standard operating procedure: jeol tem-2100 · standard operating procedure: jeol tem-2100 purpose...

Electron Microscopy Facility – WVU SRF 1

STANDARD OPERATING PROCEDURE: JEOL TEM-2100

Purpose of this Instrument: Essential tool for structural characterization of natural or synthesized nanostructures.

Location: WVU - Engineering Sciences Building (EBS) – Room: B-63 (basement)

Primary Staff Contact: Dr. Marcela Redigolo (304) 680-3007 Office: ESB G75D - (304) 293-9973

The Shared Research Facilities are operated for the benefit of all researchers. If you encounter any problems with

this piece of equipment, please contact the staff member listed above immediately. There is never a penalty for

asking questions. If the equipment is not behaving exactly the way it should, contact a staff member.

1) INITIAL CHECK

This text is a guide to operating the JEOL 2100 TEM. A more detailed and thorough account of these procedures can be found in

the JEOL Operating Manual. A glossary for acronyms can be found at the end of this document.

1. Log in your TEM session on the FOM. The computer to the left of the microscope and closest to the wall is connected to the

internet for this purpose. (fom.wvu.edu/fom)

2. Check log sheet to see the notes of previous users. This will inform you about anything unusual that occurred before.

3. Write down your name, supervisor, start time (same as FOM) and specimen information on the log sheet.

4. Check the Ion Pump Gauge reading (the blue number in the middle) on the left rack. It is usually around 0.91.510-5 Pa. If

the reading exceeds 3.510-5 Pa, do not continue and contact SRF personnel immediately.

5. Check the Filament Meter (below the Ion Pump Gauge) and record the filament hours on the log sheet.

6. Check the Cooling Water Flow meters on the back wall. Typical reading should be around (left to right): DP 46 OL 32 CL 14

Gate 42. Small variations (around 2 to 3 units) isn’t critical. More than that please contact SRF personnel immediately.

7. Check the HT Tank Gauge reading on the right side of microscope in the back. It should be around 0.015 MPa. If the

reading exceeds 0.02 MPa, do not continue and contact SRF personnel immediately.

2) START-UP

1. Take out the Anti-Contamination Device (ACD) heater from the ACD container if you are the first user of the day.

2. Cover the glass viewing window of the microscope with the protective lid and the eyepieces of the microscope binocular

if they are not covered. Place the plastic funnel at the ACD container to make it easier to fill with liquid nitrogen.

3. Get liquid nitrogen from the liquid nitrogen tank. There is always one tank of liquid nitrogen in the TEM room.


IMPORTANT: You are required to wear the apron, gloves and the face shield while handling

liquid nitrogen. Failure to do so can result in your being prohibited from using the TEM

4. Fill the ACD container with liquid nitrogen. If necessary, use the rolling ladder in the TEM room. Add more liquid nitrogen

after 10 minutes (once the system reaches equilibrium temperature).

IMPORTANT: Do not allow liquid nitrogen to contact the window glass, as the glass could

crack, causing serious damage to the interior of the microscope column.

5. Liquid nitrogen in the ACD container will last for about four hours. Make sure the ACD container is filled with liquid

nitrogen during your entire session. You may need to add more during the session.

IMPORTANT: Poor vacuum will occur when the liquid nitrogen in the ACD runs out, which may

cause instabilities to the TEM and damage when the filament and high voltage are on.

6. If it’s not opened yet, start the software program <TEMCON> on the computer on the right-hand side of the microscope

(the closest one to the TEM). The top of the screen when opened should read “Controller for JEM2100/HR”.

7. Check the stage name and the position on the right of the <TEMCON> program window. It should read <SINGLE TILT

HOLDER>.

IMPORTANT: Double click the Stage Neutral button if the stage is not neutralized. Pay special attention to the tilt reading TX and TY. Values should be zero.

8. IMPORTANT: Check the switch position of the upper digital camera on the TEM column. It should be in the “out” position

(switch pointing to the right) as shown in Fig. 1. If not, flip the switch to the right to retract the upper digital camera from

the column

Fig. 1: Upper camera. When switch is to the right, camera is out.

9. Take off the protective lid for the glass viewing window and check the phosphor screen position. The screen should be

DOWN. If the screen is not down, press F1 on right control panel to lower down the screen. Cover the lid again. If there

are any problems with this step, do not continue and contact SRF personnel immediately.


10. If you find the microscope with any of these start-up steps in different settings than what they should be, report the details

in the log sheet and make sure to put the microscope back in the right setting before you start using the equipment. SRF

staff will contact the previous user.

11. Check the magnification condition on the right control panel. The system should be in MAG 1 mode (light on) at a

magnification of 3060 K (reading on the TEM Control software window). If the system is not in MAG 1 mode, press

the MAG 1 button (right panel) and set the magnification between 30K and 60K with MAG/CAM knob on right panel.

