Practical Electron Microscopy and Database

• Open the User Interface (UI) through the Windows quick launch toolbar or the Start menu.
• Navigate to Workset → Setup → FEG Control (User). Verify that the FEG Control parameters are configured as follows: HT = 200kV, Extraction Voltage = 3800V, and Gun Lens (GL) = 4. If you need to adjust the extraction voltage, input the desired value and then press the Enter button located next to the field.
• Navigate to Workset → Setup → Vacuumto confirm the vacuum levels in the system:
  • The gun vacuum should always read 1.
  • The column vacuum should be below 20 log or <10^-7 Torr).
  • The Col. Valves Closed button is illuminated yellow, indicating that the valves are closed. The column valves must remain closed if the column vacuum exceeds 20 log or when the microscope is idle. Opening the column valves under high vacuum conditions can severely damage the field emission gun.
• Launch the digital camera control software, e.g. TIA.

• Magnification: 2,000x - 5,600x.
• Spot size: 3–4.
• C1 aperture: 2000 mm.
• C2 aperture: 100 mm.

• Users interact with the TEM Server—and consequently the microscope—through the User Interface (UI), which serves as a secondary application layer. The UI enables access to essential microscope functions, with control panel knobs and buttons designed to simulate traditional TEM controls. In practice, these controls interface with the computer, which manages all microscope operations.
• The UI includes various panels and windows. The central area is allocated for supplementary programs such as TIA and others. The lower section of the user interface primarily displays information panels, such as the Message panel, Status panel showing current microscope parameters, and others. [1] The vertical section of the UI includes multiple control panels for managing various microscope parameters. Each control panel includes a collection of controls associated with a primary microscope function, such as Field Emission Gun (FEG) control, CompuStage (stage control), camera control, and more. All of these control panels are grouped into a Workset and can be accessed by selecting the corresponding tab at the top. Drop-downs are used to expand the list of available options or choices on certain control panels. The Workset serves as an organizer for commonly used microscope controls and facilitates access to the Control panels. A complete list of available microscope controls can be accessed through the Popup panel located at the bottom-right corner of the UI. The Popup panel allows users to open Control panels (alongside the Workset) and manage items in the Workset, including adding, removing, or renaming them.
  

  Figure 0364a. Microscope User Interface. Adapted from [1]

  F1 function key: You can press the F1 function key to access the UI help pages from any Control panel. Simply position the cursor over a specific item and press F1, and the corresponding help pages for that item or Control panel will appear automatically.

  • The Vacuum Control panel displays the vacuum levels, e.g. listed in Table 0364, in various sections of the microscope, such as the gun and the column. [2] The column valves should remain closed when the microscope is not in use or if the vacuum reading in the column exceeds 20 Log or 10^-7 Torr. A yellow button indicates that the valves are currently closed, while a gray button signifies that the function or device is not active. When the "Column Valves Closed" button appears yellow, the valves are securely closed. Clicking this button changes its color to gray, indicating that the column valves have been opened.

    Table 0364. Typical values (log) for the FEI TEM vacuum system.[1-12]

    Gun or Accelerator	IGP3	1
    Column	IGP1	1-6
    Detection limit		13
    Buffer tank		53
    Camera	P3	20
    Backing line		88
    Liquid nitrogen	If applicable	> 10%

    

    Figure 0364b. Vacuum Status. [1, 6]

    This control panel below can be accessed exclusively through the Popup panel located in the bottom-right corner of the user interface. Various colors indicate the quality of the vacuum: cyan signifies an optimal vacuum level for the specific component associated with that color.

    • GP – Ion-Getter Pump.
    • TMP – Turbo-Molecular Pump.
    • Pir, Pen – vacuum gauges.
    • V - valves
    .
    

    

  • At 200kV, the extraction voltage is set to 3800V, and the gun lens is adjusted to 4 (within the range of 3 to 6). A yellow Operate button signifies that the FEG is active, while a yellow High Tension button indicates that the high voltage is enabled.
    

