This document provides instructions for using the JEOL 2000FX transmission electron microscope at North Carolina State University. It outlines safety procedures and describes how to prepare the microscope, align the illumination system, perform imaging alignments, and shut down the microscope. Appendices provide additional details on specific tasks like adjusting the condenser aperture, acquiring images with the CCD camera, and handling liquid nitrogen.

1. JEOL 2000FX
User Instructions
TEM Mode
North Carolina State University
Material Science and Engineering
Atomic Resolution Electron Microscopy Facility
1046 Engineering Building One
Raleigh, NC 27695-7907
(919) 515-8765

2. TABLE OF CONTENTS
SAFETY..........................................................................................................3
TEM SESSION PREPARATION.....................................................................4
TEM Session Check...................................................................................4
Log/Invoice .................................................................................................4
Prepare Refrigerant Tank ...........................................................................5
Sample Cleaning Procedure.......................................................................5
Specimen Holder Insertion .........................................................................5
TEM ALIGNMENT PROCEDURE...................................................................6
Illumination Source Setup...........................................................................6
Establish Accelerating Voltage ...........................................................6
Establish Beam Emission Current ......................................................6
Illumination Source Alignment ....................................................................7
Find the Beam ....................................................................................7
Gun Tilt Alignment..............................................................................7
Gun Shift Alignment............................................................................7
Illumination Beam Alignment ......................................................................8
Condenser Variable Aperture Centering.............................................8
Condenser Lens Astigmatism Correction ...........................................8
Imaging Lens Alignment .............................................................................8
Z-Axis Eucentric Z-Height Adjustment................................................8
Image Wobbler Tilt Balance Alignment...............................................8
Objective Lens Focus (amplitude contrast imaging)...........................9
Voltage Centering Alignment..............................................................9
Intermediate Lens Astigmatism Correction.........................................9
Projector Lens Centering..................................................................10
Objective Lens Astigmatism Correction............................................10
Objective Lens Focus (phase contrast imaging)...............................11
TEM DIAGRAMS ..........................................................................................14
Vacuum Layout.........................................................................................14
Column Lens and Coils ............................................................................15
Column Construction................................................................................15
TEM SESSION SHUT DOWN PROCEDURE ..............................................16
INSTRUCTION PHOTOGRAPHS.................................................................17
SELECTED AREA DIFFRACTION PROCEDURE .......................................17
LOW MAGNIFICATION ALIGNMENT PROCEDURE...................................18
DARK FIELD (CENTERED) ALIGNMENT PROCEDURE ............................18
JEM-2000FXI - 1 - 11/4/2008

3. TABLE OF CONTENTS
(Continued)
APPENDICES...............................................................................................20
A Variable Condenser Aperture Instructions........................................20
B Gatan CCD Camera Setup & Image Acquisition ..............................21
C Dispensing Liquid Nitrogen...............................................................23
D Exchanging JEOL 2000FX Camera Film..........................................25
E Fischione Plasma Cleaner Instructions ............................................26
F Specimen & Holder Decontamination Procedure .............................28
G Storing Specimen Positions in Memory............................................29
JEM-2000FXI - 2 - 11/4/2008

4. Personal and Instrument Safety
Transmission electron microscopes (TEM) are complex instruments that present
dangerous hazards such as high voltage, x-rays, and liquid nitrogen. Misuse of a TEM can
cause serious personal injury.
If there is any questions about the safe use of the instruments, then
stop and seek advice from the laboratory staff.
Use the TEM and all instrumentation in the correct manner as described in the available
manufacturer’s instrument manuals as well as the user instructions provided in the labs.
• NEVER attempt to repair or modify the TEM or its peripheral instrumentation,
including computer hardware and software anywhere within the Facility.
• DO NOT use an instrument or perform a task for which you have not received the
proper training.
• DO NOT attempt to use a TEM or any instrumentation when it is being serviced,
“tagged” with a problem or a problem has been logged by a previous user.
• DO NOT operate a TEM that has not been surveyed and labeled to meet safe X-ray
radiation levels by the campus Radiation Safety Office.
Always operate the microscopes with extreme care following the instructions in this
manual; particularly the most critical steps which include:
• inserting and removing the specimen holder
• increasing the high voltage and gun emission current
• handling, filling, transporting and pouring liquid nitrogen
• loading and unloading film magazines
• wet chemical processing of photographic film
• using methanol solvent
If any abnormality or problem is encountered during the operation of the TEM, contact the
laboratory staff and log the problem in the LOGBOOK.
In case of fire or medical emergency call 911
• Identify and become familiar with the location of the main electrical disconnect for
each instrument.
• Identify and become familiar with your emergency exits and routes.
In case of any abnormal occurrences that may be potentially hazardous to personnel or
instrumentation please contact the lab manager- 513-0751, building engineer- 608-3540,
department administration- 515-7724 or campus safety hotline 515-5445. If in doubt, then
contact something regardless.
JEM-2000FXI - 3 - 11/4/2008

5. BASIC TEM ALIGNMENT PROCEDURE
JEM-2000FXI ELECTRON MICROSCOPE
BEFORE BEGINNING TEM SESSION CHECK—
• JEOL 2000FX is powered ON.
• The instrument logbook to determine the
status of the JEOL 2000FX
• Vacuum gage meter on the Sputtering Ion
Pump power supply console reads ≤ 5x10-5
Pa on the blue scale.
• ACD/SIP toggle switch on the Power
Supply Console is in the down position.
• Toggle switches (L2) for the LENS POWER
SUPPLY and ACCELerating VOLTAGE are
ON in the full up position.
• Adjust the brightness of the CRT {52}
• Condenser Mini (CM) lens is ON and the S
mode switch is OFF (L1) as indicated by L
mode (conventional TEM) displayed on the
CRT page 1 and to the right of the SPOT
SIZE digit.
• ACCEL VOLTAGE READY green light (L1)
is ON.
• Column valves V2 and V3 displayed on CRT page 3 are open (solid green bowtie).
• If HT is ON (red button {17} is lit), then check that the BEAM CURRENT displayed
value (L1) is one-half (+/-2 μA) of the ACCELerating VOLTAGE value displayed on the
CRT page 1, e.g. 101 μA for 200kV.
• FILAMENT knob {14} is fully CCW “OFF”
• Specimen holder X- & Y- positions display zero on CRT page 2.
• Goniometer x-tilt is at zero {5} and locked {7}.
• Objective {3} and SAD {9} apertures are out.
• Condenser aperture lever {2} is positioned to the left and largest aperture selected.
• Complete the first section of the Invoice/Log.
• Fill the liquid nitrogen trap {1}. Make sure the viewing screen is covered{12}
COMPLETE FIRST PART OF INVOICE/LOG BOOK—
• Account number, user name, phone number, email, PI contact information is required
on the invoice/log form prior to the beginning of a TEM session.
DO NOT ATTEMPT ANY OF THE ALIGNMENT PROCEDURES IF
YOU HAVE NOT BEEN PROPERLY TRAINED.
JEM-2000FXI - 4 - 11/4/2008

