JEM 2100 Manual

Operation and Basic Alignment Instructions

1. Verify the vacuum:

Check the vacuum levels
(power supply closet)
Column (blue scale): < 2.5x10-5 Pa
If vacuum is not good enough, contact somebody from the LME staff.

Verify the vacuum in JEOL PC / TEMCON / Valve Status window

VACUUM SYSTEM
GUN/CAMERA valves
V1 and V2 = OFF (black)
Pirani gauge status
PIG-2 <30 A
PIG-1 <30 A
PIG-4 254 A
PIG-3 < 30 A
PIG-5 100 A

2. Complete Cold Finger Dewar with Liquid Nitrogen:

Fill with LN2, wait for a few minutes and complete the Dewar after it
stops boiling.

The microscopes view port must be covered

before this procedure. The window can crack
under thermal shock.
Wear appropriated protective eyeglasses and
gloves when manipulate LN2 to avoid accidents.

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Julho/2011

ATTENTION!!! Complete the dewar with LN2 at each 6 working

hours. In working days, in the morning (7 oclock AM) and in
the afternoon (1 oclock PM).

3. Check the camera:

Check if the shuter box (TVIPS camera) is in CCD mode
(right side of the TEM Column). Put a picture
Check if CCD ES 500W is ON
(left side of the TEM Column).

4. Verify the TEMCON / Controller window (JEOL PC):

-

If the program is not open click double-click on the TEM Controller icon in
the PC monitor screen.
Check the points bellow:
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4

1)
1) High Voltage (HT) : Acc. = 160kV (Start) or 200kV (Middle of the Day);
2) Spot Size = 1, Alpha = 3;
3) X = Y = 0, Z = 0, TX = 0 (TY doesnt matter);
4) Select the sample-holder (SH) type that you use:
Single Tilt: EM-21010 = Single Tilt Holder;
Double Tilt: EM-31630 = Specimen Tilt Holder (DTC);
Single Tilt Rotation: EM-31650 = Rotation Holder (STR);
Double Tilt Beryllium: EM-31640 = Specimen Tilt Holder Be (DTB);

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5. Turning on the Accelerating Voltage

Make sure that the reading of the column pressure gauge is < 2.5 x 10-5
Pa

Make sure that the HT Status = Ready (HT allowed) on the right upper
corner of the window High Voltage

For 1st user of the day:

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160.00

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4

1) Verify that Acceleration voltage has been set to Acc = 160 kV

2) If not, choose the Voltage Step = 10 kV in the right side of HT
menu and using Down button decrease the HT to 160 kV;
3) Click on HT ON icon. Current on Beam Current indicator must
increase gradually. When Beam Current = 81 A, Voltage
reached the correct value HT = 160 kV.
4) Increase voltage from 160 to 200 kV (Target = 200kV): In Auto
HT Step = 0.1 kV and Time = 3 sec (Time to Finish = 20 min).
(PS: If the microscope has not been used for several days use 40
minutes Time/Step = 6 s).
5) Click on START to increase HT to 200 kV. While the
Accelerating Voltage window is open, you cannot access any
other windows

For 2st user of the day:

3

1) Verify that Acceleration voltage has been set to Acc = 200 kV

2) Verify that the HT icon is on .
3) Current on Beam Current indicator must be 102 A. If not,
repeat the step for 1st user.

6.

Introducing the sample holder (SH):

Always use glove when to manipulate the sample holder or
your sample. The gloves are not for your protection. You are
the main source of contaminations.

Put your sample on the adequate SH.

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Remember!!! Dont use the scalp to manipulate your sample. It

can seriously contaminate it. Use the pick-up vacuum system on
the working table.

For single tilt holder, loosen two screws TWO turns, rotate the cover
plate away and mount specimen with film side UP. For double tilt holder,
loosen two screws TWO turns, rotate the two plate-clamping fingers and
mount sample facing DOWN. NEVER OVERTIGHTEN THE SCREWS!!!

After to put firmly your sample, always check that the SHs o-rings are
completely free of dust or lint, under the optical microscope. Use tweezers
to remove the contamination.
Be Careful!!! Dont introduce the SH on the microscope until
be sure that it is completely free of dust or lint. One can
induce vacuum leak!!!

