JEOL JSM-6390 LA User Manual

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Scanning Electron

Microscope (SEM)

JEOL JSM-6390 LA

User's manual

Julien M. Allaz

March 14, 2021

Version 1.4

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Page 1 Scanning Electron Microscope (SEM) JEOL JSM-6390 LA User’s manual Julien M. Allaz March 14, 2021 Version 1.4...
Page 3: Table Of Contents
A.3) First things to do when you arrive ................2 A.4) Overview of the JEOL console ................. 3 A.5) Overview of the “JEOL Scanning Electron Microscope” program ......4 B) Starting your session ....................7 C) Sample loading or unloading ..................9 C.1) Opening the sample chamber ..................
Page 4 I) SE, BSE, or CL imaging with Thermo NSS ..............29 I.1) SE, BSE, or CL imaging ................... 29 I.2) SE, BSE, or CL mosaic imaging ................31 I.3) Tips on image acquisition time & magnification ............33 I.4) Exporting your images ..................... 33 J) Quantitative (or qualitative) EDS analysis ..............
Page 5: A) Generalities About The Jeol Sem @ Igp
BSE (backscattered electron) and CL (cathodoluminescence) imaging capabilities and can provide accurate standard-based quantitative analyses of major and some minor elements by EDS (energy dispersive spectrometry). See Figure Figure 1. Overview of the JEOL JSM-6390 at ETH Zürich, D-ERDW / IGP. SEM manual ETHZ v1.4...
Page 6: A.2) Computers
The SEM is controlled by two computers that are always ON: • The LEFT computer is the main JEOL computer controlling the instrument itself. It is used to control the electron source, to set up the instrument parameters, to perform the beam alignment, and to move the stage (X, Y, Z), among other…...
Page 7: A.4) Overview Of The Jeol Console
A.4) Overview of the JEOL console The JEOL SEM has a console that is used to control the stage motion (X, Y), and the electron imaging capabilities (magnification, brightness & contrast, etc.; Fig. • The left side of the console controls the stage motion.
Page 8: A.5) Overview Of The "Jeol Scanning Electron Microscope" Program
A.5) Overview of the “JEOL Scanning Electron Microscope” program On the LEFT computer, there is a single program running constantly: “JEOL Scanning Electron Microscope”. It is subdivided in three main parts as shown in Figure • Top section: menu bar & main buttons.
Page 9 Figure 5. Overview of the main buttons in the TOP section of the SEM program. SEM manual ETHZ v1.4...
Page 10 Figure 6. Overview of the MIDDLE section of the SEM program. Figure 7. Overview of the BOTTOM section of the SEM program. J. M. Allaz © March 14, 2021...
Page 11: B) Starting Your Session
B) Starting your session Check if a notice with special instructions is on the table (e.g., in case of an outage, a problem with a detector, etc.). 2. Turn ON both computer screens. 3. Ensure that nothing is currently running (e.g., overnight EDS element map work). If an analysis is still running , contact the former (e.g., mosaic BSE or EDS mapping on the right computer)
Page 13: C) Sample Loading Or Unloading
C.1) Opening the sample chamber 1. In the JEOL SEM program, set the signal to SEI in the bottom section of the program. 2. If the CL detector was in use, turn it OFF (red button on the CL control box).
Page 15 Figure 11a. Loading a new sample and taking an overview image of your sample (SNS). SEM manual ETHZ v1.4...
Page 17: D) Stage Motion
D) Stage motion D.1) Horizontal displacement (X, Y) There are several ways to navigate along the X- and Y-axis in your sample: • Click-and-drag the mouse on the electron image. • Double-click on a feature on the electron image. • Use the joystick on the console (in X/Y mode). •...
Page 19: E) Activate The Electron Beam
The optimum is set by the lab manager or the assistant. • The “Filament heating” should read between 20 and 30 µA. • An SE image should now be visible in the JEOL SEM program. • Perform a beam alignment following the instructions in Section E.2) Activating a W electron source...