6. PREPARE REFRIGERANT TANK
- COVER THE VIEWING WINDOW USING THE SHIELD!
- If the liquid nitrogen is already present and tank is cold, then add until full per Appendix B
- If anti-contamination device is plugged in, then be sure it is off before removing, then fill
refrigerant tank per Appendix B and wait at least 1/2 hour before inserting specimen holder
SPECIMEN CLEANING PROCEDURE
Choose method of cleaning based on the stability of your sample. For example, all holly-carbon
or diamond carbon films are to be annealed at 80-120 C for 10 minutes (the plasma cleaner can
damage your sample). See Appendix E: TEM specimen holder/specimen decontamination
procedure and Appendix D for the complete operating instructions for the Fischione Model 1020
Plasma Cleaner, which are only briefly outlined below.
1. Switch on and vent plasma-cleaner
2. Remove plug and insert specimen holder with sample and switch on vacuum
3. Wait 2 minutes after all red light bars are out and green vacuum ready is on
4. Choose time by selector and depress “Set”, click “Timer” to “Auto on”
5. Set on timer and switch “Plasma” on
6. When completed vent chamber and extract the rod, reinsert the plug and switch on
vacuum ⇒ wait 15-20 sec and switch plasma cleaner off
SPECIMEN HOLDER INSERTION
• Holder o-ring is free of dirt lint, etc. and coated with Fomblin vacuum grease as evident
by a black shiny surface appearance. Do not touch the sample holder end beyond the
o-ring without gloves or finger cots.
• FILAMENT is OFF; knob {14} is fully CCW.
• With the pin on the holder shaft at 9 o’clock position and your left hand on the
goniometer body, insert the specimen holder straight in to the goniometer using your
right hand until it stops.
• Push the holder in without rotating/twisting it until the goniometer red lamp is lit. This
begins the vacuum pumping cycle sequence of the goniometer specimen chamber.
• At the end center of the holder, maintain a slight finger pressure towards the column until
the gurgling sound of the vacuum roughing pump is no longer heard, after which you may
let go of the specimen holder.
• The first cycle of the evacuation sequence will cease when a sufficient vacuum in the
specimen chamber is attained, as indicated by the red lamp is OFF. Wait for at least
two evacuation cycles to be completed (red goniometer light goes OFF twice).
• When the red lamp is OFF, rotate/twist the specimen holder CW 45 degrees until it
stops and then guide it in to the goniometer until it stops. Since at this point the
specimen holder is under vacuum, it will be pulled into the column by the vacuum,
DON’T LET GO OF THE SPECIMEN HOLDER, until it comes to a complete stop.
CAUTION! The holder may be pulled from your hand by the vacuum and cause
severe damage. Grip the holder firmly!
• If using the double tilt holder, carefully plug the holder cable into the connector H1 {4}
on the goniometer. Be careful not to bend the connector pins
• Check that the ACCEL VOLTAGE READY lights remains ON.
• Wait until the gun and column ion pump vacuum comes back down to ≤ 5x10-5
Pa. as
read on the blue scale of the meter located on power supply console.
JEM-2000FXI - 5 - 11/4/2008

7. ILLUMINATION SOURCE SETUP
ESTABLISH ACCELERATING VOLTAGE (High Tension)
If the HT is OFF and Emission Current 000 μA, then:
• Check ACCEL VOLTAGE value displayed on CRT page-1 {40}, set the accelerating
voltage to 181kV using ACCEL VOLTAGE toggle switch {16}.
• Turn ON the accelerating voltage using the red HT push button switch {17}.
• Increase accelerating voltage to 200kV (or chosen working voltage) one step at a time
(0.5kV/step). DO NOT HOLD THE ACCEL VOLTAGE TOGGLE SWITCH in the up
position when increasing the voltage.
• Observe the filament dark BEAM CURRENT at each voltage step increase. The
filament current should not surge more than 4 μA and if it surges, it should immediately
return to the initial value or the initial value plus 1 μA.
• When the desired acceleration voltage is attained, the BEAM EMISSION current meter
(L1) should read a value half of the display accelerating voltage value +/- 3, e.g.,
120kV will correspond to 060 μA.
If the HT is ON and Emission Current 40 to 103 μA
• Check ACCEL VOLTAGE value displayed on CRT page-1 {40}, set the accelerating
voltage to 200kV (or the working voltage of choice) one step at a time (0.5kV/step). DO
NOT HOLD THE ACCEL VOLTAGE TOGGLE SWITCH in the up position when
increasing the voltage.
• Observe the filament dark BEAM CURRENT at each step increase of the accelerating
voltage. The filament current should surges no more than 4 μA and then immediately
return to the initial value or the initial value plus 1 μA.
• When your working HT is attained the emission current meter should read a μA value
half of the HT kV value +/- 3 μA, e.g., 120kV will correlate to 60 μA.
If the Emission Current surges and hangs >4 μA and/or becomes erratic, then do not
proceed with the TEM session. Switch HT OFF and contact the TA or lab manager.
ESTABLISH BEAM EMISSION CURRENT
• Slowly increase the FILAMENT current knob {14} to position 3 and wait 3 minutes, then
slowly increase to position 4 and wait 1 minutes, followed by a slow increase to the
filament stop. DO NOT FORCE/MOVE THE FILAMENT STOP
• Do not allow the light BEAM EMISSION current to exceed the dark BEAM EMISSION
current by more than 10-15 μA. It may be necessary to lower the GUN BIAS {15}
before further increasing the FILAMENT current.
If the filament is in good condition and installed correctly, then the GUN BIAS values
should be in the range of 2-0 to 6-0. If GUN BIAS is outside this range, then do not
proceed with TEM session.
JEM-2000FXI - 6 - 11/4/2008

