05. Mapping

To map the fitted elements, click on Map Fittings in the toolbar. Only those fittings which are enabled in your Peak Fitting list will be mapped. It is recommended that you enable all fittings for mapping as each fitting results in an individual map which can be disabled later.

For extremely large maps, you may see some performance gain from disabling some fittings, especially if you are using data filtering or Optimizing/Least-Squares Curve Fitting or Fitting Solver algorithms.

Peakaboo’s mapping window

After the mapping is complete, a window will appear with a coloured map, a scale, and a list of the mapped element lines. For datasets which contain dimension information, map widths and heights are automatically set to appropriate values. Otherwise, Peakaboo can attempt to find dimensions that produce contiguous images. If this does not work (it usually does), you will have to adjust the dimensions yourself.

All fittings will be represented in the initial map. To get the individual element maps, uncheck all other fittings in the Peak Fittings tab in the sidebar, leaving the element fitting you wish to view. Maps can have filters applied to them the same way that spectra can, which can help reduce outlier values and noise. For more information, see the section on Map Filtering.

Map Modes

Composite

Composite is the default map mode. It sums the intensities from different fittings into a single map. The data is displayed with a heat map colour scale, but can also be shown using different colour palettes by selecting View in the toolbar. See the Map Colour Palettes section below for available options.

Composite maps are scaled against a global maximum of all fittings. If you wish to scale a fitting to its own highest intensity, select Visible under the Sort By section in the sidebar. A minor element will show very a low intensity distribution using All, but appear much more intense with Visible when displayed alone.

Overlays

Select the Overlay option from the dropdown list under the Peak Fittings sidebar tab to use this mapping mode. It allows you to assign different color groups to various fittings, which are then overlaid on the map. Each color represents the intensity of its respective fitting group, providing a visual distribution of multiple elements simultaneously.

Caution: Be mindful when selecting colors for overlays, as some combinations may create ambiguity. It’s important to select distinct colors to clearly represent each fitting group. Since Red, Green, and Blue are primary colors used in computer displays, choosing them can help minimize this issue.

Overlay of Iron and Zinc concentration

The Scale By settings in Overlay mode dictate how the colors of fitting groups relate to each other:

• All: This setting uses the highest intensity from all fitting groups as a benchmark to scale colors for every group, providing a uniform intensity comparison across all colours in the map.

• Colour: Each color group is scaled according to the highest intensity found within that specific group. Caution While this method highlights each group distinctly, it will distort quantitative accuracy, rendering the map more suitable for qualitative analysis.

To enhance the clarity of overlays where different elemental maps blur together, consider using the Low Signal Removal map filter. This filter truncates weaker intensities, making it easier to distinguish between overlapping maps. For detailed instructions on applying this and other map filters, refer to the section on Map Filters.

Ratios

In Peakaboo, you can map the ratios of elements by selecting Ratio from the Peak Fittings dropdown list. Choose the fittings you want to compare and assign a color to each from the dropdown lists provided next to the fittings.

Ratio of Iron and Zinc

The Scale By settings in Ratio mode dictate how the colors of fitting groups relate to each other:

• All: Scales the fitting groups based on the highest intensity from either group, applying this maximum value to both groups. This method provides a unified view of intensity across the mapped ratios.

• Colour: Each group is normalized individually against its own greatest intensity before ratios are calculated. Caution: This approach enhances the visual distinction between groups but will lead to quantitatively inaccurate representations. It's best used for qualitative insights where visual separation is more important than accuracy.

Correlations

To explore the relationships between different elements in your dataset, select Correlation from the Peak Fittings dropdown list. Choose which fittings to analyze and set their respective axes using the controls provided next to each fitting.

Correlation maps are two dimensional intensity histograms, illustrating how often map points fall within specified intensity ranges. This graphical representation helps identify patterns or relationships between the selected elements.

Adjust the number of intensity ranges (or bins) using the Granularity control located at the bottom of the sidebar. This allows you to change the resolution of the correlation map, tailoring the detail level to your analytical needs.

Correlation of Iron and Zinc

Map Colour Palettes

Colour palettes control how intensity data is visually represented in maps. Choosing an appropriate palette can help with data interpretation and presentation. Peakaboo uses Gouldian as the default palette, which works well for most analyses. Colour palettes can be changed on a per-map basis or set globally for new maps.

Peakaboo provides nine colour palettes:

• Gouldian (default) - Perceptually accurate palette with a good portion of the colour spectrum.
• Lipari - Perceptually accurate palette.
• Navia - Perceptually accurate palette.
• Red Hot - Perceptually accurate gradient from black to red to yellow.
• Rainbow - Legacy palette ranging from blue to green to yellow to red. This is not a perceptually accurate palette, although effort has been made to minimize the deviation.
• Black to White - Perceptually accurate monochrome gradient for greyscale visualization.
• Amber - Inverted palette from white to yellow to orange to purple where low signal values appear light.
• Cranberry - Perceptually accurate inverted palette from icy light blue to cranberry red where low signal values appear light.
• White to Black - Perceptually accurate inverted monochrome gradient.

Palette Selection Guidance:

Perceptually accurate palettes provide consistent visual representation of intensity differences across the entire range of values. This makes them well-suited for quantitative analysis where accurate interpretation of relative intensities is important.