12. Check to see if Objective Aperture and Selected Area Aperture are inserted. If they are, remove them from the path of

the beam by aligning the red dot on knob 1 with the black dot (reference mark) on the column. (See representation on

Fig. 3)

3) HIGH VOLTAGE

1. Open the <DIALOGUE> window at the <TEMCON> program, then <HIGH VOLTAGE CONTROL> window.

2. Check the HT reading in the window. It should read 180 kV. If it does not, modify the value to 180 kV with the <DOWN /

UP> arrows in the <HT> section of the window.

3. In <HT> section, click <ON> to start high voltage at 180 kV. Wait till HT ON is complete.

4. Check the Beam Current in the <HIGH VOLTAGE CONTROL> window. It should be stabilized at around 92 A.

5. In the <HIGH VOLTAGE CONTROL> window, under the <AUTO HT> section, check the settings: <TARGET> voltage

200 kV, the <STEP> 0.1 kV, and <TIME / STEP> 6 sec. These settings should never be changed!

6. Click on <START> in the <AUTO HT> section. The HT Voltage will gradually increase and will take approximately

20 minutes to stabilize at 200 kV. While the filament voltage is increasing, prepare the specimen holder.

Do not alter these settings to raise the HT Voltage faster!! Use this time to prepare your sample on the specimen holder…

4) LOADING THE SPECIMEN HOLDER (SH)

1. ALWAYS wear dust-free gloves (IMPORTANT) while handling the specimen holder.

2. Ensure that samples, tweezers and other tools are absolutely clean and free of contamination from contact with fingers,

any surface which might not be clean or might have had any contact with fingers or contaminants.

3. NEVER “blow on” or exhale on samples to dry them! Always use a clean, dry gas source when preparing your samples.

4. Prepare samples in advance, allowing the solvent used to fully dry, before bringing the sample to the microscope.

5. Make sure you always have a sure grip of the SH. Always ask if you have a question. The staff is here to help and guide

you.


6. IMPORTANT: Do NOT breathe on the holder. It is very difficult to pump water vapor in TEM! Besides, it will take a long

time before the system vacuum gets ready for the measurements. Never touch the O-rings, even with gloves!!

Fig. 2: Detail of Specimen Holder (SH)

7. For the single-tilt holder, inset the cartridge-handling tool into the cartridge clamp hole at the end of the SH (see Fig. 2).

8. Open the clamp by tilting the cartridge-handling tool, then using the tweezers remove the cartridge from the holder.

9. Mount the cartridge onto the cartridge support with the guide pin on the support inserted into the guide hole on the

cartridge.

10. Loosen the two little screws from the cartridge TWO turns.

11. Rotate the retainer away and mount the sample grid with your sample facing UPWARD.

12. Return the retainer to the original position (make sure of that) and secure it with the two little screws. IMPORTANT:

Never overtighten the screws!!

13. Insert the cartridge-handling tool into the cartridge clamp hole at the end of the SH and open the clamp.

14. Attach the cartridge to the holder so that the guide hole on the cartridge aligns with the guide pin on the clamp.

15. Clamp the cartridge by returning the cartridge-handling tool to the clamping position.

16. Turn the holder 180o to have the sample facing downward. Tap the base of holder rod with gloved finger to ensure that

the sample does not fall out.

IMPORTANT: This is an important step because if a sample falls inside the microscope, the

microscope will have to be opened to remove it, meaning the vacuum must be broken and the

column unavoidable contaminated. This requires total shutdown of the machine.

17. Make sure there is no dust and/or lint on the specimen holder O-rings. Use the magnifier lens and lamp at the desk to

check.


IMPORTANT: Always ensure that the SH O-rings are completely and definitively free of dust or fibers. Check very carefully with the magnifier lens and lamp. Be really sure before introducing the SH into the microscope!!!!

18. While waiting for the voltage to reach 200 kV, add more liquid N2 to the ACD heater to reach the full level. Remember

to cover the protective lid for the glass viewing window of the microscope and the binocular eye-pieces whenever you

are using liquid nitrogen around the microscope.

5) INSERTING THE SPECIMEN HOLDER (SH)

These steps are shown in diagrams attached to the end of this SOP and also taped to the microscope column.

1. Verify that the stage position is neutral (on the right/top corner of <TEMCON> screen) and that the airlock switch is set

to AIR position (at the microscope column, below the goniometer).

2. Align the SH guide pin with the guide groove on the microscope column (horizontal left side).

3. Insert the holder into the goniometer until position 1. This will be a long path. When the SH guide pin finally reaches the

entrance of the goniometer, you will be reaching position 1. Clicking sounds will be heard immediately after.

Never, never turn the SH clockwise before pumping. IMPORTANT: Never use excessive force when inserting the SH, especially sideways!!

4. Set the goniometer switch to PUMP. Yellow light ON.

5. WAIT until the green light on the goniometer is lit.

6. Check the vacuum reading for the specimen chamber on the <TEMCON> program. For that, open <MONITOR>, then

<VACUUM SYSTEM>. The window VALVE STATUS will open. Check for the SPECIMEN/PiG 4 reading on the right

corner of the window. It should be 36 A or less, and the status should be EVAC READY.

a. Note: The system starts evacuating the goniometer. If this process takes too long, the sample inside might be

degassing or have some contamination (hand sweat, grease, moisture, etc) that might be preventing the vacuum.

