1

JEOL 2100 Basic operating instructions

May 2012

This manual contains information regarding the basic operation of this microscope for

conventional imaging.

These are the only procedures you should carry out, unless you have received specific additional

training.

The information contained in this manual is subject to change without notice. Please follow

the current procedures correctly.

If you are unsure what you are doing, please check with CMM staff before continuing.

2

Important!!!

If you stop for lunch, etc. please turn off the beam by pressing the [BEAM] button on the left-hand control panel or in the HT Window, or the [FIL] button in the HT window. In an emergency, turn off the beam by pressing the [BEAM] button and leave the building immediately. Only operate the microscope beam current at Dark Current + 5µamps Normal Imaging Conditions:

i.e. at 103.6 + 5.0 = 108.6µamps as this will prolong the lifetime of a sharp filament.

Note 1: HRTEM = dark current + 2.5µamps Note 2: AEM (analytical) = dark current + 10.0µamps After using these settings, please return to Filament to normal (prolonged filament life) imaging conditions.

3

Please note:

• This microscope has been optimized for physical sciences imaging, 200kV.

• The microscope can be used at voltages between 80kV and 200kV.

• Standard TEM operating voltages of this microscope are: 80kV, 120kV, and 200kV.

• Standard STEM operating voltages of this microscope are: 120kV and 200kV.

• During normal working hours (9am-5pm, Monday-Friday) the voltage will be left switched ON, at 200kV.

• Other times it will be left ON at 150kV. But note that after the ACD heater has been applied the HT may not turn back on automatically. If this is the case, then simply ensure/set the HT to 150kV, then press the HT button (in the HT menu box) by using the [left mouse button].

• If you wish to operate the microscope at a different voltage, ensure that a microscope alignment exists for that particular accelerating voltage.

Note: It takes approximately 1 minute to change the voltage from 150kV to 200kV.

4

1 What to do at the start of your microscope

session 1.1 Pre-session checklist

ALL users: MUST carry out the following checks before starting their session. If you are in any doubt about any procedures, contact CMM staff. Do not proceed if you are uncertain what to do. 1.1.1 Check that the microscope is on. Look at

the Ion Pump at the rear of the microscope in the alcove and the GREEN LAMP should be ON, see Figure 1.

1.1.2 Check that vacuum levels are OK – see section 1.2.

1.1.3 If you are the first user of the day, and the

accelerating voltage is not at 200kV then either:

1.1.3.1 ensure that the accelerating voltage is at 150kV – see section 1.5.

1.1.3.2 turn on the accelerating voltage to 150kV – see section 1.5.

1.1.4 Load the sample into the holder and insert the holder into the microscope – see section 1.1.4.

1.1.5 Ensure that the anti-contamination device (ACD) is full of liquid nitrogen (LN2) – see section 1.1.5.

Note: The two computers and microscope/camera software should always be left running.

Do NOT quit either of the running software applications [TEM CON on the JEOL computer or Digital Micrograph on the Gatan computer].

Figure 1 SIP (ion pump or ion gauge) showing that microscope is in the ready state.

5

Do NOT shut down either of the computers. If you think there is a problem with the computers or software, do not try to fix it yourself, please contact a member of CMM staff.

6

1.2 Checking the microscope vacuum levels

The microscope vacuum system can be checked for operation by inspecting the Valve Status window on the JEOL computer monitor (shown in Figure 2). If the Valve Status window is not displayed on the JEOL monitor, then:

1.2.1 Select the [VAC] button located near the top left-hand corner of the screen (highlighted in RED) then the Valve Status window should appear (highlighted in RED in Figure 2).

Figure 2 The vacuum display (called Valve Status window) shows a layout of the vacuum system. The right hand

side of the Valve Status window shows the readings of the main vacuum gauges.

7

The vacuum status and levels should be as follows (from top to bottom):

GUN: Status: Evac Ready ~24-28µA

COLUMN: Status: Evac Ready ~24-28µA

SPECIMEN: Status: Evac ~252µA

CAMERA: Status: Evac Ready ~24-28µA

RT: Status: Evac Ready ~80-90µA

Figure 3 Enlarged view of the main vacuum

gauges on the microscope. If the vacuum levels are higher than expected, please consult CMM staff.

8

1.3 Checking the column vacuum level

The column vacuum can also be checked on the ion gauge located on power supply cabinet in the back right hand corner (alcove) of the microscope room (see Figure 2). The gauge should be reading less than 2.5 on the blue (middle) scale when the meter range is set to the 10-5Pa range.

Figure 4 The column vacuum gauge. It should read less than 4 on blue (middle) scale the 10-5 Pa range at the start of your session.

Note: The column vacuum gauge may be on the 10kV range when you first arrive. Remember to confirm that the meter range is on the 10-5Pa scale before checking the vacuum level.

When changing meter ranges please move the dial slowly between each range to prevent high voltage arcing within the meter and possible damage.

Important: The column vacuum must be checked again after the sample holder

has been inserted. The vacuum level must be below 2.5 x 10-5Pa and stable before the electron beam [Filament] is switched on.

9

1.4 Filling the anti-contamination device (ACD)

Caution: Always wear appropriate PPE when using liquid nitrogen (LN2).

