button located in 'Import Maps and Images'. This will open the import module and prompt you to select files.
button in Classify and select the phases. Press again the Add 
button. Note that the Classify button is only available when an appropriate dataset and training set are selected in the primary and secondary menus.
button appears above the tree menu.
to generate the calibrated maps.
button allows a set of map files to be imported. Select compatible files from the pick map file(s) pop-up window. Multiple files can be selected together. If a selected file cannot be imported (e.g. due to an incompatible format), it will be skipped during the import.
to import the selected maps into XMapTools after the corrections have been applied.
button activates the mode to draw a ROI with a circle shape. Draw a circle on the map in a region of constant intensity.
Set the colour palette to be used for the colour bar throughout XMapTools.
Check the Log (Use a log colormap) box to set a logarithmic axis for the colour bar. If this option is not selected, a linear scale is used instead.
Sets the number of colours used in the colormap (i.e. the resolution of the colour bar). Colour palettes defined with more colours are resampled. The default value is 256.
Adds a black or white layer at the bottom (lower) and/or top (upper) of the colour palette. When selected, the layer can be set to either black or white in the corresponding drop down menu.
If selected, negative values are displayed in the plotted map. By default, XMapTools ignores negative values in plots.
Defines the value of the median filter to be applied when plotting a new 3D surface (see main menu Edit > Plot 3D surface). Changing this option will not update plots already generated.
button opens and loads an existing project in XMapTools. The first map available in Intensity is automatically selected. The current working directory is automatically changed to the location of the project file.
button saves the active project as a MATLAB M-file containing all variables used by XMapTools. If no project has been saved, a new project will be saved.
button saves the active project as a new MATLAB M-file.
Display the name or the full path of the active project (if saved) depending on the selected option in the dropdown menu (File or Path).
button opens the converter for EPMA data. A description on how to convert EPMA maps is available in the 
button opens the converter for LA-ICPMS data. A detailed description of how to convert LA-ICP-MS data can be found in the 
button allows multiple maps to be stitched together in a grid. Such a mosaic allows maps of individual grains to be combined on a single image, improving the visualisation of possible variations in composition. The original coordinates of each map are not preserved. Spot analyses used as internal standards must have X and Y manually defined after the mosaic has been created using the XMapTools coordinate system. For an alternative option, see the real mosaic option below.
button merges several maps into a referenced system based on their original coordinates. It also calculates the coordinates of the new map for the Standards.txt file. This means that spot analyses obtained during the same probe session can be provided directly and used to calibrate the mosaic.
button opens the Import Tool to load map data.
button imports slice images obtained after reconstruction of CT data. Compatible image formats are 
Set the map resolution corresponding to the pixel size, also known as the step size on EPMA instruments. The default value is 20µm (arbitrary). The resolution value is automatically calculated from the map coordinates defined in Standards.txt when internal standards (spot analyses) are imported.
Activate and display the scale bar using the pixel size defined in Resolution. Two options are available from the drop down menu: white (default) or black.
button can be used to adjust the orientation of the map. The rotation angle is displayed next to the button with possible values: 0 (default orientation), 90, 180 or 270. Note that some of the display features, such as drag-for-zoom, are not available when a rotation is applied.
button has various functions depending on the item selected in the secondary menu:
button opens a new figure containing two plots (e.g. Fig. 2): the result of the algorithm on the left and the same map with the filtered grain boundaries shown in red on the right. The axes of the two plots are aligned, and zooming in on one plot automatically adjusts the view of the second plot.
(small) button available in Segmentation Parameters & Test.
button generates several plots to examine the spatial distribution of the segmented groups:
button to automatically adjust the colour range.
ROI
Path
mode to select multiple regions of interest. Simply repeat Step 3 to add more selections (circle or ROI). It is possible to edit and move any selection and the plot will be updated.
.
button to copy the content of the table to the clipboard
Histogram – requires a single variable X; a histogram is generated and plotted in the main figure (Fig. 1)
Binary plot – requires two variables X and Y; a binary plot is generated and plotted in the main figure, as well as a density image. Two histograms, one for each dimension (not shown if low resource mode is active), are plotted as additional figures (Fig. 2)
RGB – requires three variables X, Y and Z; an RGB composite image is generated and plotted in the main figure, a legend is plotted in an additional figure (Fig. 3)
Ternary plot – requires three variables X, Y and Z; a ternary plot is generated and plotted in the main plot, three histograms and a density plot (not shown if low resource mode is active) are plotted as additional plots (Fig. 4)
button activates a cross cursor and you can select vertices of a polygon around any region of interest in the main plot. Right-click to close the polygon.
Selecting the Masks check box will colour the data displayed in the binary or ternary plots according to the mask file displayed in the drop down menu.
button or the live frequency polygon (see figure below) to adjust the lower and upper limits of the color bar. Note that the color bar settings are available in the "Options" workspace.
button available in the "PROJECT & IMPORT" workspace or in the menu "File" > "Save Project".
and Pan 
buttons to adjust the field of view.
button.
button. The maps of principal components are listed in the category "Other" available in the primary tree menu.
button.
button and immediately click and drag over the map to create the ROI.
button.
button and copy the results in a spreadsheet software program. Note: now you know why this method should not be used.
button. Note that the color of the spot labels can be changed in the options of the "Project & Import" workspace.
button to open the Calibration assistant for EPMA data.
button to automatically generate a density map.
button.
button.
button.
button to calculate the maps of structural formula for biotite.
button.
