2 page 59 or by exiting and restarting LabSpec 5 3 6 Video The Video menu allows configuration of the instrument s video camera s set up of video image scaling and the laser spot marker position and when multiple cameras are present selection of the active camera Source Format Video camera configuration Offsets Laser position Image scale Laser spot marker position and video image scaling and v Internal Camera Top Camera List of installed cameras Page 66 Explore the future Automotive Test Systems Process amp Environmental Medical Semiconductor Sc
11. display spectra with X axis units of detector pixels rather than the units selected in Options gt Unit This can be useful to locate the position of a hot pixel on the detector Page 73 Explore the future Automotive Test Systems Process amp Environmental Medical Semiconductor Scientific HORIBA HORIBA os Scientific Click on Show Central Pixel to mark the central pixel position on the spectrum 3 7 1 3 Calibration Click on Show Diode to move the spectrometer to the pre set internal diode position This position allows the internal reference diode to pass through the spectrometer and confocal optics onto the sample The internal reference diode can be used for back alignment of the spectrometer and optics Tick the Open Shutter box to force the detector shutter open so that the internal reference diode spot can be viewed on the sample 3 7 1 4 Motor Calibration The Motor Calibration section allows the reference positions of the instrument s motors to be set The most common use of this section is to perform a manual calibration of the spectrometer spectro motor CAUTION CHANGING PARAMETERS IN THE MOTOR CALIBRATION SECTION COULD CAUSE THE INSTRUMENT TO CEASE WORKING OR TO WORK INCORRECTLY YOU SHOULD ONLY MODIFY PARAMETERS IN THE MOTOR CALIBRATION SECTION AFTER TRAINING BY A TRAINED ENGINEER FROM HORIBA SCIENTIFIC OR ONE OF ITS REPRESENTATIVES For a step by step guide to man
12. scale W Internal Camera v Top Camera Page 67 Explore the future Automotive Test Systems Process amp Environmental Medical Semiconductor Scientific HORIBA HORIBA os Scientific EJ Drag the green laser spot marker to the desired 22 position on the video image or type the desired coordinates into the Center X and Center Y boxes a Click and Drag i Laser Position amp Center 1 23 CenterY 1 45 Help Cancel Click OK The laser spot marker is now repositioned Note that this process is objective specific the laser spot marker position should be set for each objective on the microscope 3 6 2 2 Video Image Scale Click on Video gt Image scale to open the Image scale dialog window A resizeable scale box will additionally appear on the video image The scale box can be resized to a known size and the known values used to scale the video image Image scale Bol Scale XY Move stage to Scanner corner and click button Pecat 2 Clear Size x 74 1061 Vv Size Y 59 5496 Iv Scanner T Help Cancel 3 6 2 2 1 _ Setting the Video Image Scale Using the 1 2 Corner Positions Acquire a video image using the video icon a Ensure that the objective selected in the Control Panel see section 9 7 page 233 corresponds to the objective being used on the microscope Source Format Offsets Click on Video gt Image scale
13. Acquisition Acquisition Time section in the Control Panel is set to Auto r i and greyed out JAuto D f2 3 5 4 12 2 Turning Auto Exposure Off In Acquisition gt Options select Off from the Autoexposure drop down box 3 5 4 12 3 Setting Up the Auto Exposure In Acquisition gt Options click on Set in the Autoexposure section See section 3 5 10 page 65 to learn how the Auto Exposure function can be configured Page 42 Explore the future Automotive Test Systems Process amp Environmental Medical Semiconductor Scientific HORIBA HORIBA a Scientific 3 5 4 13 Shutter Mode The Shutter Mode function sets the operation of the detector shutter during an acquisition 3 5 4 13 1 Setting the Shutter Mode In Acquisition gt Options select Auto Open or Closed from the Shutter Mode drop down box Auto In this mode the shutter operation is set automatically by LabSpec 5 Typically this means that for standard spectrum and array acquisition the shutter will be opened during spectrum acquisition and closed during detector readout and other system processes such as moving the sample stage or spectrometer grating For ultra fast SWIFT mapping see 4 5 5 page 97 the shutter is opened at the start of the acquisition and then kept open throughout the acquisition It is closed only once the final spectrum has been acquired Open In this mode the shutter wi
14. BA HORIBA a Scientific Spectral Spectral i Spectral Spectral Window 1 i Window 2 Window 3 Window 4 I o T T T 1 000 0 1 000 2 000 3 000 Raman Shift cm T 4000 Auto scanning In Auto scanning mode the spectrometer is moved in a number of very small steps allowing the spectrum to be slowly built up step by step The advantage of this method is that any pixel to pixel variation in response can be averaged out over the spectrum In the example below data has been acquired from 4 acetylsalicylic acid in the range 100 3500cm using the Autoscanning mode The stacked spectra show the individual spectra which are acquired but they have been offset for clarity The blue spectrum shows the final spectrum as observed by the user which is an average of all the individual spectra in the range 100 3500cm Page 51 Explore the future Automotive Test Systems Process amp Environmental Medical Semiconductor Scientific HORIBA HORIBA we Scientific nnn reebeere et ants HEEE SRREESERR 1 000 0 1 000 2 000 3 000 4000 Raman Shift em 3 5 6 2 Sub pixel Acquisition Function The Sub pixel acquisition function uses the high precision fine step size of the spectrometer drive mechanism to acquire spectra which are shifted by less than a whole pixel value The result is to increase the number of data points defining a band i e sub pixel 2 results in t
15. HORIBA ow Scientific The spectrum shown to the right was acquired without the Spike Filter Spikes in the spectrum are highlighted Intensity cnt T T T T T T T 500 1000 1500 2 000 Raman Shift cm The Spike Filter algorithm compares multiple accumulations of a spectrum and calculates what peaks are real e g Raman peaks and what peaks are spikes It then automatically removes spikes from the spectrum The comparison method ensures that real peaks can never be incorrectly deleted The spectrum shown to the right was acquired with the Spike Filter active This time all peaks in the spectrum are Raman peaks and there are no spikes visible Intensity cnt 500 1 000 1500 2 000 Raman Shift cm 3 5 4 7 1 Turning On the Spike Filter In Acquisition gt Options select either On auto add or On from the Spike Filter drop down box o On auto add this mode automatically adds an extra accumulation to your measurement For example if you specify three accumulations in the control panel see section 9 9 3 page 235 the actual number acquired will be four 3 1 This mode ensures that every spectrum will be spike filtered even if you only specify one accumulation since the software will automatically acquire two accumulations 1 1 to enable the Spike Filter comparison algorithm o On this mode will activate the Spike Filter only if the number of acc
