LabSpec 5 user manual Page
Contents
1. 920 500 1 000 1500 Raman Shift cm When the Add Peak cursor is active and the _ gt fhe mouse is hovered over an existing peak label the cursor changes to a Move Peak cursor Left click and drag the Move Peak cursor to move JE 5 the peak label to a different position on the hy d qn Hy spectrum 7 Y 500 1 000 1500 Raman Shift cm l 365 T T T T T 500 1 000 1500 Raman Shift cm Page 173 Explore the future Automotive Test Systems Process amp Environmental Medical Semiconductor Scientific HORIBA HORIBA ae Scientific When multiple peaks are labelled on a spectrum the active peak label is enclosed in a dashed box Use the Move Peak cursor to activate a different peak label by left clicking on that peak label 500 1 000 1500 Raman Shift em T T T T T 500 1 000 1 500 Raman Shift em The Add Peak and Move Peak cursors should be used in conjunction with the Peak Searching and Fitting module see section 4 6 7 page 134 Available for Spectrum Spim Point Model 5 11 Adjust Peak FE Activates the Adjust Peak cursor allowing peak fit parameters to be manually adjusted prior to fitting The peak position amplitude and full width at half maximum height FWHM can be adjusted using this cursor Typically this function requires that the peak shape is visible on the spectrum so that the shape and position can be man2. Click on Delete to delete the spectrum from the Delete position indicated by the cursor position In a default spectral profile the other spectra above this position will be shifted downwards in the profile For example if spectra A B C and D are currently at positions 1 2 3 and 4 in a profile of form 1A 2B 3C 4D when spectrum B is deleted the new profile will take the form 1A 2C 3D In a spectral profile where the scale has been manually modified using the Data Range dialog window see section 3 3 2 page 20 the first and last positions of the profile will remain fixed The positions of spectra within the profile will be adjusted when a spectrum is deleted For example if spectra A B C and D are currently at positions 1 2 3 and 4 in a manually scaled profile of form 1A 2B 3C 4D when spectrum B is Page 153 Explore the future Automotive Test Systems Process amp Environmental Medical Semiconductor Scientific HORIBA HORIBA al Scientific deleted the new profile will take the form 1A 2 5C 4D If necessary the profile can be rescaled using the Data Range dialog window after the spectrum has been deleted 4 6 11 Modelling AA m Opens the Model dialog window The Model dialog window is used to set up and perform a direct classical least squares DCLS modelling procedure on multidimensional spectral arrays including time profiles Z depth profiles temperature profiles XY maps
3. Scientific The profile will be created with each spectrum assigned to an integer value on the X axis and the X axis label is set to Points To modify the scaling and axis label use the Data Range dialog window accessed through the Data gt Data Range menu the Data Range icon i i amp or by using the keyboard short cut lt CTRL gt D See section 3 3 2 page 20 for more information about the Data Range dialog window Save the spectral profile in ngc format by activating the Splm window and using the File gt Save As menu or the Save icon W 4 6 10 2 Adding Spectra to a Spectral Profile To add a spectrum into an existing Spectral Profile use File gt Open menu or the Open icon So or the keyboard short cut lt CTRL gt O to open the spectrum which is to be added Select the spectrum and click on Add to Add automatically add the spectrum at the end of the spectral profile For example if the profile already has spectra at positions 1 2 and 3 a new spectrum added to the profile will be at position 4 4 6 10 3 Inserting Spectra into a Spectral Profile To insert a spectrum into an existing Spectral Profile use File gt Open menu or the Open on 8 or the keyboard short cut lt CTRL gt O to open the spectrum which is to be inserted In the profile Map window activate the cursor and Bie select the position at which the new spectrum is to be inserted Se
4. tick box See section 4 6 11 1 page 154 for more information about the modelling procedure and normalization Get Click on Get to load the currently active spectrum Get as a reference component spectrum and start the modelling procedure See section 4 6 11 4 page 157 for more information about how to use the modelling procedure Get All Click on Get All to load in multiple model spectra Get All saved from a previous modelling procedure and start a new modelling procedure using them This function is useful to apply a modelling procedure to a spectral array using identical reference component spectra used for previous spectral array modelling See section 4 6 11 4 1 page 160 for more information about using the Get All button to start a modelling procedure with previously saved reference component spectra Page 156 Explore the future Automotive Test Systems Process amp Environmental Medical Semiconductor Scientific HORIBA HORIBA m Scientific Create Click on Create to start the automatic Create Eo clustering procedure and subsequent modelling See 4 6 11 5 page 161 for more information about how to use the automatic Create clustering procedure 4 6 11 4 How to Model a Multidimensional Spectral Array The DCLS modelling procedure can be used with any multidimensional spectral array including time profiles Z depth profiles temperature profiles XY maps XZ and
5. If normalization is turned off after normalized modelling has been performed the scores are shown as their true values Unnormalized Modelling When the modelling procedure is unnormalized i e the Normalize box is unticked prior to performing the modelling procedure the reference component spectra loadings are used with their raw intensities during the modelling procedure Unnormalized modelling must be used if quantitative analysis is required since the actual intensity of each reference component spectrum relates directly to the its concentration Page 154 Explore the future Automotive Test Systems Process amp Environmental Medical Semiconductor Scientific HORIBA HORIBA Scientific The scores are shown as their true values If normalization is turned on after unnormalized modelling has been performed the scores are displayed as normalized values so that the combination of all scores adds to 100 4 6 11 2 The Create Clustering Procedure The Create clustering procedure automatically identifies a number of reference component spectra loadings using a factor analysis algorithm This algorithm searches the entire multidimensional spectral array and locates a number of clusters of similar spectra where the average of each cluster is as different from the other cluster averages as possible The number of clusters is specified in the Factors drop down box Once the average spectra hav