📚
Documentation
Powerful tools for quantitative compositional mapping and analysis
XMapTools Documentation
Official documentation for XMapTools, a free and versatile software solution for quantitative compositional mapping and analysis. This site is built with VitePress and deployed via GitHub Pages.
Live site: https://xmaptools.github.io/Documentation/
Contributing
Contributions to improve or extend the documentation are welcome. Please follow the workflow described below.
Prerequisites
Setting Up the Project Locally
- Fork this repository on GitHub.
- Clone your fork:bash
git clone https://github.com/<your-username>/Documentation.git +cd Documentation - Install dependencies:bash
npm install - Start the local development server:bashThe site will be available at
npm run devhttp://localhost:5173/Documentation/. Changes to.mdfiles are reflected live in the browser.
Repository Structure
.
+├── index.md # Home page
+├── getting-started.md # Getting started guide
+├── installation_guide.md # Installation instructions
+├── doc-epma.md # EPMA documentation
+├── doc-laicpms.md # LA-ICP-MS documentation
+├── bingo-antidote.md # Bingo-Antidote documentation
+├── tutorials.md # Tutorials
+├── videos.md # Video resources
+├── .vitepress/ # VitePress configuration and theme
+│ ├── config.js # Site configuration (nav, sidebar, ...)
+│ └── theme/ # Custom theme overrides
+└── package.jsonWriting and Editing Content
- All documentation pages are written in Markdown (
.mdfiles) at the root of the repository. - VitePress supports standard Markdown syntax plus additional features such as custom containers, code highlighting, and frontmatter.
- Images are hosted in the separate Documentation_Images repository. Reference them using raw GitHub URLs with an HTML
<img>tag:html<img src="https://raw.githubusercontent.com/xmaptools/Documentation_Images/main/Figures/my-image.png" alt="description" style="max-width: 100%; height: auto; display: block; margin: 0 auto;"> - Navigation and sidebar links are configured in .vitepress/config.js.
Submitting Changes
- Create a new branch for your changes:bash
git checkout -b my-contribution - Make your edits and verify them locally with
npm run dev. - Commit your changes with a clear message:bash
git add . +git commit -m "docs: describe your changes" - Push to your fork:bash
git push origin my-contribution - Open a Pull Request against the
mainbranch of this repository. - Wait for review and approval before merging.
Style Guidelines
- Use clear, concise language.
- Use headings (
##,###) to structure content logically. - Prefer numbered lists for sequential instructions and bullet points for unordered items.
- Include screenshots or diagrams where they help clarify a concept.
- Keep filenames lowercase with underscores (e.g.,
installation_guide.md).
Building for Production
bash
npm run buildThe static site is generated in .vitepress/dist/ and automatically deployed to GitHub Pages via the CI workflow on push to main.
License
This project is licensed under the GNU General Public License v3.0.
button allows multiple maps to be stitched together in a grid. Such a mosaic allows maps of individual grains to be combined on a single image, improving the visualisation of possible variations in composition. The original coordinates of each map are not retained. Spot analyses used as internal standards must have X and Y manually defined after the mosaic has been created using the XMapTools coordinate system. For an alternative option, see the second mosaic option below.
-
-Procedure for creating a mosaic using a predefined grid:
-
-- From the the main menu, set the working directory to a directory containing a Mosaic (case sensitive) folder: XMapTools > Set Working Directory
-- The Mosaic folder should contain a set of maps with the same elements in the same format (e.g. TXT or CSV, not a combination of the two). Each dataset must be stored in a separate subfolder and already be in the XMapTools format after conversion from the raw EPMA
-
- data. Note that the subfolder name is used to define the order of the map in the mosaic. Use folder names such as 01_Map34; 02_Map4; 03_Map1 to define the order before importing.
-- If a folder name starts with a minus symbol (−), the folder will be skipped and not imported when the mosaic is created
-- Important: The maps must have the same spatial resolution. If a map has a different spatial resolution, the resolution must first be adjusted manually. Note that XMapTools assumes that the maps have the same spatial resolution and does not check this during mosaic creation
-- Press the Generate Mosaic (Grid) button
-- Set the number of columns in the dialogue box
-- XMapTools generates the mosaic and saves the new maps in a new selected directory and change the edit the current working directory automatically.
-
-
button merges several maps into a referenced system based on their original coordinates. It also calculates the coordinates of the new map for the Standards.txt file. This means that spot analyses from the same microprobe session can be provided directly and used to calibrate the mosaic.
-
-
-To create a referenced mosaic:
-
-- From the main menu, set the working directory to a directory containing a Mosaic (case sensitive) folder: XMapTools > Set Working Directory
-- The Mosaic folder should contain a set of maps with exactly the same elements. Each dataset must to be stored in a separate subfolder. Note that the subfolder name is used to define the order of the map in the mosaic. Use folder names such as 01_Map34; 02_Map4; 03_Map1 to define the order before importing. Each folder must contain a Standards.txt file containing the map coordinates. If a Classification.txt file exists, it will be skipped.
-- The spatial resolution of each map is automatically adjusted to the settings of the map with the higher spatial resolution. Resampling is performed using a linear interpolator for raster data.
-- Press the Generate Mosaic in Original Coordinate System button
-- XMapTools generates the mosaic, saves the maps in the working directory, generates a file Standards.txt containing only the first block with the map coordinates. The order of the oxides (second block) and the analyses (third block) must be added manually.
-
-