16. Test exposure time s Min exposure time s Max exposure time s Desired intensity cnt Help Cancel Test exposure time s Set the initial test acquisition time in seconds s Typically an acquisition time between 0 3s and 1s is suitable although it can be increased if most samples are very weak Raman scatterers Minimum exposure time s Set the minimum acquisition time which can be selected by the software for the final measurement Typically an acquisition time between 0 1s and 0 5s is suitable Maximum exposure time s Set the maximum acquisition which can be selected by the software for the final measurement For weak Raman scatterers the final acquisition time required to reach the Desired intensity may exceed the Maximum exposure time In this case the final acquisition time will be equal to the Maximum exposure time and the achieved intensity may be less than the Desired intensity Page 65 Explore the future Automotive Test Systems Process amp Environmental Medical Semiconductor Scientific HORIBA HORIBA os Scientific Desired intensity cnt Set the desired maximum signal level in counts cnt for the final spectrum ensuring that it is below the saturation point of the detector being used Remember that the larger the desired intensity the longer the measurement will take but the better the spectrum quality For weak Raman scatterers the Desired intensity may not
17. ally are The observed spectrum is not correct since it aA r T r T r 7 T 7 ji 500 1000 1500 2000 2500 3 000 3500 is perturbed by instrumental factors Raman Shift em Page 43 Explore the future Automotive Test Systems Process amp Environmental Medical Semiconductor Scientific HORIBA HORIBA oes Scientific By applying the HORIBA ICS intensity correction factor the perturbed Raman spectrum peak intensities can be restored as illustrated in the corrected spectra shown right 3 5 4 14 1 How is the HORIBA ICS Correction Factor Calculated The HORIBA ICS intensity correction factor is created individually for each instrument at the time of manufacture The output from a calibrated white light source is passed through the system and the recorded response spectrum is compared with the calibrated source spectrum of the white light source The correction factor is calculated as correction source response The obtained correction factor is a multiplicative factor which means that each spectrum acquired is multiplied by the correction factor to yield the corrected spectrum A correction factor is created for each and every pairing of laser wavelength and diffraction grating available on the instrument e g 532nm 600gr mm 532nm 1800gr mm 633nm 600gr mm 633nm 1800gr mm_ etc When the automatic intensity correction is activated the software automatica
18. applied once at the beginning to find the optimal focus point and the 100 data points will then be acquired at the same optimal focus point This mode is useful when you wish to use autofocus for single spectrum acquisition or for surface mapping of a flat smooth sample Before each point In this mode the autofocus procedure will be applied for each individual spectrum being measured in the acquisition For an array acquisition including time profiles Z depth profiles temperature profiles XY maps XZ and YZ slices and XYZ datacubes this means that the autofocus will be performed before each point in the array For example if an XY map comprising 10 x 10 data points is to be acquired the autofocus procedure will be applied at each XY coordinate prior to spectrum acquisition This mode is useful when you wish to use autofocus for mapping of a rough and or non flat tilted sample If the sample is smooth but non flat tilted then the In limits point mode is recommended see below In limits point In this mode the autofocus procedure will be applied at four intermediate positions in a rectangular surface XY mapping area to calculate the tilt of the sample The focus position will then be adjusted at each measurement point to compensate for the tilt In the diagram below showing a surface XY mapping area the intermediate In limits point autofocus points are marked with with For example if an XY ma
19. ature of the detector The current temperature in degrees celsius C will be displayed in the adjacent indicator box 70 a Page 58 Explore the future Automotive Test Systems Process amp Environmental Medical Semiconductor Scientific HORIBA HORIBA _ Scientific Tick the box to have the current temperature el m continuously updated Note that the current temperature of the active 70 detector is also displayed next to the detector indicator icon in the Status Bar 3 5 7 2 Setting the Detector Temperature To set the temperature of the detector type in the desired value in degrees celsius C and click t f Set Set 3 5 8 Autofocus The Autofocus function in LabSpec 5 automatically finds the optimum focus position for a sample and ensures that the best quality spectrum with maximum signal level can be easily achieved It is a useful tool for samples where manual focusing is difficult such as highly polished clean surfaces So long as the sample is relatively close to focus the Autofocus procedure will find the correct focus position and give a good quality spectrum Autofocus also is invaluable when acquiring XY surface maps of samples which have significant surface roughness Without autofocus whenever the measurement position in the map is out of focus the signal level will be reduced and analysis of the map data will be difficult With the autofocus running the focus po
20. ctrometer window in the control panel see section 9 5 page 230 and or selected via Options gt Unit see section 3 4 1 page 22 Note that multiple spectral windows can be set up by ticking the check boxes on the right hand side Up to five spectral ranges can be defined Each spectral range can be acquired with a specific integration time see Time below Multiple spectral ranges can be contiguous e g 100 200 200 500 500 2000cm or discrete e g 100 1500 1750 1900 2900 4000cm For most standard measurements it is generally sufficient to use a single spectral range covering the whole range desired Time The acquisition time for each spectral range can be set up in two ways o Time in this mode the time in the Extended Range dialog window is specified as a percentage of the acquisition time set in the Control Panel see section 9 9 2 page 235 For example if the Control Panel has the acquisition time set as 10s then if Time is set to 50 in the Extended Range dialog window the acquisition will be made with 5s per spectral window Explore the future Automotive Test Systems Process amp Environmental Medical Semiconductor Scientific LabSpec 5 user manual 6000 4000 4 3000 4 Intensity a u 2000 4 1000 510 515 520 525 Wavenumber cm 1 Multi windows v Sub pixel number 11 100 Combine data M Min overlap pix iy Vv