8. ILLUMINATION SOURCE ALIGNMENT
FIND BEAM
• Remove all the variable objective and selected area apertures with the lever positioned
to the right.
• Remove the variable condenser aperture per Appendix A.
• Increase to the largest SPOT SIZE {18}; displayed as 1L on the CRT page 1 {40}.
• Set the selected MAG1 or MAG2 at magnification {20} less than 5kX.
• Adjust BRIGHTNESS {19}, SHIFT {25, 41}, or DEFlector {28, 42} controls to mid-
range. Set the BRIGHT 16X switch {26} to fine or coarse as needed.
• Insert the largest Condenser Aperture {2} and center per Appendix A.
IF BEAM IS STILL NOT FOUND, THEN TRY THIS:
• Move or remove the specimen if you suspect that it is blocking the beam. LOW MAG
{21} mode may help locate a vacuum region or an electron transparent specimen area.
• Check the objective lens voltage for the acceleration voltage selected. For example, for
200KV the objective lens voltage is ~6.9.
• Set GUN SHIFT X & Y {55, 56} and GUN TILT X & Y {53, 54} at mid-points. Depress
GUN SCAN (L2) and adjust GUN TILT and GUN SHIFT to obtain the most rapid
oscillating beam. Turn GUN SCAN off.
• Insert the largest Condenser Aperture and center per Appendix A.
GUN TILT – varies the 1st
and 2nd electron gun beam deflector coils.
• Set the BRIGHT 16X switch {26} to fine or coarse as needed for the BRIGHTNESS
{19}, SHIFT {25, 41}, or DEFlector {28, 42} controls.
• Set Magnification MAG1 or MAG2 to 10-20kX
• Center beam on the screen using SHIFT X {25} and SHIFT Y {41} knobs
• Set the SPOT SIZE {18} to the maximum size (minimum number displayed on the CRT
page 1) you expect to use, typically 1L or 2L.
• Adjust the BRIGHTNESS {19} to crossover.
• Adjust GUN TILTs X and Y {55, 56} for maximum brightness. Center the beam
with GUN SHIFTs X, Y {53, 54}.
• Desaturate the filament by slowly and carefully turning down the FILAMENT {14}
knob (less than one division) and center the filament tip image in the halo with
GUN TILTs X and Y. Resaturate filament.
GUN SHIFT – varies the 1st
electron gun beam deflector coil.
• Set the SPOT SIZE {18} to the minimum size (maximum number displayed on the CRT
page 1) you expect to use, typically 3L or 4L.
• Center beam on the screen using SHIFT X {25} and SHIFT Y {41} knobs
• Switch the SPOT SIZE {18} to the maximum size (minimum number displayed on the
CRT page 1) you expect to use, typically 1L or 2L.
• Adjust the BRIGHTNESS {19} to crossover and center the beam with GUN SHIFTs X,
Y. Repeat until spot centers coincide for maximum and minimum SPOT SIZEs.
Continuously align the GUN TILTS as described in the previous alignment step.
GUN TILT and GUN SHIFT alignments are interactive and require alternating between
the two alignments until a good gun alignment is achieved.
JEM-2000FXI - 7 - 11/4/2008

9. ILLUMINATION BEAM ALIGNMENT
CONDENSER VARIABLE APERTURE CENTERING
• Select the appropriate size condenser aperture per the instructions in Appendix A.
• Center beam on screen at crossover with SHIFT X and Y (25, 41).
• Spread the beam with BRIGHTNESS to ~90% of screen and center the illumination
with aperture (X, Y) drives per Appendix A.
• Follow this procedure anytime you change a condenser aperture.
• Converge the beam to crossover with BRIGHTNESS; if it is not centered repeat this
process.
CONDENSER LENS ASTIGMATISM – varies condenser lens stigmator coil.
• At the working SPOT SIZE select MAG1 or MAG2 and adjust SELECTOR {50} to 10 to
20 kX
• Go to crossover with BRIGHTNESS {19} and center the beam on the screen using
SHIFT X {25} and SHIFT Y {41}
• Setup to Stigmate the filament tip image or the beam spot by selecting COND STIG
{21} and BRIGHT 16X {26}
• Adjust the DEFlector X {28} and DEFlector Y {42} to obtain a sharp tip image and a
symmetrical spot. Beam is round as it passes through crossover.
• Alternatively, if a sharp image is not discernable, then adjust for a circular beam shape
just slightly on the each side of crossover.
SPOT SIZE – switch {18} varies the 1st
condenser lens excitation.
BRIGHTNESS – control knob {19} varies the 2nd
condenser lens excitation.
MAGNIFICATION – selector switch {50} varies system of intermediate lenses.
IMAGING LENS ALIGNMENT
Z-AXIS EUCENTRIC Z-HEIGHT – knob varies the specimen vertical height.
(Standard Focus)
• Adjust the OBJective lens {43} to bring the specimen image into focus.
• Center the X and Y stage {13} drives (displayed on CRT page 2).
• Select MAG1 or MAG2 and SELECT a magnification of 4-5000X as displayed on CRT
page1.
• Move a recognizable feature of the specimen to the center of the screen.
• Unlock the X-tilt drive {7} on the goniometer.
• Manually tilt the goniometer stage {5} by 5-10 degrees about zero and note movement
of the feature. Return the feature to the screen center with the Z adjust knob {6} on the
bottom front of the goniometer. Return the stage to zero tilt and refocus the objective
lens and repeat.
• Greater precision of this alignment is achieved by successively increasing the
magnification (no more then 40kX) with the feature object remaining centered with
minimal sweep.
JEM-2000FXI - 8 - 11/4/2008

10. • When finished, tilt the goniometer back to zero and lock the tilt motor drive. Refocus
the OBJective lens. Check page 4 of the CRT, OBJ should read ~7.02 at 200kV. *See
OL vs. kV Table posted on column for values at different accelerating voltages.
JEM-2000FXI - 9 - 11/4/2008