This is why it is crucial to have a clean environment when preparing (in your lab) and loading the sample onto the

SH!

b. If this process takes more than 10 min, contact SRF personnel immediately.

7. Slowly turn the SH clockwise until position 2, while firmly holding it, because it might be pulled into the goniometer to

position 3. Be careful!! This will be a very short distance.

8. Carefully HOLD (DO NOT PUSH) the SH until position 3. This will be a very short distance.

9. Slowly turn the SH clockwise until position 4, while firmly holding it. This will be a short distance. This step might

require a little bit of more strength, but it will be just a small amount more than before. Do not force the SH in.


10. HOLD (DO NOT PUSH) the SH until it reaches position 5 and black pin is in place.

IMPORTANT: All procedures here must be done slowly and carefully. Do not let go of the SH

because the vacuum will pull the SH into the column! Do not let the SH hit the end of the

goniometer!! Any collision can cause serious damage to the SH and the microscope!!

6) GETTING AN ELECTRON BEAM

1. Select the SH name <SINGLE TILT HOLDER> from the list in the holders on the <TEMCON> screen. (top right

position), if it wasn’t selected yet.

2. Record the <BEAM CURRENT> reading on HIGH VOLTAGE CONTROL window onto the log sheet. It should be

around 101102 A. If not, contact SRF personnel immediately.

3. Click on <ON> in the FILAMENT section of the HIGH VOLTAGE CONTROL window. The beam current will increase

and stabilize at around 110 A. If not, contact SRF personnel immediately.

4. Wait till the beam current stabilizes. During this time, uncover the lid to observe the beam. Turn OFF the lights of the

room and in the left panel click [ROOM LAMP].

5. Record the <BEAM CURRENT> reading on HIGH VOLTAGE CONTROL window onto the log sheet.

6. Verify that the [TEM] button on the left panel is ON (if not, press it).

7. <SPOT SIZE> must be 1, and <ALPHA> must be 3. They appear on the top of the <TEMCON> software screen.

8. Select coarse sample movements by pressing [CRS] on the SPEC CONTROL (trackball) that is the small controller

sitting on the left side of the microscope column. It will light up.

7) FIND THE BEAM AND FOCUS IT

Note: If you can’t see the electron beam on the phosphor screen, follow the steps below. If you can see the electron beam as a

small dot, turn the [BRIGHTNESS] knob to spread it on the screen and use the trackball to move the grid out of view, in case any

part of the copper grid is showing up. Go to step 2, if you already see the electron beam.

1. Set magnification to 10K ([MAGNIFICATION] knob on right control panel) and move the sample using the trackball until

the beam appears completely on the phosphor screen.

a. Note: If the beam does not appear on the screen, decrease the magnification or select LOW MAG mode by

pressing the [LOW MAG] button on the right control panel.

b. Turn the [BRIGHTNESS] knob and observe if the beam appears.

c. Check to see if Objective Aperture and Selected Area Aperture are inserted. If they are, remove them from the

path of the beam by aligning the red dot on knob 1 with the black dot (reference mark) on the column. (See

representation on Fig. 3 below)

d. If you still cannot find the beam, ask SRF personnel for help. {

IF YOU

CAN’T

SEE THE

BEAM

YET…


Fig.3: Representation of the knobs for Objective Aperture and for the Selected Area Aperture.

2. Set magnification to 50K for standard corrections. ([MAGNIFICATION] knob on right control panel).

3. Check the Condenser Aperture. (the top one)

a. The second biggest size is the standard. It must be always there. If not, align the 2nd largest white dot on the knob

1 with the small black dot (reference mark) on the column. (See Fig. 3 for reference)

b. If you use another aperture during your work, you must always put back the condenser aperture in the column

before leaving and LEAVE IT ALIGNED.

4. Press [STANDARD FOCUS] button (right control panel) to bring the beam into focus

5. Focus the beam into the smallest possible spot using the [BRIGHNESS] knob (left control panel). If you need to center

the beam, use the [SHIFT X] and [SHIFT Y] buttons on the right and left control panels to do so. .

8) CENTER THE CONDENSER LENS APERTURE (CLA)

Note: Change the [BRIGHTNESS] so that the beam is going through the crossover (the smallest size of the beam on the

phosphor screen) and see if the beam center is swinging. If yes, the Condenser Lens Aperture needs centering.

1. Focus the beam to crossover on the phosphor screen with [BRIGHNESS] knob and then center it using the [SHIFT X]

and [SHIFT Y] knobs on left and right control panels.

2. Adjust the [BRIGHTNESS] knob to expand the beam before and after crossover and see if the beam moves off screen

center as you turns.

3. Center the beam using the end and side knobs on the Condenser Lens Aperture. They are knobs 2 and 3,

respectively, on Fig. 4 below.

IMPORTANT: move the CLA knobs carefully. The amount of movement required to align the

aperture is minimum.

Fig. 4: Condenser Lens Aperture knobs: (1) aperture size, (2) and (3) alignment.


4. Repeat steps 1 to 3 till there is no beam swinging. Verify the result by turning the [BRIGHNESS] knob back and forth

through the crossover and see if the beam expands and contracts coaxially.

