PeakCounter 2.1.5 User manual - Computer programs produced by
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1. see Fig 9 NB The brightness and contrast of the X radiograph can be changed by using 140 the corresponding scroll bars in the PeakCounter 2 1 5 control panel which will NOT change the 141 values saved in the additional column i e the function is only to enhance visibility on the monitor 142 without altering signal quality 143 144 5 2 XRF data 145 Click on the Import XRF data button in the PeakCounter 2 1 5 control panel Fig 2 or go to 146 File Import XRF data navigate to your XRF data csv file or choose the XRF data csv file 147 from the sample data folder select it and click open or double click the file This opens five 148 other active windows which contain element profiles plotted in green on a background of the X 149 radiograph image This also opens two scale bars one showing the full core section length above 150 the X radiograph preview window A in Fig 3 defined by the core scan length and the other 151 showing the length of the active windows B in Fig 3 defined by the active window selector The 152 scale bars automatically reflect the analytical resolution stepping interval recorded in the XRF 153 data file The position of the windows can be changed by clicking and dragging them They can be 154 arranged and aligned by right clicking on the upper most window and clicking Align forms Fig 155 4 or going to Tool Align forms in the control panel menu A single2. Brightness Contrast Import core photo Brightness Contrast Show tools Save Quit FE aa Svigetsu les bat Varves 2006 Ill PeakCounter 53 4 Ti Ti _v C Ratio Active years Level 1 Level 2 Level 3 Level 4 Level 5 Level 6 Level 7 Level 8 Level 9 Retract coo oOAN wa 17 Fig 9 Output file showing additional columns created by PeakCounter 2 1 5 PeakCounter 2 1 5 User manual AM AN AO AP AQ AR 1825 446 2128 523 220 2492 580 216 2561 593 211 2802 627 206 2767 659 200 2743 585 198 PRATA RAR 197 aes 18 Suigetsu arves 2006
3. mm 268 Fig 8 as indicated by the position of the marked varves in the clearly varved section The bar can 269 be placed anywhere and the circles will move accordingly NB this tool should only ever be used 270 as an approximate guide and any varve limits marked using the tool should be marked at an 271 accordingly low degree of certainty i e a high level number 272 273 6 3 Labelling laminae and making notes on sediment character 274 To precisely mark a particular sedimentary structure right click in an active window at the desired 275 position and select Labelled lamina Fig 4 This opens a separate window were the user can 276 label the lamina in the first box and describe it in the second Fig 4 Click OK to close the 277 window A blue line will appear in the marked position in all active windows The lamina label 278 and note in brackets text will appear when the user hovers the active cursor line over the blue 279 line in any of the active windows The labelled lamina may be deleted by hovering the active 280 cursor line over the particular marked line right clicking and selecting Delete NB this cannot 281 be undone A blue line also appears in the X radiograph window of the full core section which 282 makes it easier for the user to align and re scale if required i e when not using the core photo 283 from the Itrax scan the core photo to the X radiograph image using the position of the distinct 284 sedime
4. surface reflectance Fig 6 To re 203 scale stretch the Y axis click and drag vertically on the image anywhere outside the dashed white 204 lines 205 206 5 4 Screen resolution 207 One pixel in each active window precisely corresponds to one measurement by the Itrax core 208 scanner Users are advised to reduce their screen resolution to improve the visibility of extremely 209 fine scale changes in parameter profiles A trial and error approach is advocated so that the user 210 can view the programme at a reduced resolution while maximising use of screen space In Vista 5 PeakCounter 2 1 5 t arves User manual 2006 211 this can be done by right clicking on the desktop selecting Personalize then clicking Display 212 settings 213 214 6 0 Using PeakCounter 2 1 5 215 6 l Further active window manipulation 216 All the components displaying the multi parameters derived from the Itrax core scanner should 217 now be arranged so they are all visible and fill the screen Figs 6 and 7 218 The drop down menu at the top left corner of each of the six active windows can be used to 219 select from the list which of the parameters is plotted in the window As well as all of the elements 220 of interest selected by the Itrax user to measure this list includes greyscale kilo counts per 221 second kcps and mean square error of prediction MSE In active windows 4 6 it is also 222 possible to plot element and or parame