Introduce the SH in the microscope. Follow the instructions contained at

the end of this manual, or in the copy that is Always over the TEM
console. (Be careful and always look at the Vacuum indicator).

Remember!!! After step (1) wait several minutes till

Specimen/PIG4 indicator is just below 32 A (ideally 30 A).
After this vacuum level be attained introduce completely
the SH (steps 2 to 5).

Suring this time, write the informations in the Microscope Notebook:

User Name,
Column Pressure
Sample Holder,
Sample name,

Check again the vacuum levels (item 1)

If you will perform EDS analysis, insert the EDS detector at
this moment to avoid an afterward gun misalignment.

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7. Heating the filament:

Verify

that Filament Status: READY (Filament Enabled).

NEVER PRESS CONDITIONING BUTTON ON HT CONTROL

WINDOW:
This buttom implements HT conditioning and is used only when a
JEOL service engineer asks you to operate

In Right Lower Corner of High Voltage Control Window choose in

Filament Control Speed the Heating Mode DEGAS SETUP - 30 min (1st
user of the day) and NORMAL SETUP (2st user of the day).

Normal Setup:
Degas Setup:

Applies the current to the filament at the speed set in the

factory.
Click on this button when degassing the filament. Specify
the ascending time in the combo box.

ALWAYS CHECK IF SOFTWARES NORAN SYSTEM SIX IS CLOSE

BEFORE HEATING THE FILAMENT!!!

To Heat the Filament click ON button under HT in the Left Middle of

High Voltage Control Window.

A small window opens: Filament Setting the Filament: going from 0 to

~57%. Wait until this window close and Beam Current = 112 A. While the
Filament window is open, you cannot access any other Windows.

When the filament shutdown is complete, the Filament window closes

and you have got an electron beam in the phosphorous screen of the
microscope
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TEM MODE ALIGNMENT

Control Panels

Most of the commands on the control panels (right and left) related to
Standard Operation, Apertures and Movements of the Stages can be accessed
in Operation menu.

8. Finding the electron beam:

If the beam is not visible on the phosphor screen, set to a lower
magnification (10 kx) with the MAG/CAM L knob, and move the sample
using the track ball until the beam be visible. Put the sample in an open
region.
Set magnification to 50 kx with the MAG/CAM L knob for the initial
adjustments.

9. Centering the Condenser Aperture:

To insert the Condenser Aperture press CL button and choose the
Aperture #2 to be inserted (If other Aperture # is Light On, means that you
are changing CL aperture. If no aperture is inserted, OPEN Lights On).
The second biggest aperture is the standard one.

a) Remember to always compensate the condenser lens hysteresis

(BRIGHTNESS knob, counterclockwise-crossover-clockwise).
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b) Focus the beam using the BRIGHTNESS knob to obtain the crossover
and bring it to the center of the phosphor screen using the BRIGHTNESS
SHIFT knobs X and Y.
c) Defocus (clockwise) the beam till approximately the same screen
diameter. If the beam is not centered use the aperture position adjust to
center it (left panel).
Important: Remember to check the condenser aperture
alignment from time to time. It is mechanical and it will
misalign more often than you imagine.

10. Sample Height (Eucentric Center)

a) Press Standard Focus STD FOCUS button in the Upper Right Control
Panel to optimize the focus of Objective Lens (OL).
b) Use IMAGE WOBBLER X or Y (right panel). The image will start to
oscillate. You need to stop it from moving by adjusting Z control buttons
(right panel) at the right position.
c) Disable IMAGE WOBBLER X or Y.

11. Optimizing the Gun Tilt:

Focus the beam with BRIGHTNESS knob, and center it on the screen
using BRIGHTNESS SHIFT knobs X and Y.
b) Press the GUN button (F4 button on the Keyboard Right Control Panel).
Turn DEF X and Y knobs until maximize CUR. DENS. (Current Density =
pA/cm2) measurement of the Mic. Computer screen.
a)

Disable F4 gun buttons by clicking on it again!!!

