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Iolite 3 User`s Manual

1. import Baselines Reference Materials Samples lalite v3 Five Seconds Basalt Images Results General Settings Stats for baselines Mean no outlier reject Crunch Data Stats for normal selections Mean with 3 S D outlier reject M Current Data Reduction Scheme Trace Elements 15 DRS Specific Settings DRS Report 12 59 15 PP The DAS Trac Elementa 157 requires a Vei La35 LPS 61576127 in the folder splines 55 proceed further Index Channel 243 Referance Material G_NIST 12 Default intensity Units CPS Standardisation method Internal Elemental Standard 1 Output Units ppm BeamSeconds method Rate of Change Threshold to use when masking low signals 5000 Seconds to trim before after low signals 1 BeamsSeconds Sensitivity 4 TableFormat Normal DefaultindexCantentin sample 1 Figure 2 3 DRS Tab of the Main lolite Window Default Intensity Units This can be set to either volts V or counts per second cps Relevant waves will be given in these units Standardisation Method This is used to specify whether a fully quantitative approach e g Longerich et al 1996 including an internal standard element or semi quantitative approach which compares the sensitivity of the reference material to the sample to calculate the concentration of each element is used Output Units The units used for calculated concentrations Beam Seconds Method T
2. BHVO2G 13 19 49 5 0 sec C BIR 13 20 17 5 0 sec M NIST612 13 20 57 5 1 sec BCR2G 13 22 09 5 0 sec BHVO2G 13 22 39 5 1 sec BIR 13 23 07 5 0 sec V NIST612 13 23 47 5 0 sec BCR2G 13 24 29 5 0 sec BHVO2G 13 24 58 5 1 sec BIR 13 25 26 5 0 sec NIST612 13 26 06 5 0 sec BCR2G 13 27 17 5 0 sec BHVO2G 13 27 47 5 0 sec BIR_G 13 28 15 5 0 sec V NIST612 13 28 55 5 0 sec BCR2G 13 29 36 5 0 sec BHVO2G 13 30 06 5 0 sec BIR 13 30 33 5 0 sec V NIST612 13 31 14 5 0 sec BCR2G 13 32 26 5 0 sec BHVO2G 13 32 55 5 0 sec BIR_G 13 33 23 5 0 sec Vf NIST612 13 34 03 5 0 sec BCR2G 13 34 45 5 0 sec BHVO2G 13 35 14 5 1 sec BIR_G 13 35 42 5 0 sec V NIST612 13 36 22 5 1 sec BCR2G 13 37 34 5 0 sec BHVO2G 13 38 03 5 0 sec BIR 13 38 30 5 0 sec V NIST612 13 39 11 5 0 sec BCR2G 13 39 53 5 0 sec BHVO2G 13 40 23 5 0 sec BIR 13 40 50 5 0 sec V NIST612 13 41 30 5 0 sec BCR2G 13 42 42 5 0 sec BHVO2G 13 43 12 5 0 sec BIR 13 43 39 5 0 sec 8 NIST612 13 44 19 5 0 sec BCR2G 13 45 01 5 0 sec C BHVO2G 13 45 31 5 0 sec BIR_G 13 45 58 5 0 sec NIST612 13 46 38 5 0 sec BCR2G 13 47 20 5 0 sec BHVO2G 13 47 50 5 0 sec BIR_G 13 48 17 5 0 sec
3. L Show sample labels s run 3 42 um 3 23 12 PM 11 6 sec 54 3 42 um 3 23 41 PM 13 2 sec 53 run4 4 42um 4 10 50 PM 39 sec 53 rund 4 42um 4 12 12 PM 42 7 sec H run4 4 42 4 30 28 PM 33 6 sec a E rund 4 42um 4 31 45 PM 44 4 sec Ed 4 42um 4 50 06 PM 41 8 sec 53 rund 4 42um 4 51 29 PM 41 9 sec E rund 4 4Zum 5 09 50 PM 31 sec 54 rund 4 42um 5 10 25 PM 5 89 sec 54 rund 4 42um 5 11 10 PM 42 4 sec Raw Age 206 238 S 1000 3 00 PM 3 30 PM 4 00 PM 4 30 PM 5 00 PM 5 30 Ph T 3 08 Analysis Time mum E Figure 3 7 Selections for the secondary reference material Z Temora2 3 2 U PB GEOCHRONOLOGY 3 DEMO 21 Step 4 Samples Proceed to the Samples tab and bring up the Automatic Selection function Using either the select from beam intensity method select all of the remaining wave peaks that do not belong to the two standards used in this session 91500 and Temora 2 and apply them to the Output 1 selection type Figure 3 8 aono Automatic integrations from beam Select All Deselect Al Urs i Saec Channel Select Channel c o Clos 68 of 104 periods selected 5 greater than 5 greater than 5 groster than is Add j Rem O m Minimum duration 2 iR rM XI runa 4 42um 4 34 11 PM 47 6 sec Bf runa 4 AZum 4 45 33 PM 47 7 sec O runt 4 4 4 47 12 PM 48 Zoom Auto 8 runa 4 us CR op ee Ip Out Manual Chan
4. Set Ref Mats IS values v Set GSD Standards Internal standard file Notused Set BCR standards Element Ca43 Set Sample runs Import IS values Set STD IS vals E Run Traces DRS Move Missed Shots Good Epidote Shots Check Data before Export Export data Figure 4 22 A processing template with a lot of actions 4 File or Folder import Select whether you want to import a single file or an entire folder of mass spec files Note that if you choose folder it will not check subfolders for files It will only load files from the selected folder 5 Date format this is only for Agilent and X Series files which have ambiguous time datestamp formats within the raw data files If you don t know what format to use try opening your file using the Import Tab in the Main lolite Window It will show you the timestamp in your file Usually once this is set you don t need to change it and can use Use Default for this option 6 Machine Type This is only used when you are doing split stream LASS ap plications and have two instruments of the same type e g two X series one measuring trace elements and the other measuring U and Pb isotopes If you re not interested in mass spec syncing just leave this as Automatic T File path this is where you specify which file you want to import Click on the button to select the file folder you want to import The full path to the se
5. 0 0 12 30 PM 12 45 PM 1 00 PM 1 15 PM 1 30 PM 1 45 PM 2 00 PM 31 8 11 Time Navigation Window shor a uro a oe l Figure 2 2 Baseline Tab of the Main lolite Window Implementing a correct baseline fit is the most important step in data deconvo lution Once a particular fit is chosen using one reference wave it is essential to check the other input waves to make sure that the fit is good for all channels as different elements can all behave rather differently in terms of wash out or memory effects Simply choose a new primary channel from the channel drop down list and the selected baseline intervals will be there to visualise Also note that different spline types can behave rather unpredictably especially when fitted to low numbers of data points which is another very good reason to check the fit for each wave separately Once baselines are selected and the user is happy with the fit to the data throughout the session the user may progress to the Reference Materials Tab If the user hits the Crunch Data button in the DRS Tab the Intermediate Channels will now be available in the channel drop down list 2 3 Reference Materials Tab The Reference Materials Tab allows the user to define selections for one or multi ple reference materials analysed during a mass spectrometry experiment The use of sample standard bracketing allows for the correction of instrumental drift over an experimental session The u
6. 20 of 20 periods selected 31 run 3 42 um 2 38 21 PM 45 6 sec B run 3 42 um 2 39 44 PM 45 7 sec Ed run 3 42 um 2 41 05 PM 45 6 sec e 82 run 3 42 um 2 59 20 PM 45 7 sec el integration typa Se Ef run 3 42 um 3 00 43 PM 45 9 sec Bf run 3 42 um 3 18 56 PM 46 sec B run 3 42 um 3 20 19 PM 46 sec Ed run 3 42 um 3 38 33 PM 46 sec 82 run 3 42 um 3 39 56 PM 45 8 sec 54 4 4 42m 4 06 36 PM 45 7 sec Bf runa 4 42um 4 07 59 PM 45 6 sec 52 runa 4 42um 4 09 20 PM 45 6 sec Bd rund 4 42um 4 27 30 PM 45 8 sec EH rund 4 42um 4 28 53 PM 45 9 sec 52 runa 4 42um 4 47 13 PM 45 7 sec runa 4 42um 4 48 35 PM 45 8 sec Bd runa 4 42um 5 06 55 PM 45 9 sec Ed runa 4 42um 5 08 17 PM 45 8 sec EH runa 4 42um 5 26 35 PM 46 2 sec Bf runa 4 42um 5 27 57 PM 46 2 sec TotalBeam m ANF A UM 3 00 PM 3 30 PM 4 00 PM 4 30 PM 7 3 08 5 30 P Analysis Time Figure 3 6 Selections for the primary standard Z 91500 Select All Deselect All 22 61 22 periods selected d run 3 42 um 2 42 38 PM 40 6 sec run 3 42 um 2 44 04 PM 18 9 sec 8 run 3 42 um 3 02 15 PM 41 7 sec 53 run 3 42 um 3 03 35 PM 23 9 sec Ed run 3 42 um 3 04 03 PM 2 34 sec E run 3 42 um 3 04 10 PM 3 77 sec 4000 d run 3 42 um 3 21 53 PM 12 5 sec 53 run 3 42 um 3 22 10 PM 8 33 sec E run 3 42 um 3 22 23 PM 2 sec run 3 42 um 3 22 29 PM 3 44 sec 3000 5 run 3 42 um 3 23 28 PM 8 89 sec
7. 43 Terminology 44 3 8 3 0 4 5 Baseline Subtraction 0 4 6 Time Series Tabs Baselines Reference Materials 4 7 Active Selection 48 Spline 6 4 9 Manual 58 6 0 4 10 Automatic Selection 4 10 1 Information from import 4 10 2 Laser log file 4 10 3 Detect from beam intensity 4 11 Editing Selection Periods 4 12 Channel Panel CONTENTS lii 4 13 4 14 4 15 4 16 4 17 4 18 4 19 4 20 4 21 4 22 4 23 4 24 Sample Info Panel 35 Standard uuo see es Boe EA AE EOP aw 36 Trace Element Control Panel 36 lolite Menu osos 37 View Reference Values a a a 40 EXPORT Data amp 2 23x o3 enh Sb anwa a 4 9x o8 3 XoRo ou 4 41 Trace Elements IS DRS 41 Limits of Detection 000 ee 42 U Pb Geochronology 3 85 43 Downhole Fractionation Correction 44 Cell5pace Images so comm om xoxo Bee de Xe Eom xo 47 4 23 1 How it works oes 48 4 23 2 A note about resolution and image size 40 4 23 3 Mask by integration type menu 40 4 23 4 Zooming in on the image 50 4 23 5 Mapped Image Layer
8. V NIST612 13 48 57 5 0 sec O BCR2G 13 50 09 5 0 sec BHVO2G 13 50 39 5 1 sec BIR 13 51 06 5 0 sec vf NIST612 13 51 46 5 0 sec BCR2G 13 52 28 5 0 sec BHVO2G 13 52 58 5 0 sec BIR 13 53 25 5 0 sec Vf NIST612 13 54 05 5 0 sec BCR2G 13 55 17 5 0 sec BHVO2G 13 55 46 5 0 sec BIR_G 13 56 13 5 0 sec M NIST612 13 56 53 5 0 sec BCR2G 13 57 36 5 0 sec O BHVO2G 13 58 05 5 0 sec BIR 13 58 33 5 0 sec V NIST612 13 59 13 5 0 sec BCR2G 14 00 25 5 0 sec O BHVO2G 14 00 54 5 0 sec BIR_G 14 01 22 5 0 sec V NIST612 14 02 02 5 0 sec O BCR2G 14 02 44 5 0 sec BHVO2G 14 03 14 5 0 sec O BIR_G 14 03 41 5 0 sec V NIST612 14 04 21 5 0 sec BCR2G 14 05 33 5 0 sec BHVO2G 14 06 02 5 0 sec BIR_G 14 06 30 5 0 sec V NIST612 14 07 10 5 0 sec BCR2G 14 07 52 5 0 sec O BIR_G 14 08 23 5 0 sec BHVO2G 14 08 50 5 0 sec 8 NIST612 14 09 35 5 0 sec BCR2G 14 10 48 5 0 sec Figure 3 2 Making reference material selections using the Automatic integrations from metadata window 31 TRACE ELEMENTS IS DEMO 17 Proceed to the Samples tab and bring up the Automatic Selection function Using either the laser log file or select from beam intensity methods select a few selections and apply them to the Output 1 selection type Step 5 DRS Proceed to the DRS tab and se
9. You can zoom in on any part of the image by dragging a marquee around the area you d like to zoom in on and clicking within the marquee and selecting Expand 4 23 5 Mapped Image Layers There are five image layer drop down menus You can use these menus to open new mapped images or to change the order in which images are displayed Unfortunately Igor Pro currently doesn t have a suitable transparency option so you can t change the transparency of the images even if they are overlapping The reason there are five layers is to allow five separate images to be opened If you have opened a registered image but then hide it by selecting None from the image layer drop down menu and then select a channel to map the formatting of the page may be a little off i e the data will be there but it might be a little hard to read the axis title etc You can fix this just by selecting any image from the image layer drop down menus To reset the image limits set both the lower and upper limit to zero lolite will automatically calculate the lowest and highest image values and set these as the limits 4 23 0 Exporting Images There are three export button on the bottom right Fig 4 17 Export Current ex ports whatever is currently visible in the CellSpace imaging window Export Selected will create a map for any channel that has saved values any saved colour maps or limits Export All creates a map for each channel in turn
10. informational selection provides the user with information about the version of lolite being used By clicking on Register olite the user can enter their lolite registration number lolite Main Window This command brings the Main User Interface to the forefront of the desktop 30 CHAPTER 4 SOFTWARE FEATURES DIRECTORY import Basetnes Reference Materias Samples DRS Results images General Settings Stats for baselines Mean cutlier reject Stats for normal selections Mean with 3 5 53 outlier reject DRS Specific Settings Current Data Reduction Scheme Trace Elements D Index Channel Ca43 Reference Material G NIST612 Default Intensity Units CPS Standardisation method internal Elemental Standard Output Units ppm Crunch Data DRS did not finish See report for details DRS Report 12 59 15 PM The 085 Trece Eiements JS requi imei Ca4S CPSDNISTG 127 in the folder 591 3 3 67058 Terther 3 16 47 PM The DAS Traca Elemani n cham 5 a Wave Jac di Vn th folder Trece Elementa JS apis Cece 1 ferthe 5 58 46 PM The DAS Trace A aa rz n pe ele ire lin the folder Trace Terther BeamSeconds method Curaff Thresholi Threshold to use when masking low signals 20 Seconds to trim before after low signals 1 BeamsSeconds Sensitivity 4 C Trace Element Control Panel Open Int Std data Interna
11. z8 04 A Bases i zs uezoriossrs 31 8111 1246 14 4501 99698 112 7 aC A E 4 Baseline 25 M 20110831 d 31 8 1 1 1 7 4127 12405 M 20110831 4 DA TA EE iam E 16999879188891 145303 ad am eszel RO 1 a o BEER BECHER E BEE 7 9z8 ese 0658 8621 6277 L a OA EEC 2201 rasa MIE CCE a EE El Baseline 30 M 20110831 d 31 8 11 12 44 13 a a OOO 30 31 MFz0110831 6 31 8 11 12 44 40 7 903 M z0110831 4 11 1 8 RR if nase CECI IET AMICS IM 889418288886 188 af ea IT IE IA os or 22 6 1 53142011681 1 3u amp ri 124521 3741jwzoriossra 1032 os 864 291 628 505 am 1 341 4501108314 31 8 111 tensa 127650 2911899 161 1 64 1 651 918 615 E UNIT UTE IDA NN 65666667 566 6667 6 566 BB yq E A AA EE EE 57162911691 319811 124811 2778 52989 1 3a A 06541 0059 CEIC IET 1845 1279957878841 vos 1 1 5541 6 osal 681 i Ke a xe teen a RH T Figure 2 7 Data Table display of the Results Tab The fifth blue button Export allows the user to export the lolite experimental results However it is
12. BCR2G 13 22 09 5 0 sec BHVO2G 13 22 39 5 1 sec BIR_G 13 23 07 5 0 sec NIST612 13 23 47 5 0 sec BCR2G 13 24 29 5 0 sec BHVO2G 13 24 58 5 1 sec BIR 13 25 26 5 0 sec Automatic from metadata li nli rere Close Vf NIST612 13 26 06 5 0 sec BCR2G 13 27 17 5 0 sec BHVO2G 13 27 47 5 0 sec BIR_G 13 28 15 5 0 sec V NIST612 13 28 55 5 0 sec BCR2G 13 29 36 5 0 sec BHVO2G 13 30 06 5 0 sec O BIR_G 13 30 33 5 0 sec o NIST612 13 31 14 5 0 sec BCR2G 13 32 26 5 0 sec a BHVO2G 13 32 55 5 0 sec BIR_G 13 33 23 5 0 sec NIST612 13 34 03 5 0 sec BCR2G 13 34 45 5 0 sec BHVO2G 13 35 14 5 1 sec O BIR_G 13 35 42 5 0 sec z NIST612 13 36 22 5 1 sec BCR2G 13 37 34 5 0 sec BHVO2G 13 38 03 5 0 sec BIR_G 13 38 30 5 0 sec V NIST612 13 39 11 5 0 sec BCR2G 13 39 53 5 0 sec BHVO2G 13 40 23 5 0 sec BIR_G 13 40 50 5 0 sec E NIST612 13 41 30 5 0 sec BCR2G 13 42 42 5 0 sec BHVO2G 13 43 12 5 0 sec BIR_G 13 43 39 5 0 sec NIST612 13 44 19 5 0 sec C BCR2G 13 45 01 5 0 sec BHVO2G 13 45 31 5 0 sec BIR_G 13 45 58 5 0 sec V NIST612 13 46 38 5 0 sec BCR2G 13 47 20 5 0 sec BHVO2G 13 47 50 5 0 sec O BIR_G 13 48 17 5 0 sec V NIST612 13 48 57 5 0 sec BCR2G 13 50 09 5 0 sec C BHVO2G 13 50 3
13. 22 PM 24 7 sec MI 20110831 d 12 43 03 PM 27 4 sec E MI 20110831 d 12 43 46 PM 12 4 sec 0 l 84 1 2 d 12 44 14 j ip ojo siue 12 30 PM 12 45 PM 1 00 PM 1 15 PM 1 30 PM 1 45 PM 2 00 PM MI 20110831 d 12 44 40 PM 7 9 sec 31 8 11 MI 20110831 d 12 44 57 PM 8 8 sec MI 20110831 d 12 45 21 PM 57 4 sec Analysis Time SS 4 Figure 4 5 The Automatic integrations from beam window 10010 Baseline 1 Automatic 0 8 0 6 TotalBeam 0 4 0 2 0 0 12 46 PM 12 47 PM 12 48 PM 12 49 PM 12 50 PM 31 8 11 analysis Time Figure 4 6 Activating the Channels Drop down List 34 CHAPTER 4 SOFTWARE FEATURES DIRECTORY analytical session labelled TotalBeam or Waves displaying individual measured iso tope masses as either a non time dependent total count Input Channels counts per second CPS and ratios of two masses Intermediate Channels or parts per million ppm Output Channels 1 in Figure 4 7 It is important to note that only masses measured during experimental analysis can be viewed as a channel during data reduction As the user progresses through the data reduction procedure additional Channels will become available After a baseline has been defined and the Data Crunched Intermediate Channels will be viewable After the reference material selections have been defined in the Reference Materials Tab and the Data Crun
14. Baseline 1 D Set GSD Standards l Start crop 1 sg Endcrop 62 LIMES im pline type Spine Smooth Med5 Existing delete Set Sample runs Match text impot S values Set STD IS vals Run Traces DRS Move Missed Shots Good Epidote Shots Check Data before Export Import my laser log file Figure 4 26 Options for the create selections from file action any spaces or non word characters i e anything other than A Z 2 0 9 or _ and that it isn t longer than 16 characters long 5 Start Crop This is how much to trim off the start of each selection Please see Figure 4 4 to understand how negative and positive numbers affect this cropping 6 End Crop This is how much to trim off the end of each selection Please see Figure 4 4 to understand how negative and positive numbers affect this cropping 7 Spline Type What spline type to use for this selection group Note that this is only used for reference materials and Baseline_1 samples are not splined 8 What to do with existing selections If there are already selections in this group this option allows you to choose what to do with them Use delete to delete any selections already in this group Use append to add to this group keeping the selections already there 9 Match Text Selections will only be added when their filename matches the text in this field Use to match any filename e g when you re adding a baseline before every sa
15. C H 1967 Smoothing by spline functions Numerische Mathematik 10 3 p 177 183 to fit a smoothed cubic spline through all data points taking into account the individual uncertainties of each he smoothing factor specified by the user determines how tightly the curve is fitted through each data point no smoothing will result in a cubic spline fitted through all data points and as the factor is increased the spline will become smoother and eventually approach a straight line When the curve fit window first appears the default settings altered in the DRS tab are used to calculate a model of down hole fractionation for the ratio based on the average of all selected analyses of the reference standard The user is then free to alter the model using the controls on the right hand side of the curve fit window Figure 4 16 These controls operate in two separate ways either by masking the beginning and or end of the average or by manually altering the parameters of the fit note that the latter option is unavailable when using Running median or Smoothed cubic spline Masking of the beginning or end of the average pattern is particularly useful as there will often be small sections at the start and end of the graph that are averages of only one or two waves and are thus highly susceptible to the signal noise of these analyses By masking these portions so that they are not included in model calculation a significantly better fit t
16. CHAPTER 4 SOFTWARE FEATURES DIRECTORY Integrations This is which selection group you d like to export the results for Note that you can only export the stats for each selection group using this action To export time series use the iolite menu s Export Data item Outputs this is which channels you d like to export results for Each channel name must be an exact match and should be separated by a Use default to export the usual channels Sort by This is how the selections will be sorted in the exported file By integra tion then time will sort each group of selections by time keeping them in their groups By time will sort the selections according to their start times irrespec tive of their selection group By annotation will sort the selections according to the selection label annotation irrespective of their groups Export path this is the path to the folder where the export files will be saved Use the button to select a folder This folder must exist before the export action is executed as it will not create the folder for you Export name the name of the file to be saved Uncertainties Whether to report the internal uncertainties external uncertain ties or both See the website for more details on how the external uncertainties are calculated https iolite software com uncertainty propagation how it works Bibliography 1 Longerich H P S E Jackson et al 1996 La