5. the number of XRF measurements In other words the resolution stepping interval 75 needs to be identical for both X ray radiography and XRF scanning This is the only requirement 76 for the scanner settings Optical core images can be taken in different resolution and using 77 different devices such as digital cameras Users can include as many elements as they want for 78 detection by model fitting The scanning resolution defined by the user must be constant within 79 each scanned segment PeakCounter 2 1 5 displays one XRF measurement in one pixel on the 80 monitor Therefore the use of a coarse step size results in images that are too small Generally 81 speaking PeakCounter may not be the best analytical tool for materials that do not require high 82 resolution scanning The SG06 core was scanned at 60 Um stepping 83 2 PeakCounter 2 1 5 t arves User manual 2006 84 3 0 Installation of PeakCounter 2 1 5 85 PeakCounter 2 1 5 runs on Windows XP Service Pack 3 SP3 or later NB it has been reported 86 by several users that it does NOT run on Windows XP SP2 or earlier Currently there is no plan 87 to develop PeakCounter for Macintosh or Linux An installer package of PeakCounter 2 1 5 can be 88 downloaded from the web page lt http dendro naruto u ac jp nakagawa gt The download has no 89 limitation and is free of charge Extract the downloaded zip file and double click SetUp exe file 90 Next simply follow the ordinary pr
6. the study of laminated sediments Journal of Paleolimnology 19 33 40 Francus P Lamb H Nakagawa T Marshall M H Brown E Suigetsu 2006 Project Members 2009 The potential of high resolution X ray fluorescence core scanning Applications in paleolimnology PAGES News 17 93 95 Holtia Hovi E Saarinen T Kukkonen M 2007 A 2000 year record of solar forcing on varved lake sediment in eastern Finland Quaternary Science Reviews 26 678 689 Marshall M H Schlolaut G Nakagawa T Brauer A Lamb H Bronk Ramsey C Yokoyama Y Suigetsu 2006 Project Members In prep A novel approach to varve counting for the Lake Suigetsu 2006 Varved Sediment Core Project Combining u XRF and X radiography with thin section microscopy Quaternary Geochronology Nakagawa T 2007 Double L channel an amazingly non destructive method of continuous sub sampling from sediment cores Quaternary International 167 168 Supplement 298 doi j quaint 2007 04 001 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 PeakCounter 2 1 5 e arves User manual 2006 Nakagawa T Gotanda K Haraguchi T Danhara T Yonenobu H Yokoyama Y Brauer A Tada R Takemura K Staff R A Payne R Bronk Ramsey C Suigetsu 2006 Project members in press SG06 a perfectly continuous varved sediment core from Lake Suigetsu Japan stratigraphy and potential for improving radiocarbon calibration model and und
7. vertically i e the short axis 172 of the core by clicking and dragging the image If the overlap between images encompasses the 173 active window selector on the X radiograph red rectangle an active window selector will also 174 appear on the optical image Fig 5 This will move horizontally when the user changes the 175 position of the active window selector on the X radiograph image It can be moved vertically by 176 clicking and dragging within it in the core photo window If the user changes the position or size 177 of the core photo then it is necessary to click on the active window selector in the core photo to re 178 align it to that within the X radiograph image preview window 179 180 5 3 1 Magnifying the core photo 181 Right click on the core photo and select Crop to open a magnified image of the core section 182 defined by the active window selector in a separate window Fig 5 This can be moved and 183 resized both vertically and horizontally The brightness and contrast can be changed by using the 184 corresponding scroll bars in the PeakCounter 2 1 5 control panel Once in the required position i e 185 aligned with the active windows right click and select Align scale Fig 6 to align the active 186 window scale below the cropped core photo and to align the active cursor line orange line with 187 cross hair between this and the other active windows The method for aligning the active cursor is 188 defined by e