Page 20 Figure 12. Activation of the electron beam in LaB -mode. Two different processes depending on the electron source currently used: LaB cathode or W filament. Refer to Appendix A2 if the SEM is in W-mode! J. M. Allaz © March 14, 2021...
Page 21: F) Beam Alignment
6. Set the Working Distance (WD) to 10 mm by clicking on the WD value on the bottom of the JEOL SEM program, and clicking on 10 mm. 7. Do NOT change the electron beam focus anymore, as it will modify the WD! 8.
Page 22: F.3) Beam Alignment For Cl Imaging
11. Continue increasing the magnification up to at least 2000x to 4000x, relocate an even smaller particle, readjust the brightness & contrast, and perform a final adjustment of the Z-stage position; final Z position should be somewhere between 10 and 11 mm. 12.
Page 23 Figure 13. Complete procedure for beam alignment. SEM manual ETHZ v1.4...
Page 24 Figure 14. Detail on the adjustment of the Z-stage position for quantitative analysis and SE/BSE imaging (optimum Z ~10 to 11 mm at a fixed Working Distance WD = 10 mm) versus cathodoluminescence imaging (optimum Z ~16.5 mm). J. M. Allaz © March 14, 2021...
Page 25 Figure 15. Detail on the beam alignment procedure to obtain the best image quality. SEM manual ETHZ v1.4...
Page 26 Figure 16. Optimization of brightness & contrast. Constantly adjust B & C to reveal what you need to see. Avoid under- (black) or over-saturated (white) areas, unless a high contrast is required to reveal a small signal variation (e.g., discreet zoning, phase of similar density). J.
Page 27: G) Using The Cathodoluminescence (Cl) Detector
G) Using the Cathodoluminescence (CL) detector G.1) Inserting or removing the CL detector WARNING! Whenever you insert remove the CL detector, ensure that the Z stage position is at 30 Figure 17a. Inserting (or removing) the CL detector. WARNING! Ensure you have locked the CL detector when you are done! SEM manual ETHZ v1.4...
Page 28: G.2) Activating The Cl Detector
IMPORTANT: Brightness & contrast (B&C) for CL image are first adjusted using the “Brightness” & “Contrast” buttons on the CL control box! Once the right B&C is found on the control box, then adjust the B&C of the JEOL SEM program. Figure 17b. Control box for the “Centaurus” CL detector.
Page 29: H) Thermo Nss Program
The Thermo “NSS” program controls the EDS system and acquires electron images (SE, BSE, or CL). The JEOL SEM program can also acquire images, but it is not as easy to use and certainly not as versatile as the “NSS” program.
Page 31: H.2) Overview Of Nss And The Different Analysis Modes
H.2) Overview of NSS and the different analysis modes The program NSS consists of several panels described in Figure 19. The present manual only covers the essential functionalities of the modes “Electron Imaging”, “Spectrum”, “Point & Shoot”, or “Spectral Imaging” (= hyperspectral maps). For more details, ask for assistance. Figure 19.
Page 33: I) Se, Bse, Or Cl Imaging With Thermo Nss
(recommended: 1024 x 768). Ignore the bottom section “Live…”. 3. Enter a name for your image in the textbox “Base name”. 4. Adjust the signal & field-of-view on the JEOL SEM program: • Select the desired electron signal: SEI for secondary electron, BEIW for backscattered electron (BSE), or BEIC for cathodoluminescence.
Page 35: I.2) Se, Bse, Or Cl Mosaic Imaging
(recommended: 1024 x 768). Ignore the bottom section (“Live…”). 3. Enter a name for your image in the textbox “Base name”. 4. On JEOL SEM program, select the desired electron signal: SEI for secondary electron, BEIW for backscattered electron (BSE), or BEIC for cathodoluminescence.
Page 37: I.3) Tips On Image Acquisition Time & Magnification
I.3) Tips on image acquisition time & magnification • Always use aperture 2 when acquiring images. (or 1) • You can try to increase/decrease the current and adjust the counting time. A medium current is recommended for most applications (spotsize 70-80) as it gives a strong signal and a decent sub-micron imaging resolution.
Page 39: J) Quantitative (Or Qualitative) Eds Analysis