6. XZ and YZ slices and XYZ datacubes using a set of reference component spectra This procedure is used to identify the distribution of the reference component spectra within the spectral array to create a profile image based on the component distribution The component spectra can be either manually selected from previously saved spectra or from within the spectral array or automatically created by LabSpec 5 using a clustering algorithm 4 6 11 1 The DCLS Modelling Procedure At each position within the multidimensional spectral array the DCLS modelling procedure finds a linear combination of the reference component spectra which best fits the raw data The resulting profile image is created by showing the contribution score of each component loading as a profile image For example if there are three loadings A B and C with scores x y and z the sum S of the linear combination is represented by S x A y B 4 z C A B C are the loadings e g reference spectra of pure components X y Z are the scores e g the amount of each loading necessary so that S matches the raw data Normalized Modelling When the modelling procedure is normalized i e the Normalize box is ticked prior to performing the modelling procedure the reference component spectra loadings are normalized before the modelling procedure takes place The scores are normalized so that the combination of all scores adds to 100
7. Model Page 168 Explore the future Automotive Test Systems Process amp Environmental Medical Semiconductor Scientific HORIBA HORIBA _ Scientific 5 6 Intensity Shift 2 Activates the Intensity Shift cursor allowing the upper display limit of the intensity axis Y axis for spectra and profiles Z axis for images to be manually scaled When this icon is active the mouse cursor N T changes to the Intensity Shift cursor Left click and drag the Intensity Shift cursor on the spectrum profile or image window to adjust the 10 000 scaling 5 000 Intensity cnt o Dragging upwards as in the example shown right will make the upper display limit of the intensity axis be reduced This is equivalent to zooming in on the 500 l 1 000 1500 intensity axis for images the affect will be Karan Shift em to brighten the image o Dragging downwards will make the upper display limit of the intensity axis be increased This is equivalent to zooming 5 0004 out on the intensity axis for images the 1 effect will be to darken the image 40007 a 30004 2 0004 1 000 T 500 1 000 1500 Raman Shift cm Intensity cnt Note that this function is purely a display function it does not affect the actual data of the spectrum Available for Spectrum Video Splm Point Map Score Model 5 7 Scale Shift P Activates the Scale Shift cursor allowing the display scales of the
8. click and drag the Add Constant cursor on the 20 000 spectrum window to shift the spectrum up or down iso o Dragging upwards as in the example shown right will shift the spectrum upwards to a higher intensity position 5 000 equivalent to adding a constant to the spectrum 500 i 1 000 o Dragging downwards will shift the Raman Shift em spectrum downwards to a lower intensity position equivalent to subtracting a constant from the spectrum 10 000 Intensity cnt T 1500 20 000 15 000 10 000 Intensity cnt 5 000 T T T T 500 1 000 1500 Raman Shift cm This function is related to the Const function available in the Math dialog window see section 4 6 6 page 130 Available for Spectrum Point Model 5 9 Multiply by Constant ite Activates the Multiply by Constant cursor allowing all pixels in the active spectrum to be multiplied or divided by a constant value to be added to or subtracted from all pixels in the active spectrum i e to increase or decrease the entire spectrum intensity When this icon is active the mouse cursor N 3083 changes to the Multiply by Constant cursor Page 171 Explore the future Automotive Test Systems Process amp Environmental Medical Semiconductor Scientific HORIBA HORIBA an Scientific Left click and drag the Multiply by Constant cursor 20 000 on the spectrum window to shift the spectrum up or dow
9. shortcut lt CTRL gt S When the spectral array file is next opened the Score and Model windows will also open 4 6 11 4 1 Using a Previously Saved Set of Reference Component Spectra The How to Model a Multidimensional Spectral Array procedure outlined above is based on each reference component spectrum being selected and modelled individually on a one by one basis It is also possible to recall a previously used set of reference component spectra and load all spectra simultaneously This is useful if you wish to model a number of spectral arrays in exactly the same way using exactly the same reference component spectra Saving the Reference Component Spectra To save a set of reference component spectra associated with a multidimensional spectral array model activate the Model window and save the reference component spectra as a single file in ngs or tsf formats using File gt Save All Opening and Loading the Reference Component Spectra The procedure described here assumes that a spectral array file is currently open with the Splm Point and Map windows visible Open the single file in ngs or tsf format containing the reference component spectra using File gt Open the Open icon Cia or the keyboard short cut lt CTRL gt O The spectra will be opened within a Model window Open the Model dialog window by clicking on the IAA fA Modelling icon Activate the Model win
