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.

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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.

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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.

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Figure 6. Overview of the MIDDLE section of the SEM program.
Figure 7. Overview of the BOTTOM section of the SEM program.

SEM manual ETHZ v1.4 7
B) Starting your session
1. 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 (e.g., mosaic BSE or EDS mapping on the right computer), contact the former
user, and see if you can wait for the completion or if you can cancel the analysis.
4. Turn ON the infrared camera (“Deben”, small screen on the left; Fig. 8).
Figure 8. Main SEM detectors and components visible on the Deben infrared camera.
5. If a sample is currently loaded in the SEM, you will need to remove it (Section C).
6. Prepare your sample (Fig. 9): choose the thin-section or the 1-inch round mount.
WARNING! If your sample does not fit the thin section or the 1’’ round holder, you MUST
contact the lab manager or the assistant before continuing!
7. Proceed to the sample loading (see Section C).

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Figure 9. Preparing the sample holder (for thin section or for 1’’ round mount).

SEM manual ETHZ v1.4 9
C) Sample loading or unloading
The sample change procedure is summarised below. Refer also to Figures 10 and 11a,b.
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).
3. Turn ON the Deben infrared camera (if not already on).
4. Open the window “Stage” and move the stage to Z = 30 mm (absolute position).
5. If the CL is inserted (check on the IR camera!), you MUST remove the CL detector
(see Figures 12 and 13).
6. On the SEM column, close the valve VT-3 (tight, with the strength of two fingers).
7. Back to the JEOL SEM program, open the window “Sample” and click “Vent”.
WARNING: When the SEM is in LaB6 mode, check the vacuum gauge while venting
(see on the left side of the SEM) to ensure you don’t lose vacuum. This can sometime
happen due to the valve VT-3 leaking. Only the light “column” should turn orange, all other
lights should stay green. If you lose vacuum, ask immediately for assistance!
This warning does NOT apply if the SEM is in W-mode (see Appendix A2).
8. When fully vented, open the sample chamber (see C.2 and Figure 11).
C.2) Removing/Loading a sample & closing the chamber
1. Open the sample chamber up to the back stop (use two hands!)
2. Remove the sample and/or load your sample (thin section or 1’’ round mount)
3. If you are loading a new sample, take a snapshot with SNS…
a. Place your sample on the holder.
b. Click the button “SNS” in the top section.
c. Click “Snap”. The stage will drive to the centre of the optical camera.
d. Wait a few seconds until a snapshot of your sample appears in the SEM
program. If you think the SNS image is not properly centred, refer to the
calibration section to calibrate the SNS in Appendix A1.
e. IMPORTANT! Lower again the stage to Z = 30 mm after using SNS!
4. Close the sample chamber while looking simultaneously at the IR camera to avoid a
disaster (e.g., sample holder touching a detector).
5. Open the window “Sample” and click “Evac” while pressing on the sample chamber
door. Wait a few seconds until the vacuum catches up.
6. Wait until the signal “Ready” appears.
If this is the end of your session, you are done. Otherwise…
7. Open valve VT-3.
8. Remove the “Beam blank” and proceed with the gun activation (Section E) and the
beam alignment (Section F).

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Figure 10. Opening the sample chamber (to remove or place a sample).

SEM manual ETHZ v1.4 11
Figure 11a. Loading a new sample and taking an overview image of your sample (SNS).

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Figure 11b. Evacuating (pumping) the sample chamber after (un-)loading a sample.