9) ALIGNING THE OPTICAL AXIS OF GUN AND CONDENSER SYSTEMS “GUN 1 CLA 5”

Note: Perform this alignment to correct a shift of beam position when you change the spot size.

1. Select <MAINTENANCE> from the <TEMCON> menu and click on <ALIGNMENT> to open the ALIGNMENT PANEL

FOR MAINTENANCE window.

2. Set magnification to 100K.

3. Set the [SPOT SIZE] knob (left panel) to 1 (number appears on the top of the <TEMCON> program) and focus the

electron beam to the crossover with the [BRIGHTNESS] knob.

4. Click on <GUN> on DEF SELECT window.

5. Center the electron beam using the [SHIFT X] and [SHIFT Y] knobs.

6. Set the [SPOT SIZE] knob to 5 and focus the beam with the [BRIGHTNESS] knob.

7. Click on <CLA> on DEF SELECT window or press the [BRIGHT TILT] button.


9. Repeat steps 38 until the electron beam stays at the center of the screen when the [SPOT SIZE] knob setting is

changed.

10. Keep the [SPOT SIZE] on 1. Whichever is clicked, <CLA> or <GUN>, press it again to turn it OFF.

10) CORRECT THE CONDENSER LENS ASTIGMATISM “SHAPE OF THE BEAM”

Note: Perform condenser astigmatism correction ONLY if the beam is not circular (elongated) when it is open or near crossover.


2. Focus the beam to crossover using the [BRIGHTNESS] knob and center the beam with [SHIFT X] and [SHIFT Y]

knobs.

3. Spread the beam on the phosphor screen and center the Condenser Lens Aperture with the end and side knobs. They

are knobs 2 and 3, respectively, on Fig. 4.

4. Press the [COND STIG] button (left control panel) or click on the <CL STIG> in STIGMATOR section of the

ALIGNMENT PANEL FOR MAINTENANCE window.

5. Slowly turn the [BRIGHTNESS] knob back and forth through the crossover and adjust the [DEF/STIG Y] and

[DEF/STIG X] knobs so that the shape of the beam spot becomes round immediately before and after the crossover.

6. Check the beam condition by spreading the beam on the screen and see if it is round and centered.

ONLY IF

THE

BEAM IS

NOT

CIRCULAR


7. Click on the <CL STIG> in STIGMATOR section of the ALIGNMENT PANEL FOR MAINTENANCE window to turn it

OFF.

11) CONDENSER LENS DEFLECTION COIL TILT X / Y ADJUSTMENT TILT X / TILT Y

Note: This is to make sure that beam tilt and shift are independent, that is, the beam can stay at the same place while it is being

tilted.


2. Focus the electron beam to crossover using the [BRIGHNESS] knob.

3. Press [BRIGHT TILT] button (left panel) or click on <CLA> in DEF SELECT section of the ALIGNMENT PANEL FOR

MAINTENANCE window.


5. Click on <TILT> in the COMPENSATOR section of the ALIGNMENT PANEL FOR MAINTENANCE window.

6. Click on <TILT-X> in the WOBBLER section of the ALIGNMENT PANEL FOR MAINTENANCE window.

7. Using the [DEF/STIG X] knob (left panel), bring the two splitting beam spots together.

a. Note: If the beam is going too far out the screen, turn OFF the TILT Y and TILT. Repeat this procedure from step

3.

8. Turn OFF by clicking again the <TILT-X> in the WOBBLER section of the ALIGNMENT PANEL FOR MAINTENANCE

window.

9. Click on <TILT> in the COMPENSATOR section of the ALIGNMENT PANEL FOR MAINTENANCE window to turn it

OFF.

10. If the beam moves off center as you turn the [BRIGHNESS] knob, press the [BRIGHT TILT] button or click on <CLA> in

DEF SELECT section, and use the [SHIFT X] and [SHIFT Y] knobs to center the beam.

11. Click on <TILT> in the COMPENSATOR section of the ALIGNMENT PANEL FOR MAINTENANCE window.

12. Click on the <TILT-Y> in the WOBBLER section of the ALIGNMENT PANEL FOR MAINTENANCE window.

13. Using the [DEF/STIG Y] knob (right panel), bring the two splitting beam spots together.

a. Note: If the beam is going too far out the screen, turn OFF the TILT Y and TILT. Repeat this procedure from step

10.

14. Turn OFF by clicking again the <TILT-Y> in the WOBBLER section of the ALIGNMENT PANEL FOR MAINTENANCE

window.

15. Click on <TILT> in the COMPENSATOR section of the ALIGNMENT PANEL FOR MAINTENANCE window to turn it

OFF.

{

{


16. If the beam moves off center as you turn the [BRIGHNESS] knob, press the [BRIGHT TILT] button or click on <CLA> in

DEF SELECT section, and use the [SHIFT X] and [SHIFT Y] knobs to center the beam.