11. IMAGE WOBBLER TILT BALANCE – varies 1st
and 2nd
condenser deflectors
(AKA Condenser Deflector Tilt Interlock Balance)
• Focus the image with the OBJective knob {43} at magnification from 5kX to 40kX
depending on imaging goals.
• Go to crossover with the BRIGHTNESS knob and then center the beam on the screen
using SHIFT X {25} and SHIFT Y {41}.
• Depress WOBBLER IMAGE X button {44} and converge the two beam spots on the
screen using IMAGE WOBBLER Adjust X knobs {57}.
• Depress WOBBLER IMAGE X button {44} to turn off the wobbler
• Repeat with WOBBLER IMAGE Y {45}.
OBJECTIVE LENS FOCUS (Amplitude Contrast Imaging) – varies objective lens
• Assuming that you just completed the previous BALANCE alignment, spread the beam
with the BRIGHTNESS knob {19} and find sharp distinguishable (best contrast)
features on the specimen nearest area of interest.
• If not on, then depress (turn on) the WOBBLER IMAGE X or Y button {44, 45}.
• Adjust the OBJective lens knob {43} until the double appearance of the image features
converge to a single image, i.e. wobbling appears to be minimized.
• Reduce the beam with the BRIGHTNESS knob {19} to about half the screen diameter
to check for losses in the IMAGE WOBBLER balance alignment.
• Repeat the IMAGE WOBBLER TILT BALANCE ALIGNMENT and the OBJECTIVE
LENS FOCUS until both the beam wobble and image wobble are both simultaneously
minimized at the working magnification of interest.
VOLTAGE CENTERING –bright (beam) tilt varies 1st
and 2nd
condenser deflectors
• Note: For best results this alignment must be performed using the mini-
screen/binoculars or the TV camera.
• Depress MAG1 {20} and SELECT {50} a magnification of 120kX,
• Locate a small point object or feature in the specimen and center it on the screen.
• Spread the beam with the BRIGHTNESS knob {19} to point that the image features are
just barely visible. Set the coarse mode with BRIGHT 16X {26}.
• Depress the WOBBLER HT {46} and note the direction of image movement. Minimize
the movement with BRIGHT TILT {23} DEFlectors X {28} and Y {42}.
• For improved alignment (especially in preparation for HRTEM) the TV camera may be
used for greater precision. Make sure the CCD camera, which located above the TV
camera, is retracted using Digital Micrograph.
INTERMEDIATE LENS ASTIGMATISM – varies intermediate lens stigmator coils
& DIFFRACTION FOCUS – varies 1st
intermediate lens excitation
• Spread beam with BRIGHTNESS fully CW and select the DIFFraction {37} Mode.
• Set camera length to 100 cm using SELECTOR {50}.
• Adjust DIFF FOCUS {38} to obtain a small but easily observable caustic image.
• Adjust the intermediate lens stigmator controls INT STIG X {61} and Y {62} for a round
and symmetrical caustic.
• Adjust DIFF FOCUS {38} to obtain a very small and distinctly visible spot.
CAMERA LENGTH SELECTOR – switch varies system of intermediate lenses.
JEM-2000FXI - 10 - 11/4/2008

12. PROJECTOR LENS CENTERING – varies projector lens deflector coils
AKA Central Diffraction Spot Centering
• Center the diffraction spot on the screen with projector lens deflector controls PROJ
ALIGN X {59} and Y {60} to position the spot.
• Return to imaging mode by depressing MAG1 {20}.
OBJECTIVE LENS ASTIGMATISM – varies objective lens stigmator coil
• Select a magnification higher than that which be used for your session.
• Select objective stigmators OBJ STIG 1 or OBJ STIG 2 {20} and select the coarse
mode BRIGHT 16X {26}
• Stigmate the focused image with DEFlectors X {28} and Y {42} using one of the three
methods described below.
Method 1 (Striations)
• Locate a thin specimen edge and center on screen.
• Insert an OBJECTIVE APERTURE {3} and FOCUS {43}.
• Use either the binoculars or TV camera.
• Obtain an in-focus condition with the OBJ-FOCUS control.
• Go to either under-focus or over-focus. If a streaked image is observed, then the
objective astigmatism needs correction.
• With the OBJ STIG 2 {20} selected, adjust the DEFlector X {28} and Y {42} knobs to
minimize the unidirectional features in the image.
• Check the astigmatism by adjusting the OBJ-FOCUS back and forth through in-focus
from under/over-focus to over/under focus.
• Repeat the above steps until objective lens astigmatism correction is achieved
• Turn OFF the DEFLECTOR – OBJ STIG switch.
Method 2 (Fresnel Fringes)
• Find a circular hole or ~180 degree arc in your specimen or support film and center.
• Insert an OBJECTIVE APERTURE {3} and FOCUS {43}.
• Obtain over-, in- and under-focus conditions using the OBJ-FOCUS control.
• Observe a Fresnel fringe the edge in the under- (bright fringe) and over-focused (dark
fringe) conditions. If the fringe width is not uniform, then objective astigmatism needs
correction.
• Select OBJ STIG 2 {20} and adjust the DEFlector X {28} and Y {42} knobs to make the
Fresnel fringe width uniform along the hole/arc edge.
• Turn OFF the DEFLECTOR – OBJ STIG switch.
Method 3 (Live FFT)
• Work at a magnification of ~200kX, use a ~100um condenser aperture, and, if in the L-
mode select a Spot Size of 2L or 3L.
• Set up the Gatan CCD camera and Digital Micrograph software per Appendix B.
• Click on SETUP on the MSC command pallet (rabbit-turtle-camera) and select the
RECORD mode and change the exposure time from 1 to 0.25 seconds.
• Acquire images using the SEARCH command (turtle) on the MSC command pallet.
The continuous image acquisition may be interrupted to save to a file by pressing the
SPACE bar and then restarted by re-selecting the turtle.
JEM-2000FXI - 11 - 11/4/2008