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12. Optimizing the Gun Shift (Gun

Condenser Lens Coupling):

a) Repeat 9a to 9d.
b) Set SPOT SIZE to 5. Focus the beam with BRIGHTNESS knob, and
center it by using the SHIFT knobs.
c) Set SPOT SIZE to 1 and refocus the beam with BRIGHTNESS knob.
d) Press F4 button (Gun command) and center the beam with the SHIFT
knobs. Disable F4 button.
e) Repeat the procedures a to c several times till the focused beam dont
move from the center when the spot size is modified from 5 to 1. Disable
F4.

13. Condenser Lens Astigmatism Correction:

a) Repeat 9a to 9d.
b) Set magnification to 250 kx.
c) Focus the beam with the BRIGHTNESS knob (at fine) to smallest size
as possible.
d) In HIGH VOTAGE CONTROL window, in the menu FILAMENT
CONDITION click on FILAMENT IMAGE in order to see the filament
image desaturating it.

e) Press COND STIG and improve the image quality with DEF X and Y
knobs to obtain the smallest and brightest spot.
f) With BRIGHTNESS knob check if there is astigmatism (i.e. the image is
distorted in perpendicular directions if the BRIGHTNESS knob is turned
from under-focus to over-focus).
g) Repeat e till a good correction. Disable COND STIG.

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14. Beam Tilt Correction (Condenser Lens

Coupling):

Objective Lens

a) Press STD FOCUS.

b) Repeat 9a to 9d.
c) Focus the beam with the BRIGHTNESS knob (at fine) to smallest size
as possible.
d) In tool bar click Maintenance Alignment.
e) In Alignment Panel click TILT X on
Wobbler box.
f) Click TILT on Compensator box.
g) Use DEF X knob to stop the longitudinal
movement of the central bright spot.
h) Click ANGLE on Compensator box.
i) Use DEF X knob to stop the transversal
movement of the central bright spot.
j) Click TILT Y on Wobbler box.
k) Click TILT on Compensator box.
l) Use DEF Y knob to stop the longitudinal
movement of the central bright spot.
m) Click ANGLE on Compensator box.
n) Use DEF Y knob to stop the transversal
movement of the central bright spot.
o) Disable TILT Y.

15. Voltage Center (Coma-Free alignment):

a) Put the sample at the correct height (in focus)
b) Press WOBBLER HT. The image will oscillate.
c) Press BRIT TILT and use DEF X and Y to minimize the oscillation. If
properly adjusted, the image will pulsate symmetrically.
d) Disable WOBBLER HT and BRIT TILT buttons.

If you prefer, you can use the ESW 500 camera to adjustment the
voltage center. To use the camera, adjust the BRIGHTNESS knob until
the illumination larger than the phosphor screen. Also lower the screen
before you change the TEM magnification or its mode. In the

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Remember to never image the diffraction pattern or

the focused beam directly on the camera.

18. Objective Lens Astigmatism Correction:

To take an image of your sample, adjust the image focus using the OBJ
FOCUS knob (right panel).
Correct the objective astigmatism pressing OBJ STIG (left panel) and
using the DEF X/Y knobs (left/right panels). Adjust the focus and the
astigmatism, one at a time until you get the sharpest image. The
astigmatism will cause the image to smear in one particular direction when
you focus/defocus the image on the screen.
Start the adjustment at a low magnification and then move to a higher one.
You can use the little phosphor screen to do the rough adjustments, and
then move to the camera to do the final touch.
Camera TVIPS

1. Open the EMMENU program

Click on icon in the PC monitor screen.
2. Save the images
Tools options image manager:
Prefix name: The image names are created out of the prefix first (this is a fix
string) followed by a number.
Number format: The number can be a simple number (1, 2, 3, ...), a 2-digit
number (01, 02, 03, ...), a 3-digit number (001, 002, 003, ...) or a 4-digit number
(0001, 0002, ... ). With each acquisition the image number is increased. The start
number can be specified in this dialog too.
Default Image Buffers: Each folder in the image manager has a number of empty
image buffers at creation time. The value of "Default Image Buffers" specifies
exactly this number.
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During the training do not save acquired images to HDD: the acquired
images are stored as 16 bit TIFF files in the specified folder. Unselect the button
with the ellipsis (...) to select the folder. It is also possible to create a new folder
by clicking on the "Create folder ..." button

Be sure that the images are not being saved on the hard drive (HD)

3. Objective Lens Astigmatism Correction

To use the camera, the illumination is spread until it covers an area slightly
larger than the whole phosphor screen (turn the BRIGHTNESS knob clockwise)
until the CUR DENS reaches values around 10 pA/cm2.