J) Quantitative (or qualitative) EDS analysis In the following, it is assumed that… • The “Thermo NSS” program is running. • You have created an NSS project folder or opened an existing one (see Section H.1). EDS acquisition can be considered as “qualitative” (i.e., just checking the presence or absence of some major to minor elements), or “quantitative”...
Page 40 • Click “OK” to validate, wait a few seconds and the table “Standards” should indicate the currently selected standard. Verify this list is correct. You can also open the tab “Element Setup” in the bottom-left panel: all elements that have now a standard defined will be highlighted as purple (see Fig.
Page 41 Figure 23. Loading standards into your project for quantitative EDS analysis. SEM manual ETHZ v1.4...
Page 42: J.2) Single Spectrum
J.2) Single Spectrum To acquire a single EDS spectrum (Fig. 24)… 1. Select “Spectrum” on the analysis mode panel. 2. Click on “Acquisition Properties > [tab] EDS” to set the EDS acquisition conditions; default options are OK if you loaded the template “silicate calibrated analysis”: a.
Page 43 Figure 24. “Spectrum”: Acquiring a single EDS spectrum over the currently scanned area. SEM manual ETHZ v1.4...
Page 44: J.3) Point & Shoot
J.3) Point & Shoot To acquire multiple EDS analyses in a given (BSE) image (Fig. 25)… 1. Select “Point & Shoot” on the analysis mode panel. 2. Click on “Acquisition Properties > [tabs] Imaging or EDS” to set the “Imaging” (see Section I.1) and “EDS”...
Page 45 Figure 25. “Point & Shoot”: Acquiring multiple EDS analyses selected on an electron image. SEM manual ETHZ v1.4...
Page 46: J.4) Eds Data (Re)Processing
J.4) EDS data (re)processing J.4.1) Options for analysis processing Locate the tab “Analysis Setup” in the bottom-right panel. Providing you have loaded the template “Silicate calibrated analysis” when creating your NSS project, you should be fine in most situation with the default parameters. The following parameters should never be changed (see also...
Page 47: J.5) Exporting Quantitative Eds Data
J.5) Exporting quantitative EDS data J.5.1) Choice of data to export You can choose the data to be exported under the menu “Edit > Properties”, under the tab “Quant Results”. Below are the key entries to consider in this tab (in bold are the most important entries, in normal are the optional ones, and )…...
Page 49: K) Eds Element Mapping
3. Move to the area of interest, adjust the Z-stage focus, and set a magnification ≥ 100x. 4. Set the appropriate “beam spot” (= beam current) on the JEOL software in order to yield 20 to 30% dead time (DT, bottom right). At a rate of 5 to 7 (= medium time constant), it corresponds to a stored rate of ~50’000 to ~80’000 counts per second.
Page 50 8. At the end of your acquisition, you can add or remove identified elements using the periodic table in the tab “Element Setup” on the bottom-left panel and request to reprocess the data to extract more elements (see more in Section K.2).
Page 51: K.2) Treating Element Or Phase Maps
K.2) Treating element or phase maps K.2.1) Extracting “Element maps” To extract element maps (see Fig. 27): 1. Select your Spectral Imaging acquisition (under “Base Name”). 2. Mark the element as “Always identified” to force the identification of an element even if the software does not think it is present.
Page 53 Figure 28. Calculating and extracting phase maps. SEM manual ETHZ v1.4...
Page 54: K.3) Additional Tips On Map Treatment After Extraction
Figure 29. Extracting a spectrum from an element map. K.3) Additional tips on map treatment after extraction • To overlay one or more map(s) on the BSE image, select or unselect an element or phase map by clicking on its name (background will turn black when selected). •...
Page 55: Appendix
Appendix A1) Adjusting the SNS (Sample Navigation System) The SNS image is not very accurate, yet it should drive the stage within a couple millimetres of the target. The calibration of this system is regularly checked by the manager. However, if you want to check and possibly adjust it (because someone screwed it up…), please, strictly follow this procedure: •...
Page 56: A2) Activating The Sem In W-Mode