The ACD (located on the left-hand side of the column see Figure 3) should be filled with liquid nitrogen (LN2) before you insert your sample. Be careful when filling the ACD as it will overflow when full.

Important: Before filling the ACD, make sure that the viewing screen cover is in place, and that the binoculars are covered at both ends. Liquid nitrogen (LN2) must not come into contact with the glass.

Note: At the beginning of the day, the dewar should be filled twice. When first filled, the nitrogen will boil rapidly. After a few minutes the boiling will stop and the dewar can be filled again. You should wait ~10 minutes after the first filling of the dewar before inserting your sample.

Figure 5 Anti-contamination device with ACD heater inserted.

Note: The dewar is usually filled by CMM early in the morning on weekdays and will only require a small top up at the beginning of the morning session. Similarly for the afternoon session, the morning session user will fill the dewar and thus only a small top up will be required. After hours users will need to fill the dewar at the beginning of their session, say 5:00pm and then top up the dewar at about 9:00pm.

Once cold, the ACD must be kept filled until the end of the day. EVERY USER should top up the ACD with liquid nitrogen BEFORE they start their session. Once it has been refilled, replace the plastic stopper (to reduce ice build-up on the outside of the ACD).

Caution: Take care if using the “Steps” to fill the anticontaminator device.

10

1.5 Turning on the accelerating voltage

If the HT box (top left corner of left monitor) is grey then the HT is off and you will not be able to get an electron beam by pressing the BEAM button. To turn on the HT follow the steps below: 1.5.1 If the High Voltage Control window is not visible, press the HT button in the top left corner

of the left monitor – this will open the High Voltage Control window (see Figure 4).

1.5.2 Check that the HT reading (top right of High Voltage Control window) is set to 150kV. If it is not, use the Down/Up arrows (top ones) to set the HT to 150kV.

1.5.3 Turn the HT on by pressing the ON button for the HT.

1.5.4 The HT will now be turned on slowly – wait until it is on before doing anything else. The grey HT button will become green when the voltage is on.

Pressing the small HT button in the top left corner makes the High Voltage Control window appear. Pressing the HT ON button turns on the HT causing the HT indicator (next to the voltage read out) to become green.

When the HT is off, the HT indicator is grey.

Figure 6 High Voltage Control Window with HT Off.

Figure 7 High Voltage Control Window with HT On.

11

1.6 Changing the accelerating voltage

Important: You should only change the accelerating voltage if you have been shown how to do so by a member of CMM staff. Do NOT follow these instructions unless you have been trained to do so. In the High Voltage Control window tick the More box in the bottom right-hand corner – this will open up the bottom section of the window

1.6.1 To increase the voltage from 150kV to 200kV:

1.6.2 Make sure that the beam is turned ON at 150kV

1.6.3 At 150kV, the beam current should be stable ~77µA.

1.6.4 If it is not, contact a member of staff.

1.6.5 In the High Voltage Control window, set a target voltage of 200kV, a step size of 1kV and a time step of 2s.

1.6.6 Hit the [Start] button – this will automatically increase the voltage from 150kV to 200kV.

1.6.7 Once it has reached 200kV, the beam current should become stable at ~103µA within a few minutes. If it is stable at this value, then it is OK to insert your sample, turn on the beam, and proceed using the microscope.

1.6.8 If it is not, please consult a member of staff.

1.6.9 To decrease the voltage from 200kV to 120kV:

1.6.10 Ensure that the beam is turned OFF.

1.6.11 In the High Voltage Control window, set a target voltage of 120kV, a step size of 1kV and a time step of 10sec.

1.6.12 Hit the [Start] button – this will automatically decrease the voltage from 200kV to 120kV.

1.6.13 Turn the beam on using the Filament [ON] button.

1.6.14 The beam should stabilize at ~xxxxxxµA.

12

2 What to do at the end of your microscope session

2.1 Ending your TEM session

The purpose of these steps is to leave the microscope in a suitable state for the next user. Please ensure that all steps are completed.

2.1.1 If you have used the digital camera, stop the live image acquisition and press F1 to lower the viewing screen.

2.1.2 Retract the CCD camera by unticking the Camera Inserted check box.

2.1.3 Ensure that the view and record settings are set to standard conditions.

2.1.3.1 View Mode – bin 4, User mode, 0.1 secs.

2.1.3.2 Record Mode – bin 1, User mode, 1.0 sec.

2.1.4 Ensure the microscope is in TEM mode.

2.1.5 Select Condenser Aperture 2.

2.1.6 Select Spot Size 2.

2.1.7 Select Alpha selector 2.

2.1.8 Select a Magnification of 200kx.

Note: These are optimal BF TEM operating conditions, so if you don’t change them you should still be in this set up, and the microscope is usually left it this configuration. This is mainly to ensure that carbon films are not blown apart when the beam is turned ON, and also these operating parameters allow one to obtain high resolution images. This selected magnification is to keep the lenses warm, ready for stable high resolution imaging, with less sample drift. It could be up to one hour (1hr) before the specimen becomes stable. Please do NOT leave the microscope in Low Mag mode.