17. Remember to turn OFF the [BRIGHT TILT] button or click on <CLA> in DEF SELECT section.

12) CENTERING CURRENT AXIS (OBJECTIVE LENS ALIGNEMENT) OBJ

Note: Perform current axis adjustment if you observe a shift of image when you change the focus (i.e., changing the objective

lens current).

1. Obtain an image on the phosphor screen at over 100K magnification. To focus the image, first make sure you are in

the proper sample height by pushing the [UP/DOWN Z] buttons (right control panel) to adjust the Z height until the

image is in focus.

2. For further focus adjustments, use [OBJ FOCUS] knobs.

3. Spread the beam fully across the phosphor screen, and move an object in the image to the center of the screen.

4. Click on <OBJ> in WOBBLER section of the ALIGNMENT PANEL FOR MAINTENANCE window. The image will

expand and contract periodically.

5. Press the [BRIGHT TILT] button (left panel) or click on <CLA> in DEF SELECT section.

6. Adjust [DEF/STIG X] and [DEF/STIG Y] knobs so that the image expands and contracts around the center of the

phosphor screen, i.e., the object in the center do not slide while vibrating.

7. Click on <OBJ> in WOBBLER section again to turn it OFF.

8. Verify the result by turning the [OBJ FOCUS] knob to go in and out of focus and see if the image shifts.

9. Click on <CLA> in DEF SELECT section again to turn it OFF.

13) CENTERING VOLTAGE AXIS (OBJECTIVE LENS ALIGNEMENT) HT

Note: Adjust the TEM optical axis so that the image stays in the center of the screen even when the accelerating voltage is

changed. This is to ensure that the beam passes through the optical axis of the objective lens.

1. Obtain a focused image on the phosphor screen at 300K.

2. Focus the image using [OBJ FOCUS] knobs.

3. Spread the beam fully across the phosphor screen, and move an object in the image to the center of the screen.

4. Press the [HT WOBB] button (right panel) or click on <HT> in WOBBLER section of the ALIGNMENT PANEL FOR

MAINTENANCE window. The image will expand and contract periodically.

5. Press the [BRIGHT TILT] button (left panel) or click on <CLA> in <DEF Select> section.

6. Adjust [DEF/STIG X] and [DEF/STIG Y] knobs so that the image expands and contracts around the center of the

phosphor screen, i.e., the object in the center do not vibrate.


7. Press the [HT WOBB] button or click on <HT> in WOBBLER section again to turn it OFF.

8. Click on <CLA> in DEF SELECT section again to turn it OFF.

14) OBJECTIVE LENS ASTIGMATISM CORRECTION

Note: Perform Objective Lens astigmatism correction if you observe asymmetrical Fresnel fringes appear along the rim of a hole.

If the correction of objective lens astigmatism is inadequate, it is very difficult to obtain an in-focus image no matter how you try

to focus.

Method 1: Fresnel Fringe Method

1. Set magnification between x20K and x100K.

2. Adjust the [BRIGHNESS] knob for optimum brightness of the image.

3. Press [BRIGHT TILT] button (left panel) or click on <CLA> in DEF SELECT section.

4. Adjust the [SHIFT] knobs to center the beam.

5. Focus the image using [OBJ FOCUS] knob.

6. Move the image of a small hole or a curved edge on the sample to the center of screen.

7. Press [OBJ STIG] (left panel) or click on <OL STIG> in DEF SELECT section of the ALIGNMENT PANEL FOR

MAINTENANCE window.

8. Adjust the [OBJ FOCUS] knobs so that the Fresnel fringes appear along the rim of the hole or edge. The Fresnel

fringes are the white lines seen along the edge in a slightly over focused condition. If there is astigmatism in the

objective lens, these fringes will be asymmetrical.

9. Adjust the [DEF/STIG X] and [DEF/STIG Y] knobs so that Fresnel fringes appear to be symmetric (have same contrast

and same width in all directions).

10. Press again [OBJ STIG] (left panel) or click on <OL STIG> in the DEF SELECT section of the ALIGNMENT PANEL

FOR MAINTENANCE window to turn it OFF.

Method 2: Granularity of an amorphous sample

The supporting film itself is amorphous and can be used for astigmatism correction at high magnifications.

1. Obtain an image at your desired magnification. (over x100K)

2. Adjust the [BRIGHNESS] knob for optimum brightness of the image.

3. Press [BRIGHT TILT] button (left panel) or click on <CLA> in DEF SELECT section of the ALIGNMENT PANEL FOR

MAINTENANCE.

4. Adjust the [SHIFT X] and [SHIFT Y] knobs to center the beam.

5. Focus the image using [OBJ FOCUS] knobs.

CHOOSE

ONE OF

THE

METHODS


6. Move a suitable image of an amorphous region on the sample (or support film) to the center of the screen.

7. Press [OBJ STIG] (left panel) or click on <OL STIG> in the DEF SELECT section of the ALIGNMENT PANEL FOR

MAINTENANCE window.

8. Slowly turn [OBJ FOCUS] knob back and forth through the focus position to observe the variation of phase contrast. If

there is astigmatism, the granularity of the amorphous film will be observed with preferred directionality.