A2) Activating the SEM in W-mode In a normal situation, the SEM is working under ultra-high vacuum (UHV) using an ion pump in the gun. However, some situation might force us to shut down the ion pump and to work only under “high vacuum”...
Page 57 Figure A2. Saturation of the W-filament in W-mode. When the optimum is reached, the emission current should read 30 to 50 µA (or higher). SEM manual ETHZ v1.4...
Page 58: A3) Characteristic X-Ray
A3) Characteristic X-ray Figure A3. All common electron transitions and characteristic X-ray generation. From Goldstein et al. (2003) “Scanning Electron Microscopy and X-Ray Microanalysis” (Fig. 6.9, p. 280). Original in Woldseth (1973) “X-Ray Energy Spectrometry”. J. M. Allaz © March 14, 2021...
Page 59: A4) Image Resolution
A4) Image resolution Relationship between the actual pixel resolution (expressed as micrometre) and the magnification & image resolution. • For regular SE / BSE images: a resolution of 1024 x 768 px is recommended. Higher resolutions are possible with Thermo NSS. However, keep in mind that if you double the width &...
Page 60: A5) Eds Mapping Time & Element Map Quality
A5) EDS mapping time & element map quality For element mapping by EDS, you should consider the total X-ray counts received on each pixel. A minimum of ~1000 counts on each pixel is recommended. Above ~4000 there is no significant gain of extractable information for most applications, except maybe if you need to identify a significant zonation in a specific phase (e.g., Ca-Na in plagioclase).
Page 61 Figure A5.2 Relationships between magnification, map pixel size, and counting time. Use these plots to estimate the best analytical conditions for your needs. SEM manual ETHZ v1.4...
Page 62: A6) Thermo Nss Toolbars (From The Nss Manual)
A6) Thermo NSS toolbars (from the NSS manual) J. M. Allaz © March 14, 2021...
Page 63: A7) File Handling In Thermo Nss
A7) File handling in Thermo NSS Below is a list of the important files created by Thermo NSS during EDS analysis. A7.1) “Spectrum” mode • EMSA [text file] EDS data including energy vs counts data (at the end). A7.2) “Point & Shoot” mode •...
Page 64: A8) "Ispectra" By Christian Liebske
A8) “iSpectra” by Christian Liebske iSpectra* is an open-source toolbox for the analysis of spectral images and provides the following features: • RGB mapping tools, • Principle component analysis, • Transparent way of creating phase maps, • Particle analysis, • Batch processing to create large scale phase maps, •...
Page 65: A9) Troubleshooting For Bad Analysis & Other Known Problems
• Have you properly set the Time Constant to “Rate 2” in the “Acquisition Properties”? • Is the Working Distance (WD) set at 10 mm on JEOL? If so, Thermo NSS should indicate WD 9.700 mm on NSS at 15 keV (or 9.800 mm at 20 keV).
Page 66 A9.3) Other common problem • If the ammeter is not responding, this is likely due to the fact that someone turned it OFF. To reactivate it, start Thermo NSS, and ask to run one analysis. This will force to activate the ammeter. When you first do this, the ammeter will generate an error and should normally re-initiate itself.
Page 67 A9.4) Abnormal and known hardware-software bugs WARNING: The following list abnormal behaviour that will hopefully be fixed one day… A9.4.1) Wrong EDS energy calibration Starting in April 2019, we have observed a few times a shift in the X-ray peak position. This is due to the EDS hardware losing its calibration.
Page 68 Acknowledgments: This manual would not be so complete without inputs from Dr. Christian Liebske regarding the Thermo NSS sections, numerous discussions with Dr. Eric Reusser, and inspiration taken from the original 7-page SEM manual from Dr. Lukas Martin. Many thanks to them! Comments, suggestions, questions about this manual? Contact…...

JEOL JSM-6390 LA User Manual

A) Generalities about the JEOL SEM @ IGP

B) Starting Your Session

C) Sample Loading or Unloading

D) Stage Motion

E) Activate the Electron Beam

F) Beam Alignment

G) Using the Cathodoluminescence (CL) Detector

H) Thermo NSS Program

I) SE, BSE, or CL Imaging with Thermo NSS

J) Quantitative (or Qualitative) EDS Analysis

K) EDS Element Mapping

Appendix

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