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1. Clicking into the appropriate workspace (Objects), capture an image as described in the above section.
2. Click on the image to draw the point, set of points, or area over which you would like to acquire spectrum.
3. Use Select all to highlight all objects.
4. Click on the dropdown arrow on the Acquire button to open the Acquisition menu.
   1. Set Acquisition parameters
      1. Automatic:
         1. Fast (50000 counts) for major elements
         2. Precise (250,000 counts) for minor elements (recommended)
         3. Exhaustive (1,000,000 counts) for elements close to the detection limit
      2. Manual: If Manual is selected, the acquisition must be stopped manually by deselecting the Acquire button
      3. Real time: The acquisition will stop after the time entered in the dialog box has elapsed
      4. Live time: The acquisition will stop after the dead time-corrected acquisition time has elapsed
      5. Counts: The acquisition will stop after the predefined number of counts is recorded.
   2. Optionally, set Automatic Quantification if desired. If Continuous or After acquisition is selected, the spectrum is quantified during or after the acquisition. Load a quantification method using the button.
   3. Optionally, set Spectrum numbering settings if desired: the numbering will start after the entered Spectrum number.
   4. Optionally, set Auto save settings: Select Add to report to send the data automatically after acquisition to the report, and/or select Save to file to save the data automatically after acquisition via pop-up dialogue.
5. Click Acquire to Acquire a spectrum. If Acquisition is set to Manual, the acquisition must be manually stopped by deselecting the Acquire button. All other acquisition parameters will automatically stop the acquisition when the set parameter (time or counts) has been reached.
6. The acquired spectra will appear in the spectrum list (see Figure 2). Right click into the spectrum chart to Save or Add to report.

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Figure 2: Example of object mapping.

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1. Clicking into the appropriate workspace (Linescan), capture an image as described in the above section.
2. Highlight the line and drag/adjust the endpoints to the desired position.
3. Set Point count of the line scan. Alternatively select Distance [μm] between measurement points. The distance between points and electron beam spot size is shown in a display and will change depending on whether Point count or Distance [μm] has been selected. The calculation of the spot size depends on the voltage used.
4. Click on the dropdown arrow on the Acquire button to open the Acquisition menu. Select the desired parameters.
   1. Set Acquisition parameters: 
      1. Automatic:
         1. Fast (50000 counts) for major elements
         2. Precise (250,000 counts) for minor elements (recommended)
         3. Exhaustive (1,000,000 counts) for elements close to the detection limit
      2. Manual: If Manual is selected, the acquisition must be stopped manually by deselecting the Acquire button
      3. Real time: The acquisition will stop after the time entered in the dialog box has elapsed
      4. Live time: The acquisition will stop after the dead time-corrected acquisition time has elapsed
      5. Counts: The acquisition will stop after the predefined number of counts is recorded.
   2. Optionally, set Automatic Quantification if desired. If Continuous or After acquisition is selected, the spectrum is quantified during or after the acquisition. Load a quantification method using the button.
   3. Optionally, set Spectrum numbering settings if desired: the numbering will start after the entered Spectrum number.
   4. Optionally, set Auto save settings: Select Add to report to send the data automatically after acquisition to the report, and/or select Save to file to save the data automatically after acquisition via pop-up dialogue.
5. Click Acquire to acquire a spectrum. If Acquisition is set to Manual, the acquisition must be manually stopped by deselecting the Acquire button. All other acquisition parameters will automatically stop the acquisition when the set parameter (time or counts) has been reached.
6. Use the elements icon to identify elements. Elements are automatically identified by Auto ID and element list can be modified by clicking on Element ID or Finder.
7. Select elements in the thumbnail bar by ticking the boxes below the individual element images to display their profiles in the Profiles tab
8. Use the right mouse key in the scan iage to extract region of interest spectrum from the line scan.
9. Right click into the desired element to Save or Add to report, or use the I/O icon.

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Figure 3: Example of line scan.