10. 83 Explore the future Automotive Test Systems Process amp Environmental Medical Semiconductor Scientific HORIBA HORIBA ee Scientific Note that only information visible within the window will be active for copy and paste functions Thus it is important that axes titles scales and the spectrum profile image display are kept within the boundary of the window Available for Spectrum Video Splm Point Map Score Model 5 17 Points Mapping Activates the Points Mapping cursor allowing positions for an automated multipoint acquisition to be specified on the active video image When this icon is active and the mouse is hovered over the video image the cursor will change from to the Add Points cursor Left click with the Add Points cursor to add a multipoint position to the video image Page 184 Explore the future Automotive Test Systems Process amp Environmental Medical Semiconductor Scientific HORIBA HORIBA ae Scientific The points which are added are sequentially numbered starting at 1 They will be analysed in the order they are added When the Add Points cursor is active and the mouse is hovered over an existing multipoint position the cursor changes to the Move Delete Points cursor Left click with the Move Delete Points cursor to delete the existing multipoint position The other points displayed on the video will be renumbered accordingly _ ODS ar 17 M Fi
11. HORIBA HORIBA os Scientific If the Multi function is active see section 3 4 2 page 23 then all open spectra will be added to the spectral profile when it is created In this case the active spectrum will be added first followed by all other open spectra in the order they appear within the right hand Data bar See section 4 6 10 1 page 151 for further information Add Click on Add to add the active spectrum to the Add end of the spectral profile See section 4 6 10 2 page 152 for further information Insert Click on Insert to add the active spectrum to the reat spectral profile at the position shown by the cursor in the Map window See section 4 6 10 3 page 152 for further information Delete Click on Delete to delete a spectrum from the Delete spectral profile The spectrum at the position shown by the cursor in the Map window will be deleted See section 4 6 10 4 page 153 for further information XYZ XYZ Click on XYZ to rotate an XYZ multidimensional spectral array so that the data is formatted in the default Z Y X format e g a Z stack of YX maps See section 4 5 5 3 page 99 for information about controlling the acquisition order for multidimensional spectral arrays Page 150 Explore the future Automotive Test Systems Process amp Environmental Medical Semiconductor Scientific HORIBA HORIBA Scientific 4 6 10 1 Creating a N
12. HORIBA a Scientific Load Click on Load to load a cursor parameters file in lea ngp format so that a previously saved configuration of the Map Analysis dialog window can be recalled and applied Save Click on Save to save a cursor parameters file in BEE ngp format so that the current configuration of the Map Analysis dialog window can be saved and recalled at any time Convert Click on Convert to convert an existing image file Conver into the LabSpec 5 multidimensional spectral array format including Splm Point and Map windows 4 6 10 Create Spectral Profile Db Opens the Spectral Profile dialog window The Spectral Profile dialog window allows a 1D multidimensional spectral array to be created from individual spectra and for spectra to be added to deleted from and inserted into an existing 1D multidimensional spectral array This function is useful to create profiles from spectra where there is sequential change in some experimental parameter e g reaction temperature or concentration Name Type the desired name for a new profile in the Spectral profile Name text box before clicking on New to create the profile New Click on New to create a new spectral profile ia using the active spectrum as the first spectrum in the profile Page 149 Explore the future Automotive Test Systems Process amp Environmental Medical Semiconductor Scientific
13. Score window Once the modelling procedure has been iii Dp _ mee a gai A A model_1 13 3 completed the Point window displays the model_2 29 4 del_3 27 0 following spectra model 4 21 3 4 Error 7 9 o Raw data 3 o Sum i i o Components In addition in the top right hand corner of the window a summary of the modelling result is displayed This shows the contribution of each 1000 nm reference component spectrum and the error The contribution is displayed as actual score if Normalize model is unticked or as relative percent if Normalize model is ticked Page 159 Explore the future Automotive Test Systems Process amp Environmental Medical Semiconductor Scientific HORIBA HORIBA ws Scientific Sum spectrum will only be displayed if Model sum is ticked and its color will be according to the color drop down box Components will be sequentially colored using a default palette The first three components are displayed as red green and blue The display color of the error text will be according to the Error text color drop down box The modelling results can be saved with the spectral array data by activating the Splm window and saving the file in LabSpec 5 ngc format The save dialog window is accessed using File gt Save As clicking on the Save icon a or using the keyboard
14. Spec 5 Spike Filter section 3 5 4 7 page 37 Despike section 4 6 4 1 2 page 125 Denoise section 3 5 4 15 page 46 and section 4 6 4 1 1 page 124 Available for Spectrum Point Model 5 4 Correct Shape EN Activates a pencil drawing tool allowing manual modification of spectral features When this icon is active the mouse cursor N gt w changes to the Correct Shape cursor Left click and drag the Correct Shape cursor to draw the new spectrum shape as desired Available for Spectrum Point Model Page 167 Explore the future Automotive Test Systems Process amp Environmental Medical Semiconductor Scientific HORIBA HORIBA ae Scientific 5 5 Zoom Activates the Zoom cursor allowing a small area of a spectrum profile image to be studied in detail This icon can be activated with the lt CTRL gt M keyboard shortcut When this icon is active the mouse cursor N G changes to the Zoom cursor Left click and drag the Zoom cursor to select the area which will be displayed in the window Raman Shift cm T T T i T 500 600 700 Raman Shift cm To rescale the window do one of the following o Click on the Scale Normalization icon in ere amp the Icon bar see 4 4 1 page 91 o Use the lt CTRL gt N keyboard short cut for Scale Normalization o Right click and select Rescale Available for Spectrum Video Splm Point Map Score