17. Materials Proceed to the Reference Materials tab and navigate to the Automatic Selections tool Since the 5 Seconds Basalts experiment was undertaken with the aid of a laser log file we can use the Laser Log File method to automatically choose the selections for the reference materials The Automatic integrations from metadata window will appear Figure 3 2 Select one of the reference materials analysed in this experiment from the drop down menu such as NIST612 Then query all periods that have NIST612 in their labels using the Match text section of the window All NIST612 analyses periods will be automatically selected Crop the first and last 0 5 seconds of the signal using the crop data tool at the top of the page removing the incline and decline portions of the signals Repeat these steps for the three remaining reference materials BCR 2G BHVO 2G and BIR 1G Once the selections for all of the reference materials have been selected click the Close button at the top right of the window Back in the Reference Materials tab choose the appropriate spline types for these selection types Step 4 Samples The Trace Elements IS DRS requires the user to select some selections for sample unknowns However in this sample dataset all of the analysed materials have corre sponding standard files In order to proceed with the example we will select some selection periods as unknowns so that iolite allows us to proceed which we will sub s
18. Pb Geochronology 3 data reduction namely the modelling and correction of down hole elemental fractionation the propagation of uncertainties and the calculation of error correlations In addition to the internal precision of individual analyses a number of other sources of error exist and the DRS attempts to account for these during export Although a number of studies have attempted to quantify individual sources of uncertainty and propagate these appropriately the use of complex down hole fractionation models in lolite s U Pb Geochronology 3 DRS makes this approach difficult to implement In addition this approach requires that all sources of uncertainty are explicitly identified and it remains clear from many laser studies that this is not always the case lolite s U Pb Geochronology 3 DRS employs an approach that requires no a priori knowledge of the source of uncertainties instead using analyses of the reference standard as pseudo secondary standards by removing them individually from the dataset and reprocessing the data Although this approach is extremely computationally intensive it can be used in combination with complex down hole fractionation models and has the added benefit of inherently including unidentified sources of error However because the method estimates uncertainties based on the reference standard it is important to understand that the relative contribution of different sources such as baseline noise to unknow
19. Spectro tad files e Thermo iCapQ iCapQ exports lolite universal files which were developed in collaboration between ThermoFisher and the lolite team e Los Gatos Research Water vapor isotope analyzer lolite will import LGR txt files e Any other mass spectrometer that exports the lolite Universal filetype csv 4 2 Data Reduction Scheme The first task of a DRS is to specify which data channels if any it requires to be loaded into memory to operate i e MC ICP MS techniques such as in situ Hf or Sr isotope analysis require specific combinations of mass collector pairs whereas a generalised elemental procedure may be able to operate on any available mass channels from a single collector instrument A DRS usually also specifies the requirement of an interpolated baseline for each available channel which is automatically created after the user has defined one or more time intervals as baseline selections Similarly A DRS will also sometimes require user input to define selection periods for one or more specific standards over the course of a session After data are loaded a DRS proceeds by interpolating the required channels onto a common time scale although in many cases this step is redundant From this point on any desired data processing may 24 43 TERMINOLOGY 25 be undertaken as new data become available e g interpolated baselines are usually subtracted from all channels as a first step once the user identifies t
20. Trace Elements IS DRS on the DRS tab Step 6 Results Proceed to the Results tab to view your reduced data Choose U_ppm_m238 as the channel to plot and the average U ppm values for each selection type will be listed in the table at the top of the window Figure 3 4 Your values should look very similar to the ones displayed in the Figure 3 4 18 CHAPTER 3 COMMON DRS DEMONSTRATIONS lolite v3 Five Seconds Basalt import Baselines Reference Materials Samples DRS verage Uncertaint Regie 3 Pica Options amp weighted propag 2 5 absolute E nao value lt 5 valid values lt 5 valid values af mos uncertainty 1 609 0 03 37 38 0 04 f Mensur O of 40 0 4155 0 58 LJ Prepagas 0 of 40 0 0115 lt 0 03 Order by 0 of 162 0 032 BCR_2G 1 609 0 025 U ppm 238 Figure 3 4 Results for the 5 Seconds Basalts experiment 3 2 U Pb Geochronology 3 Demo Here we will run through the zircon U Pb example dataset which we will reduce using the U Pb Geochronology 3 DRS This dataset consists of analyses of a number of unknown zircons using Z 91500 as the primary reference material and Z_Temora2 as the secondary standard Step 1 Import Data First open lolite and proceed to the Data Import tab in the User Interface Select the varian prn file type and load the zircon U Th Pb example dataset file using the blue Import button Step
21. are calculated Once time resolved data processing has been completed the data can be visualised or exported in a number of ways including as 2 or 3 dimensional spatially resolved data Igor Pro is available from Wavemetrics as a fully functional 30 day trial version after which it will revert to a limited functionality demonstration version until registered It is thus possible to trial lolite before committing to purchase Igor Pro Please see the Wavemetrics website to check pricing for academic licences lhttp www wavemetrics com 2 CHAPTER 1 INTRODUCTION Discounts for student users are also on offer lolite is built around an internal data format in which every imported time resolved channel be it a mass or element recorded by a single collector instrument or a mass collector pair from a multi collector is stored as an x y series versus its own absolute date time This is a flexible approach which makes no assumptions about the nature of any stored data except that they are time series allowing for instance the combination of data sets containing different numbers of measured masses over the course of one or more days or of simultaneously acquired data where more than one instrument is coupled to a single laser All available metadata are also collected from the source time resolved files during data import and are preserved through to data export where they are included with the output data lolite was designed for a mixed researc
22. either a selection group or the entire experiment or by loading values for your reference materials from their standard file e g loading the NIST612 IS value from the G_NIST612 standard file Import from file t Igor Pro 6 36 File Edt Data Analysis Macros Windows Graph Mpc Help Gizmo Zoom lolite Image Actions Edit actions Template bg Settings for Import IS values cion type Create Load 15 Values Method Import from file D a nternal standard file CiUsers Bence Documents Testers e Import IS values Set STD IS vals Run Traces DRS Move Missed Shots Good Epidote Shots Check Data before Export Export data Import my laser log file Figure 4 31 Options for the load IS values from file action 1 Action Name set this to make it clear what your action does 2 Action Type although already set you can change action types by using this dropdown menu 3 Method set how you d like to assign IS values here 4 S file Select a file containing your IS value The format must be either comma separated value csv or tab delimited txt text The first column must be the sample names and must match the selection labels for those samples Each column after that is an elements concentration Each column should be headed by the element symbol e g Na for sodium This is so that iolite can read the 66 CHAPTER 4 SOFTWARE FEATURES DIRECTORY appropriate column to load Use the button to se
23. individual selection periods by manually clicking the appropriate boxes or querying selection labels using the Match text box The user can then choose which selection group these selections will be added to as well as crop the selection periods by using the Crop data in seconds tool at the top of the window See Figure 4 4 for an illustration of the effect of increasing or decreasing the start and end crop times Once satisfied with the selections the user may click the purple Add integrations button 4 10 3 Detect from beam intensity Once the Detect from beam intensity option is selected from the Automatic Selection pop up window the user will be prompted to the Automatic integrations from beam pop up window Figure 4 5 This window is broken up into three regions the data display in white the data filters in green and the filtered data periods list in the blue area In the main data display the user is able to select which channel they would like to view which selections type the user wants to apply the selections to and whether they wish to view the sample labels or not In addition the zoom tools in the top left corner of the window allows the user to manipulate the scale of the of the data display The same techniques discussed in Wave Navigation and Operations can also be used to navigate the data The data filters at the top of the pop up window can be used to filter out individual selections periods from the data wav
24. integration for 291500 55 proceed further BeamSeconds method Cutaff Threshal Dewn hole correction modal Exponential amp 10 38 03 AM DRS finished BeamSeconds Sensitivity 1 Threshold to use when masking low signals 20 Seconds to trim before after low signals 1 ignore 235U Yes Sample238 235Ralio 137 88 DefaultStartMask 0 DefaultEndMask 0 MaxBeamDuration 60 FitOutlier Tolerance 1 5 Figure 3 9 DRS settings for the demo zircon U Pb experiment view the final computed 206 238 207 235 208 232 and 207 206 U Pb ages Figure 3 10 3 2 U PB GEOCHRONOLOGY 3 DEMO 23 weighted propag 25E absolute D 6 value 26 valid values 1062 2 30 0 93 419 9 26 E eS da amp amp z eu E LL Figure 3 10 Results of the demo zircon U Pb experiment Chapter 4 Software Features Directory 4 1 Supported Instruments and Formats e Nu Plasma first generation MC ICPMS lolite will import Nu run files e Nu Plasma csv files e Nu Plasma txt files multi cycle files still in beta e Nu AttoM lolite will import AttoM csv files e Bruker Varian 800 series lolite will import iso prn e Agilent 4500 7500 7700 lolite will import Agilent csv files e Thermo X series lolite will import X Series csv files e Perkin Elmer Elan lolite will import Perkin Elmer xl files e Thermo Neptune Element2 and Triton data lolite will import fin2 files e Spectro MS lolite will import
25. is present in every analysis Because iolite is written to allow flexibility not every channel must be present in all files except for the Index channel which must be present throughout the entire analysis lt is also usually the most abundant element measured by convention Reference standard This is which standard should be used as the primary stan dard and will be included in the concentration calculation for all samples All other standards are treated exactly the same as samples and are therefore good independent guides as to accuracy precision etc lf no selections have been added to this group the DRS will finish after calculating ratio channels 68 CHAPTER 4 SOFTWARE FEATURES DIRECTORY Igor Pro 6 35 Ele Edt Data Analysis Macros Windows Graph Misc Help Gazmo Zoom lote Image Pa Processing templates Actions Edit actions Templabe liog import data Settings for Import IS values Ke scion type Run DAS TraceBlements 5 D Sel Baselines annel Cada Set GSD Standards _ e standard 6 5 612 4 Set BCR standards Set Sample runs Import IS values Set STD IS vals Run Traces DRS Move Missed Shots Good Epidote Shots Check Data before Export Export data import my laser log file Figure 4 33 Options for the run trace elements DRS action 5 Intensity units This is where you can set what intensity units your mass spec trometer measured in Usually it is CPS counts per se
26. manual for further info 4 4 Navigation By holding down the mouse button and dragging an area of interest marquee can be defined Clicking within this region then brings up a sub menu of operations which can be performed on this region The first six commands provide a means of zooming in and out of specific regions of interest by expanding or shrinking in the vertical and or horizontal direction respectively You can also use the Zoom Widget at the bottom of the tab in the Time Series Tabs More information about navigating your data is included below in the Time Series Tabs section and the Channel Panel section 4 5 Baseline Subtraction As in any mass spectrometric analysis it is important to ascertain the level of back ground noise in any signal This baseline level can then be subtracted from the total signal to calculate a baseline subtracted intensity that in this case represents only the material sampled by the laser It is common practice in laser ablation studies to analyse a gas blank in which all gas flows and instrumental parameters are identical to those encountered during sampling but the laser beam is either turned off or is physically blocked by a shutter 26 CHAPTER 4 SOFTWARE FEATURES DIRECTORY In lolite raw signal intensities can be viewed individually or together and scaled in such a way that the user can easily assess the background intensities of many beams simultaneously The time scale can be a
27. originally packaged with the lolite program The original assumed a constant internal standard concentration between samples This is fine if you re working with mono mineralic samples such as calcite where Ca can be used as an internal standard with a constant value However some users will be measuring a variety of materials within the same run with significantly different internal standard element concentra tions Thus the new Trace Element 15 DRS provides functionality for users to import a table of internal standard element concentrations for their samples The Trace Elements IS DRS matches internal standard concentrations by integra tion annotation aka Selection Label We recommend using the Automatic Selections 42 CHAPTER 4 SOFTWARE FEATURES DIRECTORY e oto View Reference Values Rotae ag mE e eo Row GNIST612 1 D NISTe12 O iG NIST612 1 6 NIST612 2 y Units Val ue Uncertainty yg ppm 22 3 Al ppm 10744 l 2 AS ppm 25 7 8 9 5 Au ppm 4 77 1 72 4 B m 34 3 12 2 Select A Ref Mat 5 Ba ee z9z 0 9 6 De ppm 21 1 5 7 Bi ppm 30 2 e 9 Ca ppm 95036 715 J Cd ppm 25 1 6 10 Ce ppm 38 4 0 7 11 Cl ppm 142 55 12 Co ppm 35 5 1 13 Cr ppm 36 4 26 3 14 Cs ppm 42 7 1 5 15 Cu ppm 37 8 16 3 16 Dy ppm 35 5 0 7 17 Er ppm a8 0 9 18 Eu ppm 35 6 0 6 19 F ppm 80 59 20 Fe pom 51 2 Ga ppm 36 9 1 7 22 Gud ppm 27 3 0 9 23 Ge ppm 36 1 12 1 24 Hf ppm 36 7 1 2 ppm 28 25 u a zb In ppm 30 9 2 1
28. suggested that if you require error correlations etc you use the export options that are available by going to the olite menu Export Data 2 7 Images Tab When initially viewing the Images Tab two blue buttons are displayed labelled Cre ate CellSpace Image and Create Image from Selections There functionalities are described below e Create Cell Space Image See the CellSpace Images section for full details on how to create a CellSpace image e Create Image from Selections This option is used to create images by stitching your selections together as rows into an image Chapter 3 Common DRS Demonstrations 3 1 Trace Elements IS Demo Here we will run through the Five Seconds Basalts example dataset which we will reduce using the Trace Elements IS DRS This dataset consists of a repeated rotation of 5 second analyses of the NIST 612 glass reference material and three basalt references BCR2G BHVO 2G and BIR 1G Step 1 Data Import First open iolite and proceed to the Import tab in the User Interface Select the agilent csv file type and load the 5 seconds basalt file using the blue Import button Step 2 Baselines Proceed to the Baselines tab Choose an appropriate spline type and proceed to the automatic selections tool iolite Automatic Selections or Cmd 2 Ctrl 2 on PC J Choose the Detect from beam intensity method from the pop up window In the Automatic integrations from beam window
29. to run when the action is created Criteria choose here what the channel must be doing to be considered a match Criteria on checkbox this checkbox must be on for the criteria to be taken into account Criteria Value Set here the value the channel must match be greater than be less than etc to be included in the selection From LaserLog la 2 Action Name set this to make it clear what your action does Action Type although already set you can change action types by using this dropdown menu Method set how you d like to create selections here Group to add to Set here which group the created selections will be added to You can use the dropdown menu marked as to select from your standard list Baseline 1 or type some text in the field to create a new selection group If what you type is exactly the same as the name of a standard or Baseline 1 it will add the selections to that standard group or Baseline 1 Make sure that if you type a new selection group name that it begins with a letter doesn t include any spaces or non word characters i e anything other than A Z 2 0 9 _ and that it isn t longer than 16 characters long 4 24 PROCESSING TEMPLATES 61 Igor Pro 6 36 Ele Edt Data Analysis Macros Windows Graph Misc Help Ga mo Zoom Iolte Image Actions Edi actions Templatedog Settings for Good E pidote shots 2 Action type Create Selections Met
30. to select one of your standards or baseline 1 groups If the group doesn t exist when you re editing this action you can type 4 24 PROCESSING TEMPLATES 63 the name of the selection group here It must exist when the action runs to avoid an error Group to add to Set here which group the selections will be moved to You can use the dropdown menu marked as to select from your standard list Baseline 1 or type some text in the field to create a new selection group If what you type is exactly the same as the name of a standard or Baseline 1 it will add the selections to that standard group or Baseline 1 Make sure that if you type a new selection group name that it begins with a letter doesn t include any spaces or non word characters i e anything other than A Z a z 0 9 _ and that it isn t longer than 16 characters long Channel Name the name of the channel whose uncertainty measurement will be used to determine whether to move the selection The channel must exist when the action runs and must match the channel name exactly no typos please In the example shown any selections that have a 2SE of greater than 500 CPS for the Ca43_CPS channel will be moved to the MissedSpots selection group Logic what comparator to use in the decision to move the selection Move value the value used with the comparator Preserve original selections checkbox Whether a copy of the original selection should be left in the From group c