Focusing the beam directly on the detector may cause

permanent damages to the detectors scintillator.

Press F1 (right panel) to up the fluorescence screen.

Click on the camera

2 icon (2k x 2k RS), exposure time (200 s). With

these buttons it is possible to switch between camera formats with different
exposure time settings.

Press the "Continuous exposure" button

and acquire consecutive

images;

To visualize the FFT image, click in

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An amorphous material will image as below. If properly adjust it will image .

The astigmatism creates the asymmetry of the FFT. Once it is corrected, you
will see concentric rings whose number will decrease as you approach to the
right focus. Remember that this method works better if you are already close
to the right focus condition.

Figure 1: Image with strong astigmatism: (a) under-focus, (b) focus, and (c) over-focus. After
almost fully correcting the astigmatism: (a) under-focus, (b) focus, and (c) over-focus

Press

icon to stop the continuous exposure process before change

the camera for acquire image.

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4. Acquiring Images
Click on camera1

icon (4k), exposure time (600s).

Press the "Viewport options" button and it will open a popup menu.

- Checked Auto increment: each click on the exposure button will store
the image in the next available image buffer in the image manager. If it is not
checked, the image in the current image buffer will be overwritten without a
warning.
- Checked "Scale bar", a scale bar is shown above the image data.
The position and appearance of the scale bar can be modified in EMMENU 4's option
dialog. There are 4 different predefined positions to display the scale bar: upper left,
upper right, lower left and lower right corner.

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 The color bar displays the distribution of the virtual memory.

Dark red: used virtual memory. Light green and dark green areas indicate the
available memory. Light green: greatest contiguous part of free memory. If the
available memory is too low, the dark red area becomes red. The yellow area
indicates that the contiguous memory is very low.

Finishing your session (middle of the day)

Turn off the filament
-

Just turn off the filament. You can leave the TEM HT at 200kV.
Click on FILAMENT OFF on HIGH VOLTAGE CONTROL window.
BEAM CURRENT must decrease gradually from 112 A down to 102 A
(means that just HT is ON = 200 kV).Wait!!!

TEM phosphor screen must be down (no beam going to the cameras).
Remove the objective and the SAD apertures if you did use them.
CCD Camera (Gatan MSC794): Leave it on, but the CAMERA key must
be down (position OUT).

Removing Sample Holder (SH)

Important: Before removing the SH, neutralize!

To neutralize: JEOLPC: TEMCON Double click on black button StageNeutral

(on right upper corner of software window) to neutralize SH position. Make sure
sample shifts and tilts are zero.

To remove the SH follow the instructions on the page at the end of this manual. A
copy of it is also on the TEM. Read it before removing the SH.
REMEMBER: The vacuum will pull the SH into the TEM. You
should never rotate and pull the SH simultaneously. Do only one
movement at time. If not, you may leak air and crash the TEM.
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Before leaving CHECK PLEAAASSE!!!!!!!!!!!!!!!!!!!!!!

Acceleration Voltage (HT) is 200 kV
Filament is OFF, Filament Control Speed on Normal Setup
High Voltage (HT) is ON (Beam Current = 102 A)!!!
TEM phosphor screen is down.
TEM viewing port is covered.
TEM telescope eyepiece is capped.
Optical microscope is covered (table).
MAG 1 is on, and magnification set to 50k.
All the Apertures: CL, EDS, OL, HC and SA must be OPEN (Removed)
LCD Microscope Computer screen OFF.
VACUUM IS OK.

Use the same setting for interrupt your session or

exchange sample !!!