15. The spectrum display window for individual spectra acquired using the real time display RTD acquisition ie Ue and spectrum acquisition i lt modes Video The video display window for optical images acquired with the integrated microscope camera s Spim The overlay of all spectra within a multidimensional spectral array Point The spectrum at the current cursor position within a multidimensional spectral array Map The cursor intensity profile image display created from a multidimensional spectral array Score The score profile image created by DCLS modelling of a multidimensional spectral array Model The reference component spectra used for DCLS modelling of a multidimensional spectral array 5 1 Pointer Activates the cursor pointer so that individual X axis and or Y axis values can be read from the window The cursor values will be displayed in the Status bar see section 7 5 page 201 The cursor can be configured using the Cursor dialog window by right clicking and selecting Cursor see section 8 11 page 218 A number of cursor modes are available Page 164 Explore the future Automotive Test Systems Process amp Environmental Medical Semiconductor Scientific HORIBA HORIBA Scientific Spectrum Spim Point Model windows o Line single vertical line cursor displaying the X axis position S of the cursor and the intensity 1 of the spectrum at the cursor position
16. X and Y axes to be shifted to higher or lower values When this icon is active the mouse cursor N L i changes to the Scale Shift cursor Page 169 Explore the future Automotive Test Systems Process amp Environmental Medical Semiconductor Scientific HORIBA HORIBA ae Scientific Left click and drag the Scale Shift cursor on the spectrum profile or image window to shift scales of 10 000 the X and Y axes Intensity cnt wn i S T T T r T 500 1 000 1500 Raman Shift cm 10 000 Intensity cnt wn 2 s T T T 0 500 1000 Raman Shift cm To reset the X and Y axes scales do one of the following o Click on the Scale Normalization icon in era amp the Icon bar see section 4 4 1 page 91 o Use the lt CTRL gt N keyboard short cut for Scale Normalization o Right click and select Rescale Available for Spectrum Video Splm Point Map Score Model 5 8 Add Constant Activates the Add Constant cursor allowing a constant intensity value to be added to or subtracted from all pixels in the active spectrum i e to shift the entire spectrum up or down in the intensity Y axis When this icon is active the mouse cursor N ie changes to the Add Constant cursor Page 170 Explore the future Automotive Test Systems Process amp Environmental Medical Semiconductor Scientific HORIBA HORIBA a Scientific Left
17. YZ slices and XYZ datacubes The procedure described here assumes that a spectral array file is currently open with the Spim Point and Map windows visible Open the Model dialog window by clicking on the AA fA Modelling icon Select whether loading scores can take both positive and negative values or just positive values Properties using the Allow negative scores tick box If peis Meee Allow negative scores is ticked the scores for the M S loadings can take both positive and negative ees values If it is unticked the scores for the loadings I Show error map can only take positive values See section FZ Model sum gt 4 6 11 1 page 154 for an explanation of the Enortext E modelling procedure and what the scores and M Normalize model loadings are In general Allow negative scores should be unticked and it is recommended that it is ticked for specialized analysis only Select the normalization mode of the modelling procedure by either ticking or unticking the Properties Normalize model box For general analysis of the Name modei spectral array and characterisation of component Factors fa distribution normalized modelling will be suitable ea E If quantitative analysis of component distribution ot ee within the spectral array is required unnormalized dieen TE modelling must be used See section 4 6 11 1 Error text X page 154 for more information ab
18. alize model Properties Name model_1 Factors 4 X Th 10 I Allow negative scores I Show error map V Model sum Error text V Normalize model Create Automotive Test Systems Process amp Environmental Medical Semiconductor Scientific LabSpec 5 user manual Page 162 HORIBA HORIBA ee Scientific 4 7 Stop Active Function Icon 4 7 1 Stop Active Function D Stop the current software function including data acquisition and data processing Page 163 Explore the future Automotive Test Systems Process amp Environmental Medical Semiconductor Scientific HORIBA HORIBA al Scientific 5 Graphical Manipulation Toolbar The Graphical Manipulation toolbar located on the left hand side of the LabSpec 5 graphical user interface GUI provides access to a range of spectrum manipulation and analysis functions This is an active toolbar and its appearance and content will update according to the currently selected window For example the options appearing in this toolbar when a spectrum is active will differ from those appearing when a video image is active Note that when clicked an icon will be locked gt gt N down Only one icon can be active and locked down at a time At the end of each icon s description a list of windows where the icon is available in the Graphical Manipulation toolbar is given The possible windows are as follows Spectrum
19. at low intensity spectra will be excluded from the Create clustering procedure spectra with a maximum signal level less than the threshold value in percent of the highest signal intensity within the entire spectra array will be ignored For general analysis 10 is suitable but the value should be adjusted as required Select from the Factors drop down box the number of component spectra which are to be created using the clustering algorithm Note that the number of component spectra should be chemically meaningful If in doubt start with a small number and increase it if the modelling results do not look correct Click on Create to start the Create clustering procedure and subsequently launch the modelling procedure using the created component spectra The Score and Model windows showing the results will be created once the modelling procedure has been completed The modelling results can be saved with the spectral array data by activating the Splm window and saving the file in LabSpec 5 ngc format The save dialog window is accessed using File gt Save As clicking on the Save icon a or using the keyboard shortcut lt CTRL gt S When the spectral array file is next opened the Score and Model windows will also open Properties Name model_1 Factors 4 X Th 10 I Allow negative scores I Show error map V Model sum Enortext E V Norm