31. 0 sec BHVO2G 12 51 57 5 0 sec O BIR 12 52 24 5 0 sec o NIST612 12 53 04 5 0 sec BCR2G 12 53 46 5 0 sec z BHVO2G 12 54 16 5 0 sec O 8 12 54 43 5 0 sec Vf NIST612 12 55 23 5 0 sec BCR2G 12 56 34 5 0 sec BHVO2G 12 57 04 5 0 sec BIR 12 57 31 5 0 sec NIST612 12 58 11 5 0 sec BCR2G 12 58 53 5 0 sec e BHVO2G 12 59 23 5 0 sec BIR_G 12 59 50 5 0 sec V NIST612 13 00 30 5 0 sec O BCR2G 13 01 41 5 0 sec BHVO2G 13 02 11 5 0 sec BIR 13 02 38 5 0 sec V NIST612 13 03 18 5 0 sec BCR2G 13 04 00 5 0 sec BHVO2G 13 04 29 5 0 sec BIR_G 13 04 56 5 0 sec V NIST612 13 05 36 5 0 sec BCR2G 13 06 47 5 0 sec BHVO2G 13 07 18 5 0 sec O BIR_G 13 07 45 5 0 sec d NIST612 13 08 24 5 0 sec BCR2G 13 09 06 5 0 sec BHVO2G 13 09 36 5 0 sec BIR_G 13 10 03 5 0 sec V NIST612 13 10 43 5 0 sec BCR2G 13 11 55 5 0 sec BHVO2G 13 12 24 5 0 sec BIR_G 13 12 51 5 0 sec V NIST612 13 13 31 5 0 sec BCR2G 13 14 13 5 0 sec BHVO2G 13 14 42 5 0 sec BIR 13 15 09 5 0 sec V NIST612 13 15 49 5 0 sec BCR2G 13 17 01 5 0 sec BHVO2G 13 17 31 5 0 sec BIR_G 13 17 58 5 0 sec E NIST612 13 18 38 5 0 sec BCR2G 13 19 19 5 0 sec BHVO2G 13 19 49 5 0 sec BIR_G 13 20 17 5 0 sec V NIST612 13 20 57 5 1 sec
32. 10831 d 12 31 12 PM 13 3 sec Mi 20110831 d 12 31 42 PM 10 sec BJ MI 20110831 d 12 32 19 PM 13 sec Dn 5 MI 20110831 d 12 32 48 PM 26 2 sec 100x107 Ed wi 20110831 d EA Mi 20110831 d be 201 10831 Eg 201 10831 bd M 20110831 d Mi 20110831 d be M1 20110831 d Ef MI 20110831 d Ed Mi 20110831 d Ed Mi 20110831 d Ef M1 20110831 d Bf M1 20110831 0 Ed Mi 20110831 d 12 33 32 PM 11 2 sec 12 34 00 PM 10 3 sec 123427 PM 23 2 sec 12 35 07 PM 28 6 sec 12 35 44 PM 19 6 sec 12 36 20 PM 13 3 sec 12 36 49 PM 10 8 sec 12 37 16 PM 8 8 sec 12 37 33 PM 5 4 5 12 37 56 PM 21 1 sec 12 38 39 PM 12 7 sec 12 38 08 PM 10 9 sec 12 39 34 PM 24 1 sec TotalBeam 60 40 ZO Ed MI 20110831 d 12 40 14 PM 4 9 sec UH Ed MI 20110831 d 12 40 28 PM 43 6 sec MARET 52 MI 20110831 d 12 41 28 PM 12 4 sec EM MI 20110831 d 12 41 56 PM 10 6 sec A RU 1 bd MI 20110831 d 12 42 23 PM 24 4 sec 0 M A mm mam mem maae m Bf 8 201 10831 12 43 03 PM 27 4 sec 82 M 20110831 d 12 43 46 PM 12 1 sec 12 45 PM 1 00 PM 1 15 PM 1 30 PM 1 45 PM Ed MI 20110831 d 12 44 14 PM 10 9 sec Bd we20110831 12 44 45 PM 3 4 sec Analysis Time Figure 3 1 Selecting the baseline using the Automatic Selections tool for the 5 Seconds Basalts experiment Step 3 Reference
33. 2 Baselines Proceed to the Baselines tab Choose an appropriate Spline Type and proceed to the Automatic Selections tool Choose the Detect from beam intensity method from the pop up window In the Automatic integrations from beam window select U238 for the channel from the drop down menu in the data filter section in green at the top of the window Select is less than and enter a low value that excludes the data peaks such as 600 The portions of the wave that this filtered region pertains to will be highlighted in bright green in the data display portion of the window These periods will also appear in the filtered data list in blue at the left side of the window Enter a starting crop of 5 seconds and an end crop of 3 seconds in the Crop data tool at the top right of the screen Then click select all from the filtered data list at 3 2 U PB GEOCHRONOLOGY 3 DEMO 19 the left of the screen Choose the selection type you wish to apply these selections to Baseline 1 in this case and click Add Integration at the top right of the window Then click the close button at the top right of the screen Back in the Baseline tab make sure that the selected baseline fits all of the mea sured channels well Figure 3 5 eoo lelite v3 Untitled Experiment T nessanes Samples Das Results 25 10 Baseline 1 5 8 Smooth Mega 38 Primary 0 Song e Log Ma
34. 35 Down Hole and Raw 208 232 Down Hole windows Figure 4 16 These windows have similar lay outs The fit controls are on the right hand side described in text below A graph illustrating all individual analyses of the reference standard coloured from blue to red is in the top left of the window with the black line representing the calculated average of the analyses and the red curve representing the exponential equation that best models changes in the average with time The residuals of the fit marked in red calculated by subtracting the exponential curve in this case from the average value for each data point are displayed in the bottom left A quality of fit panel is displayed in the bottom right corner of the window to provide additional feedback to the user on the quality of their model of down hole fractionation again based on the black average values To model down hole fractionation within an analytical session the data from indi vidual analyses of the reference standard are combined to generate an average pattern of changes in the elemental ratio with ablation time This averaging generates a more representative pattern and reduces the effects of signal noise There is no requirement for the selected segments of reference standard analyses to be the same length or to be continuous This means that the user is free to avoid sections of individual analyses that are clearly inaccurate as may result from for example surface Pb c
35. 6 5 0 sec BCR2G 10 12 51 29 5 0 sec BHVO2G 12 51 57 5 0 sec O BIR_G 12 52 24 5 0 sec V NIST612 12 53 04 5 0 sec BCR2G 12 53 46 5 0 sec BHVO2G 12 54 16 5 0 sec O BIR_G 12 54 43 5 0 sec 8 NIST612 12 55 23 5 0 sec O BCR2G 12 56 34 5 0 sec CHAPTER 3 COMMON DRS DEMONSTRATIONS BHVO2G 12 57 04 5 0 sec BIR 12 57 31 5 0 sec V NIST612 12 58 11 5 0 sec BCR2G 12 58 53 5 0 sec BHVO2G 12 59 23 5 0 sec C BIR_G 12 59 50 5 0 sec NIST612 13 00 30 5 0 sec BCR2G 13 01 41 5 0 sec BHVO2G 13 02 11 5 0 sec BIR G 13 02 38 5 0 sec V NIST612 13 03 18 5 0 sec BCR2G 13 04 00 5 0 sec BHVO2G 13 04 29 5 0 sec BIR 13 04 56 5 0 sec V NIST612 13 05 36 5 0 sec BCR2G 13 06 47 5 0 sec BHVO2G 13 07 18 5 0 sec BIR 13 07 45 5 0 sec V NIST612 13 08 24 5 0 sec BCR2G 13 09 06 5 0 sec BHVO2G 13 09 36 5 0 sec BIR_G 13 10 03 5 0 sec M NIST612 13 10 43 5 0 sec BCR2G 13 11 55 5 0 sec BHVO2G 13 12 24 5 0 sec BIR G 13 12 51 5 0 sec V NIST612 13 13 31 5 0 sec BCR2G 13 14 13 5 0 sec BHVO2G 13 14 42 5 0 sec BIR 13 15 09 5 0 sec V NIST612 13 15 49 5 0 sec BCR2G 13 17 01 5 0 sec BHVO2G 13 17 31 5 0 sec BIR_G 13 17 58 5 0 sec V NIST612 13 18 38 5 0 sec BCR2G 13 19 19 5 0 sec
36. 8 56 Options for the import laser log 8 0 57 Options for the create selections from file 8 08 58 Options for the create selections from channel action 59 Options for the create selections from laser log action o1 Options for the move selections by channel 2SE action 62 Options for the move selections by selection label action 64 Options for the load IS values from file action 65 Options for the create IS values from single value action 66 Options for the run trace elements DRS action 68 Options for the run U Pb DRS action 70 Options for the export action 0 0 2 000000 8 71 Chapter 1 Introduction lolite is a software package designed for deconvolution of data obtained by Inductively Coupled Plasma Mass Spectrometry ICP MS Laser Ablation ICP MS LA ICP MS and Thermal lonization Mass Spectrometry TIMS LA ICP MS allows the analyst to rapidly acquire very large bodies of data a feature which can be both an asset and a curse The requirement that parameters such as baseline intensities and elemental fractionation factors must be considered for every analysis over the course of a day with reference to standard analyses often located in other files can lead to an overwhelming level of processing burden often taking much longer than the data acquisition i
37. 9 5 1 sec O BIR_G 13 51 06 5 0 sec E NIST612 13 51 46 5 0 sec BCR2G 13 52 28 5 0 sec z BHVO2G 13 52 58 5 0 sec O BIR_G 13 53 25 5 0 sec Vf NIST612 13 54 05 5 0 sec BCR2G 13 55 17 5 0 sec II BHVO2G 13 55 46 5 0 sec _ BIR_G 13 56 13 5 0 sec a NIST612 13 56 53 5 0 sec _ BCR2G 13 57 36 5 0 sec BHVO2G 13 58 05 5 0 sec BIR_G 13 58 33 5 0 sec V NIST612 13 59 13 5 0 sec BCR2G 14 00 25 5 0 sec BHVO2G 14 00 54 5 0 sec BIR 14 01 22 5 0 sec V NIST612 14 02 02 5 0 sec BCR2G 14 02 44 5 0 sec BHVO2G 14 03 14 5 0 sec BIR_G 14 03 41 5 0 sec V NIST612 14 04 21 5 0 sec BCR2G 14 05 33 5 0 sec BHVO2G 14 06 02 5 0 sec BIR 14 06 30 5 0 sec d NIST612 14 07 10 5 0 sec _ BCR2G 14 07 52 5 0 sec BIR_G 14 08 23 5 0 sec BHVO2G 14 08 50 5 0 sec V NIST612 14 09 35 5 0 sec BCR2G 14 10 48 5 0 sec 3l AA E Figure 4 3 The Automatic integrations from metadata window of the select from laser log file tool 32 CHAPTER 4 SOFTWARE FEATURES DIRECTORY ve Start Crop ve Start Crop tve End Crop ve End Crop Laser On Laser Off Figure 4 4 Illustration showing how positive and negative crop times affect the dura tion of a selection Note that the same effect occurs when creating selections from files I
38. BCR standards 3ync method Syne window D 5 a A 3 6 Set Sample runs Import IS values Set STD IS vals Run Traces DRS Move Missed Shots Good Epidote Shots Check Data before Export Export data import my laser log file Figure 4 25 Options for the import laser log action loaded the log file in a separate action See Import Laser Log above for details on loading laser log files From File 1 Action Name set this to make it clear what your action does 2 Action Type although already set you can change action types by using this dropdown menu 3 Method set how you d like to create selections here 4 Group to add to Set here which group the created selections will be added to You can use the dropdown menu marked as to select from your standard list Baseline 1 or type some text in the field to create a new selection group If what you type is exactly the same as the name of a standard or Baseline 1 it will add the selections to that standard group or Baseline 1 Make sure that if you type a new selection group name that it begins with a letter doesn t include 58 CHAPTER 4 SOFTWARE FEATURES DIRECTORY Igor Pro 6 36 Ele Edt Data Analysis Macros Windows Graph Mpc Help Gizmo Zoom Iolite Image Template _Epidote Resume Actions Edit actions Template lag import data settings for Set Baselines Om type Create Selections D Method From He D dto
39. Baseline Tab for the demo zircon U Pb experiment Selections for the primary standard Z 91500 Selections for the secondary reference material Temora2 Unknown sample selections for the demo zircon U Pb experiment DRS settings for the demo zircon U Pb experiment Results of the demo zircon U Pb experiment The Time Navigation Window and corresponding portion of the data wave displayed in the main browsing window Selecting the Spline Type in the main browsing window The Automatic integrations from metadata window of the select from laser log file 10 Illustration showing how positive and negative crop times affect the duration of a selection Note that the same effect occurs when creating selections from files Information from Import The Automatic integrations from beam window Activating the Channels Drop down List The Channels drop down menu highlighting the channel selections and Add Channel drop down 6 5 LIST OF FIGURES 4 8 4 0 4 10 4 11 4 12 4 13 4 14 4 15 4 16 4 17 4 18 4 19 4 20 4 21 4 22 4 23 4 24 4 25 4 26 4 21 4 28 4 29 4 30 4 31 4 32 4 33 4 34 4 35 The Channels drop down menu highlighting the scaling tools Make Primary Get settings from and Auto Setup buttons
40. Data E Settings for Import My Data Action type Import D File type X seres csv I Data as file el Date format use default Le Machine type Automatic File path select a path for import am Figure 4 21 A new action in the main processing templates window to save the file interactively By saving the template log you can then later see exactly what happened when you ran the Template This can be really useful with troubleshooting later on If you would like to inspect your experiment for example before exporting your results you can add a Pause action This will simply pause the Template while you have a look at your results and then you can resume your experiment when you re happy with your experiment The following subsections describe the options available for each of the processing template actions 4 24 1 Import 1 Action Name set this to make it clear what your action does 2 Action Type although already set you can change action types by using this dropdown menu 3 Import File Type what type of raw mass spec file to open 54 CHAPTER 4 SOFTWARE FEATURES DIRECTORY hi Igor Pro 6 36 File Edit Data Analysis Macros Windows Graph Misc Help Gizmo Zoom Iolite Image ji Processing templates ba a a Template KENN Actions Edit actions Template log import data Settings for Set STD IS vals Action type Create Load IS Values El Set Baselines Method
41. E ppm 62 5 2 4 28 La ppm EL 0 7 29 ppm 40 2 5 2 Figure 4 15 View Reference Values window with the values for the reference material NIST612 shown function to choose your selections instead of manually labelling each selection period Note that for standard selections the DRS will look in the standard files and extract a value from there if there is an entry for the internal standard element lf not it will use the default value set by the user 4 20 Limits of Detection The limits of detection based on Longerich et als 1996 work are defined as 1 1 1 LOD 3 x1 4 1 S Np L So where the LOD is the limit of detection for the element lo is 1 standard deviation of the background measurement for this element n is the number of measurements in the background selections e g number of sweeps in the background measurement for a 60 s background measurement 60 s x 2 sweeps per second 120 background measurements n is the number of measurements in the sample selection as for backgrounds and S is the sensitivity e g cps ppm 4 21 U PB GEOCHRONOLOGY 3 DRS 43 Sensitivity is calculated by S Tamal x E x Sei 4 2 oet Ry Scal CT D sam where Rancal is the count rate of the analyte e g 5Sr in the calibration standard e g NIST612 usually in cps Canet is the concentration of the analyte in the calibration standard Rygsam is the count rate of the internal standard IS isot
42. Figure 3 1 select Ca43 for the channel from the drop down menu in the data filter section in green at the top of the window Select is less than and enter a low value such as 20 The portions of the wave that this filtered region pertains to will be highlighted in bright green in the data display portion of the window These periods will also appear in the filtered data list in blue at the left side of the window Enter a starting crop of 5 seconds and an end crop of 3 seconds in the Crop data tool at the top right of the screen Then click select all from the filtered data list at the left of the screen Choose the selection type you wish to apply these selections to Baseline 1 in this case and click Add Integration at the top right of the window Then click the close button at the top right of the screen 14 3 1 Select All Deselect All 178 of 179 periods selected D MI Z0110831 d 84 201 10831 12 24 59 PM 115 sec 12 27 11 PM 13 sec E 8 201 10831 6 12 27 40 PM 26 5 sec 64 M1 20110831 d 12 28 30 PM 6 7 sec TRACE ELEMENTS IS DEMO 15 Automatic integrations from beam Close Add integrations E ium duration _ Zoom Auto An Out Manual Channel to view TotalBaam Integration type Basalina 1 Show sample labels Mi 20110831 d 12 28 52 PM 11 2 sec E MI Z0110831 d 12 29 19 PM 24 1 sec m MI 20110831 d 12 29 59 PM 57 1 sec Ed MI 201
43. For each export option any currently visible Geostar images will be saved as part of the exported image At the moment the only export format for images is pdf but 4 24 PROCESSING TEMPLATES 51 if enough users wish to export files in another format options can be added other possible file types include PNG TIFF JPEG EPS etc 4 24 Processing Templates Processing Templates are essentially macros that perform repeated tasks that are common to each dataset If your lab is routinely using the same parameters such as naming conventions for files background measurement times etc then Processing Templates may save you a lot of manual interaction You can start with a blank template set it up for one dataset and then use it to process other datasets To start a Processing Template go to the iolite menu and select Processing Templates or hit Cmd 3 Cntl4 3 on PC on the keyboard The main window will look like Figure 4 19 hi Igor Pro 6 36 File Edit Data Analysis Macros Windows Graph Misc Help Gizmo Zoom lolite Image Y Processing templates Template Actions Edit actions Template log click on an action to edit its settings Figure 4 19 he main processing templates window The buttons along the top allow you to Save and Load Templates which are stored as simple text files with the file extension tpl You can open an existing tpl file and read it in a text editor and even edit it there if yo
44. Hide Show file labels and Show selection labels boxes and the Add Channel drop down menu 35 Location of the Sample Info button indicated by the blue arrow in the main browser window This feature is available in the Baselines Reference Materials and Samples tabs 36 The Sample Info window showing a number of unknown sample selec tions A single selection has been chosen in the Sample Info window marked in red and the corresponding selection box has been auto matically highlighted in the main browser window 37 The Trace Elements Control Panel 2 38 Internal Standard Values 0 39 Export Settings window sx cox os a a e mess sees 40 Edit lolite s default settings window 41 View Reference Values window with the values for the reference ma terial NIS TOI2 shown 23x 9 eR x9 a 42 Down hole fractionation correction window 4T The CellSpace Imaging 48 CellSpace explanation 40 The main processing templates 00 51 Processing templates add action dialog 52 A new action in the main processing templates window 53 A processing template with a lot of actions 54 A processing template 1 55 Options for the import 8 0
45. Info window showing a number of unknown sample selections A single selection has been chosen in the Sample Info window marked in red and the corresponding selection box has been automatically highlighted in the main browser window Name Table and choose a location to store the file Once this is done the user must load the table by clicking on the Open Int Std data button and selecting the file pertaining to data being deconvoluted The user can then check whether the load has been successful by clicking on the now visible Show Int Std data button A window will appear Figure 4 12 in which the user can select any of the existing selections for that lolite experiment and check the Internal Standard Values in wt for each individual selection The Internal Standard Value for any reference material should match the value in its corresponding standard file The user can check a standard file by clicking on the lolite Menu and selecting View reference values The Internal Standard Value for the unknowns should match the user defined DefaultIndexContentInSample value in the DRS Specific Settings in the DRS Tab 4 16 lolite Menu The lolite menu found above the Main User Interface contains a number of sources of information lolite commands and tools summarised below About lolite By clicking on About iolite from the lolite Menu the user has two options About iolite and Register iolite The About iolite