• EDS acquisition and analysis (Esprit: Bruker spectrometer system, and Velox)
.
• The level of control varies based on the user's position within FEI's user-account hierarchy: factory → service → supervisor → user. While users have sufficient control to operate the microscope across all available modalities, their ability to alter critical TF20 settings or adjustments is restricted.
• Each user has their own standard Windows account secured with a password.
• Each new account adopts the supervisor settings active at the time of its creation. These settings can later be modified and saved by the user within their account.
• Users can access and apply settings from others, including those of the supervisor, highlighting the benefits of a digital interface.

• Intensity (brightness).
• Magnification.
• Focus.
• Focus-step.
• Dark field.
• Diffraction.
• Wobbler.
• Stage X-Y joystick.
• Beam shift trackball.
• Z-height.
• Programmable buttons. The system includes a set of user-defined programmable buttons that operate as switches. These buttons can be customized to perform frequently used functions, such as adjusting the screen lift or spotsize.
• Multifunction knobs X and Y (MF).
  • The default function of the MF knobs is "user beam shift X & Y."
  • They can also be linked to other functions, such as beam tilt, astigmatism correction, and more.
  • The current role of the MF knobs is displayed in the UI's “Binding” window.
  • MF knobs and programmable buttons can be assigned to various microscope functions, offering versatility and ease of operation.

Figure 0364d. FEI Microscope Control Panels. Adapted from [1]

• The beam should cover the circle evenly.
• If not, spread the beam slightly beyond the outer circle on the fluorescent screen. Access the aperture control panel (Workset E > Setup E > Motorized Apertures). Check the "Center" box next to "Condenser 2" or click on “Adjust” at "Condenser 2" depending on the specific microscope model.. [6] Use the MF knobs to adjust the position of the C2 aperture. Proper alignment is achieved when the beam spreads evenly around the center of the screen.[9]

• Choose "Condenser" (the button will highlight in yellow). [11]

Use the “Multifunction” knobs (both controls pads) to make the beam round; select “None” when finished.

• After each alignment, click “Done” in the Direct Alignments window to reserve the current Gun tilt conditions.
• Gun Tilt (Optional). Select Gun Tilt in the Direct Alignments menu. Use MF to adjust the beam intensity to its maximum. Then, click the Done button.
  • Press L3 (left panel) or R3 (right panel) to select illumination Spot Size 3.
  • If the beam is off-center, go to Gun Shift in the next step, and use the MF-X and MF-Y knobs to adjust the beam to the center before resuming Gun Tilt alignment.
  • Adjust MF-X and MF-Y to maximize beam Current.
• Gun Shift.
  • Configure the programmable buttons L3 and R3 for “+ spot size” and “- spot size,” respectively. Adjust the spot size to 3 using these buttons. Condense the beam and select Gun Shift. Center the beam on the screen using the MF knobs. Switch to spot size 9 using the R3 button, condense the beam, and select Align Beam Shift. Again, use the MF knobs to center the beam. Repeat the process until the beam is centered for both spot sizes 3 and 9.
  • Repeat the steps above until both spot sizes beams are centered.
  • Center the other spot sizes in between (4 – 8) using Gun Shift.
• Beam Tilt (X/Y) (or called condenser deflector balancing).
  • Adjust the microscope to a high magnification (e.g. 500,000x) and locate an empty specimen area.
  • Select "Beam tilt pp X." The beam will start to wobble. Adjust the MF knobs to eliminate the wobbling, ensuring the beam remains stationary at the center of the screen, namely, make the beams overlap. Once aligned, click the "Done" button. Next, choose "Beam tilt pp Y" in the Direct Alignments menu and repeat the same procedure to align the Y pivot points.
• Beam Shift. Select Beam Shift, and use the MF knobs to align the beam to the center of the screen. Ensure the procedure is completed by clicking the Done button.
• Rotation Center.
  • Set the microscope at a high magnification (e.g. 500,000x).
  • Re-center the beam on the screen using the trackball.
  • Align the sample using a visible feature as a reference.
  • Expand the beam to illuminate the entire screen area.
  • In the Direct Alignments menu, choose the Rotation Center Alignment option. The feature's image will begin shifting; adjust the movement using the MF knobs to minimize the image movement. Once alignment is complete, click the Done button.
  • Employ high magnification for enhanced precision.
• Coma-free Pivot Point X and Y.
  • Adjust the microscope to a high magnification, such as 500,000x, and identify a reference object.
  • Converge the beam and adjust the MF-X and MF-Y knobs to make the beams overlap.
• Coma-free Alignment X and Y. [9]