13. • Locate a uniform and amorphous region nearest your working area of interest, if
applicable, your aligned zone-axis of your specimen.
• Select the Digital Micrograph ‘Process’ menu and the ‘Live FFT’ option, which will
open a continuously updated FFT of the scanned specimen image. You may need to
adjust BRIGHTNESS slightly in order to attain a good contrast in the FFT window.
• Find and establish 2 to 3 Thon rings by adjusting the Objective Focus. Under focus the
objective lens (turn the objective focus knob counter-clockwise and observe the Thon
rings get smaller) range not far from the Gaussian focus. The Thon rings should be
close to an oval shape. If not, you will need to adjust the objective stigmators. A
negative defocus value corresponds to an underfocus condition (weakened objective
lens).
• Make sure the diffraction pattern ring diameters get smaller when the current in the
objective lens of the microscope is decreased (typically by rotating the objective lens
focus knob counterclockwise). If the ring diameters increase, while rotating the
objective knob counterclockwise, then you are at overfocus and need to go to the other
side of Gaussian focus (minimum contrast). To make this change, rotating the
objective knob counterclockwise, adjust the defocus so that the rings become so large
that they disappear, and then change it further so that the rings reappear with the
correct defocus sign.
• Adjust the objective astigmatism by pressing the OBJ STIG button on the upper left
panel and the X and Y DEF knobs. If the astigmatism is bad you may notice streaking
that flips 90 degrees on either side of focus. Start slightly under focus (bright Fresnel
fringe at the sample edge) and adjust the objective stigmators to make the FFT Thon
rings circular.
Recommended: Correct the objective astigmatism with OBJ STIG 2 selected: if you’re
unsuccessful or the image worsens, then select OBJ STIG 1 to restore the original
values.
OBJECTIVE LENS FOCUS (Phase Contrast Imaging) – varies objective lens
• Typically used for High Resolution TEM mode when attempting to image at
magnifications needed for lattice and/or atomic structures.
• Correct the Objective Lens Astigmatism using Method 3 above.
• Digital Micrograph images should be acquired using Multi-Scan Record (turtle) rate
setup for a binning of 2 and exposure time of 0.25 sec.
• If amorphous regions are available, then use a magnification range of 120kX - 200kX.
• Locate the under focus condition using the Thon rings in the live FFT.
• Minimize the number of Thon rings by decreasing under focus using the OBJ Focus
knob turned CW.
• Adjust Objective Focus to produce Scherzer condition of only one slightly broad and
distinct dark ring surrounding a circular brighter area.
JEM-2000FXI - 12 - 11/4/2008

14. Instruction Reference Photos
JEM-2000FXI - 13 - 11/4/2008

15. JEM-2000FXI - 14 - 11/4/2008

16. JEOL 2000FX 1 Diagrams
Vacuum Diagram Lens and Coil Positions
JEM-2000FXI - 15 - 11/4/2008

17. JEOL 2000FX 1 Column Construction.
JEM-2000FXI - 16 - 11/4/2008

18. SHUT DOWN PROCEDURE (Check Off on Invoice/Log )
• Select MAG1 and 40kX (R1)
• Select Spot Size 3L
• Expand the beam CW (BRIGHTNESS) to cover the entire screen (l1).
• Place the protective cover on the viewing chamber window(s)
• Remove objective and SAD apertures.
• Select the largest condenser aperture (lever to the left and largest dot).
• Turn FILAMENT CCW to OFF slowly (L1).
• Step the HT value display on CRT to 181 kV (L1).
• Tilt goniometer to zero and lock down x-tilt motor drive.
• Center goniometer X-Y stage to zero.
• Make sure EDS detector is fully retracted
• If less than 20 unused negatives, then exchange with full film box and set to 50.
• Turn down CRT screen brightness and panel light controls (R1)
• Remove specimen holder and specimen; cover and return to storage box.
• Insert ACD heater and depress ACD heat switch (L2)
• Retract CCD camera (32).
• Turn off TV control (30) and TV monitor (33).
• Flip the toggle switch UP on the Power Supply Console (green lamp lighted).
• Unlock goniometer X-tilt motor to turn off goniometer lamp.
• Complete Log
• Turn off ALL room lights.
All instrument conditions or problems must be recorded in the logbook.
JEM-2000FXI - 17 - 11/4/2008

19. PHOTO MICROGRAPH ACQUISITION
1. Select automatic or manual exposure time (Page 1 of the CRT) by depressing the
SHUTTER button (A or M is displayed).
2. Lower the small screen to measure the exposure time.
3. Cover the screen and turn off the room lights.
4. For automatic film advance press FILM ADVANCE AUTO button (built-in lamp will
light).
a. For automatic film advance press PHOTO button, wait for the green exposure
light to turn on then turn off.
b. For manual film advance press PHOTO button, wait until the button lights up,
then press again and observe the green exposure light to turn on then turn off.
SELECTED AREA DIFFRACTION PROCEDURE
1. Carry out the column alignment for the TEM mode at the accelerating voltage of
interest.
2. Locate the specimen area of interest and correct the Z-axis. Depress SAM/ROCK
button (R1) and select suitable mag with SELECTOR (R1), then focus the image.
3. Center the region of interest on the screen. Depress DIFF button (R1) and adjust
the BRIGHTNESS knob CW to produce a diffraction pattern. Select a large camera
length (100-270) cm with the SELECTOR switch (R1)
4. Adjust the DIFF FOCUS knob (R1) to obtain a sharp central spot. Center the spot
on the screen with the PROJ ALIGN knob (R2).
5. Insert and center the largest selected area diffraction (SAD) [aka field limiting]
aperture to include the area (field) of interest and center the aperture on screen.
Hint: If SAD aperture hole is difficult to locate and the beam is blocked, then reduce
the magnification. If the beam is present but the SAD aperture edge is not
visible, then increase the magnification.
6. Select and center the desired SAD aperture size and focus the diffraction pattern
with DIFF FOCUS (R1)
7. Remove (if inserted) the objective aperture. Select the desired Camera Length
(13cm-270cm only) and again focus the spot with DIFF FOCUS.
8. Maintain the diffraction pattern centered on the screen with PROJ ALIGN X,Y (R2)
9. Reduce illumination (SPOT SIZE or Condenser Aperture) and adjust DIFF FOCUS
knob to obtain the smallest possible spot.
10.Block the central beam with Beam Stop prior to raising the large screen!
11.For photo micrography, use a suitably long exposure to give sufficient illumination
with the smallest diffraction spots.
JEM-2000FXI - 18 - 11/4/2008