46. Shots m Good Epidote Shots Check Data before Export Figure 4 24 Options for the import action Offset if you already know the offset between the laser data and the mass spec data 6 Laser log file and mass spec data Offset if you ve set the Sync Method to Specified Offset use this field to set the offset between the laser log file data and the mass spec data NOTE importing laser logs and creating selections based on them are separate actions See Creating Selections for how to create selections based on an imported laser log file 4 24 3 Create Selections This action allows you to create selections automatically using one of three methods From File if each sample is recorded in its own file and you use regular timings for each sample you can use this option for creating selections From Channel create selections based on the values within selected channels Can be based on up to three criteria From LaserLog This will create selections based on an already loaded laser log file NOTE to create selections based on a laser log file you must have already 4 24 PROCESSING TEMPLATES 57 d Igor Pro6 36 File Edt Data Analyses Macros Windows Graph Misc Help Gaz me Zoom lote Image Template Actions Edt oho Template lag import data Settings for Import my laser log file Don type Import Laser Log Set Baselines Set GSD Standards File path method Prompt user 184 3 Laser log file Nobtused Set
47. alues that may overlap this spot and calculates the average e g Fig 4 18 b and c This has a smoothing effect but also reflects that for parts of the spot area we have more than one measured value 4 23 CELLSPACE IMAGES 49 5 5 5 615 5 8 18 8 5 51515 5 5 ep zi dde o St ne vw um 8 5 5 5 5 3 A A 6 18 18 158 5 5 T 30 3 30 3X0 32 19 18 18 15 19 5 8 7 A 29 30 3X X a 18 18 18 Y 30 30 30 50 19 30 8 6 d e Figure 4 18 CellSpace explanation The magnitude of these smoothing effects should be limited to areas within spots and thus features less than a couple of spot widths may be smoothed out Please be aware of this effect and it is strongly suggested that all users are aware of features in the raw data and whether these are transmitted to the processed data lolite repeats this step for each mass spectrometer measurement see masking below 4 23 2 A note about resolution and image size GeoStar exports images by default with a very high resolution nearly one pixel per micron This is fine for very small scale stuff but for large images i e larger than a millimetre square this will end up being a really large file in lolite Also the first GeoStar image you open will determine the resolution of the sample image i e the laser ablation data image Because lolite calculates the value of each pixel over the ablation area a high resolution may take a long time to calculate For examp
48. an be viewed for each mass analysed and any changes to the period of an individual baseline or to spline parameters e g the degree of smoothing are instantly displayed In addition to smoothing splines a number of different forms of interpolation are available to the user including more conventional methods An individual baseline spline spanning the duration of all data being reduced is calculated for every mass measured Baseline subtracted beam intensities are calcu lated by subtracting the baseline spline from the raw beam intensity at each data point lolite has a number of options available to use in the calculation of statistics for baseline data including various forms of outlier rejection and a choice between using mean or median based approaches These different statistical approaches can be chosen in the DRS tab By default baseline statistics are calculated as the mean of the data with no outlier rejection Although outlier rejection is often useful when processing laser ablation data it can cause significant problems when applied to low level baselines This is because for typical dwell times a single count will translate into tens of counts per second for example a 30 ms dwell time will extrapolate a single count to 33 counts per second For low background levels e g several counts per second this effect results in beam intensities consisting predominantly of 0 counts per second punctuated rarely by cou
49. an set what intensity units your mass spec trometer measured in Usually it is CPS counts per second for quadrupole instruments and V volts for multi collector instruments This setting has no effect on the calculated results and is only used to name baseline subtracted channels e g Sr88 Sr88 CPS after baseline subtraction 6 Beam second method This is how iolite should determine when the laser switches on which is a proxy for pit depth This is important because we want to be able to compare the same depth within our standards and our samples We shouldn t assume that every selection begins when the laser switches on and ends when the laser switches off due to inclusions growth zones drill throughs etc More details about this is provided on the website lhttps iolite software com downhole corrected upb ages and general workflow of the u th pb https iolite software com estimating laser pit depth using the beam seconds channel 10 CHAPTER 4 SOFTWARE FEATURES DIRECTORY Igor Pro 6 36 File Edt Data Analysis Macros Windows Graph Misc Help Gizmo Zoom lobhte Image 10 Processing templates o t Actions Edi actions Template lag import data Settings for Import IS values 4 2 iction type Run DRS UPbGeochrond Set Baselines ndex channel U23868 e ES Reference standard 2_91500 4 SelBCRstandards Z ntensity units CPS sel GSD Standard
50. and main browser window which has seven tabs Import Baselines Reference Materials Samples DRS Results and Images The tabs in the main browser window are generally used in a left to right workflow 2 1 Import Tab bolite w3 Untitled Experiment 600 import Baselines Reference Materials Samples ORS Results images File Type Nu Plasma time resolved rum 5 Import Import Type Single select a single file to import Import Report Date formal ddimenyyyy Freres Machine Nama Automatic 5 Figure 2 1 Import tab of the main iolite window The Import tab Figure 2 1 allows the user to select the File Type to be im ported The user must then select the Import Type of the desired data file either a Single data file from one experimental session or an Entire Folder of data files if data types for which import modules have been created will be listed in this menu 6 CHAPTER 2 USER INTERFACE the user wants to import all the files from within a folder Note that files in subfolders are not loaded It is important for the user to make sure that the Date Format selected on the Import tab matches the date format of the data file the user wishes to import If not the data will not be imported successfully The Nu format file box is used for older Nu Plasma run files only These files contain no header information so iolite has no way of working out what each colum
51. at if you type a new selection group name that it begins with a letter doesn t include any spaces or non word characters i e anything other than A Z 2 0 9 _ and that it isn t longer than 16 characters long 60 10 L1 12 13 CHAPTER 4 SOFTWARE FEATURES DIRECTORY Start Crop This is how much to trim off the start of each selection Please see Figure 4 4 to understand how negative and positive numbers affect this cropping End Crop This is how much to trim off the end of each selection Please see Figure 4 4 to understand how negative and positive numbers affect this cropping Spline Type What spline type to use for this selection group Note that this is only used for reference materials and baseline 1 samples are not splined What to do with existing selections If there are already selections in this group this option allows you to choose what to do with them Use delete to delete any selections already in this group Use append to add to this group keeping the selections already there Minimum duration set here how long each match must last for to be included This is to avoid cases where the background noise just happens to match your criteria Usually this will be for a very limited amount of time usually lt 1 s which we can avoid using this field Channel name Specify here what channel to base your criteria on This channel must exist when the action runs but does not need
52. ber and activation key sent to you in an email from iolite Install iolite using the iolite installer You should have received an email from iolite with a link to the iolite 3 download Download that file and install iolite 3 by double clicking the installer Run Igor Pro as an administrator by right clicking on the Igor Pro item in the start menu and selecting Run as administrator When lgor Pro starts up you should see a small iolite welcome image with Loading written on it When prompted click Yes to start the 7 day trial You will need to make sure your internet connection is working before starting the trial Once you ve clicked Yes you should see a window saying that your trial has started and when the end date is You now have a fully functional trial working on your machine To register iolite go to the iolite menu and select About lolite Register iolite Then enter your details along with the iolite licence key you received in your email from iolite Click OK and you should see a message thanking you for registering iolite You are now using a fully licensed version of iolite 3 For those who have iolite v2 x already installed on their computer ht tp www wavemetrics com 4 CHAPTER 1 INTRODUCTION 1 Make sure that you have the latest version of Igor Pro on your computer Check for updates using the item in the Igor Pro Help menu 2 You will need to delete the links to iolite v2 x You can do
53. ched the Output Channels will be available Multiple Channels can be viewed simultaneously Once a second channel is selected by selecting from the Add Channel drop down menu 2 in Figure 4 7 the user will be able to choose which channel is Primary by clicking on the Make Primary button next to the different channels 3 in Figure 4 8 The y axis of main display window will correspond to whichever channel is currently Primary The button next to the Primary Channel at any given time will not be selectable and be labelled Primary KR 238 Primary Scaling Auto A Co our gt Log Manual m Hide 2 Add Channel Get settings from AutoSetup Show file labels Show selection labels Figure 4 7 The Channels drop down menu highlighting the channel selections and Add Channel drop down menus Below each channel in the Channel Drop down List are the Scaling Tools 44 in Figure 4 8 The Scaling Tools allow the user to zoom in and out of the wave by alternating the y axis scale The user may select for this scale to be determined automatically or manually in which the user may type in the y axis minimum and maximum values by using the corresponding buttons adjust the scaling by clicking the up and down arrows and switch between and linear Lin or logarithmic Log scaling The user is additionally able to change the colour of a channel s wa
54. cond for quadrupole instruments and V volts for multi collector instruments This setting has no effect on the calculated results and is only used to name baseline subtracted channels e g Sr88 Sr88_CPS after baseline subtraction 6 Threshold to use when masking low signals this setting is important Any time the index channel drops below this value the intermediate and output channels will be blanked set to NaN and you won t get any results for these periods This is to make it easier to see variation in ratio channels without having to look at all the noise in the baselines If you see your samples being clipped check that you haven t set this value too high You can also set it to 0 to see what effect it has when it s turned off 7 Seconds to trim before after low signals This is how many seconds will be trimmed cropped see Figure 4 4 before after each time the Index Channel drops below the Threshold described in 6 Set this to 0 to show the sharp boundaries each time the index channel crosses the threshold Usually this is set to 1 so that baseline spikes aren t included in the un masked data 4 24 PROCESSING TEMPLATES 69 8 LOD method How to calculate the Limits of Detection LOD Use Normal to use the Longerich et al 1996 method which is 3 x background_1_sigma x S where S is a sensitivity factor See Longerich et al 1996 for full details Note that this method will produce an LOD value of 0 for channels that
55. cs for their data in some cases it may be sufficient to use lolite s median based statistical methods Note an ideal bell curve can be toggled on or off behind the histogram to assist in comparisons 4 23 CELLSPACE IMAGES 47 eoo Raw 206 238 Down Hole The equation for the fit is 0 22 y a b Exp CX 0 20 Exponential function Auto Manual 0 18 a 0 183672 b 0 0516657 c 0 0778352 0 16 masking of start end 0 14 start trim seconds 0 E end trim seconds 0 ls quality of fit 0 12 Standard error in X 1 048 Residuals of the fit to the average black wave expressed as Bias of fit in 0 0309 4 0 kW A RM wi 21 Oe ee 0 10 20 30 40 2 0 2 4 Seconds since shutter open 8 Show ideal Gaussian curve Figure 4 16 Down hole fractionation correction window 4 23 CellSpace Images To use this functionality you must be using a laser system that creates a valid laser log file that records the laser spot position versus time To be able to plot laser ablation data onto referenced images currently you must be using ASI s GeoStar software to produce a coord file to go with your transformed image See GeoStar s help manual for more info on saving out coordinated images Start by importing your data as normal Then add baseline integrations by hand and create output and standard integrations using the laser log file Make sure that the sync between the mass spectrometer data a
56. ctions and editing their options until you ve effectively programed your data reduction process This might include selecting various samples reference materials baselines and running a DRS An advanced template might also include making selections based on certain channels or move selections based on certain criteria such as its 2SE for a particular channel or its selection label When you have finished adding and editing features you can save the Template as a new template file by clicking the Save As button at the top and to save any changes afterwards by clicking the Save button Then when you want reopen the template you can just click on the Load button at the top To run the Template click the Run button at the top right The right hand side of the window will then show the Template log This will tell you what is happening as each action is performed As each action is completed it is listed as finished The currently executing action has a progress indicator showing how the action is progressing Once the Template finishes it will automatically save the contents of the log to the same folder as your import data or if your template doesn t include an import step you will be prompted 4 24 PROCESSING TEMPLATES 53 hi Igor Pro 6 36 File Edit Data Analysis Macros Windows Graph Misc Help Gizmo Zoom Iolite Image is Processing templates o mm Template vo 6 28 86 38 Actions Edit actions Template log Import My
57. d to the DRS tab and select the U Pb Geochronology 3 DRS from the Current Data Reduction Scheme drop down menu Figure 3 9 Choose U238 as your Index Channel Z 91500 as your Reference Material Cutoff Threshold as your BeamSeconds method and 20 for your threshold to use when masking low signals Step 6 Downhole Fractionation Correction Once the user presses the Crunch Data button in the DRS tab three pop up windows will appear Raw 206 238 Down Hole Raw 207 235 Down Hole and Raw 208 232 Down Hole windows These windows allow the user to implement the Downhole Fractionation Correction tool Step 7 Results Once the user has implemented the downhole fractionation correction and crunched the data in the DRS tab they may proceed to the Results tab The user can then 22 CHAPTER 3 COMMON DRS DEMONSTRATIONS lolite w3 U Pb example Reference Materials Samples images General Settings Stats for baselines Mean no outlier reject Stats for normal selections Mean with 35 0 outlier reject D DRS Specific Settings DRS Report Current Data Reduction Scheme U_Pb_Geochronology3 10 15 26 AM The DES 5 requires a index Channel U238 o Were UEa Baseline 17 in the folder splines 35 proceed further Reference Material Z 91500 a 10 28 57 AM The DRS UL Pb Dechronelegy 3 requires that Default Intensity Units CPS you select at least one
58. djusted to view large periods e g to view drift in background levels throughout an entire session down to very small details e g to examine an individual period of baseline acquisition or anywhere in between Using this information the user then selects periods of time containing suitable baseline data which will then be used by lolite in calculating baseline subtracted beam intensities If at any stage the user wishes to add remove or modify baselines this can be done quickly and easily with any changes reflected in the recalculated data In order to subtract baseline intensities from sample and standard analyses values need to be interpolated between the periods of baseline data In other data reduction packages such interpolations often involve a simple linear interpolation of the baseline data immediately adjacent to each sample standard analysis or the averaging of a large group of baseline analyses However because lolite works with the time of acquisition of each data point it is capable of more powerful interpolative methods such as smoothed cubic splines These splines can be adjusted to fit more or less strictly through each baseline analysis and can give varying degrees of weighting to individual baseline analyses based on the calculated uncertainties of each time period This means that a few seconds of baseline data will be given less weight than several minutes of high quality baseline The resulting interpolated spline c
59. e The user first selects the channel they wish to filter and then enters a value and selects whether they want to filter out portions of 410 AUTOMATIC SELECTION WC HSN Gop data in Match text NIST612 San 3 End 3 Select All Deselect All GNS 1 V NIST612 12 27 27 5 0 sec BCR2G r1 12 28 10 5 0 sec BHVO2G 12 28 39 5 0 sec 12 29 06 5 0 sec V NIST612 12 29 46 5 0 sec BCR2G r2 12 30 59 5 0 sec BHVO2G 12 31 29 5 0 sec O BIR 12 31 55 5 0 sec NIST612 12 32 35 5 0 sec BCR2G r3 12 33 18 5 0 sec BHVO2G 12 33 47 5 0 sec BIR_G 12 34 14 5 0 sec NIST612 12 34 54 5 0 sec BCR2G r4 12 36 07 5 0 sec BHVO2G 12 36 36 5 0 sec BIR_G 12 37 03 5 0 sec NIST612 12 37 43 5 0 sec BCR2G r5 12 38 26 5 0 sec BHVO2G 12 38 55 5 0 sec BIR_G 12 39 22 5 0 sec V NIST612 12 40 02 5 0 sec BCR2G r6 12 41 14 5 0 sec BHVO2G 12 41 43 5 0 sec 8 12 42 10 5 0 sec NIST612 12 42 50 5 0 sec BCR2G 7 12 43 33 5 0 sec BHVO2G 12 44 01 5 0 sec BIR 12 44 29 5 0 sec NIST612 12 45 09 5 0 sec BCR2G r8 12 46 22 5 0 sec BHVO2G 12 46 50 5 1 sec BIR_G 12 47 17 5 0 sec NIST612 12 47 58 5 0 sec BCR2G r9 12 48 41 5 0 sec BHVO2G 12 49 09 5 0 sec BIR_G 12 49 36 5 0 sec V NIST612 12 50 16 5 0 sec BCR2G r10 12 51 29 5
60. e helpful video tutorials and the iolite user forum where you can ask questions about iolite and interact with others in the LA ICP MS community 1 1 Installation and Opening Make sure you have Igor Pro version 6 36 or greater installed on your computer a 30 day trial version can be downloaded from the Wavemetrics website Download the lolite application and example files from the lolite wiki http iolite software com Shttp www wavemetrics com http iolite earthsci unimelb edu au wiki doku php id example files 1 1 Mac 1 PC INSTALLATION AND OPENING 3 Copy the lolite v3 folder to a place on your computer where you won t need to move it again soon Double click on the Run me to install this version pxp file This will tell Igor Pro where your iolite files are stored Move the file called EasyHT TP xop to the Igor Extensions folder which will be in the Wavemetrics folder in your Documents folder Start Igor Pro You should see the new blue iolite logo at startup and be prompted to start a 7 day trial Click Yes to start the 7 day trial To register iolite go to the iolite menu select About lolite Register iolite Enter your details along with the iolite licence key For those who are completely new to iolite Install Igor Pro on your computer following the instructions given on the Wave metrics website You can download the Igor Pro installer and use the serial num