The monochrome palettes (Black to White or White to Black) are useful for printing or presentations where colour is not available or desired.

Inverted palettes (Amber, Cranberry, White to Black) display low signal values as light colours rather than dark. This can be useful when you want to emphasize weaker signals or prefer lighter backgrounds in your visualization, especially in the correlation map mode.

The Rainbow palette is a legacy option that may be familiar to users of earlier versions of Peakaboo, but it is not perceptually accurate and may misrepresent the relative differences between intensity values.

Changing Colour Palettes:

To change the colour palette for the current map:

1. Click the View button in the toolbar.
2. A popup menu will appear showing the available palettes, each with a visual preview.
3. Select your desired palette from the list.
4. The change will be applied immediately to the current map.

To set the default colour palette for newly generated maps:

1. Navigate to Advanced Options from the main plotting toolbar.
2. Go to the Appearance tab.
3. Select your preferred palette from the Map Palette dropdown.
4. This setting only affects newly generated maps and does not change existing maps.

Map Filters

Just as with spectra, filters can improve the visual quality of your maps by cleaning up data. To add filters:

• Navigate to the Filters tab in the sidebar.
• Click Add Filters to view and select from the available filters, organized by type in expandable folders.
• Choose your desired filter, then click OK to apply it to your map.

Once a filter is added, adjust its parameters by clicking the Settings button next to the filter. This opens a dialog where you can modify settings and immediately see the impact on your map. To learn more about a map filter, you can view it’s description by hovering over the Help icon in the settings dialog.

Comparison of mapping of a nickel intensity distribution before and after being treated with the low signal removal filter (40% setting) and with the weighted average filter (radius:1, repetitions:1)

Comparison of mapping data before (left) and after (right) being treated with the Denoise filter where areas of high noise are replaced with a smoothed value without altering the rest of the map

Caution: Filters modify map data individually for each fitting before they are combined into the final map, which can sometimes lead to unexpected results. For instance, if a Signal Cap filter with a cap of 100 counts is applied separately to Fe K and Zn K maps before merging them, the combined peak value might reach 200 counts, not the 100 you might expect.

Exporting Map Data

To save your maps for further use or presentation:

1. Click the Export button on the toolbar.
2. Choose Export as Image for visual formats. You can save maps in:
   • Pixel Image (PNG): Best for general use where ultra-high resolution is not required.
   • Vector Image (SVG): Ideal for high-quality publications where scalability is needed without any loss of detail.

Additionally, map data can be exported directly in several formats:

• CSV (Comma Separated Values): Useful for data analysis in spreadsheet programs or specialized data analysis tools.
• All-In-One Zip Archive: This includes a CSV file and map for each fitted element and a session file for archiving or sharing.

These options ensure your data is preserved in formats that suit various needs, from detailed analysis to professional presentation.

Managing Errant Data in Maps

If you encounter missing or skewed spectra within your dataset, you can easily remove these anomalies from your maps:

1. Identify the Problematic Data Point: Hover your mouse over the suspicious data point in the mapping window. The index of this point will be displayed in the status bar at the bottom of the window.
2. Inspect the Data Point: Switch to the plotting window and ensure it is set to Individual Scan mode. Input the problematic Index # in the Scan field at the bottom of the window to view the specific data point.
3. Exclude the Data Point: Click the Exclude button to mark the scan as erroneous and remove it from the dataset.

Once excluded, the data point will not appear in future maps; instead, it will be interpolated from neighboring data points.

Methods for Selecting Map Subsections

Peakaboo offers four intuitive ways to select subsections of a map, each accessible from the Settings tab:

• Rectangular, Elliptical, and Free-hand Selections: These tools allow you to draw shapes directly on the map to create a selection mask.
• Point Selection by Similarity: Click on a point to select all contiguous points of similar intensity. Double-clicking selects all points across the map with similar intensity, regardless of their location.

Selecting a cropped subset of a data set

Selecting a series of contiguous high-intensity points from the data set

Settings for Point Selection

• Threshold: This setting adjusts the sensitivity of point selection. Setting the threshold t means that clicking on a point with intensity i selects all contiguous points whose intensities fall between i ÷ t and i × t. For instance, a threshold of 2 will select points between 50% and 200% of the intensity of the clicked point.

• Padding: Determines the inclusion of adjacent pixels around the selected points. A padding of 1 means all directly neighboring pixels are also selected. Increasing the padding value p expands the selection by p rings of pixels around the initial selection.

Advanced Selection Techniques

Hold the Control key while clicking to modify selections:

• Control + Click on an unselected point adds it to the current selection.
• Control + Click within a current selection removes that point from the selection.

These methods apply to rectangular, elliptical, and free-hand tools where dragging is involved. By combining these techniques, particularly with point selection settings, you can tailor complex selections, such as isolating a specific ring around an intensely active region without including it.

Viewing Spectra from Selected Map Regions

Peakaboo enables you to extract and analyze spectra from designated regions within your map. After using the selection tools described earlier to define a subsection of your map:

1. Click Plot Region to initiate the spectral view for the selected area.
2. A new tab will open in the plotting window, displaying the spectra from the chosen subsection.
3. You can then apply various Peakaboo tools and filters to further analyze these spectra.

This feature allows for targeted spectral analysis, providing insights specific to selected areas of your map.

Plotting window showing data for a subset of the original data set