13

2.2 Finding the beam 2.2.1 Centre the beam and expand it to cover the viewing screen.

2.2.2 Turn off the beam by pressing the BEAM button on the left hand control panel.

WAIT UNTIL THE BEAM IS COMPLETELY OFF BEFORE CONTINUING WITH THE NEXT STEP.

2.2.3 Ensure that Condenser Aperture 2 is inserted.

2.2.4 Remove the objective aperture (red dot selected).

2.2.5 Remove the selected area aperture (red dot selected).

2.2.6 Place the covers on the viewing screen and binoculars

2.2.7 Reset and remove the sample holder – see page 17.

2.2.8 Turn off the HT and run the ACD heating cycle – see page 13.

2.2.9 If necessary:- Convert all data and SAVE to your own storage devices.

2.2.10 Note: The CMM data storage area is volatile and not backed up, currently we accept no responsibility for YOUR data.

2.2.11 Turn off the computer monitors.

Important: Do not quit from any of the software, or shut down any of the computers.

14

3 ACD heater Note: At the end of the day, it is essential that the ACD heating cycle is started. Before the ACD heating cycle can be started, the HT should be turned down to 150kV. It is also recommended to turn off the High Voltage. 3.1 To turn off the HT: 3.1.1 If the High Voltage Control window is not

open, press the HT button in the top left corner of the left monitor – this will open the High Voltage Control window.

3.1.2 Turn the HT off by pressing the OFF button for the HT.

3.1.3 You will asked if you are sure you want to turn off the HT – answer YES.

3.1.4 The HT will now be turned off slowly – wait until it is off before doing anything else – The green HT button will become grey when the voltage is off.

Figure 8 High Voltage Control Window

Pressing the small HT button in the top left corner makes the High Voltage Control window appear. Pressing the HT OFF button turns off the HT causing the HT indicator (next to the voltage read out) to become grey. When the HT is on, the HT indicator is green. 3.2 To start the heating cycle: 3.2.1 Ensure that the plastic tube is pointing away from you, and then carefully insert the

ACD heater into the anti-contamination device (the hole where you pour the LN2).

Note: If the anti-contamination device is full of LN2 it may overflow or project out of the plastic tube when you insert the ACD heater, so be careful when inserting the ACD heater.

3.2.2 Plug the two pins into the socket on top of the anti-contamination device

3.2.3 On the left hand computer screen select ACD & Bake from the Maintenance menu

3.2.4 Make sure the ACD Heat tab is selected

3.2.5 Press ON. A series of valves will close and the vacuum gauge on the power supply cabinet at the back of the room will turn off, and the HT will be automatically switched OFF.

3.2.6 Turn the range selection knob on that vacuum gauge to the 10kV range – NOTE – at CMM UQ this step is optional.

15

Figure 9 Main vacuum gauge during ACD heating cycle.

Note: Range has been set to 10kV.

16

4 Inserting the sample holder 4.1 Sample insertion

Important: Failure to carry out this procedure carefully can significantly damage the microscope.

4.1.1 Load the sample into the holder (avoid touching the end of the holder or the ends of the tools that come into contact with the holder with bare hands).

4.1.2 Make sure the sample is held securely in the holder.

If using the standard sample holder, ensure the copper plate is correctly positioned in the recess and is holding the sample in position.

4.1.3 Check that the O-rings are clean.

If fibres are found on an O-ring, carefully remove them with your fingernail.

Do NOT use tweezers.

UNDER NO CIRCUMSTANCES should you wipe the O-ring with a tissue or any other material. Seek assistance from CMM Staff.

4.1.4 Insert the holder with the small guide pin positioned at the 9 o’clock. Guide the holder gently into the column until it comes to a stop. Push the end of the holder to ensure a good seal and release the sample holder, it should stay in position.

4.1.5 Try not to put any sideways or up/down pressure on the holder.

Note: Do NOT rotate the specimen holder at this time.

Figure 10 A schematic diagram of

the sample insertion process.

4.1.6 Change the goniometer switch over to PUMP.

4.1.7 Guide the holder gently into the column until it comes to a stop.

4.1.8 Try not to put any sideways or up/down pressure on the holder.

4.1.9 The SPECIMEN vacuum level will begin to drop from 252µAmps.

4.1.10 In the meantime fill the ACD with liquid nitrogen (LN2). Always wear PPE and be careful not to spill the liquid nitrogen (LN2).

4.1.11 Wait until the green light on the goniometer is lit and the SPECIMEN vacuum says VAC READY or the Specimen/PIG4 (Vacuum Window) value is ≤78µAmps.

17

4.1.12 To insert it into the column rotate the holder CLOCKWISE. 4.1.13 After ~10 degrees, the holder will move in ~1cm.

4.1.14 After a further ~80 degrees, it will be pulled into the column.

DO NOT LET GO!

4.1.15 Gently allow the sample holder to glide until it reaches a stop.

4.1.16 Check the vacuum level in the column using the ion gauge on the power supply at the back of the microscope in the alcove at the rear of the microscope room. The vacuum on the ion gauge must be below 2.5 x 10-5Pa and steady before the Filament can be turned on.

18

4.2 Sample removal

Important: Failure to carry out this procedure carefully can significantly damage the microscope.