61. e and a preliminary baseline trace will also appear an average of the single area selected Note the y axis of this box defines the 95 confidence limits As the user edits the size of the box its size will change automatically to reflect this confidence interval This is another very nice feature of lolite the user can instantly see the results of any changes made Clicking outside the dashed selection period will accept the new selection period This selection will then be assigned to the Active Selection selected at that time The user may Edit Selection Periods at any time after they have been defined 410 AUTOMATIC SELECTION 20 600 lolite v3 Five Seconds Basalt Import Baselines oReferenceMateriaiss Samples ORS 865 5 images 1 0010 G_N6T6l2 Automatic Channels 0 8 0 6 TotalBeam HA 0 2 0 0 12 30 PM 12 45 PM 1 00 PM 1 15 PM 1 30 PM 1 45 PM 000 PM 31 8 11 Figure 4 2 Selecting the Spline Type in the main browsing window 4 10 Automatic Selection Instead of manually selecting each selection period the user can use the Automatic Selection function by either selecting Automatic Selections from the lolite drop down menu or by using the Command 2 shortcut By making selections using the Automatic Selections tool the selections will also automatically be given labels further streamlining the data reduction process A pop up men
62. ed in 9 Set this to 0 to show the sharp boundaries each time the index channel crosses the threshold Usually this is set to 1 so that baseline spikes aren t included in the un masked data 4 24 8 Pause There are no settings for this action but it does allow the analyst to check the data before continuing on with the Processing Template Usually you might want to do this before exporting your results etc After you have finished checking your data you can then click on the Resume button at the top right to continue the Processing Template 4 24 9 Export Data 15 Igor Pro 6 36 File Edit Data Analysis Macros Windows Graph Misc Help Gizmo Zoom Iolite Image Di Processing templates S Actions Edi achans Template lag import data Settings for Export TE data D 2 Action type Expert ntegrations Qutput 1 Set GSD Standards i Outputs defaul P Set BCR standards un sorttype by Te 15 Set Sample runs Export path C Users Bence Documents Testers TesiData 6 ae me Export name TE Results Sample25 147 Import S values Uncertainties intemal only D Set STD IS vals Run Traces DRS Move Missed Shots Good Epidote Shots Check Data before Export Figure 4 35 Options for the export action 1 Action Name set this to make it clear what your action does 2 Action Type although already set you can change action types by using this dropdown menu 2
63. ee eee 35x10 0 5 10 15 20 25 m TotalEeam TotalBeam Frequency Seconds since start of selection nn Figure 2 6 Stack Plot display of the Results Tab 2 7 IMAGES TAB 13 SelectionLabel EE pael oe lonser mes EH AH i e L AEL eR Le iil EER anaa ei a ii i i A a E E E 122850 E E E 41 73 PESCHE BERECHNET AE E E TE ae sae E E E E EE e 11 191638 A A E E Y A 0110831 31 8 11 12 32 07 14 805 M 20110831 4 D 1 1 EE m EE ECT hp as oo 94 oust tg amp A Basse i ri urzoriossra 39 8011 3z3s3z irzosjezoriossia Tns 34 73 3 BUER 31 8111 123859 112658 291918 8 1 taal 314 372 31 2 Baseline 13 M Z0110831 d 31 amp 11 12 34 26 24 107 M 20110831 4 ae ME a 28 PECH BECKER BECHER BECHELER EECHER EECH BERECHNET REELLE EEN TE Baseline 1 15 M 20110831 d 31 8 11 12 37 54 27 708 M 20110831 d 11 66 baj G arel Baseline 20 M 20110831 d 31 8 11 12 38 39 1Z 70s M 20110831 10 6 v4 OI UU ZA A ases i zi urzorioeite 31 8111 123961 amazona 161 12 i56 zi Baseei zz uezoriossrs 39 8111 123930 2416785299 89 1 605 658 5 am
64. efore when opening a new DRS or a new file the settings will default to those of the selected DRS Once the General Settings and DRS Specific Settings are selected the user may click on the blue Crunch Data button lolite will then run the selected DRS using the specified settings to e g perform baseline subtraction interference corrections and or isotope ratio calculations Any information warnings or errors that may arise during the data crunching will appear in the DRS Report Once this has been done the user will be able to view the Results Tab 2 6 Results Tab In the Results Tab the user is able to view the outputted data generated by the application of the DRS to the experimental data The Results Tab is comprised of two general sections as seen in Figure 2 4 1 a row of five blue buttons and 2 the data display Four of the five blue buttons at the top of the Results Tab labelled Summary Stats X Y plot Stacked plot and Data Table correspond to different data dis plays The remainder of the Results Tab will display the data in the form corresponding to the data display type chosen by the user These different displays are described be low 2 6 1 Summary stats In the Summary Stats data display option a plot of channel values versus individual selections is generated Figure 2 4 The user can select the channel plotted on the y axis by using the drop down menu at the top of the windo
65. equently ignore Normally the user would choose the selections corresponding to the analysed unknown material during this stage in the process 16 We H nai Crop data in seconds Match text NIST612 San 3 End 3 Select All Deselect All G_NIST612 V NIST612 12 27 27 5 0 sec BCR2G r1 12 28 10 5 0 sec BHVO2G 12 28 39 5 0 sec BIR 12 29 06 5 0 sec V NIST612 12 29 46 5 0 sec BCR2G r2 12 30 59 5 0 sec BHVO2G 12 31 29 5 0 sec O BIR_G 12 31 55 5 0 sec V NIST612 12 32 35 5 0 sec LJ BCR2G r3 12 33 18 5 0 sec BHVO2G 12 33 47 5 0 sec BIR_G 12 34 14 5 0 sec Vf NIST612 12 34 54 5 0 sec BCR2G r4 12 36 07 5 0 sec BHVO2G 12 36 36 5 0 sec BIR_G 12 37 03 5 0 sec V NIST612 12 37 43 5 0 sec BCR2G r5 12 38 26 5 0 sec BHVO2G 12 38 55 5 0 sec BIR_G 12 39 22 5 0 sec V NIST612 12 40 02 5 0 sec BCR2G r6 12 41 14 5 0 sec BHVO2G 12 41 43 5 0 sec O BIR_G 12 42 10 5 0 sec V NIST612 12 42 50 5 0 sec BCR2G 7 12 43 33 5 0 sec BHVO2G 12 44 01 5 0 sec O BIR_G 12 44 29 5 0 sec 8 NIST612 12 45 09 5 0 sec O BCR2G r8 12 46 22 5 0 sec BHVO2G 12 46 50 5 1 sec BIR_G 12 47 17 5 0 sec V NIST612 12 47 58 5 0 sec BCR2G r9 12 48 41 5 0 sec BHVO2G 12 49 09 5 0 sec BIR 12 49 36 5 0 sec V NIST612 12 50 1
66. erials or Samples tabs the user may use the Sample Info button found in the top right corner of the main browser window Figure 4 9 Once the user clicks the Sample Info button the Sample Info window will appear Figure 4 10 The Sample Info window consists of a graph showing the mean primary channel values for each selection over the analytical session along with their uncer tainties f the user has not yet chosen selections for the given tab no data will be shown in this graph If the user clicks on a particular selection within the Sample Info 36 CHAPTER 4 SOFTWARE FEATURES DIRECTORY 600 e emm lolite v3 U Pb example Lesen 18 Basen nes Reference ce e Ma Materi rats 1 Sample 085 Results images Ar fe Re SE NN LLL LL LLL PUE OD LLL LLL orc m seme 7x10 T Output 1 zs Automatic amp Channels Output 1 78 13 TotalBeam Kiel ect Rove e 47 tpe eal RINT DE gies at Mii e iain ppt LE 3200 PM 3 30 PM 4 00 PM 4 30 PM 5 00 PM 5 39 PM Figure 4 9 Location of the Sample Info button indicated by the blue arrow in the main browser window This feature is available in the Baselines Reference Materials and Samples tabs window graph a number of pieces of information will be listed for the corresponding selection These include the average primary channel value the start and end times the total duration and the notes The user is able to edit a highlighted se
67. h environment featuring both MC and Quad ICP MS such that new techniques and data reduction algorithms could be added easily as required into the future All data reduction is handled by plug in Data Reduction Schemes DRS which can be created or edited by end users of the software and are by design essentially unconstrained in their capability The Igor Pro macro language is relatively easy to follow and most new users are soon able to modify any of the various built in DRSs where required to suit their own applications Whilst the overall package source code is not released the included DRS plug ins are open source by design t is in these where all time resolved data processing takes place Data may be imported from any ICP MS for which a time resolved import module has been written as long as that instrument s export data format includes enough information to calculate the absolute time of each time slice stored within the file A list of instruments and export formats that are supported by lolite can be found here Supported Instruments and Formats lolite was developed from an original concept by John Hellstrom under a Herman Slade Foundation Grant to Janet Hergt and Jon Woodhead Ongoing development is by Chad Paton now at STARPLAN Bence Paul and Jon Woodhead with the assistance and input of members of the Melbourne Isotope and Trace Element Geo chemistry Group Please see the iolite website for the latest versions of the softwar
68. hange action types by using this dropdown menu Method set how you d like to assign IS values here IS file Not used for Single value method Element which element to use This should be either the element symbol e g Ca for calcium or the name of an input channel which will be converted to its element symbol Selection group which selection group to assign the IS values to The IS values will only be assigned where there is a selection in this selection group Where Entire Session is used this field is not used and is equivalent to setting the default value Value The value of the IS to be assigned Units what units the IS value is in Set Ref Mats IS values The same as for other Create Load IS Values methods see above except that only the element to be used as 15 can be chosen This method will look for Reference Materials selections groups and apply the IS value from the relevant standard file to the selections in this group This will be repeated for all Ref Mat selections groups 4 24 6 Run DRS TraceElements IS This action automatically selects and runs the Trace Elements IG DRS You can edit the various settings for this DRS before it runs using this action 1 2 Action Name set this to make it clear what your action does Action Type although already set you can change action types by using this dropdown menu Index channel This is both the IS channel as well as a channel that
69. have no variation in their baselines e g a baseline that is all zeroes except when the laser is on This may suggest to some non specialists that the limits of detection are infinitely low which is rubbish The Howell method set to Howell replaces a background_1_sigma with 7 although it should be sqrt 7 for all channels that have a background with zero variation Check back here for our own approach in the future Set to None to avoid calculating LODs to speed up your Processing Template 9 Output Units What units to calculate the final results in Usually this is in ppm ug g but see the dropdown menu for other options 4 24 7 Run DRS UPb DRS Use this action to automatically select and run the UPbGeochron DRS This is a some what more complex DRS than the Trace Elements 5 DRS The reader is referred to Paton et al 2010 or the website for full details 1 Action Name set this to make it clear what your action does 2 Action Type although already set you can change action types by using this dropdown menu 3 Index channel This is a channel that is present in every analysis and is also usually the most abundant element measured usually 238U but may depend on your application 4 Reference Standard the reference material selection group to use as primary standard This group will be used for the downhole fractionation correction and well as normalisation of isotope ratios 5 Intensity units This is where you c
70. he appropriate selection periods Output time series as created and defined by a DRS are available for visualisation plotted concurrently with a variety of other time series These may include raw input data as well as intermediate series created by the DRS during processing Data processing can be iterative in that baseline or reference material selections can be added or redefined and the DRS re run or indeed more than one DRS can be run on a given data set to compare the effect of different data reduction algorithms Data within the lolite package can be saved to disk as Igor Pro Packed Experiment files which contain all time series and other data in memory plus all open graphs control panels and spreadsheets and a detailed data processing history These can be reopened for further processing or data export at any time 4 3 Terminology In keeping with Igor Pro terminology we use the term wave short for waveform to describe a one dimensional array of numbers it may be useful to think of a spreadsheet containing only a single column in our case waves are generally plotted versus time and tend to resemble a line graph The origin of the wave concept lies in the fact that Igor was originally designed to manipulate waveform data from a variety of scientific instruments such as oscilloscopes However the terminology is also suited to time resolved data acquired from laser ablation systems and so we will use it extensively See the Igor Pro
71. he method used to determine how long the laser has been on for Threshold to use when masking low signals When dealing with ratios which the majority of DRS routines do background values create nonsense ratios with enormous scatter 10 avoid the mess this causes we mask these nonsense portions of the waves this is done by replacing the noisy values with an empty data point leaving a gap in the data In choosing which sections of our analysis should be considered nonsense data we select a threshold value for the index channel and it is this threshold that this parameter refers to Note that for index channels expressed in CPS this will often be tens of thousands whereas Faraday collectors expressed in Volts may have values well below one Seconds to trim before after signals In addition to the above threshold iolite trims an additional segment off either side of the portions falling below the threshold This avoids the series of short segments that would otherwise be 10 CHAPTER 2 USER INTERFACE produced if the index wave were to sawtooth above and below the threshold point e Default Index Content In Sample This is the value iolite applies to the unknown sample selections for the index channel mass Generally this corresponds to an average concentration of the index channel mass in the material or substance being analysed Note that the chosen settings are specific to a single file Igor experiment and to a specific DRS Ther
72. he plot fit a curve to the data and select the colour gradient correlating with how long into the analytical session an individual selection was measured 2 6 3 Stacked plot If the user selects the Stacked Plot data display options lolite will construct a plot that stacks all of the individual waves for any selection type Figure 2 6 The user can select which waves they wish to stack by making a selection from the Stack analyses of drop down menu The user can similarly select which selection they want lolite to generate a Stacked Plot for with the For the selection type drop down menu The user can decide if they want the means and medians of the total and average data displayed by ticking or unticking the four boxes at the top right of the display 2 6 4 Data table When the user chooses the Data Table display type a detailed table describing the characteristics and results of each individual selection from each selection type is presented Figure 2 7 By clicking the grey Filter Channels button above the table the user may select the waves they want displayed 12 CHAPTER 2 USER INTERFACE Stack analyses of TotalBeam E Mean of all data dashed Export For the integration type Output_1 iT Mean of average only solid line E Median of all data dashed Mf Median of average only solid line q e
73. hecked or not unchecked Channel Value Exactly the same as Channel 2SE except that the average value for the selected channel will be used rather than the uncertainty for the selected channel Selection Label L 2 Action Name set this to make it clear what your action does Action Type although already set you can change action types by using this dropdown menu Method set how you d like to decide which selections to move here The from group Which selection group you d like to move the selections from Use the dropdown menu marked to select one of your standards or baseline 1 groups If the group doesn t exist when you re editing this action you can type the name of the selection group here It must exist when the action runs to avoid an error Group to add to Set here which group the selections will be moved to You can use the dropdown menu marked as to select from your standard list Baseline 1 or type some text in the field to create a new selection group If what you type is exactly the same as the name of a standard or Baseline 1 it 64 CHAPTER 4 SOFTWARE FEATURES DIRECTORY lger Pro 6 35 File Edt Data Analysis Macros Windows Graph Mpc Help Gizmo Zoom lolite Image Template _Epidote Resume Actions Edi actions Template lag import data Settings for Move Missed Shots 2 lion poe Moya Selections Method Selection Label M From group Output 1 set GSD Standards To group MissedSpo
74. hod From LaserLag w l 3 Group to add to GoodEpidote m 4 Set BCR standards Import IS values Set Sample runs sel STD IS vals Run Traces DRS Move Missed Shots Good Epidote Shots Check Data before Export E import my laser log file Figure 4 28 Options for the create selections from laser log action 5 Start Crop This is how much to trim off the start of each selection Please see Figure 4 4 to understand how negative and positive numbers affect this cropping 6 End Crop This is how much to trim off the end of each selection Please see Figure 4 4 to understand how negative and positive numbers affect this cropping 7 Spline Type What spline type to use for this selection group Note that this is only used for reference materials and Baseline 1 samples are not splined 8 What to do with existing selections If there are already selections in this group this option allows you to choose what to do with them Use delete to delete any selections already in this group Use append to add to this group keeping the selections already there 9 Match Text Selections will only be added when their comment matches the text in this field Use to match any comment Use to match any comment that doesn t contain the following text For example use INIST to select any files not containing the letters NIST Note that the match