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1. Select the Mapping workspace. Use high count rate for good count statistics.
2. Click on the Scan configurator to set Image resolution, Mapping dwell time and Line average. Image resolution defines the pixel resolution.
3. Click on the Capture button to open the Capture parameters menu. Adjust Capture parameters for the image: set single or continuous.
4. Capture an image (example in Figure 4).
5. Click on the Acquire button and set parameters for
1. Map time: Mapping is automatically terminated if Measurement time [s] or Cycles is set. When Manual is selected acquisition has to be stopped manually by clicking the Acquire button. One click terminates the scan after finishing the last frame, the button will change to Stop. Another click on the Stop button terminates the measurement immediately.
2. Map area: Choose as Map area: Full, Fixed or Variable and the Map width or Map heights in [μm]. Choose the number of acquisition Points or the Point distance in [μm]. Points are equal to pixels in the map. The number of points alters the distance between points and the electron beam spot size shown in the display on the left side. The calculation of the spot size depends on the used high voltage.
3. After measurement: Set microscope to turn off the HV after measurement, which should be done when the user is running a long map and will not be able to monitor the machine.Select Save data to save the data automatically after acquisition. In the pop up dialog the file name and the data storage location can be chosen.
6. Acquire a map. NOTE: wait time 30 minutes for 10 kcps or less, 5-20 min for 20 kcps or higher.
7. Use the workspace icon to
1. Save map data: Use file format: ***.bcf: to save HyperMaps (datacube, hyperspectral data set). Spectra for each pixel are saved. Further processing is possible only, when data is saved as a .bcf file. ***.rtm: to save element distribution images without point spectra. ***.raw: to save hyperspectral datacube for further processing with third party softwares.
2. Save selected map data: This is useful if only a part of the map area needs to be saved. Mark the area to be saved by drawing a rectangle in the map chart with the rectangle tool. Only the data of the area within the rectangle will be saved.
3. Add data to report.
4. Clear database: HyperMap database will be deleted. Element distribution images without point spectra remain as well as the selected elements. No Elements can be added/selected anymore
8. Right mouse click into the Map tab to
1. Save map image: Use image file formats (.bmp, .png, .jpg, .tif) to save the composite element image.
2. Add item to report: Composite element image will be added to the report.
9. Right mouse click into the thumbnail bar to
1. Save images: Individual element images of selected thumbnails will be saved. To select them mark the individual element images with left mouse click + SHIFT or CRTL key.
2. Add images to report: Individual element images will be added to report.
10. Process map data as desired.

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Figure 4: Example of mapping.

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• Any charging present on the surface of the sample will quickly degrade the quality of EDS spectra. In order to avoid charging: 
  • Use the lowest possible accelerating voltage that is appropriate for the material and elements of interest
  • Use an even smaller beam current
  • Ensure good electrical grounding using carbon tape,
  • Perhaps remove the sample to apply a thicker C coat to improve electron transport
  • Check to make sure that the sample isn't charging. You can often tell charging because there will be visual streaking on the image, however also you can look at a few things on the quantification and spectra. If you are seeing charging, let me know and I can give more specific results for how to try to remedy that.
    1. Check the mass% total, which should be around 100% for non-hydrous minerals (circled on attached image)
    2. Check the "Dwayne-Hunt limit" which is where the background on the spectra goes to 0. This should be around the energy of the accelerating voltage you are operating the microscope on, e.g. for 10 kV microscope setting, you should have a Dwayne-Hunt limit of 10 keV (circled on image)
    3. If there is charging, under Additional Settings, click A (circled on image) to make the software adjust the quantification down to the "effective high voltage"
• One proxy for quality of spectrum is to right click on the spectra and then select Logarithmic graph display, to make visible the background curve of the spectra. The background should taper smoothly to the highest values at the accelerating voltage used, e.g. if the microscope is being operated at 10 kV, the spectra should have smooth values up to 10 kV.
• The carbon peak can mainly be caused by sputtering: It can be disregarded in the Esprit software Sample Configurator menu. It will ignore the carbon peak in the quantification (aka it will know that the carbon is from the coating, not the sample). See page 27 of the Bruker Esprit Compact user manual
• PRECAUTION on carbon peak: Carbon peaks are tricky, carbon coating obviously will add to it, but so will just sitting in air.  Because C is so abundant in our environment, it is almost impossible to not have some C peak unless real precautions are taken to keep the sample from being exposed tot he environment.  The beam hitting the sample actually attracts all the hydro carbons in the chamber, so while the beam is one even more carbon (burn marks you see when you go from high to low magnification) is accumulating on the surface of the sample. 
• There are two quantification methods loaded. They can be changed by clicking the arrow on the Quantify button, and click Load.
  
• Check the non-normalized mass % totals, which ideally should be around 100% for non-hydrous minerals.
• In order to interpret mass percent oxides, it is helpful to have an idea of the anticipated mineralogy of the sample, then compare the compositions to the ideal stochiometric mineral compositions from an online mineral database such as Webminerals of Mindat.
• Technicians can share access to a number of technical books on electron microanalysis if desired.

III. Uploading Data to LIMS

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