21. d Image scale Scanner tick the Scanner box to start the EN Scanner motorized mirrors otherwise ensure that Move stage to eae j i x comer and click the scanner is started using the switch on the button a instrument control unit The laser beam will now 24 ee be rastored on the sample in the Y direction Sex 741061 y ap SizeY 59 5496 iv Cancel Drag the scale box in the Y dimension to match the scan height of the rastored laser beam Click Scanner to register the video scale eas Note that this process is objective specific the video image scale should be set for each objective on the microscope 3 6 3 List of Installed Cameras A list of all installed cameras is displayed at the bottom of the Video menu The currently active camera is denoted by a tick next to its name this camera will be used when the video read out is started with the camera icon 3 6 3 1 Selecting a Camera The currently active camera is denoted by a tick next to its name this camera will be used when the video read out is started with the camera icon a To change the active camera click on the camera Source Source name listed in the Video menu Format Format Offsets Offsets Laser position Laser position Image scale Image scale v Internal Camera Internal Camera EEEE Toce Page 72 Explore the future Automotive Test Systems Process amp Environmental Medical Semiconductor Scientific HORIBA
22. d by changing efficiency of the spectrometer s diffraction grating T i T T T 2 900 3 000 3 100 3 200 Raman Shift cm Combined data with Adjust Intensity unticked Adjust intensity m Note the step at 3030 cm 2 900 3 doo 3 100 3 200 Raman Shift em Combined data with Adjust Intensity ticked The Adjust intensity Vv gluing between the two individual spectral windows is seamless 2 900 3 000 3 100 3 200 Raman Shift cm Return to First Window If Return to First Window is ticked at the end of an extended range measurement the spectrometer will be returned to the starting position for the measurement so that it is ready to immediately start the next measurement If Return to First Window is unticked the spectrometer will remain at the position used for the last spectral window When a new measurement is started then the spectrometer will move to the correct starting position for that measurement Page 55 Explore the future Automotive Test Systems Process amp Environmental Medical Semiconductor Scientific HORIBA HORIBA os Scientific The Return to First Window function is particularly useful when making kinetic time based measurements with the extended range function In this case it is important that the spectrometer is ready to immediately start the measurement at the next trigger point for the kinetic run and thus it must be at the starting position f
23. e selected using the detector indicator in the Status Bar see section 7 3 2 page 201 Select the read out mode for the detector from the Mode drop down box For two dimensional array detectors such as a CCD the software has different read out zones areas configured one for spectrum acquisition and one for area intensity acquisition o Spectrum select this mode for acquiring normal spectra where the detector is used in a one dimensional configuration spectral axis o Image select this mode for specialized applications where the detector is used in a two dimensional configuration spectral axis and CCD height Sizes The Sizes section controls what area of the detector is used for the Spectrum and Image modes Type in the desired minimum and maximum pixel numbers to define the area which will be used The values in the greyed out boxes indicate the maximum pixel size of the detector in the X and Y axes Options The options visible will depend on the particular detector s installed on the instrument Please consult a trained engineer from HORIBA Scientific or one of its representatives to find out more about the options available for the detectors installed on your system In most cases the temperature sensor and control options will be present and these are described below 3 5 7 1 Displaying the Detector Temperature Click on the temperature icon to display the y ef 6 current temper
24. he Use detector function sets how multiple detectors are used during a measurement If your Raman system is equipped with a single detector only then this option will be set to Active and will be greyed out 3 5 4 10 1 Setting the Use Detector Mode In Acquisition gt Options select either Active or Both from the Use Detector drop down box Active In this mode data will only be acquired from the active detector The active detector is selected from the status bar see section 7 3 2 page 201 Both In this mode it is possible to acquire data from two detectors simultaneously but this only applies to very specific configurations For most standard systems it is only ever possible to acquire data from the active detector 3 5 4 11 Signal Mode The Signal Mode function controls whether a dark subtract procedure is implemented automatically during a spectrum acquisition Some detectors e g the InGaAs near infra red array detector have a significant fixed pattern artefact signal which can dominate the spectrum acquired from a sample with low signal level In this case it is possible to acquire a dark spectrum e g a spectrum acquired with a shutter in front of the detector so that no sample signal is observed which corresponds to the fixed pattern signal only By performing a dark subtract e g subtract the dark spectrum from the sample spectrum significant improvement in s
25. ientific HORIBA HORIBA ae Scientific CAUTION CHANGING PARAMETERS ACCESSED THROUGH THE VIDEO MENU COULD CAUSE THE VIDEO CAMERA S TO CEASE WORKING OR TO WORK INCORRECTLY YOU SHOULD ONLY MODIFY PARAMETERS IN THE VIDEO MENU WHEN INSTRUCTED TO DO SO BY A TRAINED ENGINEER FROM HORIBA SCIENTIFIC OR ONE OF ITS REPRESENTATIVES 3 6 1 Video Camera Configuration The dialog windows for Source Format and Offsets allow the configuration of the video camera s to be set up or modified The dialog windows will vary depending to the specific camera s installed on the instrument Please consult your local HORIBA Scientific engineer or representative to find out more details about the configuration options available for the cameras on your system 3 6 2 Laser Spot Marker Position and Video Image Scaling The Laser Position and Image Scale options allow the position of the laser spot marker on the video image and the scaling of the video images to be set 3 6 2 1 Laser Position Click on Video gt Laser position to set the position of the green laser spot marker on the video image 3 6 2 1 1 Setting the Laser Spot Marker Position Acquire a video image using the video icon 3 ii ae aiy ail Ensure that the objective selected in the Control Panel see section 9 7 page 233 corresponds to the objective being used on the microscope Click on Video gt Laser position Source Format Offsets Image