8. 5 sain arves User manual 2006 125 click the file This opens the full radiograph image in the X radiograph Preview window at the 126 top of the screen with the core top to the right including the file location path Fig 2 The red 127 rectangle is the active window selector Fig 1 and denotes the smaller core section of X 128 radiograph image that is plotted in the first of the active windows that is also opened Fig 2 1 129 Grey scale See below for details on the Active years window that is also opened The position 130 of the active window can be changed by clicking inside the active window selector and dragging 131 to the required position down up core and can be resized by clicking and dragging either side of 132 the selector The green line is the greyscale profile Fig 2 calculated from the area between the 133 two dashed white lines on the X radiograph image the position and width of which can be 134 changed by clicking and dragging within or on the lines in either the active window where the 135 width in pixels is also shown or in the full X radiograph preview window see Fig 2 The Y axis 136 scale can be edited by changing the limits of greyscale value at the top and bottom right hand 137 corners NB The position of the greyscale selector determines the values that are saved in the 138 additional column labelled greyscale created in the output file one column to the right of 139 coh
9. Colour setting and selecting Default 254 The user can Undo their last marked level lines by right clicking on any of the active 255 windows and selecting the appropriate command Fig 4 or by using Ctrl Z The undo function 256 can be repeated for up to 50 times Marked lines may be deleted by hovering the active cursor line 257 over the particular marked line right clicking and selecting Delete NB this cannot be undone 258 An additional column is created in the output file labelled year where the marked level number 259 is recorded in the spreadsheet row corresponding to the exact Position mm from the top of the 260 Itrax core scan Fig 9 one row in the spreadsheet corresponds to one pixel in active window 261 If the varve clarity and or signal are poor in places then more clearly varved sections can be 262 used to estimate the spacing position of varves in the poorly varved section i e sedimentation 263 rate Either click the Show tools button in the PeakCounter 2 1 5 control panel Fig 8 which 264 will also bring the Active year window to the front or go to Tool Show elastic scale 265 which will open show the Elastic scale bar aligned with the active windows Click and drag 266 horizontally inside the bar to reveal markers and circles in the bar and active windows 267 respectively The user can drag them to the desired spacing noted in the elastic scale bar in
10. active windows Unlike Labelled lamina the line does not appear in the X radiograph preview window The note may be deleted by hovering the active cursor line over the particular marked white line right clicking and selecting Delete NB this cannot be undone The note will be recorded in the note column in the output file Fig 9 7 0 Saving When saving the output file for the first time click the Save as button in the PeakCounter 2 1 5 control panel This opens a window where the user can navigate to the desired folder location for saving Alternatively use File Save as select the output file or change its name and click Save For saving after the first time either click on the Save button in the PeakCounter 2 1 5 control panel or go to File in the control panel Save By clicking File Save summary a separate csv file is created in which the sum of each level number 1 9 between each labelled lamina is recorded This is extremely useful when comparing varve counts between marker layers in parallel core sections 8 0 Closing PeakCounter 2 1 5 Either click on the Quit button on the control panel or go to File Quit 9 0 Questions and bug reports Queries and bug reports should be sent directly to the author of the software E mail takeshi nakagawa newcastle ac uk References Cooper M C 1997 The use of digital image analysis in
11. active window can be 156 viewed by right clicking the window of interest and clicking on Hide others Fig 4 Users can 157 also right click and click Show 1 3 to just show the first three active windows or alternatively 158 Show 4 6 Fig 4 To display all six windows right click and select Show all Fig 4 or go to 159 Tool Show all in the control panel menu 160 161 5 3 Core photograph 162 Click on the Import core photo button in the PeakCounter 2 1 5 control panel Fig 3 or go to 163 File Import core photo navigate to your core photo bmp jpg file or choose the Core 164 photo bmp jpg file from the sample data folder select it and click Open or double click the 165 file Once open the window displaying the optical image can be aligned to the X radiograph 166 image Fig 5 The window can be resized both horizontally i e along the long axis of the core 167 and vertically by clicking and dragging at its edge If you resize it horizontally then the optical 4 PeakCounter 2 1 5 t arves il User manual 2006 168 image stretches or shrinks to the width of the window This function is particularly useful when 169 you are trying to align the core image independently taken by a digital camera to the X 170 radiograph Vertical resizing only trims the core image which is useful to save space on the 171 monitor The position of the image within the window can be moved