SEM manual ETHZ v1.4 13
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).
• Double-click on the SNS image of your sample (inaccurate but close enough…).
• Use the window “Stage” and either…
o Click on one of the coordinates and change the value in the window
“Positioning”. Ensure you are in ABSOLUTE mode and click “Go”!
o Click on the map view (bottom section of window “Stage”) and click “Go”.
o Note that in the Stage window, the “Go” button will change to “Stop” as soon
as the stage is moving. Keep your mouse on this button so you are ready to
stop the stage if it is approaching too dangerously from a detector!
o Other possibility (rarely used): Move the mouse along the X or Y axis of the map view. When
the mouse pointer changes to a single or a double arrow, click to move by one step or maintain
the click for a continuous motion. A single-arrow indicates a slow motion (micron-sized), a
double-arrow indicates a faster motion (with acceleration feature).
D.2) Vertical displacement (Z)
WARNING: Any time you significantly move the Z-axis you should ALWAYS turn ON the
infrared camera and WATCH that IR camera to ensure that the stage does not bump into
the BSE or the CL detector! Repairs can be costly!
To move the sample up or down along the Z-axis:
• Open the window “Stage”, and (two options)…
• (Safest) Use the cross-section view on the top-right of the “Stage” window:
o Move the mouse over the vertical axis until the mouse pointer changes to a
single-arrow (slow motion) or a double-arrow (fast motion).
o Click a single time to move one step at a time or click and hold for a continuous
drive (the stage will stop as soon as you release the click).
• To move to a fixed (absolute) value, click on the Z-stage position (top-left of the
“Stage” window) and enter a new absolute Z position. BE CAREFUL not to set a Z-
stage position that would drive the sample holder into the BSE or the CL detector!
D.3) Rotation (R)
The sample holder can be rotated manually using the small rotation knob situated between
the X and Y stage motors on the front of the SEM door. It is best practice to rotate the sample
on loading (i.e., before you take a snapshot using the button “SNS”), and then NOT to rotate
the sample anymore, otherwise you won’t be able to double-click on the SNS picture and
locate a feature.
D.4) Tilting (T)
DO NOT USE IT! There is a high likelihood of damaging the detectors (SE, BSE, EDS, or
CL) when you tilt your sample and move in along any direction (X, Y or Z). The tilting is
manually controlled by the knob on the bottom-right side of the SEM door. Leave it at 0°
(horizontal)! If you absolutely need this option, contact the lab manager.

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SEM manual ETHZ v1.4 15
E) Activate the electron beam
WARNING! Different procedure to activate the electron beam if a W or a LaB6 electron
source is loaded (Fig. 12)! Check the note W or LaB6 below the computer screen!!!
If you see a BLUE sign W-mode , refer to Appendix A2 for separate instructions.
E.1) Activating a LaB6 electron source in “LaB6 mode”
When a lanthanum hexaboride (LaB6) electron source is loaded, it is left active at optimum
filament heat all the time, and only the gun bias is adjusted to control the electron emission.
LaB6 offers a higher stability, a better image resolution, and a longer lifetime. However, it is
fragile and expensive; it can be damaged when warmed up or cooled down too quickly.
Please, strictly respect the following to activate the electron beam:
• Ensure that the window “Sample” indicates “Ready” (= high-vacuum condition).
• Check that VT-3 is opened and that the “Beam blank” is OFF.
• Open the window “Gun”.
• Click on “Set Bias” and click “Preset”. This calls back the default bias value (~100 to 150).
• Do NOT change anything else in the window “Gun Alignment”! NEVER change
the filament heat! 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 F.
E.2) Activating a W electron source in “LaB6 mode”
The tungsten (W) electron source is usually left in “standby” condition; the filament heat is
just enough to keep the filament warm, but not enough to emit electron. You’ll need to
perform a filament saturation by setting the filament heat to its optimum:
• Ensure that the window “Sample” indicates “Ready” (= high-vacuum condition).
• Check that VT-3 is opened and that the “Beam blank” is OFF.
• Saturate the W-filament…
o Insert the Faraday cup by pressing the button “PCD”.
o Press the top-left button “LOCAL / CONFIGURATION” on the ammeter. This
will activate the live beam current reading. If the wording “CONFIGURATION”
appears on the ammeter display, press another time on the same button. If
you still don’t see a live reading of the beam current, press the button “TRIG”.
o The ammeter should indicate a varying value around zero.
o Set the “Spotsize” around 74 to 78 (= medium to high beam current).
o Open the window “Gun” and increase the filament heat until the emission
current and the beam current increase. Continue increasing the heat, until the
beam current decrease again (= “false peak”). Continue increasing the heat
until the beam current increases again. You will reach the saturation point
when the increase in beam current slows down or drops down slightly.
o The emission current should read ~30 to 60 µA (or more), and the ammeter
should read ~2 to 3 nA at the beam aperture #2.
o Note that with a W filament, you can increase the heat rapidly. This saturation
should not take you more than a minute…
o When done, click on “PCD” to remove the Faraday cup.
• An SE image should now be visible in the JEOL SEM program.
• Perform a beam alignment following the instructions in Section F.

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Figure 12. Activation of the electron beam in LaB6-mode. Two different processes
depending on the electron source currently used: LaB6 cathode or W filament.
Refer to Appendix A2 if the SEM is in W-mode!