4.2.1 Stop the live camera image (Press Stop View).

4.2.2 Untick the ‘Camera inserted’ box.

4.2.3 Turn off the beam by either pressing the BEAM button on the left hand control panel or selecting the FILAMENT button in the HT window.

4.2.4 Reset the sample holder to its initial position by double clicking on the Stage Neutral button in the top right hand corner of the left monitor (black square with white letters).

4.2.5 Press OK after it has initialized.

4.2.6 For removal of double-tilt holders – select the standard TEM holder and remove the double-tilt cable from the microscope connection point.

4.2.7 To remove the specimen holder, pull until it comes to a stop. Try to do this steadily and without placing any lateral or vertical pressure on the holder.

4.2.8 Now rotate the holder ~80 degrees ANTICLOCKWISE.

DO NOT PULL WHILE ROTATING THE HOLDER

4.2.9 Gently slide the holder out until it hits the next stop (~1cm).

4.2.10 Carefully rotate the holder the final ~10 degrees ANTICLOCKWISE.

Then WAIT!

YOU MUST NOT PULL ON THE HOLDER WHILE ROTATING OR YOU WILL PULL THE HOLDER OUT OF THE MICROSCOPE

which will cause the microscope to turn off and may cause damage.

4.2.11 Once the holder is fully rotated, change the goniometer switch to AIR.

4.2.12 Wait for the pressure in the goniometer to reach air pressure. SPECIMEN vacuum display will change to AIR and vacuum level will rise. After ~30s valves V21 and V16 will close, indicating you that it is now safe to remove the holder.

4.2.13 The holder should now glide out easily, as it should not be under vacuum at all.

19

Figure 11 Schematic diagram of sample holder insertion and removal procedure.

20

5 Basic alignment 5.1 Basic alignment

The following alignments should be carried out at the start of each microscope session. The alignments 5.1.8-5.1.10 should be repeated whenever the operating voltage or operating mode (TEM, EDS, NBD, CBD) is changed, and whenever the Spot Size, Alpha-selector or Condenser Aperture size are changed.

5.1.1 Insert Condenser Aperture 2.

5.1.2 Turn on the beam by pressing the FILAMENT button in the HT window.

5.1.3 Find the electron beam – see page 20 – and your sample.

5.1.4 To carry out the alignments, set the magnification to ~20kx.

5.1.5 Centre the electron beam (using the beam SHIFT X and Y controls).

5.1.6 Find a recognizable feature in your sample.

5.1.7 Press the STD FOCUS button on the right hand control panel.

5.1.8 Press the IMAGE WOBB X (or Y) button on the right hand control panel.

5.1.9 Adjust the Z-HEIGHT of the sample until the image movement is minimized.

This positions the sample at the eucentric height. This is required as it firstly makes sample tilt easier, and secondly ensures that the scale bar is correct.

5.1.10 Turn off the IMAGE WOBB X.

5.1.11 Choose which CONDENSER APERTURE size to use (the optimal setting is to use the second largest aperture).

5.1.12 Align the CONDENSER APERTURE – see page 21.

5.1.13 Correct the CONDENSER STIGMATION – see page 22.

5.1.14 Correct the BEAM TILT (often referred to as the VOLTAGE CENTRE) – see page 23.

5.1.15 Insert and align the OBJECTIVE APERTURE – see page 24.

5.1.16 If necessary, correct the OBJECTIVE STIGMATION.

5.1.17 Press the NEUTRAL button on the LH-panel, or set the OBJECTIVE STIGMATOR X & Y values you used (and recorded last time for your sample at your preferred magnification.

Note: These values may change depending upon changes made to you sample.

Note: These values are dependent upon the magnification.

21

5.2 Finding the electron beam If the beam does not appear on the screen, the sample or grid might be blocking the beam. If the beam is still not visible upon the viewing screen then try the following: 5.2.1 Press the LOW MAG button.

5.2.2 Increase the beam size by turning the BRIGHTNESS knob clockwise until it beeps – you may need to recentre the beam [SHIFT X] and or [SHIFT Y].

5.2.3 You should remove the OBJECTIVE APERTURE.

5.2.4 You may need to remove the CONDENSER APERTURE.

5.2.5 You may need to change from SPOT SIZE 3 to SPOT SIZE 1.

5.2.6 Move the sample [TRACKBALL] until a hole (or the required thin area) appears in the middle of the screen.

5.2.7 You should insert the OBJECTIVE APERTURE.

5.2.8 Then move your area interest to the centre of the aperture. [TRACKBALL].

5.2.9 Then remove the OBJECTIVE APERTURE.

5.2.10 You SHOULD reinsert the CONDENSER APERTURE to avoid sample damage.

5.2.11 Return to higher magnification by pressing the [MAG1] button.

5.2.12 Adjust the [BRIGHTNESS] knob to obtain a suitable image).

Note: If your sample is beam-sensitive, e.g. biological, insert an OBJECTIVE APERTURE BEFORE pressing [MAG1].

5.2.13 Centre the beam using the [SHIFT X] and [SHIFT Y] control knobs.

22

5.3 Aligning the CONDENSER APERTURE Note: The optimal setting on this microscope for basic imaging at 200kV is to

use the second largest CONDENSER APERTURE (CA2). The CONDENSOR APERTURE size can be selected by turning the Aperture size knob on the front of the aperture control (marked with the red and white dots in Figure 11). The aperture can be moved using the Aperture translation knobs on the front and side (Figure 11).