Finishing your working session (end of the day)

Turning Off the Filament:
- Click on FILAMENT OFF on HIGH VOLTAGE CONTROL window.
- BEAM CURRENT must decrease gradually from 112 A down to 102 A (means
that just HT is ON = 200 kV).Wait!!!
Turning Off the High Voltage:
- Verify the filament is effectively OFF
- Click on HT OFF button on HIGH VOLTAGE CONTROL window. BEAM
CURRENT must decrease gradually from 102 A down to ZERO (HT = 0 kV) BEAM
CURRENT must be 0 A.
- Set the next user initial acceleration voltage to 160 kV.

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 Removing Sample Holder (SH)

Important: Before removing the SH, neutralize!
-

To neutralize: JEOLPC: TEMCON Double click on black button StageNeutral

(on right upper corner of software window) to neutralize SH position. Make sure
sample shifts and tilts are zero.

To remove the SH follow the instructions on the page at the end of this manual. A
copy of it is also on the TEM. Read it before removing the SH.
REMEMBER: The vacuum will pull the SH into the TEM. You
should never rotate and pull the SH simultaneously. Do only one
movement at time. If not, you may leak air and crash the TEM.

Write the following information in the Microscope Notebook:

Filament: ??????????? Power:
Fil: ???????? (Number of Hours of Filament Used)

Before leaving CHECK PLEAAASSE!!!!!!!!!!!!!!!!!!!!!!

Acceleration Voltage (HT) must be set to 160 kV
Filament is OFF, Filament Control Speed on Degas Setup
High Voltage (HT) is OFF (Beam Current = 0 A)
TEM phosphor screen is down.
TEM viewing port is covered.
TEM telescope eyepiece is capped.
Optical microscope is covered (table).
MAG 1 is on, and magnification set to 50k.
PANEL LIGHT is off.
All the Apertures: CL, EDS, OL, HC and SA must be OPEN (Removed)
LCD Microscope Computer screen OFF.
TEM computer screen is off (contrast and brightness to the minimum).
VACUUM IS OK..
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Inserting the Sample Holder into TEM Column

1. To insert the SH align the guide pin with the notch on
the goniometer, located at 9 oclock. Insert the SH.
2. Gently press the SH toward the column (step 1). You
will hear the valves from the TEM.
3. Set the switch to PUMP position to pre-vacuum the
SH. The yellow lamp will light on. Wait.
4. After about 10 minutes, the green light will turn on. If it
does not turn on, please contact somebody from the
staff.
5. Wait several minutes till Specimen/PIG4 indicator is
just below 32 A (ideally 30 A).

PUMP/AIR

~70o

Never, never turn the SH

clockwise before finishing
the PUMP step.

STOP

~20o

Black Pin

Guide Pin

6. Slowly turn the SH clockwise ~20o (step 2). The

vacuum will pull the SH after completing this step. Do
not let it go and smash into the TEM.
7. Carefully hold the SH and insert it (step 3).
8. Slowly, turn the SH clockwise ~70o (step 4). Again, do
not let it go and smash into the TEM after finishing
turning the SH.
9. Finish inserting the SH (step 5). The SHs black pin
will fit in its place (small slot on the goniometer located
at 3 oclock). The gap between the SH and the
goniometer is ~3mm.

All the steps have be done slowly and

always
observing
the
column
vacuum. If after inserting the SH the
vacuum does not recover after few
minutes, look for the staff.

Elaborado: Marina Magnani

Fevereiro / 2011

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Removing the Sample Holder from the TEM Column

1. Neutralize the SH before start removing.

2. Be careful!! Slowly pull out the SH (step 1). Do not let
the SH smash against the TEM column.
3. Turn the SH counterclockwise (ccw) ~70o (step 2).
DO NOT PULL, JUST TURN IT CCW.
4. Slowly pull out the SH (step 3).
5. Turn it ccw ~20o (step 4) and stop. DO NOT PULL,
JUST TURN IT CCW.

Never, never remove the SH

before finishing venting the
TEM (AIR switch).
~70o

STOP

~20o

PUMP/AIR

4
6. Set the switch to AIR.
7. Wait for ~30 seconds.
8. Remove the SH (step 5).

These procedures are done

slowly and always observing
the column vacuum.

Elaborado: Marina Magnani

Fevereiro / 2011

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