12. arves User manual 2006 PeakCounter 2 1 5 t 1 PeakCounter 2 1 5 a user friendly Windows programme for high resolution 2 analysis of multi parameter data from the Itrax core scanner 3 4 Michael H MARSHALL Takeshi NAKAGAWA Suigetsu 2006 Project Members 5 6 Institute of Geography and Earth Sciences Aberystwyth University Aberystwyth SY23 3DB 7 Wales UK 8 A Department of Geography University of Newcastle Newcastle upon Tyne NE1 7RU UK 9 3 http www suigetsu org 10 11 Corresponding author E mail takeshi nakagawa newcastle ac uk 12 13 Abstract 14 This paper describes new software PeakCounter 2 1 5 that was specifically developed for using 15 multi parameter data from the Itrax core scanner for varve counting but it is also an extremely 16 useful tool for all fine scale analysis of such data The X radiograph and the optical images can be 17 viewed adjacently An active window selector plots up to six different parameters e g greyscale 18 from X radiograph chemical elements and or ratio between them as well as any other parameter 19 measured by the scanner The active area of the optical image can also be viewed in a separate 20 window magnified A cursor line moves simultaneously in all active windows allowing the user 21 to check correlation between different curves Recognised varve laminae limits can be marked 22 with the numbers denoting the varve clarity to the human counter allowing a meas
13. cal image optical tif can simply be saved as a bmp jpg file using standard 109 graphics software e g Adobe Photoshop GIMP etc as can the X radiograph image 110 radiograph tif although this must first be converted to an 8 Bits Channel image from 16 111 Bits Channel before it can be saved as a bmp jpg file Standard image enhancements e g 112 brightness contrast may need to be made prior to the conversion in order to avoid loss of signal 113 resolution 16 bit grey scale divides the range from white to black into gt 65 000 levels whereas 8 114 bit signal can resolve only 255 levels However remember that all core sections from the same 115 master sequence should be edited using identical settings to allow consistent master profiles to be 116 constructed from the X radiograph images Any available optical image of the core section may be 117 used whether that recorded by the Itrax scanner or taken in the field 118 119 5 0 Importing files and user interface manipulation 120 5 1 X radiographic image 121 Navigate to the location of PeakCounter 2 1 5 and open the programme Fig 1 Click on the 122 Import radiograph button A in Fig 1 in the PeakCounter 2 1 5 control panel or go to File 123 B in Fig 1 Import radiograph navigate to your radiograph bmp jpg file or choose the 124 Radiograph bmp jpg file from the sample data folder select it and click Open or double a3 PeakCounter 2 1
14. erstanding of climate changes Quaternary Science Reviews Ojala A E K Francus P 2002 X ray densitometry vs BSE image analysis of thin sections a comparative study of varved sediments of Lake Nautaja rvi Finland Boreas 31 57 64 Petterson G Odgaard B V Renberg I 1999 Image analysis as a method to quantify sediment components Journal of Paleolimnology 22 443 455 Ripepe M Roberts L T Fischer A G 1991 Enso and sunspot cycles in varved Eocene oil shales from image analysis Journal of Sedimentary Petrology 61 1155 1163 Saarinen T Petterson G 2001 Image analysis techniques In Last W M Smol J P Eds Tracking Environmental Change Using Lake Sediments vol 2 Physical and Geochemical methods Kluwer Academic Publishers Dordrecht pp 23 40 Weber M E Reichelt L Kuhn G Pfeiffer M Korff B Thurow J W Ricken W 2010 BMPix and PEAK tools New methods for automated laminae recognition and counting Application to glacial varves from Antarctic marine sediment Geochemistry Geophysics Geosystems 11 QOAA05 doi 10 1029 2009GC002611 9 PeakCounter 2 1 5 o User manual 2006 Fig 1 Initial window of PeakCounter 2 1 5 Preview Active window selector PeakCounter 2 0 0 Control panel AJA Suigetsu VAN Varves 2006 mie 10 PeakCounter 2 1 5 aa arves User manual 2006 Fig 2 PeakCounter 2 1 5 window after X radiograph image impor