Figure 12 CONDENSOR APERTURE (CA) control mechanism.

The procedure for aligning the CONDENSOR APERTURE is as follows:

5.3.1 Move off your sample to prevent electron beam damage.

5.3.2 Set the magnification to ~20kx.

5.3.3 Select the size of CONDENSOR APERTURE you want to use.

5.3.4 Make the electron beam small by adjusting the [BRIGHTNESS] control.

Note: Do not make the beam too small as it will burn a hole in your sample!

5.3.5 Centre the electron beam on the screen using the [SHIFT X] and [SHIFT Y] control knobs.

5.3.6 Enlarge the electron beam by turning the [BRIGHTNESS] control clockwise. 5.3.7 If the CONDENSOR APERTURE is correctly aligned, the beam should expand

concentrically about the centre of the screen.

5.3.8 If the beam does not expand concentrically about the centre, then move the CONDENSOR APERTURE (CA) translation knobs to centre the beam.

5.3.9 Repeat steps 4-8 until the beam expands about the centre of the screen.

Aperture size knob

Aperture translation knobs

Figure 13 Concentric CONDENSER swing using the [BRIGHTNESS] knob.

23

5.4 Correcting the CONDENSER STIGMATION

The beam should be reasonably symmetrical (but perhaps a little triangular) when the [BRIGHTNESS] control is adjusted to make the beam small. If the electron beam looks distorted on the screen you may need to adjust the CONDENSER STIGMATORS. To check if the CONDENSER STIGMATION is correct: 5.4.1 Use the [BRIGHTNESS] control to make the electron beam small.

5.4.2 Adjust the size of the beam by turning the BRIGHTNESS control clockwise or anticlockwise from the smallest point.

5.4.3 The shape of the beam should remain circular for both the clockwise and anticlockwise directions. If the shape is elliptical for either of the two directions, the CONDENSER STIGMATION is wrong.

5.4.4 To correct the CONDENSER STIGMATION, select [COND STIG] button from the left-hand control panel.

5.4.5 Use the [DEF/STIG X] and [DEF/STIG Y] knobs to adjust the shape of the beam.

The control can be changed from coarse to fine by pressing the [CRS] button next to the [DEF/STIG X] knob.

5.4.6 Continue to make adjustments to the shape of the beam until the beam shape is circular as the [BRIGHTNESS] is adjusted either clockwise or anticlockwise from the smallest beam.

5.4.7 Turn off [COND STIG] by pressing the button again (the light in the button will go off).

Note: The CONDENSER APERTURE alignment and CONDENSER

STIMATION will need to be repeated if one or more or the following settings are changed: CONDENSER APERTURE size, SPOT size, or ALPHA setting.

24

5.5 Correcting the beam tilt (voltage centre) To check the voltage centre: 5.5.1 Find your sample again, usually at higher magnifications, e.g. >250kx.

5.5.2 Ensure that the sample is focused at the eucentric height.

5.5.3 Centre the beam using the beam [SHIFT X] and [SHIFT Y] knobs.

5.5.4 Spread the beam by turning the [BRIGHTNESS] knob clockwise until the beam fills the viewing screen.

5.5.5 Centre a recognisable feature by moving the sample with the {TRACKBALL].

5.5.6 Press the [HT WOBB] button (on the right hand control panel).

5.5.7 Select [BRIGHT TILT] on the left hand control panel and adjust the [DEF/STIG X] and DEF/STIG Y] knobs until image movement is minimized.

5.5.8 Turn off the [HT WOBB] button (the light will go off).

5.5.9 Turn off the [BRIGHT TILT] button (the light will go off).

25

5.6 Aligning the OBJECTIVE APERTURE Note: If the OBJECTIVE APERTURE is badly aligned, then the image quality will

be reduced, the OBJECTIVE STIGMATION will be incorrect, and the OBJECTIVE APERTURE may block the field of view.

This procedure should be repeated every time the OBJECTIVE APERTURE is inserted or a different OBJECTIVE APERTURE size is selected. To align the OBJECTIVE APERTURE: 5.6.1 Insert the SELECTED AREA APERTURE (SAA – the bottom one) by turning the aperture

mechanism to the largest white spot

5.6.2 Roughly centre the SELECTED AREA APERTURE in the image plane.

5.6.3 Press [SA DIFF] on the right hand control panel to obtain an electron diffraction pattern.

5.6.4 Adjust the [DIFF FOCUS] (right hand panel) to make the centre spot in the diffraction pattern as small as possible. The [CRS] button may be selected/deselected as required.

5.6.5 Insert the OBJECTIVE APERTURE (choosing the aperture size you want) using the aperture control – RED means no aperture, the white circles represent the different aperture sizes.

5.6.6 Adjust the position of the SELECTED AREA APERTURE using the arrows on the left hand panel until it is centered on the middle of the diffraction pattern.

5.6.7 Press [MAG1] to view the image – you may need to make a final small adjustment of the aperture while looking at the image.