20. dow and click on Get All Get All in the Model dialog window pee The modelling procedure will be launched using all of the reference component spectra The Score and Model windows will be created once the modelling procedure is completed Page 160 Explore the future Automotive Test Systems Process amp Environmental Medical Semiconductor Scientific HORIBA HORIBA _ Scientific 4 6 11 5 How to Automatically Create a Model for a Multidimensional Spectral Array The procedure described here assumes that a spectral array file is currently open with the Spim Point and Map windows visible Open the Model dialog window by clicking on the AA fA Modelling icon Select whether loading scores can take both positive and negative values or just positive values Properties using the Allow negative scores tick box If lal Allow negative scores is ticked the scores for the TEESE IM E loadings can take both positive and negative EES values If it is unticked the scores for the loadings I Show error map can only take positive values See section Model sum M 4 6 11 1 page 154 for an explanation of the Enortext modelling procedure and what the scores and I TNomekze model loadings are In general Allow negative scores should be unticked and it is recommended that it is only ticked for specialized analysis only Select the normalization mode of the
21. e been identified in this way they are used as loadings in the DCLS modelling procedure as described above section 4 6 11 1 page 154 4 6 11 3 The Model Dialog Window The Model dialog window allows reference component spectra to be manually added to the modelling procedure in addition to automatic generation of component spectra with subsequent modelling using the Create clustering procedure The display mode of the modelling result can also be configured through the dialog window Properties Name fmodel_1 Factors 4 J Thiz fo F Allow negative scores Show error map V Model sum Error text Ha V Normalize model Name Type in a name in the Name text box for each reference component spectrum to be used in the modelling procedure prior to clicking on Get to start the modelling See section 4 6 11 4 page 157 for more information about how to use the modelling procedure Factors Select the number of factors to be automatically created using the Create clustering procedure See section 4 6 11 5 page 161 for more information about how to use the automatic Create clustering procedure Thr Type in a value in percent in the Thr text box to set the intensity threshold for the automatic Create clustering procedure The threshold ensures that low intensity spectra will be excluded from the Create clustering procedure spectra with a maximum signal level
22. ew Spectral Profile Using File gt Open menu or the Open icon 8 5 open the individual spectra which are to be used to create the spectral profile Open the Spectral Profile dialog window by clicking on the Create Spectral Profile icon Type into the Name text box a name for the new Spectral profile profile Name ffNewProfile Select the first spectrum to be added to position 1 New in the new profile and click New to create the profile The new profile will be created in two ways depending whether the Multi function is active see section 3 4 2 page 23 o Multi active the active spectrum will be added to position 1 in the profile followed by all other open spectra in the order they appear within the right hand Data bar o Multi inactive the active spectrum will be added to position 1 in the profile No other spectra will be added to the profile Additional spectra can be added to the profile using the Add button see section 4 6 10 2 page 152 or Insert button see section 4 6 10 3 page 152 When the profile is created the standard Splm Point and Map windows associated with a multidimensional spectral array will be displayed The profile can now be analysed in the normal way using cursors and modelling Page 151 Explore the future Automotive Test Systems Process amp Environmental Medical Semiconductor Scientific HORIBA HORIBA os
23. fth Page 185 Explore the future Automotive Test Systems Process amp Environmental Medical Semiconductor Scientific HORIBA
24. ght FWHM o Dragging away from the peak as in the example shown right will increase the full width at half maximum height FWHM o Dragging towards the peak will decrease Jo the full width at half maximum height Raman Shift cm FWHM o e a 500 520 540 Raman Shift cm The Adjust Position and Adjust Width cursors should be used in conjunction with the Peak Searching and Fitting module see section 4 6 7 page 134 Available for Spectrum Spim Point Model 5 12 Remove Peak X Activates the Remove Peak cursor allowing a peak label to be removed from a spectrum When this icon is active and mouse is hovered jy m over a peak the mouse cursor changes to the Remove Peak cursor Page 176 Explore the future Automotive Test Systems Process amp Environmental Medical Semiconductor Scientific HORIBA HORIBA ae Scientific Left click on a peak label to remove it from the spectrum 500 1 000 1500 Raman Shift em 920 365 T T T T 500 1 000 Raman Shift cn T 1500 The Remove Peak cursor should be used in conjunction with the Peak Searching and Fitting module see section 4 6 7 page 134 Available for Spectrum Splm Point Model 5 13 Integral i Activates the Integral cursors and opens the Integral dialog window allowing the integrated area sum of a region of the spectrum to be calculated Note that this func
25. lect the spectrum which is to be inserted and veers click on Insert to insert it at the position indicated Ene by the cursor In a default spectral profile the other spectra originally at and above this position will be shifted Page 152 Explore the future Automotive Test Systems Process amp Environmental Medical Semiconductor Scientific HORIBA HORIBA _ Scientific upwards in the profile For example if spectra A B and C are currently at positions 1 2 and 3 ina profile of form 1A 2B 3C when spectrum D is inserted at position 2 the new profile will take the form 1A 2D 3B 4C In a spectral profile where the scale has been manually modified using the Data Range dialog window see section 3 3 2 page 20 the first and last positions of the profile will remain fixed The positions of spectra within the profile will be adjusted when a spectrum is inserted For example if spectra A B and C are currently at positions 1 2 and 3 in a manually scaled profile of form 1A 2B 3C when spectrum D is inserted at position 2 the new profile will take the form 1A 1 66D 2 33B 3C If necessary the profile can be rescaled using the Data Range dialog window after the spectrum has been inserted 4 6 10 4 Deleting Spectra from a Spectral Profile In the profile Map window activate the cursor and ERa select the position from which a spectrum is to be deleted uw a S 3 u te g E
