JEOL JSM-6390 LA User manual

Scanning Electron
Microscope (SEM)
JEOL JSM-6390 LA
User’s manual
Julien M. Allaz
March 14, 2021
Version 1.4

Table of Contents
A) Generalities about the JEOL SEM @ IGP ................................................................... 1
A.1) Lab overview ............................................................................................................ 1
A.2) Computers ................................................................................................................ 2
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 .................................................................................. 9
C.2) Removing/Loading a sample & closing the chamber ............................................... 9
D) Stage motion ............................................................................................................... 13
D.1) Horizontal displacement (X, Y) ............................................................................... 13
D.2) Vertical displacement (Z) ........................................................................................ 13
D.3) Rotation (R) ............................................................................................................ 13
D.4) Tilting (T) ................................................................................................................ 13
E) Activate the electron beam ........................................................................................ 15
E.1) Activating a LaB6 electron source in “LaB6 mode” .................................................. 15
E.2) Activating a W electron source in “LaB6 mode” ...................................................... 15
F) Beam alignment ........................................................................................................... 17
F.1) Tilt & shift optimisation ............................................................................................ 17
F.2) Beam alignment for quantitative analysis or SE/BSE imaging ............................... 17
F.3) Beam alignment for CL imaging ............................................................................. 18
G) Using the Cathodoluminescence (CL) detector ....................................................... 23
G.1) Inserting or removing the CL detector .................................................................... 23
G.2) Activating the CL detector ...................................................................................... 24
G.3) Deactivating the CL detector .................................................................................. 24
H) Thermo NSS program ................................................................................................. 25
H.1) Starting “Thermo NSS” ........................................................................................... 25
H.2) Overview of NSS and the different analysis modes ............................................... 27

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 ................................................................ 35
J.1) Load standard data ................................................................................................. 35
J.2) Single Spectrum ...................................................................................................... 38
J.3) Point & Shoot .......................................................................................................... 40
J.4) EDS data (re)processing ......................................................................................... 42
J.4.1) Options for analysis processing ........................................................................ 42
J.4.2) Reprocessing data ............................................................................................ 42
J.4.3) Navigating in the Spectrum panel ..................................................................... 42
J.5) Exporting quantitative EDS data ............................................................................. 43
J.5.1) Choice of data to export ................................................................................... 43
J.5.2) Exporting a single Spectrum ............................................................................. 43
J.5.3) Exporting a Point & Shoot analysis .................................................................. 43
K) EDS element mapping ................................................................................................ 45
K.1) Acquiring an element map with the mode “Spectral Imaging” ................................ 45
K.2) Treating element or phase maps ............................................................................ 47
K.2.1) Extracting “Element maps” ............................................................................... 47
K.2.2) Extracting “Phase maps” .................................................................................. 47
K.2.3) Extracting and quantifying a “Spectrum” from of an element map ................... 47
K.3) Additional tips on map treatment after extraction ................................................... 50
Appendix .......................................................................................................................... 51
A1) Adjusting the SNS (Sample Navigation System) ..................................................... 51
A2) Activating the SEM in W-mode ................................................................................ 52
A3) Characteristic X-ray ................................................................................................. 54
A4) Image resolution ...................................................................................................... 55
A5) EDS mapping time & element map quality .............................................................. 56
A6) Thermo NSS toolbars (from the NSS manual) ........................................................ 58
A7) File handling in Thermo NSS ................................................................................... 59
A8) “iSpectra” by Christian Liebske ................................................................................ 60
A9) Troubleshooting for bad analysis & other known problems ..................................... 61

SEM manual ETHZ v1.4 1
A) Generalities about the JEOL SEM @ IGP
A.1) Lab overview
The scanning electron microscope (SEM) at ETHZ D-ERDW / IGP has SE (secondary
electron), 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 1.
Figure 1. Overview of the JEOL JSM-6390 at ETH Zürich, D-ERDW / IGP.