  

  • Lift the fluorescent screen and activate the camera view on an amorphous specimen area at approximately 500,000x magnification.
  • Activate the live FFT and adjust the microscope focus until the ring patterns become visible (see page1965).
  • Turn the MF-X and MF-Y knobs to maintain the size and shape of the ring patterns.
• Astigmatism. [4]
  • Check and correct Monochromator Tune if needed.
  • Select the Stigmators option in the Alignments user interface.
  • Choose the Condenser (LM TEM) option, then balance the Stigmators by shifting the beam to the center from Step 1 to 3 (by clicking the arrows) so that we can ensure the beam is centered to prevent it from shifting while adjusting the Stigmators. Then, adjust the stigmator in Step 4. Here, we need to use the multifunction (MF) knobs to perform the correction until it forms a circle.

  

  • Do the same thing for Condenser (LM Probe).
  • Do the same thing for Condenser (µP TEM) - microprobe TEM.
  • Do the same thing for Condenser (µP Probe) - microprobe probe mode.
  • Do the same thing for Condenser (nP TEM) - nanoprobe TEM.
  • Do the same thing for Condenser (nP Probe) - nanoprobe Probe.
  • Do the same thing for Condenser (Lorentz TEM).
  • Do the same thing for Condenser (Lorentz Probe).
  • Do the same thing for Objective. Use FFT to check the stigmation. Ensure the granularity in a high-magnification image appears isotropic—using the CCD and live FFT for the best results.

  

  • Do the same thing for Objective 3fdd.
  • Do the same thing for Diffraction. Adjust to make the central spot in the defocused diffraction pattern circular.
  • Save the new alignment file.

• Ensure the beam is centered on the viewing screen and expanded clockwise from the crossover point to form a circle in a proper size on the viewing screen.
• Press the "Diffraction" button to switch to diffraction mode; the diffraction pattern will appear on the viewing screen. Adjust the camera length as needed using the "Magnification" knob.
• Position the focusing screen in the beam path, then observe the diffraction pattern through the binoculars. If the diffraction pattern is not centered on the focusing screen, adjust it using the “Multifunction” knobs.
• Select the desired objective aperture; aperture 4 is recommended for bright-field imaging, while aperture 2 is optimal for high-resolution imaging.
• Align the objective aperture with the direct beam using the aperture shifting knobs.
• Choose the "Diffraction" button to switch back to TEM mode.
• Re-center the beam using the trackball.

To manage (add, delete, and modify) alignment files, you must log in using either a supervisor or service account. However, normal users can have access to Direct Alignments shown above. And, you can backup the alignment files, and rename the backup files with alignment dates. If alignment files are copied into the Alg folder, they will not appear on the user panel right away. To make them visible on the panel, the server must be restarted.

• In Microscope Control, select the Camera tab; navigate down to the “Stigmator” control panel and select “Objective” (the button will turn yellow).
• Use the “Multifunction” knobs to adjust the live FFT so the rings are round (see page1965).
• Click “None” to save.

• The TF20 holders are more sensitive and prone to damage.
• Inspect the O-ring for any signs of cracks or the presence of dust.
• Identify the small opening at the bottom of the clamp.
• Place the tool (pin for lifting sample clamp [9]) into the hole and gently raise the clamp to a vertical position, ensuring it is securely held in place. Avoid using excessive force.

  

• With the clamp in the vertical position, insert the specimen into the carrier.
• Ensure it is properly centered and gradually lower the clamp into the closed position. Ensure the clamp is fully closed before removing the tool from the hole. The specimen should be positioned with the sample face downward, as the holder rotates approximately 140 degrees during insertion into the column.

• The pin is not properly aligned with 'Close.' The red arrow below shows the correct alignment of the pin to the holder stage when inserting the holder as shown in Figure 0364f. (a).
• The holder has not been pushed into the column with proper pressure after it was inserted.

(a)	(b)	(c)	(d)

• Remove the liquid nitrogen dewar from the cold trap.
• Open the Vacuum tab in the Workset, expand the flap-out menu, and click the Cryo Cycle On button. The TMP will begin operating, and the Cryo Cycle On button will turn yellow.