26. less than the threshold value in percent of the highest signal intensity within the entire spectra array will be ignored Page 155 Explore the future Automotive Test Systems Process amp Environmental Medical Semiconductor Scientific HORIBA HORIBA al Scientific Allow Negative Scores If Allow negative scores is ticked the scores for the loadings can take both positive and negative values If it is unticked the scores for the loadings can only take positive values See section 4 6 11 1 page 154 for an explanation of the modelling procedure and what the scores and loadings are Show Error Map If Show error map is ticked an additional score profile image will be displayed based on the error between the sum of the linear combination and the raw data Regions of high error bright intensity indicate a bad fit and could be caused by a missing reference component spectrum To remove the error profile image untick the Show error map box Model Sum If Model sum is ticked the sum of the linear combination will be displayed in the Point window in addition to the score loading information Select the colour for the sum spectrum from the drop down box Error Text Select the text colour from the drop down box for the error value displayed in the Point window Normalize Model The normalization mode for the modelling procedure can be controlled using the Normalize model
27. modelling amp procedure by either ticking or unticking the Properties Get Normalize model box For general analysis of the lat a spectral array and characterisation of component A al a distribution normalized modelling will be suitable i na If quantitative analysis of component distribution mo ei within the spectral array is required unnormalized Pitas modelling must be used See section 4 6 11 1 Error text page 154 for more information about the normalization modes Type in a generic name for the component spectra in the Name text box The created component Properties Get spectra will be labelled sequentially in the form name_1 name_2 etc This step is not essential Factors 4 E E but good naming of reference component spectra Wes i 7 a A elp can assist analysis and understanding of the F Alowregaive scams H I Show error map results obtained at the end of the modelling z v Modelsum E procedure If a name is not needed then ensure Enote the Name text box is blank delete any entry Normalize model which is already present Page 161 Explore the future Automotive Test Systems Process amp Environmental Medical Semiconductor Scientific HORIBA Explore the future HORIBA Scientific Type in a value in percent in the Thr text box to set the intensity threshold for the Create clustering procedure The threshold ensures th
28. n 15 000 ity cnt 10 000 o Dragging upwards as in the example shown right will increase the spectrum 5 000 intensity equivalent to multiplying the spectrum by a constant 500 i 1 000 1500 o Dragging downwards will decrease the Seen len spectrum intensity equivalent to dividing the spectrum by a constant Intens 20 000 15 0004 10 0004 Intensity cnt 5 0004 500 1 000 1500 Raman Shift cm This function is related to the Const function available in the Math dialog window see section 4 6 6 page 130 Available for Spectrum Point Model 5 10 Add Peak X Activates the Add Peak cursor allowing manual labelling of a peak position on the spectrum When this icon is active the mouse cursor N ay changes to the Add Peak cursor Page 172 Explore the future Automotive Test Systems Process amp Environmental Medical Semiconductor Scientific HORIBA HORIBA Scientific Left click the Add Peak cursor at the desired spectrum position to label a peak The peak label will be positioned in the X axis according to the click position the Y intensity axis position will be automatically set according to the spectrum intensity at that position Note that the actual display of the peak label will f of oF od depend on the settings in the Peak Options dialog window See section 4 6 7 4 page 143 me Raman Shift Fa ae
29. n each cursor in the pair If one or both of the cursors are not visible on the spectrum image do one of the following o Click on the Center Cursors icon in the ae et Icon bar see 4 4 3 page 92 o Right click and select Center cursor The map analysis cursors should be operated in Double mode right click and select Red cursor Green cursor or Blue cursor and select Double from the Style drop down box The Map Analysis cursors should be used in conjunction with the Map Analysis dialog window see section 4 6 9 page 147 Available for Splm Point 5 3 Remove Spike oO Activates a spike removal tool allowing random spikes also known as cosmic rays to be manually removed from a spectrum When this icon is active the mouse cursor N y L changes to the Remove Spike cursor Page 166 Explore the future Automotive Test Systems Process amp Environmental Medical Semiconductor Scientific HORIBA HORIBA _ Scientific Left click the Remove Spike cursor on a spike in T the spectrum to remove it 500 1 000 1500 Raman Shift cn T T T T T T 500 1000 1500 Raman Shift cm Note that if used on a true Raman peak the Remove Spike tool will modify the peak shape and intensity it should only be used on spikes and should be used with care Please see the following sections for other spike removal tools available in Lab
30. nd the modelling procedure will be started Two new windows will be created in addition to the standard Splm Point and Map windows o Scores window displays the profile image based on the loading scores calculated by the modelling procedure o Model window displays the reference component spectra used by the modelling procedure Note that the cursors displayed in the Map and Score windows are linked and both will move when one is manipulated with the mouse WL Page 158 Explore the future Automotive Test Systems Process amp Environmental Medical Semiconductor Scientific HORIBA HORIBA m Scientific Repeat the process to add more reference component spectra to the modelling procedure by selecting one at a time additional spectra and clicking on Get for each spectrum The Score and Model window will update each time Continue until all necessary reference component spectra have been included in the model for the spectral array The error profile map can be used to check that there are no regions of high error which often Properties indicates that a further reference component Seno a spectrum is necessary The error profile map can Factors 4 E be activated by ticking the Show error map box To I Allow negative scores V Modelsum Enortext E V Normalize model It will be displayed as another colored image in the