75. ighted region resulting in the area of viewable data to shrink or expand A OO lolite v3 Five Seconds Basalt 822 Reference Materials Samples ORS Resuts images 10x10 E 8 E T o Baseline 1 Automatic 12 46 PM 12 47 PM 12 48 PM 17 49 PM 12 50 PM 31 8 11 m o CR Figure 4 1 The Time Navigation Window and corresponding portion of the data wave displayed in the main browsing window 4 7 Active Selection Active Selection refers to the selection group the user is currently working with That is any new selections will be added to this group and the selections from this group will be shown over the data The Spline Type chosen for a particular selection group will be applied to all data assigned to that group The results arising from the 20 CHAPTER 4 SOFTWARE FEATURES DIRECTORY application of Data Reduction Schemes to the wave data are displayed by selection type in the Results Tab When operating in the Baseline Tab the Baseline 1 is automatically selected Only one baseline selection type can be applied to each inputted data file In the Reference Materials Tab the user can select from a number of reference material selections from the Active Selection pull down in the top left corner of the User Interface In order for a particular reference material to have a selection type in the pull down menu a txt file must exist pertaining to that reference material in the Standards Fo
76. ing the cumulative signal of all isotope masses measured during the mass spectrometer 4 12 CHANNEL PANEL 33 Select All Deselect All 167 of 167 periods selected Yl MI 20110831 d 12 24 59 PM 145 sec 53 mi 20110831 d 12 27 40 PM 26 5 sec 1o NN MI 20110831 d 12 28 30 PM 6 7 sec l Ed M 20110831 d 12 28 52 PM 11 2 sec n Out Manual Channel to ios Integration type Basalina i C Show sample labels El MI 20110831 d 12 29 19 PM 24 1 sec 53 mMi 20110831 d 12 29 59 PM 57 1 sec 5 Mi 20110831 d 12 31 12 PM 13 3 sec 83 wi 20110831 d 12 31 42 PM 10 sec El MI 20110831 d 12 32 17 PM 14 8 sec 5 MI 20110831 d 12 32 48 PM 26 8 sec 4000 MI 20110831 d 12 33 32 PM 11 2 sec E MI 20110831 d 12 33 59 PM 11 2 sec 83 MI 20110831 d 12 34 26 PM 24 1 sec 53 Mi 20110831 d 12 35 07 PM 56 8 sec MI 20110831 d 12 36 20 PM 13 3 sec 3000 MI 20110831 d 12 36 49 PM 10 9 sec El MI 20110831 d 12 37 15 PM 3 1 sec 53 Mi 20110831 d 12 37 33 PM 6 4 sec MI 20110831 d 12 37 55 PM 27 7 sec Ca43 MI 20110831 d 12 38 39 PM 12 7 sec SS 5 MI 20110831 d 12 39 08 PM 11 2 sec 5 Mi 20110831 d 12 39 34 PM 24 1 sec MI 20110831 d 12 40 14 PM 4 9 sec MI 20110831 d 12 40 28 PM 43 6 sec 1000 4 di ABE 83 MI 20110831 d 12 41 28 PM 12 4 sec 8 MI 20110831 d 12 41 56 PM 10 6 sec MI 20110831 d 12 42
77. is case sensitive 62 CHAPTER 4 SOFTWARE FEATURES DIRECTORY 4 24 4 Move Selections Selections can be made and then moved to a new group This may be based on a several criteria a channel s 2SE i e how much noise there is in a particular channel a channel s value or by selection label Let s look at these in turn Channel 2SE ii Igor Pro6 36 File Edt Data Analysis Macros Windows Graph Misc Help Gizmo Zoom Iolite Image Aa Actions import data Sel Baselines Set GSD Standards Set BCR standards set Sample runs Import IS values Set STD IS vals Run Traces DRS Move Missed Shots Good Epidote Shots Check Dala before Export Export data import my laser log file Edi schen Template log Settings for Move Missed Shots Mk on type Move Selections Method Channel 25E v 3 From group Output 1 m 4 To group Missedspots 5 Mh oro e Ca43 CPS d 5 greater than v Move value 500 S 8 F F Preserve original 5818 50 5 9 Figure 4 29 Options for the move selections by channel 2SE action 1 Action Name set this to make it clear what your action does 2 Action Type although already set you can change action types by using this dropdown menu 3 Method set how you d like to decide which selections to move here 4 The from group Which selection group you d like to move the selections from Use the dropdown menu marked
78. l Standard is Ca TabieFormat Normal DefaultindexCantentin Sample 1 Export 5ample Mame Table Figure 4 11 The Trace Elements Control Panel Automatic Selections See Automatic Selections for more details with regards to this tool Mass spec syncing This allows the user to sync multiple mass spectrometers This is an advanced feature Contact us if you wish to use this feature for support at supportGiolite software com Remove sync offset This is used for mass spec syncing and should only be used by advanced users Export data This allows the user to export the results generated in an lolite experiment When this item is selected from under the lolite menu a green Export Settings window will appear Figure 4 13 The user must enter the desired name for the exported data file as well as select the sampling frequency of the exported data the selections the user wants to export the results of the waves to export the uncertainties they want exported and how they want the exported results to be sorted View exported data table This allows the user to view the data just exported as a table in Igor This can then be used to plot results in Igor rather than opening Excel and using it to plot results Display Meta Data This is used to view certain metadata gathered by iolite during sample import and laser log file import This feature is no longer supported View Reference Values See View Reference Values for details on
79. lder In the Samples Tab of the User Interface the user chooses selections Manually or Automatically and assigns these selections to a Sample selection The Sample selection refers to the group that individual selections chosen from the portion of the wave that pertains to the unknown samples analysed during the experimental session are applied to The user may choose to apply these to the conventional Output 1 selection type or create a new sample selection type by clicking on the drop down menu and selecting the Add new selection group option The user is then prompted to give a name to this new group 4 8 Spline Type To the right of the Active Selection drop down list is the Spline Type drop down list Figure 4 2 The method of interpolation between the baseline selections can be specified using the Spline Type pull down menu If this is left as automatic the interpolation mode will change with the number of points from average 1 point to linear 2 points to linear interpolation 3 and to a variety of splines for 4 or more points The degree of smoothing can also be chosen for the spline fits The user should try experimenting with these various options the fit will be continuously updated 4 9 Manual Selection The user can manually select a selections by simply holding down the Command key on Mac or Control key on PC and dragging a marquee over an area of the wave A box will appear over the selected baselin
80. le an ablation area 2 x 4 mm can take almost a minute to calculate each channel As lolite re calculates the image displayed every time you change which image is displayed this can be quite time consuming and just painful So if you have a large ablation area you can reduce the resolution of the mapped image in something like Photoshop etc as long as you don t change the image proportions I d advise checking this reduced image against the original to make sure nothing went astray Just as an aside the edge effects in the image above the strange bits on the corners etc is from Photoshop so maybe choose a resampling method that doesn t do this 4 23 3 Mask by integration type menu This drop down menu allows you to choose which integration you want to map This is because as described above lolite will attempt to calculate a spot shaped image for every mass spectrometer measurement This is important because the spots you see on the image are not when the laser was firing but the mass spectrometer reading while the laser was in this location As an example if you have a laser repetition rate of 1 Hz and a mass spectrometer sweep time of 100 milliseconds i e 10 Hz you will get 10 spots on the image for every second of ablation rather than just one To create the sample image lolite interpolates the laser x and y coordinates and spot size It then creates a circle centred on the interpolated x and y coordinates with a diameter eq
81. lect the Trace Elements IS DRS from the Current Data Reduction Scheme drop down menu Figure 3 3 Choose Ca43 as your Index Channel NIST 612 as your Reference Material Cutoff Threshold as your BeamSeconds method 20 for your threshold to use when masking low signals and an appropriate Default Index Content in this example this value doesn t matter since the Ca values from the standard files will be applied to all of the reference material selections Then click Crunch Data 600 lolite v3 Five Seconds Basalt import Baseines Reference Materials Samples Results images General Settings Stats for baselines Mean outlier reject Stats for normal selections Mean with 3 SD autlier reject DRS Specific Settings Current Data Reduction Schema Trace Elements I5 12 59 15 PH The 085 Trece Elements 18 requires 8 Wave Index Channel Ca43 t Tad CP5 6G RSTS iZ in 156 folder agli 55 ba proceed further Reference Material 15 612 E i m 3 1647 Ph The DES Trace Elements 15 requires 8 Wave Default Intensity Units CPS 5 atatia in the faldar Trace_Elemants_1S be proceed further Standardisation method Internal Elemental Standard Output Units ppm BeamSeconds method Cutoff Threshali Threshold to use when masking law signals Z0 Seconds to trim befare after low signals 1 BeamSeconds Sensitivity 4 TableFormat Normal DetaultindexGonbentinSampbe 1 Figure 3 3 Selecting the
82. lect the file you want to load 5 Element which element to use This should be either the element symbol e g Ca for calcium or the name of an input channel which will be converted to its element symbol 6 Selection group which selection group to look for the selection labels IS values will only be assigned where the selection label matches the sample name in the IS file 7 Value Not used for Import from File method 8 Units what units the IS value is in Not used for Import from File method Single Value entire session or selection group Igor Pro 6 36 Ele Edt Data Analysis Macros Windows Graph Misc Help Gizmo Zoom lote Image ia Processing templates le k Actions Edit actions Templatelog import data Settings for Import IS values ction type Create Load IS Values BeGsDsundads _ Method Single value selection group 3 nternal standard file Mot used 4 Set BCR standards ement Cat3 s Set Sample runs election group Ouipur 1 6 Value 1 L 35 Import S values uu Units percent D Set STD 15 vals Run Traces DRS Move Missed Shots Good Epidote Shots Check Data before Export Export data Import my laser log file Figure 4 32 Options for the create IS values from single value action 1 Action Name set this to make it clear what your action does 4 24 PROCESSING TEMPLATES 67 Action Type although already set you can c
83. lected file will then be shown in the text field This path must not be empty when you run the template or else iolite will not know which file to open 4 24 PROCESSING TEMPLATES 55 15 IgorPro636 File Edit Data Analysis Macros Windows Graph Misc Help Gizmo Zoom lolite Image M Processing templates Template c Actions Template log import data Finished Processing template report Set Baselines Finished Added 12 selections based on a match to GSD Set GSD Standards Finished Set GSD Standards successfully completed o Starting Set BCR standards Set BCR slandards WEIER Added 8 selections based on a match to bcr Set BCR standards successfully completed Finished Starting Set Sample runs Added 40 selections based on a match to Set Sample runs Finished Import IS values Set STD IS vals Finished Epidote set Sample runs successfully completed Run Traces DRS gt iJ Starting Import IS values Matched 40 sample labels with IDs in the Move Missed Shots Pending sample table Import IS values successfully completed Good EO ae penal Starting Set STD IS vals Set IS values for 12 G_GSD_1G Check Data before Export Pending selections Export data Pending Set IS values for 8 G_BCR2G selections Set STD IS vals successfully completed Starting Run Traces DRS Processing baselines Figure 4 23 A processing template running 4 24 2 Import Laser Log 1 Action Name set
84. lection by either clicking the Edit button that appears above a selection when the user hovers their cursor over it in the Sample Info window or by holding shift and clicking on a particular selection in the main browser window Once in edit mode the user may adjust the start and end times and the sample notes by clicking on the corresponding informational lines in the Sample Info window 4 14 Standard Files Standard files are txt files that define the values lolite applies to isotope concentrations and isotope ratios for different reference materials These can be found in the lolite v3 folder on your computer The lolite v3 folder will be found wherever the user placed during lolite Installation A template for creating new standard files for reference materials can be found in the Standards folder 4 15 Trace Element Control Panel When the user clicks the blue Crunch Data button on the DRS Tab the Trace Elements Control Panel appears Figure The user must then click on the Export Sample Name Table button lolite will ask the user to name the exported Sample 416 IOLITE MENU 37 Sample Info Selection name Output 1 intear Click to edit Group Output 1 TotalBeam run 3 42 um 3 30 05 PM 47 7 6 36 0 22 x10 Start Time 07 03 2008 15 30 05 44 End Time 07 03 2008 15 30 53 21 Duration 47 8 sec Notes run 3 42 NN run 3 42 um 3 30 05 PM 47 7 sec Th Figure 4 10 The Sample
85. lolite 3 User s Manual Prepared by The lolite Team School of Earth Sciences University of Melbourne ast revised March 15 2015 Contact supportOiolite software com How to use this manual This manual begins with an overview of iolite s user interface the main windows that the user interacts with It then provides a basic demonstration of the two most popular data reduction schemes in iolite trace elements and U Pb geochronology The third part of the manual describes particular features of the software in detail If you are looking for a particular section on how to do some thing we suggest you check the Table of Contents If you are learning how to use iolite we suggest you begin at the start of the manual and work your way through Contents 1 Introduction 1 1 Installation and Opening 2 User Interface 2 1 IMPOR SD ama Rx omo dis ense 2 2 Baseline 135 2 3 Reference Materials 1 32 5 2 4 Samples Tab 25 DRS Wa osos 4a ded bao E 2 0 Results AD om xoxo et m x wm XE en x 2 6 1 Summary stats s 25 2 eG Bee Ee 20 2 XY PIO once ed oe eee xou wo 2 63 Stacked 10 2 6 4 Data table 2 Images Tab 9 4 RR RE 3 Common DRS Demonstrations 3 1 Trace Elements IS Demo 3 2 U Pb Geochronology 3 Demo 4 Software Features Directory 4 1 Supported Instruments and Formats 4 2 Data Reduction Scheme
86. lude matches For example use NIST in the match text to match all NIST runs Use INIST to select everything else i e anything that doesn t include the letters NIST in the filename The user can then choose which selection group these selections will be added to as well as crop the selection periods by using the Crop data in seconds tool at the top of the window See Figure 4 4 for an illustration of the effect of increasing or decreasing the start and end crop times Once satisfied with the selections the user may click the purple Add integrations button 4 10 2 Laser log file If a laser log file is available from the experimental session it can be used to auto matically make selection periods Once the laser log file option is selected from the Automatic Selections pop up window the user will be prompted to select the laser log file csv file Once selected another pop up window will appear showing the wave results previously imported into the experiment on the Import Tab in blue and the periods of laser activation recorded in the laser log file in green The user must sync the two signals by dragging the laser log file signal left or right Alternatively the user may tick the Snap correlate box to have lolite automatically sync the signals Once the user is satisfied with the sync they can click Done A new Automatic integrations from metadata pop up window will appear Figure 4 3 where the user can select
87. ly to data This is intended for intermediate iolite users Modify lolite s default settings Here the user may alter the default settings for lolite Figure 4 14 Reset experiment After making changes to selections standard files data re duction schemes or lolite settings the user must reset the experiment in order to apply these changes to the current lolite experiment Combine multiple laser log files This function allows the user to combine multiple laser log files into a single file Before using this item you should put all the log files you wish to combine into a separate folder that doesn t contain any other files Then use this item to identify the folder and it will combine all the contained files into a new log file Don t forget to change the file extension when prompted on screen How to cite lolite This informational tool allows the user to see a list of refer ences for lolite and specific Data Reduction Schemes 4 17 View Reference Values When the user selects the View reference values options from under the lolite Menu a window appears containing a single drop down list From this list the user can select any reference material for which a Standard File exists Once a reference material is selected the list of values from the Standard File is presented regarding the isotope concentrations and isotope ratios for that particular reference material Figure 4 15 418 EXPORT DATA 41 600 Edit lolite s default se
88. mple 4 24 PROCESSING TEMPLATES 59 From Channel Igor Pro 6 36 File Edt Data Analysis Macros Windows Graph Mpc Help Gizmo Zoom Iolite Image Actions Edit actioris Template lag import data Settings for Good Epidote Shots Ar cion type Create Selections D Wathoct From Channel D Sel GSD Standards oup to add to GoodEpidote F a Endcrop 1 Set BCR standards EXISTING delete Set Sample runs 9 7 Minimu durabio Import S values 8029 v Ca43 Si20 v Ca43 Si Gradient Set STD IS vals 5 greaterthan 8 less than v is less than J S Ml 105 d 6000 Run Traces DRS 3 Move Missed Shots Good Epidote Shots E Check Data before Export Export data Import my laser log file Figure 4 27 Options for the create selections from channel action 1 Action Name set this to make it clear what your action does 2 Action Type although already set you can change action types by using this dropdown menu 3 Method set how you d like to create selections here 4 Group to add to Set here which group the created selections will be added to You can use the dropdown menu marked as to select from your standard list Baseline 1 or type some text in the field to create a new selection group If what you type is exactly the same as the name of a standard or Baseline 1 it will add the selections to that standard group or Baseline 1 Make sure th
89. n An integral feature of the U Pb Geochronology 3 DRS is its treatment of down hole elemental fractionation This feature has been specifically developed for this data reduction scheme and employs separate windows that allow interactive modelling of the pattern of down hole fractionation for each elemental ratio The modelling and correction of down hole elemental fractionation occurs after 4 22 DOWNHOLE FRACTIONATION CORRECTION 45 baseline subtraction of beam intensities but before the correction of instrumental drift By using data that is not drift corrected some variability is often present between reference standard analyses However this variability is seen as a parallel offset of the data and has no effect on the pattern of down hole fractionation in each analysis or in the modelling and correction of this effect lt is worth noting here that in treating down hole fractionation the number of seconds since the laser began firing for a particular spot analysis referred to here as ablation time is used as a proxy for hole depth which cannot be measured directly The beginning of ablation is detected using the rate of change in an index beam intensity the 238U beam by default this approach is highly reproducible and does not require any extra information from the mass spectrometer or laser software Once the user clicks the Crunch Data button in the DRS tab three pop up windows will appear Raw 206 238 Down Hole Raw 207 2
