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CHANGELOG for XMapTools developer

XMapTools 4.5 (no build yet)

This release is highly recommended for all users as it includes new features, performance and compatibility enhancements, bug fixes and stability improvements to the software.

  • Major compiler update and compatibility notes:

    • MacOS compatibility: XMapTools 4.5 runs natively on Apple Silicon Macs using MATLAB Runtime 25.1, resulting in a significant performance gain. However, the version of XMapTools 4.5 compatible with the M-Series chip is limited to MacOS Ventura (13), Sonoma (14), Sequoia (15) and newer. The previous MATLAB runtime version v912 can be removed after installing this version.
    • Windows compatibility: XMapTools 4.5 is only compatible with Windows 10 and Windows 11. The previous MATLAB runtime version v912 can be removed after installing this version.
    • MacOS Installation and Update: The initial installation of XMapTools 4.5 and MATLAB Runtime 25.1 can be performed using the terminal command: curl -fsSL https://xmaptools.ch/install.sh | bash -s -- --install. In the future, XMapTools updates on MacOS will be distributed using the terminal command: curl -fsSL https://xmaptools.ch/install.sh | bash -s -- --update.
    • Windows Installation and Update: The initial installation of XMapTools 4.5 and MATLAB Runtime 25.1 can be performed using the terminal command: iex "& { $(irm https://xmaptools.ch/install.ps1) } --install". In the future, XMapTools updates on Windows will be distributed using the terminal command: iex "& { $(irm https://xmaptools.ch/install.ps1) } --update". Please note that you will need to run PowerShell as an administrator in order to update XMapTools.

  • New feature: introducing Spot Data

    • Add a new data type that can be used to interact extract information from the maps and spot data from X–Y positions.
    • Add tools to generate datasets and populate them with spots that have been entered manually or randomly onto the displayed data.
    • Add a sampling function that allows data to be extracted using the median value of an ROI defined around each spot. Data for each pixel can be displayed, and outliers can be manually removed.
    • Add a data management module that can load external data from a file and display it in a table.
    • Add a plot module to display the imported spot data on the displayed map using various colour and spot size options.
    • Add export functionalities for spot data to the Export module. Data can be exported to a CSV file in the MinPlot format for one or all spot datasets.

  • General:

    • Add an image converter module (in Add-ons) to convert images into numerical values stored in text files that can be imported into XMapTools. The converter module has additional tools to set the minimum and maximum value and to crop the image.
    • Enhance the Data Export module with a new mode that randomly selects n pixels to export. This can be combined with other export formats in the same file.
    • Add an option to display the "bulk value (average)" of plotted pixels in binary and ternary plots in the Data Visualisation module, improving the statistical output of the plots.
    • Add an option to change the colour of the ROI drawn in the main windows and modules. The default colour is selected when the program starts, but the user's choice is saved for each project.
    • Add an external function for olivine thermobarometry including the calibrations SC13: Shejwalkar and Coogan (2013) and B17: Bussweiler et al (2017).
    • Add the monticellite end-member to the olivine structural formula calculation.
    • Add the creation of colormap data on opening to allow modules to use the default colormap before the first map is displayed.
    • Hide the map navigation slider when an item is selected from the secondary menu. While this changes the behaviour of the interface, it prevents a lot of potential instability.

  • LA-ICP-MS:

    • Add a signal selector module to the converter module to manually select background signals if the background is not measured before each measurement. This module includes a manual mode in which each background measurement can be selected using a ROI, and an automated mode based on a similarity check from a single ROI.
    • Improve the converter module by enabling the generation of another type of map. When generating the map, if the 'Mean of non-zero sweeps' option is selected, the program will calculate the mean of the non-zero sweeps for each grid pixel.
    • Improve the converter module by automatically selecting 'step function' interpolation for the background and 'polynomial' interpolation for the primary standard.
    • Improve the converter module's compatibility by enabling it to convert FIN2 files to CSV files and import them. You can find the FIN2 converter tool in the Tools menu. Note that this format require a conversion before to be imported in XMapTools.
    • Improve the converter module by adding more date and time formats.
    • Improve the converter module to display the file date/time format selection module only if the format is not automatically detected. Note that the old behaviour can be restored by deselecting the "Skip Date/Time format confirmation" option in the Options menu of the converter module.
    • Improve compatibility by enabling the reading of files from PerkinElmer instruments. Please note that, as these files contain no date or time information, the file timestamp is used instead.
    • Add a new compatible format for automatic identification of the analysis ID. The list of compatible formats is "Name - ID", "Name-ID", "Name_ID".
    • Add a check to detect if the wrong format of the name has been selected and the analysis ID cannot be retrieved.

