Mineralogy offers quantitative geochemical and petrological data with maximum flexibility. Mineralogy now offers more capabilities to query data in a way that benefits users looking for diverse and customized post-analysis workflows.
Built around an automated mineralogy (AM) platform, ZEISS Mineralogical Software creates textural descriptions of samples across a wide range of scales, from crushed particle analysis to entire thin sections. Textural analysis and mineral classification are combined based on the chemical composition of major elements in wt%, providing easy-to-understand mineral libraries while reducing technical operator time.
The Mineralogical software is equipped with a Large Particle Visualization (LPV) user interface. It facilitates a seamless transition between image types including BSE, phase identification, and element heat maps.
A complete thin section of granulite facies metagabbro from the Lewis Gneiss Complex in northwest Scotland is shown in Figure 1. It was visualised using the conventional automated mineralogical format as well as elemental heat maps based on quantitative chemistry measured at each pixel.
Figure 1. Mineralogical offers flexibility in visualizing and exporting geochemical data stored in the software database. Here, a complete thin-section map is visualized in a) a backscattered electron (BSE) image, b) a mineralogical phase classification map, c) a quantitative EDS Fe heat map, d) a quantitative EDS Mg heat map. The bd figures are analyzed at a step size of 20 μm. Image credit: ZEISS Natural Resources
ZEISS Mineralogic is an automated scanning electron microscope (SEM) mineralogy system designed to acquire quantitative chemical data and automatically classify mineral phases directly from thin sections. The result is an innovative “all-in-one” system for sample mapping. The dynamic ZEISS Mineralogic platform offers a variety of imaging detectors that can be used in conjunction with the EDS function.
In the case presented in this paper, the capabilities of ZEISS Mineralogical based on the ZEISS Sigma 300 VP field emission SEM equipped with backscattered electron (BSE) imaging and two Oxford Instruments Ultim Max 65 EDS detectors using Tru-Q peak quantification are evaluated.
Flexible visualization of data sets
LPV facilitates the visualization of large data sets, including thin sections, with images and data stitched together. Individual pixels can be evaluated instantly for geochemical measurements and mineral classification.
The map view can be quickly switched from automated mineralogy to elemental heat map view with dynamic color scale thresholding and image zoom to highlight mineral zoning and other critical features of interest.
Figure 2 shows a Ca heat map of a complete thin section with the threshold range selected to highlight zoning within the garnet and a close-up image of a single garnet in the same range. Element heat maps provide an excellent way to visualize data and simplify the classification workflow on new or more detailed sample types.
Figure 2. a) Quantitative EDS map in full thin section (20 μm pixel pitch) of a high-strain gneiss from the Glenelg area of Scotland. This sample traces the evolution of the rock towards higher pressure through the zoning of the mineral garnet, which increases in Ca towards the margin. b) A close-up image of one of these garnets is taken at a smaller pixel pitch (5 μm). c) The LPV interface can be seen with the element Ca selected from the periodic table and a concentration range set on the threshold tool. A single click exports the image which is displayed on the screen with the associated legend. Image showing the user interface for selecting the element of interest and the threshold values of the colour scale. Image credit: ZEISS Natural Resources
Figure 3. The data exported from Mineralogic is designed to provide maximum flexibility for all your geochemical data. Here we see the element heat maps imported into XMapTools.
a) EDS quantitative analysis from Mineralogical imported directly into XMapTools (garnet data in Figure 2b). XMapTools allows median filtering and conversion of EDS data with many useful functions including
b) cation per formula unit (cpfu) for Ca in site X, and
c) calculation of the grossular end member (Ca component).
d) Line profile data is easily extracted from the EDS quantitative dataset in XMapTools. Image credit: ZEISS Natural Resources
This is true for samples containing previously unanalysed minerals or where processes such as fluid weathering have caused the chemical composition to change from stoichiometric values. Elemental heat maps allow the entire sample to be interrogated before a mineral library is established. Best practice methods can be applied to identify critical phases in the sample.
Exporting data
Exporting data in a flexible and relevant format is a key element to access such a comprehensive geochemical dataset. Exporting data from LPV consists of two parts with different purposes:
- The ability to export image data to the screen
- The ability to export geochemical data for downstream workflow needs
Exporting images
LPV allows to export with a single click the image displayed on the screen as a .png file. This is available for the BSE image, the automated mineralogical phase map and the thermal map of any element. All images can be exported using the scale bar.
Phase maps also include a legend while element heatmaps include the appropriate color scale. This single click is ideal for exporting figures. As the export will directly match the current field of view, it is possible to zoom in on a critical area, adjust the dynamic color scale or combine heatmaps with BSE to export the exact image required.
Exporting data
The data export feature was developed to provide the complete heatmap information needed for research purposes. By clicking the data export button, you are taken to a periodic table interface and can select many elements of interest. Once the target folder is chosen, these data files are exported as a .csv file for each element.
Regardless of screen zoom or element intensity threshold, the full dataset will be exported for each selected element, with the pixel value as collected. This provides the most powerful mechanism for exporting equal-sized maps, faithful to the original data. The .csv file format provides complete flexibility for importing into third-party software or custom code workflows, such as Python.
Third-party software integration
The flexibility of the data export feature allows element heat map data to be imported into a range of third-party software, including popular image and data analysis packages, such as ImageJ/FIJI and XMap ToolsIn the following case, the mineralogical export was developed with the geoscientific data analysis package XMapTools by Pierre Lanari from the University of Bern.
Exported mineralogical heat map data files can be imported directly into XMapTools as calibrated geochemical data. Many elements of interest can be imported and quantitative EDS eliminates the need to include a quantification step using an electron microprobe.
XMapTools contains several useful functions specific to geoscientific analysis, and the extensive mapping of geochemical data areas in Mineralogical provides an ideal input. In XMapTools, element heat maps can be edited to oxide weight percent, cation per formula unit (cpfu), and final element proportions.
There are additional features such as median filtering and line profile tools that work perfectly with mapped EDS data. XMapTools software also comes with thermodynamic calculation tools for specific samples, including pressure and temperature calculation of metamorphic rocks.
Summary
ZEISS Mineralogic builds on the foundations of automated quantitative mineralogy and goes further. In addition to mineral classification and textural analysis, Mineralogic offers comprehensive solutions EDS quantitative geochemical information of a given mapped sample.
Data can be easily visualized and exported, allowing the user to assemble workflows in a wide range of image and data analysis programs. The result is a scanning electron microscope system that offers users the greatest flexibility in evaluating a sample.
This information was obtained, revised and adapted from materials provided by ZEISS Natural Resources.
For more information about this source, please visit ZEISS Natural Resources.