15. ese rapid approaches 55 can only ever be used alongside conventional approaches of thin section microscopy and micro 56 facies analysis 57 PeakCounter 2 1 5 is a new programme that was developed by Takeshi Nakagawa using 58 Visual Basic 6 and thoroughly tested by Michael Marshall for varve counting using multi 59 parameter data from the Itrax core scanner for the Lake Suigetsu 2006 Varved Sediment Core 60 SG06 Project but it is also an extremely useful tool for all fine scale analysis of such data 61 Further reference to the use of the software for varve counting for the SG06 project can be found 62 in Marshall et al in prep while a brief description of the software can be found in Francus et al 63 2009 64 The software did not have instruction document for users mainly because it was originally 65 developed for internal use of the SG06 project However the performance and the user friendly 66 interface of the software attracted attention from outside of the project and therefore the demand 67 for a comprehensive user manual became high This paper is the first official document released 68 by the SG06 project aimed at helping a general audience to benefit fully from the software As of 69 26 October 2010 there has not been any other PeakCounter user manual authorised by the 70 project 71 72 2 0 Scanning configuration 73 PeakCounter 2 1 5 requires that the number of pixels along the depth axis of the X radiograph is 74 the same as
16. ing ticking the Activate 240 command Fig 4 or by using Ctrl A The user is able to mark different levels of varve signal 241 clarity resulting due to differing degrees of correlation between indicator parameters and signal 242 strength but also denoting the counter s judgement that it represents a true varve Left click at the 243 desired position in any of the active windows not including the magnified core photo to mark a 244 Level 1 line red in all active windows and to register this in the Active years counter 245 window Fig 7 which counts all marked years within the current active windows Right click at 246 the desired position in any of the active windows to select any level of certainty from 1 to 5 and 247 to 9 by selecting more which will be shown as different colour lines and registered in the 248 corresponding Active years counter window Fig 7 click more in the counter window to see 249 levels 6 9 It is also possible to move the mouse to the desired position and to use the number 250 keys 1 9 on the computer keyboard The user can change the corresponding line and count 251 colour by going to Setting in the control panel menu Colour setting selecting the level colour 6 PeakCounter 2 1 5 sain arves il User manual 2006 252 they wish to change clicking on the desired colour and clicking OK Default settings can be set 253 by going to Setting
17. ither the absolute position of the core photo compared to the X radiograph image or 189 by the relative scale between the two right click on the cropped optical image and select Pointer 190 link then either Position or Scale Fig 6 The Scale mode is more useful when the optical 191 core image was taken by the Itrax when it usually has the exact same scale as the X radiograph 192 The Position mode can better solve the problem of imperfect alignment between core images 193 taken independently by a digital camera and the X radiograph In Position mode the orange 194 cursor lines with cross hair in the cropped image and the active windows can be finely aligned 195 by changing the width of the cropped core image window and the position of the scale to which 196 the cursor line is linked Clicking on between the dashed white lines initially plots three green 197 profile lines corresponding to L a and b colour components which are derived from the area 198 between the white lines the colour profile selector Fig 6 As with the X radiograph active 199 window this area can be moved and resized by clicking and dragging between or on the dashed 200 white lines Right click on the cropped optical image and select Colour profile then either 201 RGB to change the plotted profiles to red green blue additive colour components or grey 202 scale to plot the greyscale of the image equivalent to the
18. l 4 0 0 Contrast Show tools Save Quit gt Suigetsu LEE Varves 2006 15 Suigetsu PeakCounter 2 1 5 ci User manual 2006 Fig 7 PeakCounter 2 1 5 The profile in active window 4 Ti has been smoothed using the weighted average tool The profile in active window 5 shows the use of the ratio tool and has also been smoothed using the weighted average tool Varve have also been marked using different levels of certainty ial Core photo close up SS ee U a a a a a U a a aM B A S 08 upper radiograph H Users mem Documents Lake Suigetsu Take o 2 4 Ti Ti x Ratio Ili PeakCounter C23 File Tool Setting Ri cAn oy t i Active years Brightness Level 1 5 a E Level 2 4 Contrast Level 3 3 a Level 4 2 Level 5 0 5 Fe Ti Level 6 0 Fe v Level 8 0 _ Brightness Level 9 0 ee Retract Contrast Show tools Save Quit Suigetsu oR Ay Varves 2006 16 PeakCounter 2 1 5 User manual Suigetsu Varves 2006 Fig 8 PeakCounter 2 1 5 with the elastic scale tool shown just above active window 1 Core photo close up A S 08 upper radiograph 3 95 bmp Users mcm Documents Lake Suigetsu Take 5 8 File Tool Setting
