I. Introduction

This Quick Start Guide builds on the SEC SNE-4500M Plus SEM Quick Start Guide, so it is assumed that the user first goes through and understands its contents. For more information, please see the helpful Bruker Quantax EDS User Manual.

II. Procedure

A. Sample Preparation For EDS

The analyzed surface should be clean and dry, well-polished, and have an electrically conductive coating (usually carbon) applied with the Leica EM ACE200 vacuum coater located on the ship. Typical sample preparations for EDS are polished thin sections, or polished grain mounts. Contact the Core Description technician for help with the vacuum coater and SEM-EDS, or the Thin Section technician for questions about EDS sample preparation.

B. Esprit Compact Software Startup

1. Start ESPRIT Compact by clicking the program icon on the desktop or in the start menu. The login screen is displayed, prompting for username and password.
2. Enter the username and password and click the login button.
   1. For general purposes, use username: main / password: main
   2. For technician troubleshooting purposes, use username: supervisor / password: supervisor

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Figure 1: EDS Detector configuration window, click on spectrum icon to see this.

1. Use the arrow icon on the bottom left corner of the EDS configurator (Figure 1) to open the EDS Detector Configuration dialogue and set Pulse throughput and Maximum energy to Automatic. Check that the detector temperature status indicator is green.
2. Note the input count rate (ICR) in the EDS detector configuration box. This should be between 1.0-10 kcps (thousand counts per second) at minimum, and instructions to adjust microscope parameters to increase counts are in the following section. If the input count rate is too low, try the following steps.
   1. Verify that the SEM is operating with a working distance of 7-10 mm (Focus area of Nanoeye software)
   2. Adjust the position of the second condenser lens (CL2 in the EDS menu of the Nanoeye software)
   3. Consider increasing the accelerating voltage of the SEM, up to a maximum of 20 kV. Note that this may increase the undesireable effects of built-up electric charge, which diminishes image and EDS quality.
   4. Ask a technician for help with aligning the strip aperture and aligning the electron gun.

C. SEM Imaging Prior To EDS

To prepare for EDS, the user will first use the Nanoeye software to collect a good image of the portion of the slide where they plan to conduct their EDS work, by following the instructions in the SEM SOP and using the following recommended settings and techniques:

1. Choose an accelerating voltage of 10-15 kV, or a maximum of 20 kV for more counts or if high Z major elements are expected.
2. Focus the microscope using SE (secondary electron) mode, before switching to BSE (back-scatter electron) mode for most geological applications. Obtaining a good focus on a highly polished thin section can be difficult; a helpful technique may be to focus on a piece of carbon tape, before moving to a small physical feature on the thin section.
3. The optimal working distance for EDS analyses is 7-10 mm (visible in the Focus Area panel of the Nanoeye software). This will require lowering the specimen stage (increasing the Z value to a higher positive number) in the Nanoeye software stage controls by Z = +7-10 mm and adjusting the focus accordingly, until the specimen is in focus at a working distance of 7-10 mm. Note that the focal plane should be at approximately Z - height of sample [mm] = working distance [mm].
4. Use a small spot size of 0-10%. This can be adjusted in the beam area using the Size(%) slider, or using the CL1 slider in the EDS menu.
5. Detector sensitivity can be adjusted between preset values in the EDS menu, between 1 (least sensitive) and 5 (most sensitive)
6. To increase the number of electron counts, the position of the second condenser lens can be adjusted down using the CL2 slider in the EDS menu. Aim for between 1.0-10 kcps (thousand counts per second).

The user should collect a good image of the region of the sample where they are planning to perform the EDS analyses. This image will form the basis on which EDS analyses will be uploaded into the database.

Recommended storage structure for EDS analysis data

Save EDS files taken on the same sample to a new folder created in the appropriate file hierarchy under C:\\SEM.This should follow the convention of e.g. C:\\SEM\U999\U999A\U999A-1H-1\350_U999A_1H_1W_10-11cm_DescriptionofSample_Number, along with a good SEM image taken of the region the analyses were performed.

D. Choose A Workspace

In ESPRIT Compact, there are three methods to capture electron microscope images, each which has their own section ("workspace") in the software. These are:

• Objects: for analyzing single spectra taken over a set of points or polygons
• LineScan: for analyzing spectra taken across a set of points, together forming a line. Often used to view elemental profiles across a feature of interest
• Mapping: for analyzing a map composed of a hypercube of spectra taken at a set of points, together forming a map/elemental map/elemental image

The user must select the appropriate workspace that corresponds to the type of analyses they would like to do first. Multiple types of analyses may be conducted during the same session, provided that data are saved as you go along.