31. ndow The Integral dialog window displays the integrated area sum of the spectrum between the Integral cursors and allows the information display to be configured and the cursor positions to be manually adjusted Integral 7547 hns a54 Base 381612 Full 867276 Format amp Digits Type Area X r Style Line X Fil EA From Displays the spectral position of the lower cursor The value can be manually adjusted by typing in the desired value and clicking Apply Page 178 Explore the future Automotive Test Systems Process amp Environmental Medical Semiconductor Scientific HORIBA HORIBA a Scientific To Displays the spectral position of the upper cursor The value can be manually adjusted by typing in the desired value and clicking Apply Top Displays the peak Sum or Area above the baseline in the shaded region Note that Top Full Base Base Displays the peak Sum or Area below the baseline in the shaded region Note that Base Full Top Full Displays the full peak Sum or Area in the shaded region Note that Full Top Base Format Click on the Format drop down box to select the maximum number of significant digits displayed in the Top Base and Full boxes Type Click on the Type drop down box to select whether peak Area or Sum should be calculated and displayed in the Top Base and Full boxes Line Click on the Line dr
32. o Cross cross hair cursor displaying the X axis position S and Y axis position I of the cursor o Level cross hair cursor which tracks the intensity of the spectrum displaying the X axis position S and Y axis position l of the cursor In this case the Y axis position is equivalent to the spectrum intensity at the cursor position o Double two vertical cursors displaying the X axis position S of each cursor and the width between the two cursors W o Peak three linked vertical cursors the central one locking to the maximum intensity pixel in a peak and the outer two locking to the pixels closest to the full width at half maximum height FWHM of the peak The Peak cursor displays the X axis position S intensity I and approximate full width at half maximum height W of the peak at the cursor position Video Map Score windows o Cross cross hair cursor displaying the X axis position X and Y axis position Y of the cursor and pixel intensity 1 at the cursor position For the Map and Score windows the spectrum associated with the cursor position will be displayed in the Point window o Rect rectangular cursor resizeable by left clicking and dragging the drag points displaying the X axis position X and Y axis position Y of the bottom right hand corner of the rectangular cursor For the Map and Score windows the average spectrum from within the rectangle is displayed in the Point window Lef
33. op down box to set the color width and line style used to outline the shaded area between the Integral cursors Fill Click on the Fill drop down box to set the color and style used to fill the shaded area between the Integral cursors Apply Click on Apply to update the cursor display on the spectrum according to values manually set in the From and To boxes Copy Click on Copy to copy the From To Top Base and Full values to the clipboard so that they can be pasted into other programs Note that Integral dialog window will be automatically closed when a different Graphical Manipulation icon is activated If Close is used to close the Integral dialog window the Integral icon will still be active To restore the Integral dialog window activate a different icon and then re activate the Integral icon the Integral cursors and dialog window will be displayed again Page 179 Explore the future Automotive Test Systems Process amp Environmental Medical Semiconductor Scientific HORIBA HORIBA ee Scientific 5 14 Add Baseline Points PS Activates the Add Baseline Points icon allowing baseline points to be manually added to a spectrum prior to baseline correcting a spectrum The type of baseline displayed when using the Add Baseline Points icon will depend on settings in the Baseline dialog window see section 4 6 2 page 115 When this icon is active the cursor will change ls gt from
34. out the normalization modes Select a spectrum which is to be used as a reference component spectrum in the modelling procedure The spectrum can be selected in two ways o Locate a pure reference component spectrum from within the spectral array using the cursor in the Map window Page 157 Explore the future Automotive Test Systems Process amp Environmental Medical Semiconductor Scientific HORIBA HORIBA es Scientific Click on the Point window to select the spectrum o Open an existing spectrum file saved in any standard LabSpec spectrum format using File gt Open or the Open icon or the keyboard short cut lt CTRL gt O Click on the spectrum window and select the spectrum If multiple spectra are opened ensure the correct spectrum is selected In the Model dialog window type in a name for the reference component spectrum in the Name text Properties a box This step is not essential but good naming of mae reference component spectra can assist analysis Faciosaj 4 a EE and understanding of the results obtained at the mi A end of the modelling procedure If a name is not F Alon negative snes H I Show error map needed then ensure the Name text box is blank F Model sun gt delete any entry which is already present Enoret V Normalize model cose Click on Get in the Model dialog window The selected spectrum will be loaded a