26. ill be made using the acquisition parameters set in the Control Panel see section 9 9 page 234 Page 61 Explore the future Automotive Test Systems Process amp Environmental Medical Semiconductor Scientific HORIBA LabSpec 5 user manual HORIBA Scientific Zone The Zone section of the Autofocus dialog window can be used to set up an intermittent autofocus procedure The XY mode sets the autofocus to be made after a fixed distance across the sample whilst the Time mode sets the autofocus to be made after a fixed time XY Tick the box for XY and type in the desired distance in micrometers um between autofocus operations This mode is useful when the sample has a very gradual change in focus across its surface and it is not necessary to autofocus at every map position Time Tick the box for Time and type in the desired time in seconds s between autofocus operations This mode is useful when the sample may slow move out of focus due to temperature fluctuations and it is not necessary to autofocus at every point Autofocus Z parameters Device Motorized gt continuous Range j5 j5 Step 5 um Signal Type Detector AP Range fiso feo nm Exposure 0 3 sec IV Profile Cancel Autofocus Z parameters Device Motorized v continuous Range 45 45 Step 5 pm Signal Type Detector Range 1500 1600 nm Exposure 0 3 sec MV Profile Zo
27. ion only and then subtracted from each spectral window In the case of an array acquisition including time profiles Z depth profiles temperature profiles XY maps XZ and YZ slices and XYZ datacubes the dark spectrum will be acquired once at the start of the acquisition only and then subtracted from the spectrum acquired at each measurement point This mode is useful when the dark spectrum is constant and is not expected to change between measurements Signal Dark always This mode is similar to Signal Dark discussed above However in this case the dark spectrum is acquired before each and every readout from the detector In the case of an extended range spectrum acquisition the dark spectrum will be acquired for each spectral window and subtracted from the sample spectrum In the case of an array acquisition including time profiles Z depth profiles temperature profiles XY maps XZ and YZ slices and XYZ datacubes the dark spectrum will be acquired and subtracted at each measurement point This mode is useful when the dark spectrum is expected to vary between measurements 3 5 4 12 Autoexposure The Auto Exposure function sets whether the auto exposure operation see section 3 5 10 page 65 is applied to a measurement 3 5 4 12 1 Turning Auto Exposure On In Acquisition gt Options select On from the Autoexposure drop down box When Auto Exposure is active the
28. le Note that this process is objective specific the video image scale should be set for each objective on the microscope 3 6 2 2 2 Acquire a video image using the video icon a BR Ensure that the objective selected in the Control Panel see section 9 7 page 233 corresponds to the objective being used on the microscope Click on Video gt Image scale to open the Image scale dialog window Ensure the Size X and Size Y boxes are ticked as appropriate With this procedure it is possible to scale just one dimension X or Y if desired The dimension s to be scaled must be ticked Drag the scale box in X and or Y dimensions as appropriate to match a feature of known size Typically this will be a graticule scale bar but any sample feature of precisely known size can be used Setting the Video Image Scale Manually Automotive Test Systems Process amp Environmental Medical Semiconductor Scientific LabSpec 5 user manual Image scale ma Scale XY i Move stage to 5 Scanner comer and click button Reset E Clear 150 8 Vv Help Size Y 104 4 Vv ance Size x Scanner M Source Format Offsets Laser position Internal Camera v Top Camera Image scale m Move stage to corner and click Seme Reset button o Cea Size x 74 1061 m elp Size Y 59 5496 5496 Cancel Cancel Scanner Page 70 HORIBA Explore the futu
29. ll be kept open throughout an acquisition For example for an extended range spectrum acquisition see section 3 5 6 page 49 the shutter will be opened prior to acquisition of the first spectral window and will be kept open throughout the acquisition It is closed only once the final spectral window has been acquired Closed In this mode the shutter will be kept closed throughout an acquisition it can be used to monitor the inherent background dark response of the detector This mode can be used to assess the spectrum of a detector without any light Note that in this mode you will not see a spectrum corresponding to your sample 3 5 4 14 Intensity Correction The LabSpec 5 intensity correction algorithm allows true comparison of spectra acquired using different laser wavelengths and optics Without intensity correction spectra acquired using different laser wavelengths and optics can show significant differences in relative peak intensities These differences are caused by varying performance of the instrument components including microscope objectives laser rejection filters diffraction gratings and CCD detectors at different wavelengths The spectrum shown right for 4 acetyl salicylic acid was acquired using a 785 nm near infra red laser In this case the CCD detector sensitivity decreases as the Raman shift increases Thus peak intensities at high Raman shift positions are observed to be significantly weaker than they re
30. lly applies the appropriate correction factor based on the active laser wavelength and diffraction grating pair In the event that there are multiple laser rejection filters for a single laser wavelength configured on a LabRAM HR system e g one notch filter and one edge filter for 633nm the software cannot automatically detect which filter is in place In this case the specific laser filter must be selected from Setup gt ICS Filters before the acquisition is made see section 3 7 3 page 75 for further information 3 5 4 14 2 Turning On the Automatic Intensity Correction In Acquisition gt Options select HORIBA ICS from the Intensity Correction drop down box Click OK Intensity Correction is now active and will be applied to all acquired data The Intensity Correction indicator icon is displayed MES in the Status Bar If multiple injection rejection or photoluminescence PL filters have been set up for a single laser wavelength ensure the correct filter is selected Page 44 Explore the future Automotive Test Systems Process amp Environmental Medical Semiconductor Scientific HORIBA Explore the future HORIBA Scientific from the ICS Filters dialog window by clicking on Setup gt ICS Filters Note that an intensity correction factor must have been created for the specified laser wavelength and diffraction grating pair otherwise an error message similar to that shown right will be