9. Adjust [DEF/STIG X] and [DEF/STIG Y] so that the granularity presents no preferred directionality. Under perfect

adjustment, once focused, the support film should almost disappear in the image.



Method 3: Fast Fourier Transfor (FFT)

1. Obtain an image at high magnification (around x300K), on the phosphor screen. Preferably of the carbon film on the

grid.

2. Start the Gatan <DIGITAL MICROGRAPH> software on the dedicated computer on the right-hand side of the TEM

console (the closest to the door). You will hear two beeps.

3. If the software asks whether to insert the camera, click <YES>.

4. Go to <CAMERA> menu, under <CAMERA> sub-menu, select <ES500W> camera.

5. Turn the [BRIGHTNESS] knob (left panel) to reduce the intensity of the electron beam on the phosphor screen.

(Important: The image/beam should at least cover the whole phosphor screen.)

6. If <CAMERA VIEW> is opened on the right side of the screen, click on <START VIEW> on to open the view window.

7. If <CAMERA VIEW> isn’t opened, click on <WINDOW>, <FLOATING WINDOWS>, <CAMERA VIEW> to open it. Click

then on <START VIEW>. Then, click on <START VIEW> on to open the view window

8. Change the Exposure Time from 1 second to 0.3 second.

9. On <CAMERA VIEW>, click the symbol (settings) on the lower right corner of this window. (Fig. 5)

Fig. 5: Camera view window and settings.

10. Adjust the settings to read: Top: 0, Left: 0, Bottom: 1024, Right: 1024. Click <OK> and close this window.

DO NOT

INSERT

THE

CAMERA

UNTIL…


11. Insert the upper digital camera by setting the switch to the left. (Fig. 6)

Fig. 6: Upper camera. When switch is to the right, camera is out.

12. Go to <PROCESS> on the Digital Micrograph software.

13. Select <LIVE> and <FFT>.

14. The new window that opens will have the FFT of the chosen image.

15. Press [OBJ STIG] (left panel) or click on <OL STIG> in the DEF SELECT section of the ALIGNMENT PANEL FOR

MAINTENANCE window.

16. Adjust [DEF/STIG X] and [DEF/STIG Y] so that the FFT will be as round as possible.



18. Close the FFT window.

19. Click on <STOP VIEW> on the CAMERA VIEW window.

20. Retract the camera by setting the switch to the right.

15) IMAGE RECORDING WITH THE UPPER DIGITAL CAMERA

1. Start the Gatan <DIGITAL MICROGRAPH> software on the dedicated computer on the right-hand side of the TEM

console (the closest to the door) is it is not already opened.

2. Go to <CAMERA> menu, under <CAMERA> sub-menu, select <ES500W> camera.

3. Obtain the image of interest on the phosphor screen.

4. Turn the [BRIGHTNESS] knob (left panel) to reduce the intensity of the electron beam on the phosphor screen.

(Important: The image should cover the whole phosphor screen.)

5. If <CAMERA VIEW> is opened on the right side of the screen, click on <START VIEW> on to open the view window.

6. If <CAMERA VIEW> isn’t opened, click on <WINDOW>, <FLOATING WINDOWS>, <CAMERA VIEW> to open it.

Then, click on <START VIEW>.

… HERE!!!!


7. Insert the upper digital camera by setting the switch to the left. (Fig. 1)

8. Click on <STOP VIEW> to freeze the image.

9. Click on <START ACQUIRE> at the <CAMERA ACQUIRE> window, on the right side of the DIGITAL MICROGRAPH

software screen. If this window isn’t opened, click on <WINDOW>, <FLOATING WINDOWS>, <CAMERA ACQUIRE>

to open it.

10. Once the image is acquired, click on <FILE>, <SAVE AS> and save the image in the .dm3 format.

11. When you finish recording the image, retract the camera by setting the switch to the right, even if you want to look for

another region on your sample.

12. At the end of your session, save all your data to a memory stick and take it with you. Do not store data on the

TEM computer.

13. If you need to convert images to a different format, at the end of the session, click on <FILE>, <BATCH CONVERT>.

14. Choose the folder in which your data is stored in the new window.

15. The files to be converted should be *.dm3. Choose between converting to .bmp, .jpg or .tiff formats.

16. Click <OK>.

18) SAMPLE EXCHANGE

1. If you were using the Gatan DigitalMicrograph software, click <STOP VIEW> at the <CAMERA VIEW> window. Make

sure the camera is retracted from the microscope column by setting the camera switch to the right.

2. Set the Condenser Lens Aperture at position 2 (2nd largest aperture).

3. Take the Objective Lens Aperture and Selected Area Aperture out of the column by aligning the red dot on the knob

with the small black dot on the column.

4. Set [SPOT SIZE] to 1 and [ALPHA] to 3. Reduce [MAG] to 30K 60K. Using the [BRIGHTNESS] knob, bring the

beam to the crossover and center it using the [SHIFT X] and [SHIFT Y] knobs on the control panels.

5. Turn off Filament by clicking on <OFF> in the FILAMENT section of the HIGH VOLTAGE CONTROL window. The

system might open a new window to ask confirmation to turn off the filament. In that case, select <YES>.

a. Never remove a sample with the Filament ON.

b. Wait to remove the sample untill the beam current stabilizes!