  • Bingo-Antidote:

    • Add melt detection and filtering in Bingo-Antidote if the option 'Exclude melt' is activated.
    • Change the name of the solution model for biotite from BI14 to BIO in DEF_ds62-mb.txt and add Ti and K for the calculation of Qcmp of amphibole.

  • Other:

    • Correct an error in the sampling function where the standard error not being calculated correctly. Thanks to Ryo Fukushima for reporting this issue.
    • Correct an error in the Calibrate workspace prevented an uncertainty on LBC from being estimated. Thanks to @harshal9192 for reporting the issue.
    • Correct an error that occurred in the 'Generate Mosaic (Grid)' function when an 'Import.txt' file was present in a folder containing CSV files. The behaviour of the function has been improved so that it can now automatically detect the presence of a subfolder called 'Mosaic'. Thanks to Yulu Tian for reporting this issue.
    • Correct an error in the calibration for EPMA module that prevented single masks from being selected for calibration. Thanks to Yulu Tian for reporting this issue.
    • Correct an error in the PRIP-ROI module preventing LOD to be calculated when an empty pixel was selected. Thanks to Renée Tamblyn for reporting this issue.
    • Correct an error in the extraction of the number of sweeps per pixel, which was causing rare errors in the value. Thanks to Thorsten Markmann for reporting this issue.
    • Correct an error in the LOD calculation equation with very minor effect on the LOD value. Thanks to Thorsten Markmann for reporting this issue.
    • Correct an error in the LOD calculation for the PRIP module. This error only affected the LOD calculated for ROIs, not the LOD for maps or the LOD filter. The LOD was underestimated by about 10–30% depending on the number of pixels in the ROI. Thanks to Thorsten Markmann for reporting this issue.
    • Correct an error in the data converter for the LA-ICP-MS module that prevented the manual adjustment of the integration sweep for the primary and secondary standards.
    • Correct an error in the LA-ICP-MS Converter module that prevented the secondary standard data from being plotted.
    • Correct an error in the log generator module that was preventing the 'Apply to All' option from being used.
    • Correct an error that prevented LA-ICP-MS projects generated with XMapTools 4.1 from being opened.
    • Correct an error that occurs during startup if the directory is not selected correctly, or if the Cancel button is pressed.
    • Other minor bug and fixes.

XMapTools 4.4 (build 250321)

This version is highly recommended for all users as it includes new features, bug fixes and stability improvements to the software.

  • General:

    • Add a Data Export module to export median and/or mean mineral compositions from merged quanti and result maps as csv files. This module is available from the Add-ons tab and is compatible with the new sub-mask classification.
    • Add several submask classification tools, including an unsupervised classification method based on the k-means algorithm proposed by Gies et al. (2024), Computers & Geosciences, 189, 105626 and a manual classification method in the Data Visualisation module inspired by Prêt et al. (2010), American Mineralogist, 95, 1379-1388.
    • Add multi-ROI selection tool in the data visualisation module and the ability to save the manually created maskfile (or submask to a selected maskfile) in XMapTools. These new features can be used in both binary and ternary diagrams.
    • Add the Border Removing Correction (BRC) algorithm from XMapTools 3.4 to the data visualisation module. If checked, the border pixels of the selected mask file will be filtered out.
    • Add a new structural formula calculation method for biotite based on Waters & Charnley (2002) assuming an 11 oxygen + Ti basis to account for a deprotonation substitution (added by P. Hartmeier).
    • Add a tool to duplicate and adjust the minimum and maximum total values of a set of merged maps (available from the Edit > Map > Duplicate and Adjust menu). This tool allows the user to define a minimum, maximum and sigma value and to rescale all pixels whose sum exceeds this value. It can be used to eliminate some of the artefacts of the EPMA multi-phase calibration routine, especially for mixed pixels that end up with too high totals.
    • Add the ability to define multiple ROIs to generate a local bulk composition.
    • Add an option to export a merged dataset to text files (available from the Edit > Dataset > Export (Merged) menu).
    • Add an option to convert quanti and merged maps from oxide wt% to oxide moles. These datasets can be used in the data visualisation module.
    • Add an option to duplicate a training set.
    • Improve the Select and Crop feature and enable it to crop merged maps. This addition was suggested by Cam Davidson for cropping quantitative compositional maps obtained by SEM.