20. LOW MAGNIFICATION ALIGNMENT PROCEDURE
1. With the microscope aligned in the MAG mode, remove the Objective and SAD
apertures, insert CL aperture 1 and depress the LOW MAG button (R1). Select
Optimum Underfocus (OU)=0.
2. Select maximum mag. (1000X), center the beam with Shifts X,Y. Focus the image
and correct the Voltage Center by depressing the WOBBLER HT (R1), depressing
the BRIGHT TILT (L1), and adjusting the DEF X,Y to minimize movement of the
image. Release WOBBLER HT.
3. Correct astigmatism in the following manner:
a. With the illuminating system aligned, focus the image at 1000X.
b. Bring the beam to crossover and defocus the image (CCW) 3 or 4 coarse
steps.
c. Select OBJ STIG 2 (L1) and correct symmetry of the "tails" extending from
the spot, with Deflectors X,Y.
Note: In LOW MAG mode, OBJ STIG 2 is automatically selected between
mags, X300 and X1000. For Mags. of X250 to X50, OBJ STIG 1 is
automatically selected.
d. Spread the beam and refocus the image using IMAGE X wobbler. Further
reduce image movement using DEF X.
e. Release IMAGE X and depress IMAGE Y wobbler, focus image. Adjust DEF
Y so as to minimize movement with image.
f. Repeat steps d. and e. until image remains stationary.
4. Repeat steps 2. and 3. at 250X, utilizing OBJ STIG 1.
Note: To increase contrast, insert and center a field limiting (SAD) aperture
large enough not to restrict full view of the image.
When returning to MAG range, insert and center appropriate apertures. Select
proper OBJ STIG memory. Reset Optimum Underfocus as desired.
Dark Field (Centered) Alignment
1. Perform column alignment per the Basic Instruction Manual.
2. Depress MAG 1 button and select desired magnification with the SELECTOR switch.
3. Select the desired field of view, and roughly focus the image.
4. Remove the objective lens aperture from the electron beam path.
5. Depress the DIFF button and spread the illumination with the BRIGHTNESS knob to obtain a
diffraction pattern on the fluorescent screen.
6. Set the camera length to a value between 40 and 130 cm with the selector switch.
7. Adjust DIFF FOCUS to obtain the sharpest possible diffraction pattern.
JEM-2000FXI - 19 - 11/4/2008

21. 8. Adjust PROJ ALIGN knobs to precisely center the direct (bright) spot on the fluorescent screen.
9. Depress the DARK TILT button and adjust the DEF: X and Y to precisely center the desired
diffraction spot on the fluorescent screen.
10. If the image shifts when adjusting DEF: X and Y (moving the diffraction pattern), then re-center
it with the SHIFT: X and Y knobs. This may be easier by shifting to MAG (image mode) and
centering BRIGHTNESS crossover with the SHIFT: X and Y knobs.
11. Insert the objective lens aperture into the electron beam path and precisely align the aperture
center with the screen center. The aperture image can be focused with the DIFF FOCUS knob.
12. Depress the MAG 1 button. A Dark Field image should appear on the fluorescent screen. The
Bright Field image can be obtained by depressing the BRIGHT TILT button.
JEM-2000FXI - 20 - 11/4/2008

22. Appendix A: Variable Condenser Aperture Instructions
The variable condenser apertures are selected corresponding to the KNOB 1 and the
LEVER position.
Lever Position Left Right
Knobs Active 2 and 3 2 and 4
Knob 1 Position with
respect to the DOT ●
Relative Aperture Size
Aperture Size (μm) 200 120 70 40 20 NA
• KNOB 2 and KNOB 3 are used to move the apertures in the X and Y directions when the
lever is turned to the left.
• KNOB 2 and KNOB 4 are used to move the apertures in the X and Y directions when the
lever is turned to the right.
CAUTION: To prevent gross misalignment of the condenser aperture assembly; pay
very close ATTENTION to the lever position and which of the
corresponding KNOBS 2 or 3 that is adjusted.
KNOB 3
KNOB 1
KNOB 2
KNOB 4
DOT ●
LEVER
JEM-2000FXI - 21 - 11/4/2008

23. Appendix B: GATAN CCD Camera Setup
The Gatan multi-scan camera (MSC) system attached to the JEOL-2000FX consists of:
DigitalMicrograph 3.4., Camera Plug-In software 1.2, MSC CCD camera, MSC Controller that
regulates the camera electronics and generates the digital data and a PCI DMA interface card to
provide high-speed data-transfer from the MSC controller to the computer. The Gatan camera
software allows users to operate all this stuff in only a point-and-shoot mode or to control all
aspects of the image acquisition system for optimum performance.
Preparation.
1. Perform the TEM mode alignment.
2. Set the TEM magnification at 40K.
Beam Setup
1. Converge and center the beam to fit the small screen.
2. Adjust the objective focus using Image X-wobbler.
3. Re-center the beam and check condenser stigmatism.
4. Converge the beam to approximately a 2 cm diameter disc on the large screen.
5. Insert TV rate camera and turn on the B&W monitor.
6. Raise the phosphor screens and find the beam and center on the monitor.
7. Spread the beam to fill the entire monitor screen.
Digital Micrograph Software Setup.
1. Open Digital Micrograph version 3.4 on the MAC monitor.
2. Make sure the RESULTS window is open
3. Select the SEARCH command (rabbit) on the MSC command pallet for an image window to
open. The continuous image acquisition may be interrupted by pressing the SPACE bar
and then restarted by re-selecting the rabbit.
4. Center Image on CCD.
You may select different image acquisition parameters to “customize” the acquisition to produce
high-quality images. However, when you have completed your session you are to restore the
settings per the Table on the next page. The MSC Command Palette is the gateway to setting
the image acquisition parameters and to initiate/restart acquisition.
JEM-2000FXI - 22 - 11/4/2008

24. MSC Command Palette Icons
Icon Icon Description
Setup This icon will bring up a dialog where you can set up various acquisition
parameters for each acquisition setting.
Search This icon will initiate acquisition using user-selected parameters in Search,
a fast acquisition typically used to survey a sample.
Focus This icon will initiate acquisition using user-selected parameters in Focus,
a slow acquisition of higher image quality typically used to “zero in” on a
particular feature in a sample.
Record This icon will initiate acquisition using user-selected parameters in Record,
a slow acquisition of very high image quality typically used to create a file
of the feature/sample for permanent storage.
Restart This icon allows you to restart image acquisition in the frontmost
image/image selection window.
Acquisition
Bar
This bar will display acquisition status.
The Search, Focus and Record acquisition settings have parameters that can be configured by the
user in the Setup dialog box shown below, which is brought up by mouse clicking on the Setup
icon. Once the parameters have been set for a specific acquisition, the user exits the Setup dialog
and clicks on the respective acquisition icon to initiate acquisition based on the predetermined
parameters. Continuous acquisition is interrupted by pressing the Space Bar and restarted by
clicking on the Restart icon. You can also access the Setup dialog by selecting CAMERA SETUP
under CAMERA on the main menu. Please note the dialog box shown is not an exact replica and
the settings displayed are not necessarily standard.
JEM-2000FXI - 23 - 11/4/2008