90. n of data in the file represents Instead the user needs to create a Nu format file for each type of run file they wish to use e g one for Sr isotopes one for Hf isotopes etc A video description of how to make and use these format files is available on You Tube The Machine Name selector only applies when the user wishes to sync multiple data files that are from multiple mass spectrometers If that is the case make sure the machine names and input data files correspond with one another Upon selection of a particular File Type and Import Type the user may now click on the blue Import button Figure 2 1 The user is then prompted to browse to the location of the appropriate file or folder If successful the data will then appear in the subsequent tabs Such time series data are referred to as waves in Igor Pro and we retain this terminology here to avoid confusion For further explanation of this term see the terminology section 2 2 Baseline Tab The Baseline tab is the first tab of the User Interface where the user s inputted waves can be viewed Figure 2 2 In the Baseline tab like any other tab in which an inputted wave can be viewed the standard iolite wave navigation and operations are used to navigate select and perform operations with the data The sample info panel can be used adjust selection display and characteristics This tab is designed to let the user perform baseline subtractio
91. n of their data The Baseline tab is divided into two sections the main baseline browser window in which the imported waves can be viewed and the time navigation graph at the bottom It is in the Baseline Tab that a user defines the appropriate sections of the data wave to use in baseline subtraction lolite automatically chooses the Baseline 1 active selection when the Baseline Tab is displayed The spline type iolite will apply to fit the baseline selections can be chosen by the second drop down menu to the right of the active selection drop down menu Using the wave navigation and operations procedures the user may zoom in on the wave to any desired level of detail The user may then select as many baseline selection periods as desired by manual selection or automatic selection As each baseline selection is defined iolite automatically updates the baseline fit according to the spline type chosen by the user At any time the user may edit selections previously selected http www youtube com watch v 7ydl5SGCxOc 2 3 REFERENCE MATERIALS TAB d lalite v3 Five Seconds Basalt sl Reference Materials Samples DRS Results images ETE ET AR UON 14x10 Baseline 1 Automatic Main Baseline Browser Window E 0 8 06 E m m 5 5 o i ga i 0
92. nd the log file is accurate or else your images will be offset and probably garbage Select your data reduction scheme and check that it has gone to completion and created output channels clicking on the Primary Channel drop down menu will show you which channels are available If no output channels are available check the command window Windows Command Window which prints out any messages regarding data processing it s actually a really important window so if you ever have any problems be sure to check this window You re now ready to create an image Click on the CellSpace button in the Images Tab It will ask you if you want to overlay the laser ablation data onto a mapped referenced image This is where you would load a GeoStar image if you have one If you don t have any image but do have a laser log file it is still possible to load an image Click Yes to open a GeoStar image and open the MAPPED version of the image NOT the original as we have no coordinate information about the original file See the note about resolution and image size below for more information about the implications of which file you open 48 CHAPTER 4 SOFTWARE FEATURES DIRECTORY The accompanying coord file that GeoStar creates must be in the same folder lolite then opens the image and automatically opens the coordinate file to map the image It then opens the image in a new window Fig 4 17 Laser ablaton data Mask by integration type Outp
93. nel to view 238 Integration type Qutput_1 m Show sample labels O run4 4 42um 4 50 04 PM 47 9 sec 1 run4 4 2 4 51 25 PM 48 4 sec 5 runa 4 42um 4 52 59 PM 47 2 sec Eel runa 4 4Zum 4 54 21 PM 47 3 sec 2 5x10 Ed rund 4 42 4 55 43 PM 47 2 sec 4 run4 4 4Zum 4 57 05 PM 47 2 sec E runa 4 AZum 4 58 26 PM 47 1 sec Ef runa 4 42um 4 59 48 PM 47 3 sec 2 0 E 4 4 42um 5 01 09 PM 47 6 sec E rund 4 42um 5 02 31 PM 47 3 sec 54 4 4 42um 5 03 53 PM 47 1 sec 5 runa 4 42um 5 05 15 PM 47 3 sec O runa 4 42 5 06 54 PM 48 1 sec O run4 4 42um 5 08 16 PM 48 sec O ona 4 42um 5 03 45 PM 48 9 sec O rung 4 42um 5 11 07 PM 48 3 sec 5 runa 4 42um 5 12 39 PM 47 3 sec Eel runa 4 42um 5 14 01 PM 47 3 sec E rund 4 42um 5 15 23 PM 47 2 sec Bf rund 4 42 5 16 44 PM 47 1 sec 5 runa 4 42um 5 18 06 PM 47 2 sec 0 5 5 runa 4 42 5 19 28 PM 47 2 sec MA 8 run 4 42um 5 20 50 PM 47 2 sec U238 Ed rund 4 42um 5 22 11 PM 47 1 sec Bf runa 4 42um 5 23 34 PM 47 3 sec 0 0 Bf runa 4 42um 5 24 56 PM 47 sec L run4 4 42um 5 26 34 PM 48 6 sec O run4 4 42um 5 27 56 PM 48 4 sec E 1 A ll ahh NUS 3 00 PM 3 30 PM 4 00 PM 4 30 PM 5 00 PM 5 30 P 7 3 08 Analysis Time m Figure 3 8 Unknown sample selections for the demo zircon U Pb experiment Step 5 DRS Procee
94. nformation from Import the wave that are greater than less than equal to or not equal to a particular value Additionally the user may select the portions of the wave that are not a NaN The user can add additional filters by clicking on the boxes at the bottom left of each filter column The filtered selection periods will be listed in the filtered data periods list on the left in blue The user then selects the periods of interest from the list and can add them to a selection type by clicking the purple Add integration button at the right of the screen 4 11 Editing Selection Periods Shift clicking holding down the shift key and clicking within an existing selection box places it into edit mode allowing that selection period to be modified If the user wishes to remove a selection period they simply shift click it to enter edit mode then hit the delete key The user may also move the selection period to a different selection type by hitting the m key while in edit mode e g if they selected a standard period as Baseline 1 by mistake 4 12 Channel Panel The Channel Drop down List can be accessed by clicking on the blue Channels button located at the top right corner of any tab of the User Interface that displays the data Wave Figure 4 6 Once the Channels button has been clicked the Channels Drop down List will ap pear Figures 23 and 24 The user is then able to select from either a wave display
95. ns and the reference standard may differ with factors such as U concentration or age It is therefore useful as always to use a reference standard of a similar composition and age to unknowns and to use secondary standards to assess accuracy and precision The calculation of error correlations in lolite s U Pb Geochronology 3 DRS is simple but is also arguably the most accurate method as it employs all available information in contrast for example to some arithmetic approximations To calculate the cor relation in the uncertainty of two ratios e g 206Pb 238U vs 207Pb 235U a built in Igor Pro function called StatsCorrelation is employed The function takes all data points within the relevant time period e g an analysis of a sample unknown and tests whether any correlation exists in the variation of the ratios If the data points are visualised as an X Y diagram of the two ratios of interest the function is testing whether the distribution of the data is random this would appear as a shotgun plot with the data points scattered evenly in all directions or whether the data cloud forms an ellipse indicating correlation in the scatter of the two ratios The ellipse will become more elongate as the degree of correlation between the ratios increases and will slope diagonally upwards if the correction is positive as is normally the case or diagonally downward if the correlation is negative 4 22 Downhole Fractionation Correctio
96. nts in multiples of the minimum detection level 33 67 or 100 counts per second in this case Statistical calculations using outlier rejection often reject the rare higher values producing an average lower than the true background level and an extremely low calculated uncertainty In contrast a simple average of all points will with increasing amounts of data approach the true value and should provide a more realistic estimate of uncertainty 4 6 TIME SERIES TABS BASELINES REFERENCE MATERIALS SAMPLES 27 4 6 Time Series Tabs Baselines Reference Mate rials Samples Once a user has selected a marquee containing only a portion of the total inputted wave the Time Navigation Window will show a highlighted area light blue corre sponding to the portion of the total inputted wave that is currently being displayed in the main browsing window at the top of the User Interface Figure 4 1 The user is then able to navigate through the inputted data wave by dragging the highlighted region in the Time Navigation Window Correspondingly the main browsing window will scroll in the direction the highlighted region was dragged If the user wants to alter the size of the region of the wave being displayed he or she may do so by placing the mouse cursor over an edge of the highlighted region in the Time Navigation Window The cross hair cursor will transform into a two sided arrow The user may then click and drag the limits of the highl
97. nual Hide Add Channel 5 Get settings from Aute Setup 1 5 Show Mo labels Show sobecthon labels U238 Lued hu lh d E cat ulla JL s 3 00 PM 3 30 PM 4 00 PM 4 30 PM 5 00 DM 5 30 PM 7 3 08 0 5 0 0 Analysis Time Figure 3 5 Baseline Tab for the demo zircon U Pb experiment Step 3 Reference Materials In order to see the Intermediate Channels during Automatic Selection of reference material selections the user must first hit the Crunch Data button in the DRS tab Then proceed to the Reference Materials tab and navigate to the Automatic Se lection tool Select the Detect from beam intensity method First select Z 91500 as the selection type from the drop down menu Figure 3 6 Using the data filters and these suggested settings Raw 206 238 gt 0 1 Raw 206 236 lt 0 3 Start Crop 2 seconds and End Crop 2 seconds Add the selections to the 91500 selection type Repeat these steps for the secondary reference materials Z Temora2 Figure 3 7 Temora 2 was analysed in pairs and is the only zircon in this session with a Raw Age 206 238 an Intermediate Channel around 400 Ma Once the selections for both of the reference materials have been added click the Close button at the top right of the window Back in the Reference Materials tab choose the appropriate spline types for these selection types 20 CHAPTER 3 COMMON DRS DEMONSTRATIONS Select All Deselect All
98. o the data is often achieved By clicking the Manual button the user is able to deactivate automatic calculation and manually edit all of the model parameters Note that this is not possible for the Running median or Smoothing spline methods In this way the user has complete control over the form of the fit while still having the benefit of the measures of success of the model the residuals plot and the Quality of fit section of the window The Quality of fit window provides additional information to the user on the efficacy of the chosen model of fractionation The standard error provides an indication of the scatter of the average values after correction using the model and should decrease as the quality of the model increases The Bias of fit provides an indication of whether the model biases the data towards a higher or lower ratio If an appropriate model is chosen this value should be near zero Finally all points of the average data are plotted as a histogram Given that normal statistical methods are employed it is important that the corrected data have a normal distribution and the purpose of the histogram is to assess whether this assumption is valid If data are badly skewed bimodal or otherwise differ from a normal bell curve distribution it would suggest that the fractionation model is inappropriate In addition it would indicate that the user should consider using a more flexible method of statisti
99. of different selection groups for groups of unknown samples Sample selections can be edited and their display adjusted using the sample info function Once the sample selections are defined the user may move onto the DRS Tab 2 5 DRS Tab In the DRS Tab the user is able to select the data reduction scheme applied to the input data The DRS Tab is broken up into four sections Figure 2 3 The General Settings the DRS Specific Settings the DRS Report and the Crunch Data button The General Settings is comprised of two drop down menus that allow the user to determine the statistical treatment of the baseline and the normal selections The initial drop down menu of the DRS Specific Settings titled Current Data Reduction Scheme allows the user to select the DRS that will be applied to the data Once a DRS is selected additional user interface elements pertaining to the user defined settings specific to that DRS will appear A few of the common drop down menus in the DRS Specific Settings are described here e Statistical Methods Allows the user to specify options for outlier rejection on baselines and selections e Index Channel n all DRS routines this wave is used for determining which portions of waves need to be masked masks are described below e Reference Material This specifies the reference material to be used in calcula tions like drift corrections etc 2 5 DRS TAB 9
100. ontamination cracks in the grain or the laser drilling all the way through a thin area of the grain For each time slice of the average pattern an uncertainty is also calculated this un certainty is then incorporated when calculating each model of down hole fractionation with the exception of the running median In order to remain as flexible as possible a number of different model types are provided these include Linear Exponential illustrated in Figure 4 16 Double expo nential Combined linear and exponential Smoothed cubic spline and Running median The DRS has been designed so that the user can freely switch between these different models and quickly see the effect of each on down hole corrected data Of the above models the first four employ a simple mathematical equation to calculate drift in the relevant elemental ratio y axis relative to ablation time x axis In each case the equation employed is provided at the top of the curve fit window Figure 4 16 The last two models employ Igor Pro s smooth and interpolate2 functions respectively using a degree of smoothing controlled by the user The running 46 CHAPTER 4 SOFTWARE FEATURES DIRECTORY median calculates the median for a given data point by calculating the median of all points within a window n seconds wide centered on that data point where n is the smoothing parameter specified by the user The smoothed cubic spline uses the method of Reinsch
101. ope e g Ca in the sample Rrsca is the count rate of the IS in the calibration standard Cisca is the concentration of the IS in the calibration standard and Cygeqm is the concentration of the IS in the sample The Rancal and Canca terms take into account how much of each element is in the standard and how sensitive the machine is to this element So for example if you have a standard with a really high Li content but the count rates for Li on the standard are low then your sensitivity for Li is obviously low This part of the formula just takes that into consideration and is usually in units of cps ppm or cps wt The second half of the equation could be rearranged to Rygsam Crssam gt Rrscat Crscat which is very similar to the first part of the equation except that it s looking at the sensitivity of the internal standard You can see that if it s rear ranged like this it is just the ratio of count rate unit of concentration e g cps wt 96 for the sample compared to the standard So if you have a sample with a really low concentration of your internal standard element this part of the equation will take that into consideration This second part of the equation is unitless so the units of S are cps ppm or cps wt The DRS just does a couple of things that are noteworthy Not every sample selection will have its own background selection So the program looks for the closest selection in Baseline 1 The number of points i e measu
102. rements of this baseline selection will be n in equation 4 1 Similarly na will be the number of measurements in the sample selection For every channel i e isotope measured it will then calculate the background noise as 1c and this is put into Eqn 4 1 too Sensitivity is calculated by taking the concentration values from the standard file for the standard Conca and C rgca Will both come from the standard file C75 comes from the Internal Standard Wave discussed above The count rates for Ranca and roi are determined from the splines of the standard So for example if the current element is Li the value for the Li CPS spline over the sample selection period would be used for Rancai If the internal standard element is Ca the value for the Ca CPS standard spline over the sample selection period would be used for Risca The value for Ryssam is derived from the average counts for the internal standard during the sample integration All these calculations are done in the function Create3sigmawave which is unencrypted 4 21 U Pb Geochronology 3 DRS The U Pb Geochronology 3 DRS incorporates of a number of discrete stages of data processing Some of these stages are common to any DRS in lolite but others are unique to the U Pb Geochronology 3 DRS A description of those stages common 44 CHAPTER 4 SOFTWARE FEATURES DIRECTORY to any lolite DRS is provided first followed by an in depth treatment of the features unique to the U
103. s 50 4 23 6 Exporting Images 50 Processing Templates 51 4241 Import 53 4 24 2 Import Laser Log 55 4 24 3 Create 5 0 5 56 4 24 4 Move Selections 62 4 24 5 Create Load IS 55 64 4 24 6 Run DRS TraceElements_IS 67 424 7 Run DRS UPE DRS uuu mz 264646 4464544444 ba ds 69 4 24 8 Pause 71 4 24 9 Export 318 1 List of Figures PI 2 2 2 9 2 4 2 2 0 2d 3 1 3 2 33 3 4 So 3 0 B 3 8 3 9 3 10 4 1 4 2 4 3 4 4 4 5 4 0 4 Import tab of the main iolite window Baseline Tab of the Main lolite Window DRS Tab of the Main lolite Window Summary Stats display of the Results Tab X Y Plot display of the Results Tab Stack Plot display of the Results 1 325 Data Table display of the Results Tab Selecting the baseline using the Automatic Selections tool for the 5 Seconds Basalts experiment Making reference material selections using the Automatic integrations from metadata window Selecting the Trace Elements IS DRS on the DRS tab Results for the 5 Seconds Basalts experiment