31. ne Help Cancel 3 5 8 3 Turning On Autofocus In Acquisition gt Options select the appropriate mode from the Autofocus drop down box see section 3 5 4 8 1 page 40 Click OK Autofocus is now active The Autofocus indicator icon is displayed in the AF Status Bar 3 5 8 4 Setting the Autofocus Offset In Acquisition gt Options type in the desired offset for the Autofocus position A negative offset means that the focus will be moved upwards e g analysis will be made higher in the sample than the Page 62 HORIBA Explore the future Automotive Test Systems Process amp Environmental Medical Semiconductor Scientific HORIBA a Scientific autofocus position a positive offset means that the focus will be moved downwards e g analysis will be made lower in the sample than the autofocus position See section 3 5 4 8 2 page 40 for further information 3 5 8 5 Turning Off Autofocus In Acquisition gt Options select Off from the Autofocus drop down box see section 3 5 4 8 3 page 40 Click OK Autofocus is now inactive The Autofocus indicator icon is no longer displayed in the Status Bar 3 5 9 Extra Images The Extra Images dialog window allows extra images to be recorded using other detector devices on the system such as the Autofocus reflection pin diode detector see section 3 5 8 page 59 There are two main modes o Image this allows f
32. nwards e g analysis will be made lower in the sample than the autofocus position The offset is also useful if you wish to do mapping inside a sample at a fixed position below the surface The autofocus procedure depending on the exact mode being used see section 3 5 8 page 59 will locate the surface of the sample and the positive offset will then be applied to move to a specified position below the surface 3 5 4 8 3 Turning Off Autofocus In Acquisition gt Options select Off from the Autofocus drop down box Click OK Autofocus is now inactive The Autofocus indicator icon is no longer displayed in the Status Bar 3 5 4 9 Scanning Device The Scanning Device function sets what device is used for Y axis movement in multidimensional spectral array measurements such as XY surface maps or YZ depth slices The default mode is Stage which uses the motorized sample XY stage to move the sample in both X and Y dimensions On systems which are equipped with the confocal LineScan mirror scanning hardware it is also possible to use the LineScan to acquire data in the Y axis In this case select Scanner to disable the XY motorized stage for Y axis movement during the measurement and to use the LineScan mirror Page 40 Explore the future Automotive Test Systems Process amp Environmental Medical Semiconductor Scientific HORIBA HORIBA Scientific 3 5 4 10 Use Detector T
33. or stand alone images to be recorded using the signal from the additional detector The dimensions of the image in X Y and or Z axes and the number of image pixels are defined in the Extra Images dialog window o Map this allows signal from the additional detector to be recorded simultaneously with a multidimensional spectral array measurement Such as a Raman XY surface map The dimensions of the image in X Y and or Z axes and the number of data points are taken from the Mapping Properties dialog window see section 4 5 5 page 97 and do not need to be set in the Extra Images dialog window 3 5 9 1 What are Extra Images For The Extra Images function can be useful to obtain additional information about a sample which wouldn t normally be possible on a Raman microscope One typical example is to create a map of the sample s surface topography roughness This can be done by using information obtained during the Autofocus procedure see section 3 5 4 8 page 39 If the Autofocus procedure is used for a Raman XY map of the surface at each measurement point in the map the software has calculated a focus position based on an autofocus signal These two values focus position and signal directly reflect the topography of the sample The Extra Images function allows the topography image to be created simultaneously with the Raman map Page 63 Explore the future Automotive Test Systems Process amp En
34. or the extended range in advance 3 5 6 4 Turning On the Extended Range Function In the extended range dialog window accessed via Acquisition gt Extended range or the Extended range icon select the desired extended range mode from the Mode drop down box Choose either Multi windows or Auto scanning to make an extended range measurement Set up the spectral range and other options Multi windows section 3 5 6 3 page 53 and click OK The Sub pixel number extended range function is now active Min overlappi free 2eanrea la Combine data V Adjust intensity Iv Return to first window Cancel Help The extended range indicator icon is displayed in ij the Status Bar Note that the extended range is only available for full spectrum acquisition Mf or multidimensional spectral array acquisition 6 It is not available for real time display RTD 2 18 3 5 6 5 Turning Off the Extended Range Function In the extended range dialog window accessed Extended range via Acquisition gt Extended range or the Extended range icon 0 m select the Single window mode from the Mode drop down box Multi windows Single window Sub pixel number Muli windon PN p Auto scanning N Min overlap pix ou Combine data Adjust intensity Iv Return to first window Cancel Help Page 56 Explore the future Automotive Test Systems Process amp Environmen