6. Put the stage in neutral position by double clicking the <Stage Neutral> button on the <TEMCON> window.

7. Remove the specimen holder from the goniometer following the proper procedure below (also can be found on

Appendix B). Observe the representation of these steps in the diagrams attached to the end of this SOP and also

taped to the microscope column for your convenience.


8. Be careful!! Slowly pull out the SH until it stops (position 1). Be sure to firmly hold the SH while doing this because it

might be pulled back into the goniometer due to the vacuum.

9. Turn it counterclockwise until it stops (position 2). DO NOT PULL IT, JUST TURN IT. It’s a short distance.

10. Slowly pull out the SH until it stops (position 3). It’s a very short distance.

11. Turn it counterclockwise until it stops (position 4). DO NOT PULL IT, JUST TURN IT. It’s a very short distance.

Never, never pull it before the chamber is filled with air!!!

12. Set the goniometer switch to <AIR>.

13. Wait about 30 seconds (sound of air filling the chamber will be heard briefly).

14. Remove the SH carefully, out of the goniometer.


because the vacuum will pull the SH back into the goniometer. Collision can cause serious

damage to the SH and the microscope!! Do not use force to remove the SH from the

goniometer, just hold it firmly. DO NOT pull it out with speed and strength!

15. Reinsert the SH into the goniometer by following procedure described in section 5 of this SOP or in Appendix A.

16. Click on <ON> in the FILAMENT section of the HIGH VOLTAGE CONTROL window. The beam current will increase

and stabilize at around 110 A. If not, contact SRF personnel immediately.

17. Find the electron beam and repeat all processes starting from section 7 of this SOP.

19) SHUT DOWN PROCEDURE

1. If you were using the Gatan DigitalMicrograph software, click <STOP VIEW> at the <CAMERA VIEW> window. Make

sure the camera is retracted from the microscope column by setting the camera switch to the right.

2. Set the Condenser Lens Aperture at position 2 (2nd largest aperture).

3. Remove the Objective Lens Aperture and Selected Area Aperture from the column by aligning the red dot on the knob

with the small black dot on the column.

4. Set [SPOT SIZE] to 1, [ALPHA] to 3 and reduce [MAG] to 30,000, center the beam to crossover and center it using

[SHIFT X] and [SHIFT Y].

5. Keep [MAG] between 30K60K to keep the lenses warm and stable, and prevent any water vapor condensation.

6. Turn off Filament by clicking on <OFF> in the FILAMENT section of the HIGH VOLTAGE CONTROL window. The

system might open a new window to ask confirmation to turn off the filament. In that case, select <YES>.

7. Wait till the process is finished! Never remove a sample when the filament is ON.


8. Turn OFF the HT VOLTAGE by clicking on <OFF> in HT section of the HIGH VOLTAGE CONTROL window. The

system might open a new window to ask confirmation to turn off the HT. In that case, select <YES>.

9. Wait till the beam current reaches zero!

10. Reduce HT value to 180 kV by clicking on the <DOWN/UP> buttons in the HT section.

11. Put the stage in neutral position by double clicking the <Stage Neutral> button on the <TEMCON> window.

12. Remove the specimen holder from the goniometer following the proper procedure below (also can be found on

Appendix B). Observe the representation of these steps in the diagrams attached to the end of this SOP and also

taped to the microscope column for your convenience.

13. Be careful!! Slowly pull out the SH until it stops (position 1). Be sure to firmly hold the SH while doing this because it

might be pulled back into the goniometer due to the vacuum.

14. Turn it counterclockwise until it stops (position 2). DO NOT PULL IT, JUST TURN IT. It’s a short distance.

15. Slowly pull out the SH until it stops (position 3). It’s a very short path.

16. Turn it counterclockwise until it stops (position 4). DO NOT PULL IT, JUST TURN IT. It’s a very short distance.

Never, never pull it before the chamber is filled with air!!!

17. Set the goniometer switch to <AIR>.

18. Wait about 30 seconds (sound of air filling the chamber will be heard briefly).

19. Remove the SH carefully from the goniometer.


because the vacuum will pull in the SH back into the goniometer. Any collision can cause

serious damage to the SH and the microscope!! Do not use force to remove the SH from the

goniometer, just hold it firmly. DO NOT pull it out with speed and strength!

20. Cover the glass viewing window of the microscope with the protective lid and the eyepieces of the microscope

binocular if they weren’t covered yet.

21. Log in on <FOM> to check if there is any user reserved a session after you today.

22. Log OFF on the FOM from your TEM session.

23. Sign out on the log sheet. Report any problems in the comments section and notify the SRF staff.

Procedure 1: There will be another user AFTER you

If someone has reserved a session after you:

Continue

from # 20

after

removing

your sample!


a. Save all your images and record them to your memory stick.

b. Make sure that the room is clean and organized before you leave.

c. Switch off the room lights.