E. Capture An Image

1. Select a workspace based on the type of analyses you would like to perform (Objects, LineScan, Mapping).
2. Optionally, Use the arrow icon in the bottom left corner of the Scan configurator to open the Scan Configuration menu
   1. Image resolution: 512 pixels for Object and Line data acquisition, 1000 pixels for Map acquisition
   2. Dwell time (us): 8 us
   3. Line average: 1
3. Optionally, click on the Capture dropdown arrow to set capture parameters and Image number of Automatic numbering
4. Click on the Capture button to Capture an image
5. Above the image, select Ch1/SE or Ch2/BSE according to what type of SEM image you wish to capture. Note that the corresponding detector must be selected in the SEM software in order to show up in the EDS software.
6. Right mouse click the image to change image parameters such as legend and brightness/contrast
   1. Right mouse click the image, then click Properties to change image legend
   2. Right mouse click the image, then click Histogram to change image brightness/contrast.
7. If a good image is not showing up, you may need to go into the Nanoeye software to change the SEM parameters, under the EDS pop-up menu:
   1. Detector sensitivity (the buttons 1, 2, 3, 4, 5)
   2. CL1, CL2
   3. If taking a SE image, the sliders for Gain and Sensitivity
8. Right click on the image to Save image (recommended), Copy image or Add image to report .

F. Acquire A Spectrum

The instructions to acquire a spectrum differ between the three workspaces, thus this portion of the Quick Start Guide is separated into three sections. Follow the steps in the relevant section for the analysis that you would like to perform.

For Object Scans

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.

For Line Scans

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.

For Mapping

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.

1. Only the data of the area within the rectangle will be saved.
2. Add data to report.
3. 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
1. 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.
2. 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.
3. Process map data as desired.

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Figure 4: Example of mapping.

G. Interpreting A Spectrum

Interpreting an EDS spectrum can be very complicated, especially if the goal is to use the results semi-quantitatively. Technicians can point users to resources and tips. In particular, consider the following:

• 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

The SEMUploader application is used to format the tests for uploading to LIMS. It is available through the IODPLauncher application.

1. Select that sample you used to take the test. (You may also provide the sample's Text ID, if you have it)
   
   1. If uploading EDS data to a SEM test that was already uploaded, select the 'Existing SEM' tab.
2. When done selecting the sample, click 'Select' button.
   1. If uploading EDS data to an existing SEM test, select the SEM image you would like to upload EDS data for.
3. Enter the comments and initials and click 'Done' button.
4. Add as many SEM tests for the selected sample as you need.
5. You may edit records by going to the Records tab.
6. Make a folder for the all the EDS data you would like to upload. You may upload multiple EDS folders to a single SEM test.
   1. It is strongly suggested that the user and technicians upload to LIMS all formats available for the EDS analysis (Mapping mode - .bcf; Line Scan mode - .rtl; Objects mode - .rto; spectra for each mode - .spx; ESPRIT Compact standard Report - .rpt; Microsoft Word - .doc);
7. When finished adding all the SEM and EDS data for the selected sample, clicked the 'Finish and upload' button.
8. This will create a file in the C:\data\in folder (and any other folder you may add under the Settings tab)
9. Use the MUT application to upload this file. (Make sure MUT is configured to use C:\data\in and SEM is an active analysis)

IV. Preventative Maintenance (for technicians)

The following tasks should be completed, in addition to the tasks listed in Section IV of the SEC SEM User Guide.

Regularly

• Check the energy-channel calibration as detailed in section 5.2 (pg. 43) of the Esprit Compact user manual. Use the Pelco standard, which contains a sample of pure Cu. Perform the energy-channel calibration using the uncoated standard at 30 kV, with the CL2 adjusted such that the EDS detector is receiving about 5 kcps.
• Check that the contrast/brightness of the best BSE image captured on an average sample looks good, adjusting detector sensitivity in the EDS pop-up on the SEM software. If the image cannot be optimized, go into Systems tab to change the image parameters.

IV. Credits

Version 1 of this document was written by Luan Heywood and Kara Vadman, on Exp 397T, and contains content modified from the Esprit Compact User Manual. This document was reviewed by ___ on ___.

V. Archived Versions