104. s Import S values set STD IS vals Threshold t use when mas g mw z gt Run Traces DRS seconds lo trim before after low signals 1 Move Missed Shots Good Epidote Shots Check Data before Export Export data Import my laser log file Figure 4 34 Options for the run U Pb DRS action 7 Beam seconds sensitivity depends on Beam Seconds method Please refer to the website for more information 8 Down hole correction model set the model for your downhole fractionation effect here See the websitet for more details 9 Threshold to use when masking low signals this setting is important Any time the index channel drops below this value the intermediate and output channels will be blanked set to NaN and you won t get any results for these periods This is to make it easier to see variation in ratio channels without having to look at all the noise in the baselines If you see your samples being clipped check that you haven t set this value too high You can also set it to 0 to see what effect it has when it s turned off 10 Seconds to trim before after low signals This is how many seconds will be trimmed before after each time the Index Channel drops below the Threshold https iolite software com estimating laser pit depth using the beam seconds channel https iolite software com downhole corrected upb ages and general workflow of the u th pb 4 24 PROCESSING TEMPLATES 71 describ
105. ser Ablation Inductively Cou 2 3 pled Plasma Mass Spectrometric Transient Signal Data Acquisition and Analyte Concentration Calculation Journal of Analytical Atomic Spectrometry 11 9 pp 899 904 Paton C J D Woodhead J C Hellstrom J M Hergt A Greig and R Maas 2010 Improved laser ablation U Pb zircon geochronology through robust downhole fractionation correction Geochem Geophys Geosyst 11 QOAA06 doi 10 1029 2009GC002618 Reinsch C H 1967 Smoothing by spline functions Numerische Mathematik 10 3 p 177 183 3
106. ser will first select the active selection for the appropriate reference material After then selecting the spline type and desired channels to display using the channel drop down list the user may select selections from the corresponding segments of the wave using standard wave navigation and operations manual selection or automatic selection commands These selections will then be applied to the chosen reference 8 CHAPTER 2 USER INTERFACE material channel The user may define any number of different reference material channels Reference material selections can be edited and their display adjusted using the sample info function Once the reference material selections are defined the user may move onto the Samples Tab If the user hits the Crunch Data button in the DRS Tab iolite will allow the Output Channels to be viewed in the channel panel 2 4 Samples Tab The Sample Tab allows the user to allocate selections for the unknown samples anal ysed during the experimental session The user will first select or create the active selection for the unknown samples After then selecting the desired channels to display using the channel panel the user may make selections from the segments of the wave corresponding to the unknown samples using standard wave navigation and operations manual selection or automatic selection commands These selections will then be applied to the selected output channel The user may define any number
107. this by going to C Users Your User Home Documents WaveMetricsMgor Pro 6 User Files Mgor Procedures and delete any iolite related files there There should be three short cut files to delete 3 Install iolite using the iolite installer You should have received an email from iolite with a link to the iolite 3 download Download that file and install iolite 3 by double clicking the installer 4 Run Igor Pro as an administrator by right clicking on the Igor Pro item in the start menu and selecting Run as administrator When lgor Pro starts up you should see a small iolite welcome image with Loading written on it 5 When prompted click Yes to start the 7 day trial You will need to make sure your internet connection is working before starting the trial Once you ve clicked Yes you should see a window saying that your trial has started and when the end date is You now have a fully functional trial working on your machine 6 To register iolite go to the iolite menu and select About lolite gt Register iolite Then enter your details along with the iolite licence key you received in your email from iolite Click OK and you should see a message thanking you for registering iolite You are now using a fully licensed version of iolite 3 Now every time you open Igor Pro you should have full access to the lolite platform Chapter 2 User Interface lolite s user interface is comprised of the pull down menus at the top
108. this function Edit the active data reduction scheme By choosing this option the user is presented with the ipf file of the currently active DRS where they are able to view the DRS code Here the user can make amendments to the code altering the way in which the DRS operates This is intended for intermediate iolite users Create a new data reduction scheme Here the user may create a new DRS 416 IOLITE MENU 39 eoo Internal Standard Values Select an integration 8 2G Integration Name Treated as Internal Standard Used default Internal Standard standard Element value Value wt 5 BCR2G 1 BCR 2G Ca no 5 0458 BCRZG r2 5 Ca na 5 0458 BCR2G r3 BCR 2G Ca no 5 0458 BCR2G r4 BCR 2G Ca no 5 0458 BCR2G r5 BCR 2G Ca no 5 0458 BCRZ rb RK Zt La na 5 0458 BCR2G r7 BCR 2G Ca no 5 0458 BCR2G_r8 BCR 2G Ca no 5 0458 BCR2G r9 BCR 2G Ca no 5 0458 BCR2G r10 BCR 2G Ca no 5 0458 BCRZG_1 Zt La na 5 0458 BCR2G 2 BCR 2G Ca no 5 0458 BCR2G 3 BCR 2G Ca no 5 0458 BCR2G 4 BCR 2G Ca no 5 0458 BCRZG_5 RR Zt La na 5 0458 BCR2G 6 BCR 2G Ca no 5 0458 BCR2G 7 BCR 2G Ca no 5 0458 BCR2G 8 BCR 2G Ca no 5 0458 BCR2G 9 BCR 2G Ca no 5 0458 BCR2G 10 Zt La na 5 0458 BCR2G_11 BCR_2G Ca no 5 0458 Next Figure 4 12 Internal Standard Values window 40 CHAPTER 4 SOFTWARE FEATURES DIRECTORY Continue nds c Ore P gi PL rt Default Figure 4 13 Export Settings window code to app
109. this to make it clear what your action does 2 Action Type although already set you can change action types by using this dropdown menu 3 File path method This allows you to set how iolite will know which file to open If you select Prompt User when the action runs it will ask you to select the laser log file If you select Use Specified Path you will then be able to select your laser log file using the button next to the Laser log file field If you select Look in import folder it will look for a log file in the same folder as the file you imported 4 Laser log file path this is where you select which file to open if you have selected Use Specified Path in the File path method Otherwise this field is not used 5 Sync Method Sync Window or Specified Offset Use Sync Window if you would like to interactively sync the log file with the mass spec data Use Specified 56 CHAPTER 4 SOFTWARE FEATURES DIRECTORY Igor Pro 6 36 File Edt Data Analysis Macros Windows Graph Mpc Help Gizmo Zoom lolite Image Actions Edit actions Template lag import data Settings Tor import data Mt Line type import File type X senes csv ER lata as fie D 4 Sel BCR standards late format use default D 5 Automatic 6 set GSD Standards Set Sample runs Machine type File path CUsers Bence Documents Testers 185 2 K Import IS values Set STD IS vals Run Traces DRS m Move Missed
110. ts set BCR standards Set Sample runs Move value TesiShot Import S values Sel STD IS vals Run Traces DRS Move Missed Shots Good Epidote Shots Check Data before Export Import my laser log file Figure 4 30 Options for the move selections by selection label action will add the selections to that standard group or Baseline_1 Make sure that if you type a new selection group name that it begins with a letter doesn t include any spaces or non word characters i e anything other than A Z 2 0 9 _ and that it isn t longer than 16 characters long 6 Move value If the selection label matches this text the selection will be moved Note that this is case sensitive 7 Preserve original selections checkbox Whether a copy of the original selection should be left in the From group checked or not unchecked 4 24 5 Create Load IS values Loading and or assigning internal standard IS values to samples is an important part of the Trace Elements IS DRS The IS concentration is an important part of the trace element concentration calculation and needs to be set before we can calculate our final concentrations We can do this automatically with the Create Load IS values action You can assign IS values in three main ways by loading an IS file usually a table of sample names and major element concentrations in elemental weight percent 4 24 PROCESSING TEMPLATES 65 not oxide wt by setting a constant value for
111. tself The lolite application grew out of the realisation that simultaneous visualisation and processing of an entire analytical session of data could not only reduce this burden but also greatly improve the consistency and reliability of that data processing This is particularly true with reference to interpolation of quantities such as baseline intensities and mass or elemental fractionation factors lolite is a data visualisation and processing tool which allows the processing of most laser ablation datasets covering a full day of analysis in a few tens of minutes or less if Processing Templates are used lolite is implemented as a self contained package for Igor Pro a scientific data processing and graphing application by Wavemetrics Inc of Lake Oswego Oregon USA Igor Pro was chosen for its emphasis on time series image analysis and curve fitting and comes with its own programming language In addition it includes powerful 3D graphing capabilities using the high performance Gizmo OpenGL visualisation tool lolite s critical distinguishing feature is the consistent visual display versus time at all stages of data processing of all available raw and processed data over the course of an entire analytical session regardless of the number of individual time resolved files involved Data processing algorithms are entirely user defined and can be of any level of complexity meaning that users have complete control over how their output parameters
112. ttings Save changes Cancel without saving Show info panel on main control window Show file labels V Show selection labels V Use native GUI appearance Stats method to use for baselines Mean no outlier reject D Stats method for normal integrations Mean with 3 S D outlier reject too Import file type Mu Plasma time resolved run d Import single file or folder Single select a single file to import Colour scheme to use in images YellowHot Wee Preferred import folder Macintosh HD Users bencepaul lolite Sa Overwrite existing integrations Yes delete my previous selections a Figure 4 14 Edit lolite s default settings window 4 18 Export Data After data processing is complete the user can export a table of results from lolite The results table is in tab separated format and can be directly imported into Microsoft Excel By default the U Pb Geochronology 3 DRS exports data in a format suitable for input into Isoplot using either Normal or Inverse U Pb isochrons although the content of the export table is fully customisable In addition to a simple table of statistics it is also possible to export a time series of calculated data either at the original time spacing of the data or after down sampling 4 19 Trace Elements IS DRS This data reduction scheme DRS is based on J Hellstrom s Trace Elements DRS that was
113. u like but we recommend editing it in iolite so that you don t accidentally enter invalid values The name of the current 52 CHAPTER 4 SOFTWARE FEATURES DIRECTORY template will be listed at the top center of the window When you re ready to run your template you can click on the Run button at the top or close the window by clicking the Close button The main part of the window is separated in half with the actions on the left and the action options panel template log on the right You start by adding actions to your template and editing their options Here s how to add and enter an action Click on the 4 button on the left This will bring up a dialog asking you to choose what type of action and what you want to call it The name doesn t matter at all it just makes it easier for you to be able to see what each action is doing Make sure you don t remove the starting and ending quotation marks Igor Pro hates that The dropdown menu at the top of this dialog is where you choose the action and the name is the lower part Add action Action type Action name Default Cancel Continue Figure 4 20 Processing templates add action dialog Once you select an action and give it a name you will then be able to see the options for this action In the example shown in Figures 4 20 and 4 21 we ve selected the Import Action and called it Import My Data The options for each action are explained further below You can keep adding a
114. u will appear prompting the user to choose one of three automatic selections methods 4 10 1 Information from import This option uses the start and end times of the imported files to create selections This is usually most useful where each sample is contained within a separate file For example your files may all contain a single sample starting with 30 s of background 60 s of ablation and 15 s of washout If this is the case you can create selections to match your samples where you add 32 s to the file start time and subtract 20 s from the end of the file there are a couple of extra seconds in there to allow for wash in and wash out Similarly you can select the baselines for every sample by selecting every sample cropping 1 second from the sample start time and 75 s from the sample end time This will crop off the entire ablation event thus selecting only the background part of each file It doesn t break anything to repeat this process until you get the right numbers for your files so feel free to create selections then check them in the main iolite window and then go back and overwrite the selections When you select this option a new Automatic integrations from metadata pop up window will appear Figure 4 3 where the user can select individual selection 30 CHAPTER 4 SOFTWARE FEATURES DIRECTORY periods by manually clicking the appropriate boxes or querying selection labels using the Match text box TIP Use to exc
115. ual to the spot size for each mass spectrometer measurement See Fig 4 18 a The value of this circle will be equal to the output channel at this time Note that this 50 CHAPTER 4 SOFTWARE FEATURES DIRECTORY is why getting an accurate sync between the laser log file and the mass spectrometer data is important lolite also reads out any existing pixels values that may overlap this spot and calculates the average of the existing pixel values and the value of the current spot e g Fig 4 18 b and c This has a smoothing effect but also reflects that for parts of the spot area we have two measured values Where several points are overlapping however the average is calculated between the existing values and the current spot Fig 4 18 d and e This average value will be biased towards the last measurement In the example image Fig 4 18 lolite calculates the average as 30 6 2 which is equal to 18 instead of more correctly 5 7 30 3 which is lower 14 i e the result is biased towards the last spot The magnitude of this effect should be limited to areas within spots and thus features less than a couple of spot widths may be smoothed out Please be aware of this effect and it is strongly suggested that all users are aware of features in the raw data and whether these are transmitted to the processed data lolite repeats this step for each mass spectrometer measurement see masking below 4 23 4 Zooming in on the image
116. ut 1 Channel to display Please select a wave to map Colour Table Bathymetry9 22 5 Lower Limit 0 Upper Limit D Layer 1 mall after E Layer 2 None 4 Layer 3 None E Layer 4 None Layer 5 None BS k Precrors Export Current Export Selected Export All Figure 4 17 The CellSpace Imaging window You ll notice the mapped image is on the left and there s a control panel on the right The drop down menus are described below 4 23 1 How it works lolite will attempt to calculate a spot shaped image for every mass spectrometer mea surement his is important because the spots you see on the image are not when the laser was firing but the mass spectrometer reading while the laser was in this location As an example if you have a laser repetition rate of 1 Hz and a mass spectrometer sweep time of 100 milliseconds i e 10 Hz you will get 10 spots on the image for every second of ablation rather than just one To create the sample image lolite in terpolates the laser x and y coordinates and spot size It then creates a circle centred on the interpolated x and y coordinates with a diameter equal to the spot size for each mass spectrometer measurement See Fig 4 18 a The value of this circle will be equal to the output channel at this time Note that this is why getting an accurate sync between the laser log file and the mass spectrometer data is important lolite also reads out any existing pixels v
117. ve as well choose to hide or display a particular channel wave by ticking or unticking the Hide box 5 in Figure 4 8 413 SAMPLE INFO PANEL 35 U238 Primary 4 Auto Colour MEME gt Log Manual m ini Ec Scaling Auto C Colour 888 TT _Log_ Manual Hide O 5 Add Channel 6 Getsettingsfrom AutoSetup 7 Show file labels Show selection labels Figure 4 8 The Channels drop down menu highlighting the scaling tools Make Primary Get settings from and Auto Setup buttons Hide Show file labels and Show selection labels boxes and the Add Channel drop down menu Below the different channels selected by the user are two buttons allowing the user to import channel viewing settings 6 in Figure 4 8 The first labelled Get settings from allows the user to import channel viewing settings from the other two time series tabs the other two of Baselines Reference Materials or samples The second titled Auto Setup retrieves a predetermined channel viewing setting previously designed by the user See Auto Setup for more information regarding this tool Finally at the bottom of the Channel Drop down List the user may select whether to display the file labels and selection labels by ticking or unticking the corresponding boxes 7 in Figure 4 8 4 13 Sample Info Panel When viewing data in the Baselines Reference Mat
118. w A table with the data for each selection type corresponding with the selected channel sits above the plot The user selects which selection type to be displayed in the plot by ticking the box next to the listed selection types A number of Plot Options in the top right corner of the screen allow the user to determine how the data is displayed 2 6 2 X Y plot For the X Y Plot data display option lolite presents an x y plot for each individual selection of a chosen selection type Figure 2 5 The selection type can be selected by ticking the boxes next to the desired selection type in the box above the plot These 2 6 RESULTS TAB 11 enn lolite v3 Untitled Experiment Import Baselines Reference Materials Samples DAS results images 22226228622382228 omon nm Group A MSW L opaga 3 Dutlier Rejection verape Hone weighted propag O of 187 40 45 of 41 0 of 41 of 40 O of 40 of 162 E m D m 15 Be 30 40 50 60 70 80 90 100 110 120 130 140 150 160 Figure 2 4 Summary Stats display of the Results Tab boxes correspond to the statistical information pertaining to an selection type the user desires to be displayed i e Averages error bars ellipses and time slices The waves displayed on the x and y axes are selected by the user at the two drop down menus at the top of the screen The remaining buttons and drop down menu allow the user to autoscale t

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