  • LA-ICPMS:

    • Improve the LA-ICPMS calibration module by the addition of several Pixel Reconstruction and Improved Precision (PRIP) tools. Manual PRIP mode allows ROIs to be manually selected during calibration to estimate local composition with improved LOD. A comparison with the median composition and LOD of all pixels within each ROI is also provided. The PRIP-AI module allows the calculation of pixel compositions below the LOD using neural networks. These new features are under development and limited in the public version of XMapTools; they will be documented in a publication. Contact Pierre Lanari or Thorsten Markmann for more information.
    • Add a sweep extraction routine to the converter for LA-ICPMS to export data from all measured sweeps. The generated data are stored in a new file SweepData_Import.mat.
    • The LOD filter is automatically applied in the LA-ICPMS calibration module when a new Quanti dataset is generated.
    • Add an option to the LA-ICPMS calibration module to store unfiltered maps (LOD). If this option is selected, two Quanti datasets will be generated, one filtered (default) and one unfiltered labeled as "no LOD filter".
    • Add a module to select the date format when importing files from LA-ICPMS instruments.
    • Store the results of the last standard calibration test in a last_std_calibration_test.txt file in the working directory. This file is be copied to the map folder when the maps are exported.
    • Display the mean(sweeps) obtained by the sweep extraction routine when visualising the generated maps using the show button.
    • Improve signal display and background integrations in the converter module. The count rate of a single sweep is displayed with a dot. Integrations are displayed in black if no count was taken during the interval.
    • Fix minor issues with ROI generation and plot interaction in the Log Generator module.

  • Classification:

    • Add the ability to use maps from the Other category (e.g. BSE, CL, etc.) for classification.
    • Add a button to remove all the selected maps for classification.
    • Set the number of neighbours to 5 for K-nearest neighbours.
    • Add an option to select a mask with merged data.
    • Disable the log scale of the colour bar when a mask file is selected and displayed.

  • Bingo-Antidote

    • Add the database JUN92_Pourteau2014 as used in Petroccia et al. (2025) JMG 43,21-46.

  • Other:

    • Enhance the Generator module by adding the ability to use log, log10 and exp functions.
    • Enhance the Data Visualisation module with the ability to use log scales for binary plots.
    • Add log scale compatibility to multi-plot images and to the gif creation function.
    • Improve the map display engine as a test for compatibility with future versions of MATLAB. To start XMapTools with the 4.3 legacy display engine, simply add an empty legacy.xmt file to your working directory.
    • Fix a problem with the merge function that did not work properly when multiple quanti files had the same name.
    • Fix a problem where the zoom state was lost when exporting the map to a new window.
    • Fix an aspect ratio error for the RGB image in the Data Visualization module.
    • Fix a problem in the Calibration for EPMA module that could occur if a point was outside the map boundaries; a warning message has been added. Thanks to Stephen Centrella for reporting this issue.
    • Fix a problem in the calculation of the end member fraction for andradite garnets. Thanks to Rich Taylor for reporting this problem.
    • Fix an issue that prevented the first map from being displayed when a Quanti dataset was selected.
    • Fix an issue with displaying mask names in the Data Visualization module when a mask file was selected. Thanks to Jonas Vanardois and the second year bachelor students at UNIL for reporting this issue.
    • Fix a issue in the converter for EPMA (JEOL Windows recipe) where the CL maps were not recognised.
    • Solve an issue in the Spider module that prevented the plot from being updated. Thanks to Guillaume Bonnet for reporting this issue.
    • Minor fixes in XMap_MinColors.txt and XMap_MinDensity.txt.
    • Improve compatibility of the Export Plot Tool (opens in a new window) by allowing log scale colour bars to be properly exported.
    • Change the data type from 'wt%' to 'wt/wt' in the Import module.
    • Edit the message displayed when XMapTools is used for the first time.
    • Fix a configuration error for users using the latest developer version via MATLAB.
    • Other minor bug and fixes

Release notes published on 21.03.2025, by Pierre Lanari & Philip Hartmeier.