35. p comprising 10 x 10 data points is to be acquired the autofocus procedure will be applied at the intermediate positions of the map area prior to the mapping When the map acquisition starts the focus position will be adjusted at each point based on the tilt plane calculated by the autofocus This mode is useful when you wish to use autofocus for mapping of a smooth but non flat tilted sample Page 39 Explore the future Automotive Test Systems Process amp Environmental Medical Semiconductor Scientific HORIBA HORIBA ws Scientific 3 5 4 8 1 Turning On Autofocus In Acquisition gt Options select either Before acquisition Before each point or In limits point from the Autofocus drop down box Click OK Autofocus is now active The Autofocus indicator icon is displayed in the AF Status Bar 3 5 4 8 2 Setting the Autofocus Offset Depending on the exact Autofocus mode being used see section 3 5 8 page 59 the focus position located by the autofocus procedure may correspond to a visual focus of the sample which is not always the position giving a maximum Raman signal In this case it is possible to set a Z axis offset which will be applied after the autofocus position has been located A negative offset means that the focus will be moved upwards e g analysis will be made higher in the sample than the autofocus position a positive offset means that the focus will be moved dow
36. pectrum quality can be realised 3 5 4 11 1 Setting the Signal Mode In Acquisition gt Options select either Signal Dark Signal Dark or Signal Dark always from the Signal Mode drop down box These choices what type of spectrum is acquired from the detector Signal In this mode the sample spectrum detector shutter open will be acquired and displayed on screen Dark In this mode the dark spectrum detector shutter closed will be acquired and displayed on screen Note that in this mode you will not see a spectrum corresponding to your sample Signal Dark In this mode the dark spectrum detector shutter closed will be automatically subtracted from the sample spectrum detector shutter open The dark spectrum will be acquired first followed by the sample spectrum The dark spectrum will be acquired with identical acquisition settings as the sample spectrum for example if the acquisition is set for two accumulations of 30s each then the dark spectrum will also Page 41 Explore the future Automotive Test Systems Process amp Environmental Medical Semiconductor Scientific HORIBA HORIBA ws Scientific be acquired with two accumulations of 30s each As a result the total acquisition time will be doubled In the case of an extended range spectrum acquisition the dark spectrum will be acquired once at the start of the extended range acquisit
37. re HORIBA Scientific In the Size X and or Size Y boxes type in the size of the feature to which the scale box has been match Click Scale XY to register the video scale If only one dimension X or Y has been scaled in this manner ensure that the other dimension is scaled using a similar process Both dimensions X and Y must be scaled to have correctly scaled video images Note that this process is objective specific the video image scale should be set for each objective on the microscope 3 6 2 2 3 Setting the Scanner Scale The Scanner Scale function is used to set the scan range of the confocal LineScan mirror Acquire a video image using the video icon 3 BR Ensure that the objective selected in the Control Panel see section 9 7 page 233 corresponds to the objective being used on the microscope Turn on the laser and or open the shutter so that the laser beam is visible in the video image Click on Video gt Image scale to open the Image scale dialog window Automotive Test Systems Process amp Environmental Medical Semiconductor Scientific LabSpec 5 user manual Image scale Move stage to comer and click button 24 Scanner Size x 74 1061 Vv SizeY 59 5496 M Scanner Source Format Offsets Laser position Internal Camera iv Top Camera Page 71 HORIBA HORIBA ae Scientific If the system has a software controlled motorize
38. shape and position and subtle features Such as weak shoulders on a strong band can be lost The Denoise function ensures that all this important information is retained whilst still reducing noise in the spectrum The spectra shown right illustrate the effect of the Denoise function Two main Denoise algorithms are available from the Denoise drop down box o Standard recommended for spectra with signal to noise 20 o Lite recommended for very noisy spectra with signal to noise lt 20 In addition both algorithms can be used with an integrated Despike function to remove random spikes also known as cosmic rays See also section 3 5 4 7 page 37 for more information about other spike filter options in LabSpec 5 Denoise can be applied post acquisition using the Smoothing icon and Filtration dialog window see section 4 6 4 page 124 If a spectrum has had the Denoise function automatically applied through Acquisition gt Options it cannot have the function applied again through the Filtration dialog window Page 46 Explore the future Automotive Test Systems Process amp Environmental Medical Semiconductor Scientific HORIBA HORIBA a Scientific 3 5 4 15 1 Turning On the Automatic Denoise Function In Acquisition gt Options select the desired Denoise function from the Denoise drop down box o Standard recommended for spectra with signal to noise 2 20 o Standard
39. sition will be adjusted at each measurement position in the map ensuring that good quality data is acquired across the full mapping area despite the sample s inherent roughness Spectrum acquired using 100x objective with autofocus 6 000 40004 Intensity cnt 20005 T t T 1000 1500 Raman Shift em Spectrum acquired using 100x objective without autofocus out of focus by approximately 20 um The bottom image is shown with the same intensity scale as the autofocus spectrum shown above 3505 3005 2505 Intensity cnt 2005 1505 8 000 6 0005 40004 Intensity cnt 2 0004 i E east enna i cca T 1 600 i 1500 Page 59 Raman Shift cm Explore the future Automotive Test Systems Process amp Environmental Medical Semiconductor Scientific HORIBA HORIBA es Scientific 3 5 8 1 The Autofocus Procedure The Autofocus procedure uses a software controlled motor to control the microscope focus The focus position is adjusted in small increments whilst monitoring a signal from the sample The sample signal is maximum at the focus position and thus the focus adjustment is made iteratively until the maximum signal is observed At this point the Raman measurement is made There are two main motors which are used to control the microscope focus o Z motor this motor controls the fine focus wheel of the microscope Its maximum range is limi
40. tal Medical Semiconductor Scientific HORIBA HORIBA _ Scientific All the options will be greyed out Extended range Click OK The extended range function is now inactive The extended range indicator icon is no longer show in the Status Bar 3 5 7 Detector The detector window controls the configuration of the detector s used by the Raman system In typical use these parameters do not need to be adjusted by the user and it is recommended that they are only modified when instructed to do so by a trained engineer from HORIBA Scientific or one of its representatives Detector Type EM_32 Sensor _ be Help Mode l Spectrum v Cancel Sizes foa E bg fi froze Options I High speed 1020 M Shift M High gain a r fo sal Page 57 Explore the future Automotive Test Systems Process amp Environmental Medical Semiconductor Scientific HORIBA HORIBA al Scientific CAUTION CHANGING SETTINGS IN THE ACQUISITION gt DETECTOR WINDOW MAY RESULT IN SYSTEM MALFUNCTION ON NO ACCOUNT SHOULD SETTINGS IN THIS DIALOG WINDOW BE MODIFIED EXCEPT WHEN INSTRUCTED TO DO SO BY A TRAINED ENGINEER FROM HORIBA SCIENTIFIC OR ONE OF ITS REPRESENTATIVES Type Select the detector to be used from the Sensor drop down box this list will only show the detectors installed on the instrument Note that when multiple detectors are installed the Bi active detector can also b