Procedure 2: You are the LAST user of the day

If no one has reserved the instrument for use during the next 4 hrs, follow the procedure below:

a. Remove the ACD container fill cap. Use face shield for protection from liquid nitrogen spills!

b. Insert the ACD heater into the ACD container.

IMPORTANT: Use protection clothes/face shield! Direct the plastic pipe AWAY from

your face!! Liquid nitrogen will come out through the plastic pipe when inserting the heater!

c. Insert the heater plug into the HTR socket on the connector box.

d. Select <Maintenance> from the <TEMCON> menu bar.

e. Click on <ACD & BAKE> to open the <BAKE OUT /ACD HEAT> window.

f. Click on the <ACD HEAT> tab to open the <ACD HEAT> window.

g. Click on the ACD Heat <ON> button.

h. Click <OK>.

Note: The liquid nitrogen in the ACD has to be burnt off at the end of the day. If this is not done, there is a danger

of contaminating the column and adversely affecting microscope performance.

i. Save all your images and copy them to your memory stick.

j. Make sure the room is clean and tidy before you leave.

k. Switch off the room lights.


GLOSSARY

Glossary of terms and acronyms used in this SOP. If you have any suggestions to be added here, please let us know. Thanks.

1) ACD = Anti-Contamination Device

2) CL = Condenser Lens

3) CLA = Condenser Lens Aperture

4) COND = Condenser

5) Crossover = the smallest size of the beam on the phosphor screen

6) CRS = Coarse

7) DEF = Deflection

8) DP = Diffusion Pump

9) FFT = Fast Fourier Transform

10) FOM = Facility Online Manager

11) HT = High Tension

12) MAG = Magnification

13) OBJ = Objective

14) OL = Objective Lens

15) SA = Selected Area (for diffraction)

16) SH = Specimen Holder

17) SOP = Standard Operating Procedure

18) SRF = Shared Research Facilities

19) STIG = Stigmatism

20) TEM = Transmission Electron Microscope

21) TEMCON = TEM Control software


INTRODUCING THE SPECIMENT HOLDER (SH)

1. Align the SH guide pin with the guide groove on the

microscope column (see photo below).

2. Insert the holder into the goniometer until position 1.

Clicking sounds will be heard right after.

3. Set the goniometer switch to <PUMP>. Yellow light ON.

4. WAIT until the green light on the goniometer is lit.

a. Note: If this process takes more than 10 min /

green light does not turn ON, contact SRF

personnel immediately.

5. Slowly turn the SH clockwise until position 2,

while firmly holding it, because it might be

pulled into the goniometer to position 3. Be

careful!! This will be a very short path.

6. Carefully HOLD (DO NOT PUSH) the SH until

position 3. This will be a very short path.

7. Slowly turn the SH clockwise until position 4,

while firmly holding it. This will be a short path.

a. This step might require a little bit of

more strength, but still it will be just a

bit more than before.

8. HOLD (DO NOT PUSH) the SH until it

reaches position 5 and black pin is in place.

APPENDIX A


REMOVING THE SPECIMEN HOLDER (SH)

1. Be careful!! Slowly pull out the SH until it stops

(position 1).

2. Turn it anticlockwise until it stops (position 2). DO

NOT PULL IT, JUST TURN IT.

3. Slowly pull out the SH until it stops (position 3).

4. Turn it anticlockwise until it stops (position 4). DO

NOT PULL IT, JUST TURN IT.

5. Set the goniometer switch to

<AIR>.

6. Wait about 30 seconds (sound of

air filling the chamber will be heard

briefly).

7. Remove the SH.

Always place the stage

in neutral position

before removing it!!!

APPENDIX B


EMERGENCY OPERATING PROCEDURES

If you have any questions, even if you are just slightly unsure, ASK someone who knows and can help.

There are no penalties for asking for help but there may be for not reporting damage to the equipment that

may delay or prevent others from working.

If, at any time, you need to contact someone for help, call or locate the following staff of the Shared

Research Facility (SRF):

Marcela Redigolo Office: ESB G75D Phone: (304) 293-9973 Cell: (304) 680-3007

This microscope is protected by various safety devices. If none of the above-listed individuals is available,

the user must:

Turn the filament OFF.

Turn HT OFF.

If possible, the user should stay with the microscope while trying to contact the above individuals. If it

becomes necessary to leave the microscope then the user should leave a large, legible note on both the

microscope and at least one of the above individuals’ offices, stating:

The problem (describe what happened and steps taken)

When it occurred (date and time)

User name and phone number

Prof. Xueyan Song, faculty expert in TEM, is also available for assistance if the contact above is not

available. Her office is located at ESB 537 and her office phone number is (304) 293-3269.

If a dangerous situation is evident (smoke, fire, sparks, etc), ONLY if it is safe to do so, the user

should press EM STOP switch (on the control panel under the left side of the microscope) to turn

OFF power to the entire microscope and notify the proper emergency personnel. In any case, the

user should leave the facility and contact emergency personnel as soon as possible from a safe

place.

Marcela Redigolo Office: ESB G75D Phone: (304) 293-9973 Cell: (304) 680-3007

standard operating procedure: jeol tem-2100 · standard operating procedure: jeol tem-2100 purpose...

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