XMapTools 4.3 (build 240114)

  • General
    • Add a functionality to reorder masks within a maskfile
    • Improve the correlation plots by implementing an option to select a submask
    • Improve the output format of the multi-map export function for all sampling methods
    • Improve the live plot of the sampling method strip
    • Improve the calibration module interface for EPMA data, including a description of the check calibration table
    • Add a subroutine to check the map size before classification. Display an error message with the map size if there is any problem with the data (problem discovered by Alissa Madera)
    • Update and improve the help files

LA-ICP-MS:

  • Add a multi-file mode for importing LA-ICP-MS data

  • Add a log generator module for data collected in separate files

  • Add a functionality to filter values below LOD in quanti files

  • Add standard files for: NIST614, FGS1, FGS2, STDGL3, MASS1, NiS3, MAPS4, MACS3

  • Modify the export function to append the isotope number to the file name (e.g. Al.txt is now Al_27.txt)

  • Optimize the GUI of the data conversion module for LA-ICP-MS

  • Classification:

    • Add a classification test and calculate the classification metrics (Accuracy, Precision, Recall, F1 Score); they are displayed in the Information tab, if a mask file is selected. This feature is not available for mask files created with previous versions of XMapTools
    • Improve significantly the performance of classification for sub-mask creation and fix several minor issues
    • Improve the overall appearance of the graphs generated by the Classification function
    • Improve the composition plot in the classification by implementing the mineral colors

  • Data Visualisation Module:

    • Add a submask selection option for plotting
    • Add an option to fix (hold on) the axis limits in binary plots
    • Add the specific colors of each mask for plotting
    • Improve performance of density map calculation; density maps are now displayed in low resource mode by default
    • Add an option to hide the density map in low resource mode
    • Add an option to set the density map resolution (default: 100)

  • Drift correction module:

    • Add a drift correction module to XMapTools 4 with enhanced data visualisation capabilities
    • Add a 2D correction subroutine based on a single mask that includes data renormalisation

  • Sampling Tools (thanks to @hannahcunning on GitHub for suggesting these changes):

    • Add a label showing the orientation of the stip when the shape is modified or rotated.
    • Improve multi-map export function when a mask is selected from the secondary menu
    • Improve the file format for single-map sampling
    • Add an option to the Sampling menu to hold the ROI. The ROI will not be deleted if the mask selection is changed from the secondary menu and this mode is selected

  • Other:

    • Fix an issue in the external function for rutile thermometry for the Kohn (2020) equations (pressure unit, discovered by Mona Lueder)
    • Fix several compatibility issues in the project loader for files created with previous versions of XMapTools
    • Fix an issue in the data visualisation module for binary plots after the mask option was disabled
    • Fix a display issue in the information window for map data containing NaN values
    • Fix an error in the title of the sampling strip plot where colors where switched; the blue curve represents the median and the red curve represents the mean profiles (discovered by Nils Gies)

XMapTools 4.2 RC (no build yet)

  • General

    • Add a new colour scheme "XMapTools Colour Palette for Minerals" for plotting mask images that is automatically applied to new classifications. Unrecognised classes are displayed in black
    • Add a new module "Mask Colour Editor" to edit the colours of the mask image. It is possible to (1) apply the new "XMapTools Colour Palette for Minerals, (2) edit individual colours using a colour picker, (3) apply any of the available colour palettes.
    • Add a menu option to save a result dataset to an hdf5 file available in Menu > Edit > Dataset > Export as hdf5
    • Add a menu option to update the element/oxide indexing for Quanti and Merged datasets, available in Menu > Edit > Dataset > Update Element/Oxide Indexing
    • Implement a stopwatch in the classification function; results are visible in the log file
    • Improve the sampling tools "Circle" and "Area (Polygon)" by exporting all data in a file Data.txt when the "Multiple Map" option is used
    • Improve the converter module for EPMA by automatically reading the dwell time for JEOL data sets

  • LA-ICP-MS:

    • Add a new data category in the secondary tree menu for LOD data
    • Fix a problem that prevented the AcqMethod.xml file from being read.