19. nmental signal through depth This is a particular advantage when measuring laminated 41 sediments at very high resolution The X radiographic images are also extremely useful in PeakCounter 2 1 5 t arves il User manual 2006 42 allowing greyscale profiles to be produced of sediment density variations as well as in the 43 detection of hidden clasts and sedimentary structures that are not visible from the sediment surface 44 An increasing number of studies are utilising digital analysis of optical and X ray images as 45 an objective method of analysing sediment features including varves both manually and 46 automated Ripepe et al 1991 Cooper 1997 Petterson et al 1999 Saarinen and Petterson 47 2001 Ojala and Francus 2002 Haltia Hovi et al 2007 Automated peak counting software has 48 been developed for use in charactering laminated sediments and varve counting using profiles 49 derived from images but also geochemical data and allow the option of spectral analysis on such 50 datasets Weber et al 2010 However for such approaches to be viable the laminations must be 51 extremely well preserved clearly and consistently distinguishable and continuous for the entire 52 period of interest In most laminated and varved sediment sequences this is not the case These 53 methods also detract from actually studying and characterising sediment composition and 54 understanding the process of deposition for which there is no substitution Th
20. ntary structures e g turbidites tephra as marker layers Fig 7 Two additional columns 285 are created in the output file labelled lamina and note where these are recorded Fig 9 This 286 therefore makes it easy for the user to find the marker layers in the output file which are 287 particularly useful when used to correlate overlapping core sections either when taken as parallel 288 Double L channel a k a LL channel or Nakagawa channel sub samples see Nakagawa 289 2007 Nakagawa et al in press advocated here when core scanning at extremely high 290 resolution for varve counting from the same master core section or from overlapping bore holes 291 In the same way the user can precisely mark notes at any required position by right clicking 292 in any of the active windows and selecting Note Fig 4 This opens a new window where the 293 note can be made either manually or by selecting a note from the drop down library list and then 294 clicking OK Fig 4 A short white line will appear in the active windows This note will be 7 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 PeakCounter 2 1 5 et arves User manual 2006 shown as text when the user hovers the active cursor line over the white line in any of the
21. ocedures of installing Windows software If successfully 91 installed you will find a shortcut to the PeakCounter software in your Start menu Start gt Program 92 Files gt PeakCounter gt PeakCounter 2 1 5 You do not need to restart your computer to activate 93 the software 94 If you have already installed an older version of PeakCounter and are trying to update it it is 95 usually possible to simply download the compressed version and replace the old exe file which 96 is normally in C Program Files PeakCounter unless otherwise stated on the web site The 97 PeakCounter exe file needs to be in the same directory as the References folder 98 Notice for French Windows users A malfunction of PeakCounter 2 0 0 was reported by a French 99 Windows user The more recent version 2 1 5 seems to be free from this problem If the problem 100 persists an easy solution is to use PeakCounter version 1 6 2 also available at 101 http dendro naruto u ac jp nakagawa which has less capacity to customise the user interface 102 but does essentially the same thing as the latest version 103 104 4 0 Formatting data and image files 105 PeakCounter 2 1 5 requires the data file containing the XRF data to be in csv format and the X 106 radiograph and optical images to both be in bitmap bmp or Jpeg jpg format The XRF data 107 file result txt can be imported opened in Excel and saved in a csv file using the core section 108 name The opti