2 J. M. Allaz © March 14, 2021
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…
• The RIGHT computer controls the Thermo EDS system through the program
“NSS”. The “Thermo NSS” program is used to acquire both images (SE, BSE, CL)
and compositional data (e.g., EDS spectrum, quantitative analysis, element maps).
This computer can be restarted safely anytime. Even if the NSS program crashes, all
your data are automatically saved, except for the analysis that was running when the
program crashes. The Windows login password is written on the computer.
• NEVER restart or shutdown the JEOL computer!
• NEVER exit the JEOL SEM program!
A.3) First things to do when you arrive
When you first arrive in the lab (Fig. 2)…
1. Turn ON both computer screens.
2. Check the general status of the instrument:
o Is it working and under high vacuum? Check the vacuum controller (box on
wheel on the LEFT side of the instrument with indicator on the top). The
vacuum should be in the mid to low 10-5 Pa range. (*)
o Is the HT button (high tension) on the top-left side of the screen green & ON?
o If something is wrong, call for assistance.
3. Check that nothing is running, especially on the Thermo computer; there could be
some overnight map running… Check with the previous user if it’s still running!
4. Activate the IR camera, and check if a sample is currently loaded.
5. Which electron source is currently loaded? Check the paper on the bottom of the
left screen. The starting procedure will depend on which source is currently loaded!
o W (tungsten filament – GREEN sign)
o LaB6 (lanthanum hexaboride crystal – ORANGE sign)
(*) WARNING! Exception applies when, due to some technical difficulties, the SEM is in “W-mode” with the
ion pump OFF (no vacuum reading). See Appendix A2 if you see the additional BLUE sign for “W-mode”.
Figure 2. Checking instrument status (in “LaB6-mode” with the ion pump working).

SEM manual ETHZ v1.4 3
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. 3):
• The left side of the console controls the stage motion. Leave the “Stage” setting
to “X/Y”! You can then use the joystick to move along the X and/or Y axis.
• The top-right side of the console “Scanning mode” has several options for the
different scanning rate. You will most likely use only “Scan2” (full-frame fast scan,
ideal for navigating in the sample) or “Scan1” during the alignment (fast scan over a
reduced area). Other scanning options (Scan3 or 4, Photo) are not recommended;
Thermo NSS (Section H) is used for acquiring and saving high-quality images.
• The middle-right side controls either the brightness and contrast (when STIG is
OFF) or the astigmatism correction (when STIG is ON). In any case, prefer the use
of the buttons atop of the electron image to adjust these parameters.
• The bottom side of the console has 2 similar knobs for magnification (left) and focus
(right). Pay attention to which one you twist!
o Left-one is the MAGNIFICATION knob. It controls the field of view of the
electron image, from 20-40x to 300,000x.
o Right-one is the ELECTRON BEAM FOCUS knob. It controls the focus point
of the electron beam through the objective lens and defines the working
distance (WD). Activate the “coarse” button for large changes in the focus
(e.g., rough focussing), and DE-activate this “coarse” button for fine tuning.
Figure 3. Overview of the SEM console.

4 J. M. Allaz © March 14, 2021
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 4:
• Top section: menu bar & main buttons.
• Middle section: electron image display with grey buttons used to control the image
quality, and on the right side a snapshot image of the sample holder.
• Bottom section: instrument status (voltage, WD, spot size, etc.).
Figure 4. Overview of the “JEOL Scanning Electron Microscope” program.
The next Figures 5 to 7 present an overview of the different sections of the
JEOL SEM program.
Refer to the following Sections B to F for details on the important buttons in
this program, and in Section G for the CL detector.

SEM manual ETHZ v1.4 5
Figure 5. Overview of the main buttons in the TOP section of the SEM program.

6 J. M. Allaz © March 14, 2021
Figure 6. Overview of the MIDDLE section of the SEM program.
Figure 7. Overview of the BOTTOM section of the SEM program.