41. ted only by the microscope focus mechanism and the available space between the objective and the sample o Piezo device Pifoc this motor is attached to a single microscope objective and uses piezo controllers to adjust the objective position up or down Its maximum range is limited by the piezo controllers and typically has a travel of approximately 100 um By using piezo motors this device is extremely fast and has very fine step size typically lt 50 nm There are two main signals which can be detected to find the focus position o Reflection this signal is the reflected and Rayleigh scattered light from the sample and is detected by a small pin diode detector positioned at the top of the microscope which monitors the total signal intensity without spectral information The signal will be greatest at the surface of the sample o Detector this signal is based on the Raman signal from the sample detected in the normal way using the active detector The signal will be greatest at or just below the surface of the sample The hardware present on your instrument will dictate whether autofocus is possible and if so what motor and signal will be used 3 5 8 2 Setting Up Autofocus The Autofocus dialog window accessed via Acquisition gt Autofocus allows the Autofocus to be configured Autofocus Z parameters Device Motorized continuous x Range 45 45 Step 5 um Signal Type Detector
42. to open the Image scale dialog window Internal Camera v Top Camera i Page 68 Laser position Explore the future Automotive Test Systems Process amp Environmental Medical Semiconductor Scientific HORIBA HORIBA _ Scientific Ensure the Size X and Size Y boxes are ticked PEETA E M torre Eese button EE Size X 74 1061 Flo SEa a548 Cancel Scanner Drag the scale box to cover a large proportion of Video Test DER the video image Move a small easily recognisable feature of the sample so that it is positioned exactly at the top left hand corner of the scale box Dust particles on the Silicon calibration sample are ideal for this but any sample with recognisable features can be used Click 1 The scale values in the Size X and Image scale Size Y boxes are cleared re ard cick utton Reset Clear Size x So Vv Size Y PT Scanner M Using the joystick move the XY stage so that the Video Test feature is positioned exactly at the bottom right s hand corner of the scale box Page 69 Explore the future Automotive Test Systems Process amp Environmental Medical Semiconductor Scientifi HORIBA Explore the future HORIBA Scientific Click 2 The scale values in the Size X and Size Y boxes are set according to the distance moved by the XY stage Click Scale XY to register the video sca
43. tor Scientific HORIBA HORIBA es Scientific In the description that follows the term Spectral Range refers to the specified extended range and Spectral Window refers to the individual spectra which are acquired to cover the extended range 3 5 6 1 Extended Range Acquisition Modes The Extended Range module offers three main modes for spectrum acquisition Single Window In Single Window mode only the spectral range covered by a single CCD detector readout will be used The actual range will depend on the spectrometer position see section 9 5 page 230 the laser wavelength see section 9 1 page 227 and the diffraction grating see section 9 6 1 page 231 Remember that the acquired spectrum will be centered about the current spectrometer position In the example below data has been acquired from 4 acetylsalicylic acid with the spectrometer centered at 1200cm in Single Window mode 1 000 0 1 000 2 000 3 000 4 000 Raman Shift cm Multiwindow In Multiwindow mode a user defined spectral range can be covered with the software automatically adjusting the spectrometer position and capturing multiple spectral windows to cover the desired range In the example below data has been acquired from 4 acetylsalicylic acid in the range 100 3500cm using the Multiwindow mode Page 50 Explore the future Automotive Test Systems Process amp Environmental Medical Semiconductor Scientific HORI
44. tral arrays including time profiles Z depth profiles temperature profiles XY maps XZ and YZ slices and XYZ datacubes will be saved as tvf Folder Type in the file path or browse using the file browse button for the location where the data should be saved o Ifthe folder exists already data will be saved inside the specified folder Tick the boxes for Year Month and Day to create a new folder labelled _YYYY_MM_DD which indicates the year YYYY month MM and day DD according to the computer s clock o If the folder does not already exist it will be created when the Autosave procedure is next performed If the boxes for Year Month and Day are ticked the year YYYY month MM and day DD according to the computer s clock will be appended to the specified folder name for example Folder_YYYY_MM_DD File Type in the file name for the data which is to be saved Tick the Hour Min and or Count boxes to append the hour HH minute mm and or integer count C to the file name The count number will start at the number indicated in the box to start the count at a different number type in the desired first number in the count box This number will be automatically incremented for subsequent autosaves For example with Hour and Min ticked the data will be saved as FileName_HH_mm xxx where XXX indicates the specified file format
45. ts neighbours The Min Overlap pix allows the user to define in pixels the minimum overlap which must be used Typically a value of 100 is adequate for most measurements Combine Data When Combine Data is ticked the individual spectral windows will be automatically glued together to yield a single spectrum at the completion of the measurement Spectrum acquired with Combine Data unticked Combine data E 1 doo 2 doo 3 doo Raman Shift cm Spectrum acquired with Combine Data ticked Combine data iv 1 000 a Sn 3 000 Page 5 4 Explore the future Automotive Test Systems Process amp Environmental Medical Semiconductor Scientific HORIBA HORIBA a Scientific Adjust Intensity During an extended range measurement discrete spectral windows are acquired to cover the entire range As the spectrometer is moved to capture each spectral window there is a natural small drop in efficiency of the diffraction grating which can result in slight changes to the baseline of each spectral window When these spectral windows are glued to create the final spectrum covering the extended range these baseline changes can give rise to small steps in the spectrum If Adjust Intensity is ticked the baselines of the individual spectral windows will be adjusted prior to gluing to yield a seamless final spectrum Raw data showing the individual spectral windows with a natural baseline shift cause