22. ow all ee Show 1 3 me Show 4 6 Align forms l Flip vertical T ierat bray setea E OK 13 PeakCounter 2 1 5 User manual Fig 5 PeakCounter 2 1 5 window after core photo import Suigetsu Varves 2006 94 7 cm Preview C Users mcm Documents Lake Suigetsu Takeshi Varve Counting A 08 A S 08 upper radiograph_3_95 bmp megretten lake Sager Telee ae Core photo window gt Morns se Active window selector 25 7 mm Grey v Il PeakCounter 22 File Tool Setting Brightness pann Contrast pou Import core photo Show tools Save Quit DN Suigetsu HELAN Varves 2006 Active years Level 1 Level 2 Level 3 Level 4 Level 5 More 0 ooooo 14 PeakCounter 2 1 5 Varves User manual 2006 Fig 6 PeakCounter 2 1 5 window after opening magnified crop of core photo a oo Core photo window f Greyscale profile i e surface reflectance ala f Users Colour profile 2 L a b Colour profile selector Pointer link i ad vV Grey scale anit Level 5 3 More 0 v Ratio Import core photo Brightness Align scale Illi PeakCounter 3 File Tool Setting _tnportradioaraph Active years Brightness Level 1 0 e j Levet2 0 Contrast Level 3 0 Leve
23. t Preview C Users mcm Documents Lake Suigetsu Takeshi Varve Counting A 08 A S 08 upper radiograph_3_95 bmp X radiograph preview window Active window including file location Greyscale selector 1 Grey scale PeakCounter File Tool Setting Brightness Active years Level 1 Level 2 Level 3 Level 4 Level 5 More Active years window Contrast ooooo Greyscale profile Quit 3 Suigetsu eat Varves 2006 11 PeakCounter 2 1 5 ec User manual 2006 Fig 3 PeakCounter 2 1 5 window after XRF data import 94 7 cm Preview C Users mcm Documents Lake Suigetsu keshi Va Illi PeakCounter 53 File Tool Setting _importradioaraph Active years Brightness Levelt 0 Level 2 0 Contrast Level 3 0 Level 4 0 Level 5 0 kaklas More 0 i Import core photo Brightness Contrast Show tools Save Quit s Suigetsu fat yy Varves 2006 12 PeakCounter 2 1 5 e arves User manual 2006 Fig 4 Right click window with extensions vV lt None gt 0 33 33 33 0 Movi the Petts 0 25 50 25 0 One year 20 20 20 20 20 Half year 10 20 40 20 10 Level 1 Level 2 Level 3 Level 4 Level 5 more ladedinit 2 22sming E Lae Lamina label Undo ee Delete Note vV Activate Hide others oK Sh
24. ter ratios by ticking the ratio box and selecting the 223 desired element parameter s from the two drop down menus The parameter profiles may be 224 stretched by changing the upper and lower Y axis values at the right of each active window The 225 Y axis may also be reversed by right clicking on the active window and selecting Flip vertical 226 Fig 4 Weighted moving averages equally or centrally based 3 or 5 point may be plotted by 227 right clicking on the desired active window and selecting Moving average Fig 4 and then one 228 of the possibly weightings 0 33 33 33 0 0 25 50 25 0 20 20 20 20 20 or 229 10 20 40 20 10 To bring both the active window scale bar and the X radiograph scale bar to 230 the front of all the windows at any time go to Tool Show scale in the PeakCounter 2 1 5 231 control panel menu 232 233 6 2 Varve counting 234 The active cursor line orange line with cross hair moves simultaneously in all active windows 235 allowing the user to examine correlation between elements parameters and their ratios at 236 extremely high resolution This allows varve or other laminae sediment structure limits to be 237 marked in the active windows and the output file To activate one of the six active windows the 238 user must either left or right click on the desired window The active windows can be 239 deactivated activated by either right clicking on any of them and untick
25. ure of varve 23 quality to be incorporated into the count Weighted averaging can be used to overcome noisy 24 element profiles that can result when scanning at very high resolution Distinct sedimentary 25 structures that are often used to correlate cores e g turbidites tephras can be marked and 26 described These new data appear as four additional columns in the output file greyscale from X 27 radiograph varve limit marker layer number and notes 28 29 1 0 Introduction 30 X ray fluorescence XRF core scanning of split sediment cores was developed in the late 1990s 31 Jansen et al 1998 and is a powerful analytical technique It is relatively rapid requires no 32 sample preparation is non destructive and can detect most chemical elements of the periodic 33 table down to limits of a few parts per million depending on acquisition dwell time and sample 34 conditions A new generation of XRF core scanners allowing extremely high resolution analysis 35 with improved count rates and detection limits even with reduced count time has become widely 36 available The Itrax core scanner takes high resolution radiographic and optical images at the 37 same time as XRF measurements Rather than using a single spot X ray beam which most 38 alternative scanners use the Itrax scanner is equipped with a unique flat X ray beam that means 39 that grain to grain variance is averaged in the horizontal core axis ensuring predominance of the 40 enviro
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