5.6.8 Remove the SELECTED AREA APERTURE – aperture position at the RED spot.

Note: Sometimes it will be difficult to see the edge of the aperture in the diffraction

pattern. It may be easier to see the aperture if you adjust the BRIGHTNESS to increase the intensity of the diffraction pattern. Be careful not to damage your sample.

26

6 Using the digital camera

6.1 Digital camera operation

6.1.1 Align the microscope.

6.1.2 Obtain a focused image at the required magnification on the viewing screen.

Note: The field of view of the camera is approx 2.7mm wide and 2mm high.

6.1.3 Press [F1] on the right hand control panel to raise the viewing screen.

6.1.4 Insert the digital camera by ticking the box next to CAMERA INSERTED on the right hand monitor.

6.1.5 On the right hand computer monitor, check that the camera is in Search mode and start the live image view by hitting START VIEW – if the exposure time is ~0.1s you will get around 14 frame/s readout.

6.1.6 Adjust the brightness, focus, magnification, etc. to obtain the desired image.

6.1.7 The colour bar below the START ACQUIRE button can be used to set the brightness. The black box indicates the intensity range in the image and the green area indicates an optimum intensity range.

6.1.8 Press START ACQUIRE to obtain your final image. This will interrupt the continuous acquisition and acquire a single, high quality image. If you select AUTO from the EXPOSURE MODE box the software will try to optimize the exposure time. Alternatively, you can select USER and select your own exposure time.

6.1.9 To see the image on the viewing screen, press F1 to lower the viewing screen.

6.1.10 You can leave the live image acquisition running if you want to so that when you next raise the viewing screen you will see the image on the digital camera. However, if you are not planning to use the camera for a while you should stop the live image by pressing STOP VIEW. This is handy to see if (unacceptable) drift occurred during recording of the micrograph.

Note: All final images should be acquired using the Start Acquire option as this optimizes image quality and ensures correct calibration.

6.2 To save the digital image

Important: All data should be saved in ‘Gatan format .dm3’ by choosing Save or Save As from the File menu. Each user has their own directory on the S: drive. Save the data onto the S: drive into your directory (you can create whatever subdirectories within your directory as required).

Data can also be saved in other image formats such as tiff, gif, etc. Always make sure that you first save your data in Gatan format before trying to save it in a different format. It is best to store these types of formats using Save Display As …. Or use the Batch Covert from the File menu item at the

27

conclusion of your session. This will be required if you do NOT have access to Digital Micrograph software.

28

6.3 Recording a Diffraction Pattern (DP) on the Gatan Slow-scan CCD

Note: Please carefully follow these instructions to reduce the risk of burning the Slow-scan CCD Camera

6.3.1 Select Spot Size 2.

6.3.2 Select SA DIFF.

6.3.3 Select 20cm Camera Length.

6.3.4 Insert the Objective Aperture (OA).

6.3.5 Focus the OA until sharp – use the DIFF FOCUS knob.

6.3.6 Remove the OA.

6.3.7 Focus the DP to the smallest spot using the BRIGHTNESS knob

6.3.8 Correct Intermediate Astigmatism.

6.3.9 Insert the Beam Stop.

6.3.10 Select Spot Size 2. It should be difficult to see the Diffraction Pattern. 6.3.11 Lift the Viewing Screen [F1].

6.3.12 Expose the CCD at minimal exposure times.

6.3.13 Lower the Viewing Screen and check for dark spots remaining on the CCD

6.3.14 Increase exposure time until the desired time is achieved – using care not to saturate the CCD camera.

29

6.4 To acquire a gain reference image

When using the digital camera, you may notice features in your images, small dark or bright patches, which do not move when you move the sample. These are caused by variations in the response of the CCD camera.

This problem can be overcome by acquiring a new gain reference image i.e. an image acquired with uniform intensity across the filed of view that the software uses to correct for gain variations in the camera. This will remove any artifacts coming from the response of the camera.

The response of the Orius camera depends on the voltage at which you are operating the microscope. If the last gain reference was acquired at 120kV, features from the camera will appear in images acquired at 200kV (and vice versa).

If you think you can see the effects of the camera in your images, you should acquire a new ‘gain reference’ image.

To acquire a new reference image:

6.4.1 Find a hole in the sample. This is important because if you are on the sample when you acquire the gain reference image, a picture of your sample will appear in all future images acquired on the camera!

6.4.2 Choose a magnification that makes the hole bigger than the field of view of the camera

6.4.3 Spread the beam so that it illuminates the entire camera

6.4.4 From the Camera menu in Digital Micrograph select Prepare gain reference

6.4.5 Press OK (or Yes) in response to each of the questions (do not change any settings)

6.4.6 The gain reference image will automatically be acquired and stored. It will take a few minutes. A message will appear on the screen when it is finished. Select OK

6.4.7 If the beam is too bright or not bright enough, the computer will let you know. Simply adjust the BRIGHTNESS while ensuring the beam still covers the entire camera

30

6.5 Image intensity and x-rays

X-rays will occasionally hit the camera during an acquisition causing a very high or low intensity to be recorded in a particular pixel. The contrast and brightness in the displayed image can be adjusted using the histogram on the LHS of the Digital Micrograph display or the controls beneath the histogram.