46. ual calibration of the spectrometer please see section 10 page 247 Motor Select the motor to be calibrated from the Motor drop down box Position The current position of the selected motor is displayed in motor step units Click on the left hand ar row to sequentially move lt i es gt ine fT iti 654360 I aT the motor position to lower position The position Eosin will be reduced by the increment shown in the Inc box Click on the right hand arrow to sequentially move Position 654360 OAN the motor position to higher position The position will be increased by the increment shown in the Inc box Grating The selected diffraction grating see section 9 6 1 page 231 is displayed Page 74 Explore the future Automotive Test Systems Process amp Environmental Medical Semiconductor Scientific HORIBA
47. umulations set in the control panel see section 9 9 3 page 235 is greater than 1 So if an acquisition is made with 2 3 4 accumulations then the Spike Filter will be active If an acquisition is made with only 1 accumulation then the Spike Filter will be inactive and there is the possibility of spikes being present in your spectrum This mode is useful since it allows you to easily switch between a fast analysis mode without the Spike Filter e g when the accumulation number is set to 1 and standard analysis with the Spike Filter e g when the accumulation number is set to 2 or more 3 5 4 7 2 Turning Off the Spike Filter In Acquisition gt Options select Off from the Spike Filter drop down box Page 38 Explore the future Automotive Test Systems Process amp Environmental Medical Semiconductor Scientific HORIBA HORIBA al Scientific 3 5 4 8 Autofocus The Autofocus function sets how the autofocus operation see section 3 5 8 page 59 is applied to a measurement There are three main modes of operation Before acquisition In this mode the autofocus procedure will be applied a single time at the start of a spectrum or array acquisition including time profiles Z depth profiles temperature profiles XY maps XZ and YZ slices and XYZ datacubes For example if an XY map comprising 10 x 10 data points is to be acquired the autofocus procedure will be
48. vironmental Medical Semiconductor Scientific HORIBA Explore the future HORIBA Scientific 3 5 9 2 Setting Up an Image Acquisition Tick the axis boxes to activate the X Y and Z axes as required Set the image dimensions in micrometers um using the From and To boxes and number of image pixels using the Size boxes Select the signal source additional detector which will be used to create the image by ticking the Image box es in the Sources section The most common sources are as follows o Reflection autofocus pin diode detector o Z Z axis position of the piezo Z motor Other sources may be visible in this dialog window depending on the configuration of your system Click Image to start the acquisition 3 5 9 3 Setting Up a Map Acquisition Select the signal source additional detector which will be used to create the mapped image by ticking the Map box es in the Sources section Nothing needs to be set or adjusted in the Image section of the dialog window Note that if all three image axes X Y and Z are unticked then the Image button will be greyed out This button is not used for map acquisition Automotive Test Systems Process amp Environmental Medical Semiconductor Scientific LabSpec 5 user manual Extra images Sources Map Image Reflection lr WwW Z a Image Help Extra images Image From To Size
49. wice the number of data points sub pixel 3 results in three times the number etc Note that this will increase the total acquisition time and it is suggested that sub pixel acquisition is only used over limited ranges The sub pixel acquisition function does not increase the spectral resolution of the spectrometer since this is defined principally by the laser wavelength spectrometer focal length diffraction grating and slit However the sub pixel acquisition function is useful to give increased definition of a peak by providing more data points to define that peak This can be beneficial when studying peak shape or performing peak fitting routines Sub pixel 1 on The data shown right has been acquired with om sub pixel 1 which is the default value for ia standard acquisitions Intensity a u 510 515 520 525 Wavenumber em 1 Page 52 Explore the future Automotive Test Systems Process amp Environmental Medical Semiconductor Scientific HORIBA HORIBA Scientific Sub pixel 4 The data shown right has been acquired with sub pixel 4 The increased number of data points is clearly visible 3 5 6 3 Seiting the Extended Range From and To Set the beginning From and end To spectral positions by typing in the desired values into the respective boxes The spectral units are those which are displayed in the spe
50. zo controllers and typically has a travel of approximately 100 um CAUTION TAKE CARE SETTING THE Z SCAN RANGE WHEN USING THE Z MOTOR MOTORIZED DEVICE IF THE RANGE IS SET LARGER THAN THE AVAILABLE SPACE BETWEEN THE SAMPLE AND THE OBJECTIVE THE SAMPLE OBJECTIVE MICROSCOPE AND OR Z MOTOR COULD BE SERIOUSLY DAMAGED Signal Select the autofocus signal from the Signal drop down box o Reflection this signal is the reflected and Rayleigh scattered light from the sample and is detected by a small pin diode detector positioned at the top of the microscope which monitors the total signal intensity without spectral information o Detector this signal is based on the Raman signal from sample detected in the normal way using the active detector Tick the Profile box to create a profile of signal intensity versus Z depth position during the autofocus procedure This can be a useful tool to monitor and troubleshoot the autofocus procedure If Reflection signal is selected there are no other parameters which need to be set in the Signal section If Detector signal is selected specify the spectral range which will be used to optimise the focus position and set the exposure acquisition time in seconds s which will be used for the autofocus spectrum read out Note that this exposure time is used only for the autofocus procedure once the focus position is located the sample measurement w

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