25. Standard Operating Parameters
Parameters Search Focus Record
Mode Continuous Continuous Single Frame
Processing Unprocessed Gain Normalized Gain Normalized
Exposure 0.1-0.5 sec 0.25-1.0 sec 1.0-2.0 sec
Anti-blooming Selected Selected Selected
Binning 4 2 1
Zoom 1:1 1:1 1:2
CCD Area Centered 256x256 Full CCD 512x512 Full CCD 1024x1024
Drift Setting 0 sec 0 sec 0 sec
Shutter Normally Closed Selected Selected Selected
Alternate Shutter Unselected Unselected Unselected
JEM-2000FXI - 24 - 11/4/2008

26. Appendix C: Dispensing Liquid Nitrogen for the JEOL Refrigerant Tank
General precautions for use of Liquid Nitrogen
• Do not allow any liquid nitrogen to touch any part of your body.
• Do not touch any item that has been immersed in liquid nitrogen until it has warmed to
room temperature.
• Do not store liquid nitrogen in any container with a tight fitting lid. A tightly sealed container
will build up pressure as the liquid boils and may EXPLODE after a short time.
• Many substances become brittle and may shatter when cold, sending pieces of the material
flying. Avoid common glass and large, solid plastics.
• Remove metal jewelry/watches on hand and wrists.
• Do not carry liquid nitrogen in an open Dewar on any of the elevators.
Prior to Dispensing Liquid Nitrogen Prepare the JEOL 2000 FX
• Place the protective cover over the JEOL view screen before dispensing liquid nitrogen,
since spilt liquid nitrogen can crack the glass and potentially cause extensive and
irreparable damage to the electron microscope.
• Make sure that the lamp does not light when the switch on the refrigerant tank is
depressed.
• Remove the cap or the ACD heater assembly (see ACD heater instructions) on the
refrigerant tank and insert the funnel provided.
Dispensing Liquid Nitrogen into 4 Liter Dewar
• Liquid nitrogen is to be dispensed only into the 4 liter Dewar provided, which is equipped
with a carrying handle. Do not let the fill hose touch the floor.
• Liquid Nitrogen can cause terrible burns. Wear insulating gloves and goggles (not safety
glasses) are to be worn at all times when handling liquid nitrogen.
• Wear full length trousers/pants or a full length apron, and footwear that covers the entire
foot are to be worn.
• Persons dispensing the Dewar must be in constant attendance to the filling operation.
Dispensing Liquid Nitrogen into JEOL Refrigerant Tank
• Use the step ladder with safety rail provided when filling the refrigerant tank.
• Exercise caution when filling the JEOL refrigerant tank, since the liquid nitrogen may gush
from the tank and splash on the operator during filling and discharging.
• Fill the tank with liquid nitrogen and wait for 15 minutes and replenish the tank again.
• Remove the funnel from the refrigerant tank and place on microscope left of the column.
• Place the cap on the refrigerant tank opening.
JEM-2000FXI - 25 - 11/4/2008

27. Appendix D: Exchanging JEOL 2000FX Camera Film
Room and Equipment Setup conditions
1. Make sure the GUN VALVE is switched off (V1 CLOSED).
2. Make sure the PHOTO switch lamp is NOT LIT.
3. Provide a CLEAN SURFACE at the TEM on which to place MAGAZINES.
4. CLOSE all room DOORS and turn OFF room fluorescent LIGHTS.
5. LOWER incandescent LIGHT LEVEL to lowest preset setting.
6. VENT the film DESSICATOR.
7. WEARING GLOVES, OPEN dessicator lid and REMOVE the film MAGAZINES.
8. HOLD the MAGAZINES so as to prevent the magazine lid from dropping out.
9. CLOSE the DESSICATOR LID and press the control switch to pump down the dessicator.
10. PLACE both MAGAZINES on a CLEAN surface (not the floor)
Opening the Camera Chamber
1. TURN the camera chamber DOOR LEVER 90 degrees clockwise until it stops (9 o’ clock
position).
2. WAIT for the camera chamber to VENT and OBSERVE the on page 3 of CRT.
3. When VENTING is COMPLETE the camera chamber DOOR automatically OPENS a bit
and the VACUUM GAUGE should read about 250 µA for the camera chamber.
Unloading and Loading the Camera Chamber
1. WEARING GLOVES fully OPEN camera chamber DOOR
2. Very gently PULL OUT magazine RACK, if any resistance, then STOP and contact TEM
manager.
3. DO NOT TOUCH the camera drive mechanism in the camera chamber.
4. UNLOAD the used DISPENSING MAGAZINE marked FILM and PLACE IN light tight BOX.
5. PLACE unused full DISPENSING MAGAZINE gently and squarely in the rack.
6. UNLOAD the used RECEIVE MAGAZINE with ARROW only and PLACE IN light tight BOX.
7. PLACE unused empty RECEIVE MAGAZINE gently and squarely in the rack.
8. The DISPENSING MAGAZINE marked FILM is placed to the REAR of the rack drawer.
9. The RECEIVE MAGAZINE marked with an ARROW only is toward the FRONT of the rack
drawer.
10. The MAGAZINE LID TABS are positioned nearest you and FIT DOWN inside the U-channels.
Closing the Camera Chamber
1. Carefully and slowly PUSH the RACK fully back into the camera chamber.
2. WIPE the door vacuum SEAL and mating FACE with a gloved finger to remove any debris.
3. CLOSE the camera chamber DOOR while holding the lever at the 9 o’ clock position.
4. TURN the camera door LEVER counter-clockwise 90 degrees to start AUTOMATIC
EVACUATION.
5. VERIFY VACUUM INTEGRITY by observing vacuum gauge reading below 140 µA.
6. SET the UNUSED film sheet count to 50 on the CRT monitor:
7. MOVE both used MAGAZINES to the DARKROOM under light tight conditions for processing.
TO MAINTAIN VACUUM INTEGRITY FOR GOOD TEM RESULTS
DO wear gloves while handling any and all components that are inserted into the TEM
DO maintain cleanliness by observing where you place gloved hand and TEM components.
DO minimize the time the camera chamber door is open.
JEM-2000FXI - 26 - 11/4/2008

