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I. Introduction

What is the SEM-EDS? What does the SEM-EDS do? What are additional resources (link them here)

This Quick Start Guide builds on the SEC SEM Quick Start Guide, so it is assumed that the user first goes through and understands its contents.

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. IMAGE OF THE DESKTOP ICON AND THE LOGIN POPUP <----set them up as main user
  3. Use the arrow icon on the bottom left corner of the EDS configurator 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.
  4. 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. Probably need higher counts per second for mapping, to reduce time required
    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. Instructions will go in User Guide

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

File structure and example

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:
  • LineScan:
  • Mapping:

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.

Picture of the top ribbon showing the different workspace buttons

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 menuimage
    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
    1. Recommended settings:
  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.image
  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.image
  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
    2. CL1, CL2 image
  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 see pg. 54 of user manual

  1. Clicking into the appropriate workspace (Objects, see figure #), 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. image of toolbar
  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: image
      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. Right click into the spectrum chart to Save (recommended to save as ???.txt???) or Add to report. image Expand on different ways of saving data

For Line Scans check this is correct

  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: image
      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.

For Mapping Needs work

  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.
  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.??????? 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, 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.

Map Processing

G. Quantify A Spectrum

H. Save Data

Saving annotated image
Saving spectra
Saving quantification results
Saving data for later reduction

III. Uploading Data to LIMS

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IV. Preventative Maintenance

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.
  • Check that the contrast/brightness of the BSE image captured on an average sample looks good. If not, 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

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