X-rays can be removed permanently from recorded images by selecting Point Blemish : Remove All from the Camera menu in Digital Micrograph.

X-rays will create problems with the automated image alignment process. If you think this has happened, remove the x-rays from the three images and repeat the alignment (either using the cross correlation or manually) and then compute a new elemental map.

31

7 Selected area electron diffraction 7.1 Aligning the Selected Area Aperture 7.1.1 Align the microscope as usual (eucentric height, focus, Condenser Aperture, beam tilt,

Objective Aperture).

7.1.2 Press F1 to go to the digital camera.

7.1.3 Insert the camera and start the live image.

7.1.4 Find the area of interest and centre it on the digital camera.

7.1.5 Acquire an image of the sample for future reference.

7.1.6 Insert a Selected Area Aperture and centre it on the screen – choose the size of aperture that selects the feature of interest (smaller apertures will give lower intensity diffraction patterns).

7.1.7 Choose a magnification that allows you to position the feature and Selected Area Aperture easily – the choice of magnification does not have any effect on the diffraction pattern.

7.1.8 Note: You need to be at 8kx magnification or above to do SAD.

7.1.9 Acquire an image with the Selected Area Aperture inserted so that you know exactly where your diffraction pattern comes from.

7.1.10 Spread the beam by turning the Brightness control clockwise until you hear a beep – this creates a parallel beam of electrons.

7.1.11 Press F1 to lower the viewing screen – this is important to avoid damaging the camera when you first go to diffraction mode.

7.1.12 Press the DIFF button on the right-hand control panel to see the diffraction pattern.

7.1.13 Remove the Objective Aperture as it is blocking out the edges of the diffraction pattern.

7.1.14 Choose the camera length (magnification of the pattern) using the MAG/CAM L control on the right-hand control panel.

7.1.15 Use the DIFF FOCUS control on the right-hand control panel to make the centre spot of the diffraction pattern as sharp as possible.

7.1.16 To centre the diffraction pattern press the Projector Lens Alignment (PLA) button on the left-hand control panel and use the DEF/STIG X and Y controls to centre the Diffraction Pattern.

7.1.17 Insert the beam stop and position it to block out the bright, centre spot of the Diffraction Pattern

7.1.18 Press F1 to go to the digital camera and restart the live image.

7.1.19 If necessary, make minor adjustments to the centering of the diffraction pattern, the position of the beam stop and the diffraction focus – be careful not to expose the camera to the bright, centre spot of the Diffraction Pattern for more than a few seconds.

7.1.20 If you want to make major changes to the positioning and focus, or want to change the camera length, press F1 to put the viewing screen down and make the adjustments on the fluorescent screen.

7.1.21 To record the pattern, use Record mode on the camera. Set the exposure time manually.

7.1.22 Depending on the intensities in the Diffraction Pattern you may need to set the exposure to anything between ~1s to ~20-30s to get a good quality pattern. Try short times initially and

32

check what spot intensities this gives. Make sure you are not saturating the camera – keep the max intensity below 16,384 counts.

7.1.23 Once you have decided on the exposure time, click on the tools button in the bottom right-hand corner of the Record window in Digital Micrograph (the picture of the hammer and spanner)

7.1.24 Set the acquisition to average multiple frames – we typically use 5-10 frames to get publication quality data.

7.1.25 Close the tools window and acquire the diffraction pattern.

7.1.26 To get Diffraction Patterns from a new feature of interest, go back to image mode (MAG1), remove the Selected Area Aperture and the beam stop, insert the Objective Aperture and adjust the brightness.

7.1.27 From the tools window for the camera, set it back to single frame acquisition.

7.1.28 Then repeat the whole procedure on the new area of the sample.

33

8 STEM imaging 8.1 Selecting STEM Mode 8.1.1 Align the microscope as usual (eucentric height, focus, Condenser Aperture, beam tilt,

Objective Aperture)

34

8.2 Aligning the STEM 8.2.1 Align the microscope as usual (eucentric height, focus, Condenser Aperture, beam tilt,

Objective Aperture)

8.2.2 Move to an unimportant part of your sample, preferably an area with lots of amorphous material, e.g. carbon support film

8.2.3 Physically rotate trackball control box 90 degrees clockwise so that cable is at the top.

8.2.4 In the JEOL software (left-hand monitor), go to the Dialogue menu and select ASID Control – a new window will open.

8.2.5 Start the JEOL Simple Image Viewer program by double clicking on the icon on the desktop (left-hand monitor).

8.2.6 In the ASID Control window, select ASID mode.

8.2.7 Set the Camera Length to 20cm.

8.2.8 Insert the BF detector and obtain an image – adjust the contrast and brightness accordingly.

8.2.9 In the JEOL Simple Image Viewer, select SPOT mode.

8.2.10 Click on the image to position the spot on an amorphous region of the sample.

8.2.11 Remove the Objective apertures – set to the red dot.

8.2.12 Select PLA on the left-hand control panel and use the DEF X and Y controls to centre the beam on the viewing screen.