  • Bingo-Antidote 2.1

    • New GUIwith improved workflow and advanced tools
    • All recipes and previous functionalities have been implemented
    • Add an option to save and load a Bingo-Antidote project
    • Add an option to add new phase definitions using a file AddPhaseDefinitions.txt in the working directory
    • This version of Bingo-Antidote is fully compatible with the latest version of Theriak-Domino (available at https://github.com/Theriak-Domino/)
    • The following thermodynamic databases have been tested: JUN92.bs; td-ds55-HP1.txt; td-ds62-mp50-v05.txt; td-ds62-mb50-v07.txt

  • Other:

    • Add a version tracking option in project files to make it easier to identify compatibility issues
    • Improve the scale bar and solve several display and location issues
    • Solve a major issue in the training set that prevented ROI from being added when more than one training set was created.
    • Solve an issue in the import module that prevented the imported quantitative maps expressed in oxide wt% from being used for structural formula calculations
    • Solve several minor issues in the the load function (1) when loading projects created with XMapTools 3 and (2) when the last mask file in the project was deleted
    • Fix a problem in the sampling function (circle and polygon) where zeros were included in the average calculation.
    • Fix a problem with the mask delete function
    • Fix a problem in the Structural Formula module for calculations with a fixed oxygen and number of cations.

XMapTools 4.1 (build 230102)

Release 4.1 includes new functionalities and updates to XMapTools and improvements to stability and compatibility.

  • General

    • Add tools for single-mask classification and the creation of sub-masks. At the moment, it is recommended to use the Random Algorithm forest for creating sub-masks
    • Add a point counting tool to evaluate pseudo-modes; XMapTools selects randomly pixels on the map and estimates the modal abundances (in %). A version with uncertainty estimation using Monte-Carlo can be activated
    • Add a functionality to calibrate pixels of a selection of masks for standardisation of EPMA data. Note that merged maps are only generated when the option "Apply to all maps" is selected.
    • Add entropic filters to the classification (TEXTF)
    • Add the old function to run XMapTools and open immediately a project in the MATLAB version using the command: XMapTools open ProjectName
    • Add a demo version of Bingo-Antidote 2.0 for test purposes
    • Improve stability of XMapTools when a ROI is drawn or edited

  • LA-ICP-MS:

    • Add a multi-standard calibration option which required several major changes in both the import tool and the calibration module for LA-ICPMS data. This update also includes several improvements and minor corrections. Compatibility with data generated using previous versions is not fully maintained
    • Add an option to read the sweep time values for each element from an xml file. Note that the file name should be AcqMethod.xml.
    • Improve performances for plotting and ROI interaction of the Spider module

  • Data Visualisation Module:

    • Improve the global performances of this module by implementing the low ressource mode to all plots. Only 20 % of the data points are plotted when this mode is active; this threshold can be adjusted in the option tab
    • Add an option to select a range of data (using the fields Xmin and Xmax) when plotting an histogram
    • Add a plotting report generated while plotting a ternary diagram
    • Add an option to create a single-mask maskfile from he pixels selected by the Identify
    • Add a dropdown menu to select a phase from a maskfile to plot only the pixel compositions of this phase
    • Add an option to avoid plotting zeros; this is important for the fitting tools
    • Fix several issue in the starting function that would prevent the module to open for special cases (e.g. less than 3 maps)

  • Import tool:

    • Improve compatibility of the EPMA Converter to import data from JEOL microprobes (Windows)
    • Activate map re-sampling and orientation corrections to all data types in the import tools. This resolves an issue when LA-ICPMS data are imported from Iolite. It is not recommended to use these tools for other data types

  • Other:

    • Add an option to unfreeze the interface after an error by simply requesting to close the app. This option does not require to have unsaved data as in previous versions
    • Add a checking function for the selected training set before classification
    • Add a mask file signature to ensure data compatibility throughout XMapTools and add-ons
    • Improve interface behavior for button availability, tooltips and error messages
    • Improve GUI size for screens with low resolution
    • Improve the plot behaviour of the main tree menu: if a category/dataset from Quanti, Merged, Result, Other, the first element in the list is automatically displayed
    • Export a file Last_LBCsim.txt in the main directory containing each local bulk compositions simulated by XMapTools for estimating the LBC uncertainty.
    • Fix an issue in the classification function when part of the selected maps have been deleted
    • Fix a minor issue in the variable initialisation for mask files
    • Fix several minor issues in the Converter for LA-ICP-MS; reported by Nils Gies
    • Fix several minor issues in the behaviour of ROI for training sets; reported by Nils Gies
    • Fix an issue in the project loading function
    • Other minor bug and fixes

XMapTools 4.1 Release Candidate (no public release yet)

  • Release notes:
    • Improve stability of XMapTools when a ROI is drawn or edited
    • Add a multi-standard calibration option which required several major changes in both the import tool and the calibration module for LA-ICPMS data. This update also includes several improvements and minor corrections. Compatibility with data generated using previous versions is not fully maintained.
    • Add an option to read the sweep time values for each element from an xml file. Note that the file name should be AcqMethod.xml.
    • Improve performances for plotting and ROI interaction of the Spider module
  • Data visualisation module:
    • Improve the global performances of this module by implementing the low ressource mode to all plots. Only 20 % of the data points are plotted when this mode is active; this threshold can be adjusted in the option tab
    • Add an option to select a range of data (using the fields Xmin and Xmax) when plotting an histogram
    • Add a plotting report generated while plotting a ternary diagram
    • Add an option to create a single-mask maskfile from he pixels selected by the Identify Pixel Tool.
  • Other:
    • Fix an issue in the project loading function
    • Other minor bug and fixes

XMapTools 4.0 beta 4 Developer (no public release yet)

  • Release notes:
    • Add tools for single-mask classification and the creation of sub-masks. At the moment, it is recommended to use the Random Algorithm forest for creating sub-masks.
    • Add a point counting tool to evaluate pseudo-modes; XMapTools selects randomly 300 pixels on the map and estimates the modal abundances (in %). A version with uncertainty estimation using Monte-Carlo can be activated in the developer version.
    • Add a functionality to calibrate pixels of a selection of masks for standardisation of EPMA data. Note that merged maps are only generated when the option "Apply to all maps" is selected.
    • Add entropic filters to the classification (TEXTF)
    • Activate map re-sampling and orientation correction to all data types in the import tools. This resolves an issue when LA-ICPMS data are imported from Iolite. It is not recommended to use these tools for other data types.
  • Improve compatibility of the EPMA Converter to import data from JEOL microprobes (Windows)
  • Other:
    • Improve interface behavior for button availability, tooltips and error messages
    • Add an option to unfreeze the interface after an error by simply requesting to close the app. This option does not require to have unsaved data as in previous versions
    • Add a check of the selected training set before classification
    • Solve an issue in the classification function when part of the selected maps have been deleted
    • Solve a minor issue in the variable initialisation for mask files
    • GUI size adjusted for screens with low resolution
    • Add a mask file signature to ensure data compatibility throughout XMapTools and add-ons

XMapTools 4.0 beta 3 Developer (no public release yet)

  • Release notes:
    • Add the old function to run XMapTools and open immediately a project in the MATLAB version using the command: XMapTools open ProjectName
    • ...
  • Data Visualisation Module:
    • Add a dropdown menu to select a phase from a maskfile to plot only the pixel compositions of this phase
    • Add an option to avoid plotting zeros; this is important for the fitting tools
    • Fix several issue in the starting function that would prevent the module to open for special cases (e.g. less than 3 maps)
  • Other:
    • Improve the plot behaviour of the Tree menu: if a category/dataset from Quanti, Merged, Result, Other, the first element in the list is automatically displayed
    • Export a file Last_LBCsim.txt in the main directory containing each local bulk compositions simulated by XMapTools for estimating the LBC uncertainty.
    • Fix several minor issues in the Converter for LA-ICP-MS; reported by Nils Gies
    • Fix several minor issues in the behaviour of ROI for training sets; reported by Nils Gies