28. Appendix E: The Fischione Model 1020 Plasma Cleaner Instructions
The Fischione Model 1020 Plasma Cleaner applies a low-energy, high-frequency plasma that
removes hydrocarbon contamination from all materials research specimens and specimen holders.
Free electrons are accelerated to high velocities by an oscillating electromagnetic field that excites
gas atoms and creates the plasma. This slightly increases the temperature of the material being
processed, typically a few degrees above ambient temperature. The impinging plasma impacts the
surface with energies of less than 15 eV. Complete cleaning of contaminated specimens can
occur in 2 minutes or less.
Starting the System
1. Check the process gas cylinder valve is opened and the pressure regulator set at 10 psi. The
plasma process gas is 25% oxygen/75% argon mixture (+/-2%) with a grade in excess of
99.998% purity.
2. Press the power switch located on the back of the Model 1020 to the ON position. The process
gas vent valve will automatically open, venting the plasma chamber. When the vent LED
illuminates green the system is vented.
3. Remove the specimen holder or specimen holder port plug from the specimen holder port by
pulling outward. Do not force open against a vacuum, but wait for the vent cycle to complete.
Changing the Specimen Holder Port
1. To change the specimen holder port ensure the Model 1020 is fully vented.
2. Unscrew the large black plastic ring that holds the holder port in place. The existing holder port
can now be pulled free from the housing.
3. Select the specimen holder port that is compatible with the specimen holder that is being
processed. The specimen holder port O-ring should be inspected for any possible damage or
debris.
4. Mount the specimen holder port onto the main housing and screw the black plastic ring over
the port unit it is secured.
Specimen Holder Insertion
1. The specimen holder O-ring should be inspected for any possible damage or debris which
would prevent vacuum from being achieved.
2. Carefully insert the specimen holder into the specimen holder port (located at the front of the
main housing). Be careful not to scratch the inside of the port since it serves as a vacuum
sealing surface. The specimen holder should be inserted fully.
Starting the Vacuum System
1. Depress the Vacuum On/Off key to start the vacuum pumps. The Vacuum On LED should
illuminate. After approximately three minutes the Hi Vac LED should illuminate, indicating
adequate vacuum in the plasma chamber.
2. Should the Hi Vac LED fail to illuminate within three minutes immediately depress the Vacuum
On/Off key to de-energize the vacuum pumps. This situation indicates a possible vacuum
leak. The total pumping time can vary depending on the amount of time that the system was
open to ambient conditions.
JEM-2000FXI - 27 - 11/4/2008

29. Initiating the Plasma
1. Enter a time in minutes and seconds (maximum of 3:00) using the pushbuttons located above
and below the digits of the timer located on the front of the plasma cleaner. Press the Set key.
The selected process time is now displayed on the numeric display located above the
pushbuttons.
2. Press the Plasma On/Off key. The Plasma Active LED illuminates. Verify the existence of the
plasma by observing it through the observation window located on the side of the plasma
chamber enclosure. Should the plasma not exist then press the Plasma On/Off key. The
Plasma Active LED off. Let the vacuum system pump for two more minutes and then repeat
this step again. If the plasma still not exists then contact the TEM manager.
3. Should the plasma exist, then plasma cleaning has begun. Therefore press the Timer
Auto/Man key until the Timer Auto On LED illuminates. Countdown of the timer has started
and the plasma cleaning process with cease when the timer has counted down to zero.
Venting/Specimen Holder Removal
1. When the required processing time has elapsed the cleaning process should be terminated.
2. Depress the Vacuum On/Off key to de-energize both the molecular drag and diaphragm
pumps. This action will automatically open the plasma chamber vent valve, indicated by the
Vacuum On LED being extinguished and the Vent LED illuminating red.
3. In order to prevent ambient contamination of the specimen or the specimen holder the chamber
is vented with process gas for a period of 90 seconds. After about 3-4 minutes the Vent LED
will illuminate green indicating the end of the vent cycle.
4. Firmly grasp the specimen holder and carefully remove it from the specimen holder port.
Exercise care so as not to scratch the inside diameter of the port since its surface serves as a
vacuum sealing surface. Make sure the chamber is COMPLETELY VENTED, i.e., there is not a
residual vacuum resisting the extraction of the specimen holder.
5. When the specimen holder is removed, it should be inserted immediately into the electron
microscope for use.
Instrument Shut-Down
1. After removing the specimen holder insert the specimen holder port plug and re-enerize the
vacuum.
2. Once the Vacuum Hi Vac LED becomes illuminated turn the main power switch to the OFF
position. This action removes power to the instrument prior to the vent valve opening, thereby
maintaining vacuum within the plasma chamber and minimizing the possibility of ambient
contamination.
JEM-2000FXI - 28 - 11/4/2008

30. Appendix F: Specimen & Holder Decontamination Procedure
Liquid Nitrogen should be put into the cold trap of the microscope no less than one-half hour
before beginning a TEM session.
The following procedure should be followed in the order it is listed:
1. Put sample directly on halogen lamp (on glass)
Turn the lamp on a few minutes before use but turn it off while loading the sample so as
to be sure not to look directly into the halogen bulb.
2. Put the sample holder (without the sample) into the plasma cleaner for 3 minutes.
3. Put on gloves or finger cots. Bare hands should never touch the sample holder.
4. Clean the tip of the vacuum tweezers (with vacuum turned off) using methanol followed by
1 minute on the halogen lamp.
5. After plasma cleaning the sample holder (while the sample was on the lamp) place the
sample into the holder.
6. Plasma clean for another two minutes (if possible as the plasma cleaner may cause an
oxide to form on the surface of the sample)
7. While loading the sample, do not pump the air lock for too long. In other words, when the
specimen vacuum reaches 50 µA, immediately load the sample. Additional pumping may
cause the introduction of hydrocarbons or other contaminates into the system.
Note: Ideally, everything should be done while the sample is hot. If the sample is hot,
hydrocarbons introduced to it from the air will be blown off due to the heat.
JEM-2000FXI - 29 - 11/4/2008

31. JEM-2000FXI - 30 - 11/4/2008
Appendix G: Storing Specimen Positions in Memory
STORE Specimen Position in Memory:
1. Go To Page-2 of the CRT display
2. Using the pull out keyboard key-in: S P followed by RETURN, which will display
Specimen Position =.
3. Key-In a Memory Location Number 0 thru 9.
ERASE All Stored Specimen Positions at the End of the TEM Session:
1. Go To Page-2.
2. Using the pull out keyboard key-in: Ø P O S I followed by RETURN