35. t click to position the cursor at any point on the spectrum profile image or alternatively left click and drag to move the cursor to the desired position If one or both of the cursors are not visible on the spectrum image do one of the following o Click on the Center Cursors icon in the ae aac Icon bar see 4 4 3 page 92 o Right click and select Center cursor Available for Spectrum Video Model 5 2 Map Analysis Cursors SpilmRed SpimGreen SpimBlue k hk hk Activates the map analysis cursors allowing profiles images corresponding to the average intensity between the cursor pairs to be generated for multidimensional spectral arrays Three map analysis cursor pairs are available Red SplmRed Green SplmGreen and Blue SplmBlue Page 165 Explore the future Automotive Test Systems Process amp Environmental Medical Semiconductor Scientific HORIBA HORIBA an Scientific Left click to position the closest cursor of the pair at the click position or alternatively left click and drag to move the closest cursor to the desired position Note that the map analysis cursors can be set to have a fixed width To do this right click and 3 66 Hy select Red cursor Green cursor or Blue cursor and tick Fixed width When the cursors have a fixed width left click and drag to scroll the two cursors along the spectrum In this case it is not possible to individually positio
36. the mouse cursor to the Add Baseline Points cursor Left click the Add Baseline Points cursor on the spectrum to add a baseline point to the displayed baseline curve If there is no baseline curve on the spectrum the first left mouse click in this mode will create the baseline 500 1 000 1500 Raman Shift em 500 1 000 1 500 Raman Shift cra When the Add Baseline Points cursor is active and ie fry the mouse is hovered over an existing baseline point the cursor changes to a Move Baseline Points cursor Page 180 Explore the future Automotive Test Systems Process amp Environmental Medical Semiconductor Scientific HORIBA HORIBA Scientific Left click the Move Baseline Points cursor to drag the baseline point to a new position o 1 000 1 500 Raman Shift em l 500 1 000 1 500 Raman Shift cr The Add Baseline Points cursor should be used in conjunction with the Baseline Correction module see section 4 6 2 page 115 Available for Spectrum Splm Point Model 5 15 Remove Baseline Points A Activates the Remove Baseline Points cursor allowing baseline points to be manually removed from a spectrum prior to baseline correcting a spectrum When this icon is active and the mouse is hovered N gt m over an existing baseline point the cursor changes to the Remove Baseline Points cursor Page 181 Explore the future Automotive Test Systems Process amp En
37. tion does not apply any deconvolution of overlapping peaks if the area of peaks which are overlapping needs to be calculated it is necessary to perform a full peak fitting routine See section 4 6 7 page 134 for full information about the Peak Searching and Fitting module Similarly the baseline function of the Integral cursors uses a basic linear baseline if more complex baselines are present then it is necessary to perform a full baseline subtraction routine See section 4 6 2 page 115 for full information about the Baseline Correction module Page 177 Explore the future Automotive Test Systems Process amp Environmental Medical Semiconductor Scientific HORIBA HORIBA E Scientific When this icon is active the Integral cursors are displayed on the spectrum In addition to the cursors the display includes o The shaded part of the spectrum from where the area sum value is calculated o The baseline used for the area sum calculation Intensity cnt 500 1000 1500 Raman Shift em Left click and drag on either cursor to adjust its position The values in the Integral dialog window will be automatically updated If one or both of the cursors are not visible on the spectrum do one of the following o Click on the Center Cursors icon in the Re ae Icon bar see 4 4 3 page 92 o Right click and select Center cursor Available for Spectrum Point Model 5 13 1 Integral Dialog Wi
38. ually adjusted to approximately fit the raw data The peak shape display can be set in the Peak Options dialog window see section 4 6 7 4 page 143 When this icon is active the mouse cursor N gt D fm 9 changes to the Adjust Peak cursor Depending on the position of the mouse on the spectrum this cursor has three possible forms o When the mouse hovers over a peak dry label the Adjust Position cursor is displayed Page 174 Explore the future Automotive Test Systems Process amp Environmental Medical Semiconductor Scientific HORIBA HORIBA _ Scientific o When the mouse hovers to the left of a p peak label the Adjust Width cursor is displayed o When the mouse hovers to the right of a So peak label the Adjust Width cursor is displayed Adjustment to a peak shape and position is only possible for the active peak label shape In a spectrum with multiple peak labels shapes use the Add Peak Move Peak cursor to activate the peak which is to be adjusted see section 5 10 page 172 Left click and drag on the peak label to adjust its fm position and amplitude 2 T T T T 500 520 540 Raman Shift cm Page 175 Explore the future Automotive Test Systems Process amp Environmental Medical Semiconductor Scientific HORIBA HORIBA ee Scientific Left click and drag on either side of the peak to adjust the peak full width at half maximum hei
39. vironmental Medical Semiconductor Scientific HORIBA HORIBA es Scientific Left click on a baseline point to remove it from the spectrum 500 1 000 1 500 Raman Shift em l 500 1 000 1500 Raman Shift cra The Remove Baseline Points cursor should be used in conjunction with the Baseline Correction module see section 4 6 2 page 115 Available for Spectrum Spim Point Model 5 16 Axes Activates the Axes cursor allowing the position and size of the spectrum profile image display in the active window to be adjusted When this icon is active and the mouse is hovered N gt ite over the spectrum profile image display the cursor changes to the Shift Axes cursor Page 182 Explore the future Automotive Test Systems Process amp Environmental Medical Semiconductor Scientific HORIBA HORIBA a Scientific Left click and drag the Shift Axes cursor to adjust Spectrum spectrum the position of the spectrum profile image display in the window Intensity cnt Raman Shift crn Spectrum spectrum g a Raman Shift crv When this icon is active and the mouse is hovered over one of the axis drag points the cursor changes to the Adjust Axes cursor Left click and drag the Adjust Axes cursor to adjust D00 the spectrum profile image display size in the window Raman Shift cm Spectrum spectrum Intensity cnt Raman Shift crn Page 1
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