8.2.13 In the JEOL Simple Image Viewer, select SCAN mode.

8.2.14 Insert the required STEM detector (BF or HAADF).

8.2.15 From the ASID Control window select the appropriate detector.

8.2.16 For BF STEM, use a camera length between 8cm and 40cm, use the PLA and DEF controls to maximize the signal on the detector, and insert an objective aperture to get more contrast – the aperture should be centered by maximizing the intensity in the image.

8.2.17 For HAADF STEM, use a camera length between HAADF1 and HAADF5 (HAADF5 is the shortest and best for Z-contrast imaging), use the PLA and DEF controls to centre the beam in the middle of the detector, and remove any objective aperture as this will block the signal hitting the detector.

8.2.18 Place the screen cover over the viewing screen to block out the room lights.

8.2.19 Adjust the magnification, focus, brightness and contrast to get the desired image.

8.2.20 Select the appropriate scan rate and pixel resolution (Scan rate 4 is the slowest and gives the best images) – changing from Normal to Fine scan will also improve the images, as well as increasing the number of acquisition pixels, e.g. 512 x 512 to 1024 x 1024 for example.

8.2.21 Press the ‘camera button’ to acquire the final image and then save the image.

35

8.3 To return to TEM mode: 8.3.1 In ASID Control, select no detector – the None option

8.3.2 Insert an objective aperture

8.3.3 Retract the STEM detector

8.3.4 In ASID Control, select TEM mode

8.3.5 Realign the condenser aperture – usually select the second condenser aperture at this point

8.3.6 Close the JEOL Simple Image Viewer and ASID Control windows

36

9 Performing EDS

This can be performed in a number of ways. In TEM mode, EDS mode and STEM mode.

In TEM mode, care will need to be taken not to flood the EDS detector with electrons and X-rays with high energy (up to 200kV).

A hard X-ray aperture is available for those who wish to perform X-ray analysis in TEM mode, however, this method is not recommended by CMM Staff. These 200kV electrons hit the metal cover (stainless steel) of the EDS detector and produce X-rays with energies up to 200kV as a continuum. These X-rays enter the EDS crystal and produce large numbers of electron-hole pairs which increase the dead time of the EDS detector. This slows counting and hence analysis time.

A better way to perform TEM microanalysis is to select the EDS mode (or NBD mode). This produces a focused probe rather than the spread electron beam required for imaging. These probes are better defined within the condenser lenses and produce far less scattered electrons and X-rays.

Alternatively STEM EDS map be performed. This has the advantage of scanning the sample without stopping the probe – and may reduce electron beam damage. Point, line and area X-ray analysis are possible.

37

10 Troubleshooting Problem: All of my images from the digital camera contain features that do not move

when I move the sample.

Solution: You should acquire a new gain reference image for that camera. This will remove artifacts coming from the response of the camera.

Problem: Digital Micrograph has given me an error message saying that it cannot find the ‘dark reference image’.

Solution: The software has run out of memory. Quit from Digital Micrograph and restart the software by double clicking on the Digital Micrograph icon on the desktop. Do not restart any of the other software.

Problem: I cannot turn on the beam.

Solution: Check that the HT is turned on (page 10) and that your sample is inserted (page 17).

Problem: There is an error message telling me that there is a problem with the goniometer motor control.

Solution: You should have reset the sample holder to within ±100µm before hitting Stage Neutral. Now that the error has occurred, go and find a member of staff and do nothing else.

Problem: When I go to STEM mode I cannot find the beam.

Solution: Check that you have the correct set of alignments loaded

Check that you have selected a detector, either SEI or HAADF.

38

Appendix 1: Microscope Settings at 200kV

Condenser Aperture settings (um): 150 70 50 10

Condenser Spot Size α

Aperture

Normal TEM 2 2 2

Better HRTEM 3 3 2 but exposure time increases

Some clients have found the following settings useful:

Most TEM BF Imaging 2 2 2 bin 1

Wang 3 1 2 bin 2

Yang 2 3 2 bin 2

Diffraction Patterns 2 5 2 bin 2

39

Appendix 2: Network Settings

IP Address: 172.23.79.21

40

The JED2200 EDS.

Settings:

STEM mode is preferable to TEM Mode.

EDS mode is preferable to TEM Mode.

Tilt the sample holder to ~20° optimum but 15°-25° is still better than 0°.

Note:

The EDS detector is fabricated from stainless steel.

Therefore it contains Fe plus other minor metals.

The crystal is Li-doped Silicon [Si(Li) EDS detector].

There is a silicon dead layer composed of silica (SiO2).

There is a gold contact (Au).

The thin window is a proprietary plastic film (C, H, O) with perhaps other elements present.

This thin window is supported on a Ni slot grid with a striped spacing (Ni).

The detector is protected from light and infra-red by an aluminium coating on the thin window (Al).

The pole-piece is constructed from brass and thus copper is a major component (Cu).

Your grid is most likely copper (Cu).

The planchette is chromium-plated brass (Cr, Cu).

Some of these elements may interfere or appear in your spectra.

Please be careful with qualitative analysis.

Sometimes strong NdSm rare-earth magnets are used to deflect back-scattered electrons (BSE), thus insertion of the EDS distorts the image and is not recommended for acquiring high quality images.

Si(Li)

Dead layer

Au contact

RE magnet

Ni Grid

Collimator

Stainless Steel Housing