SEM Instructions:

JEOL 5800 LV


Abbreviations, Terms, & Definitions:

Backscattered electrons = primary electrons which have bounced off sample surface or are emitted from moderate sample/substrate depth. Energy in kV. Resolution less than with SE.

BE = backscattered electron(s)

BEI = backscattered electron imaging

CCW = counter clockwise

COMPO = composition mode in BEI. Generates compositional map of sample

CW = clockwise

EDS = energy dispersive spectrometry (usually X-ray)

Emission current = load current, the current being emitted from the gun (in A)

Exposure marker = contrast/brightness scale observed when any scanning speed button is pushed twice

HT = high tension

HV = high vacuum

JEOL = Japan Electron Optics Laboratory

LC = load current

LCD = liquid crystal display

LV = low vacuum

OL = objective lens

Orifice = differential pumping aperture

Primary electrons = electron beam

SE = secondary electron(s)

Secondary electrons = electrons emitted from shallow sample depth. Energy in eV. Greatest spatial resolution (covers smallest area above sample).

SEI = secondary electron imaging

SEM = scanning electron microscope

Shadow = BEI feature which allow some topography to be seen during COMPO analysis

Spot size = probe size = probe current = beam size (diameter)

TOPO = topographic mode in BEI. Generates topographic map of sample

WD = distance from lens to sample surface as determined by focusing on sample

X-rays = emitted from greatest sample/substrate depth. Least spatial resolution.

Z = Distance from lens to the top of the sample holder

Maintenance chores:

1. Change filament when it burns out

2. Maintain water level in chiller (above white intake hose)

3. Maintain water temperature in chiller (65F)

4. Clean/change filter in chiller (remove, ultrasonicate, and rinse)

5. Activate LV foreline vacuum trap heater 2x/week (30 minutes), if LV has been used

Getting started:

1. Turn key to ON position (only if key is in OFF position)

2. Turn on water chiller (this should already be on). Note: if chiller is off, allow to operate 315 minutes before beginning SEM operation

3. Turn on IR camera and monitor (medium brightness)

Sample exchange:

1. Push VENT button next to door of sample chamber. Hold for a long second. The button will flash while the chamber vents (takes ~1 minute).

2. Open latch, door.

3. Wearing gloves, insert sample holder tool under sample holder until it clicks (for orientation, note that brass screw on bottom of sample holder will be positioned at the front of the stage after loading). Carefully slide sample holder onto stage (note lock and key fit).

Be careful not to bump into either the objective lens/BEI detector above the sample stage or into the SEI detector. Release tool by squeezing.

Note: if sample stage is not in position to accept a sample, turn outer ROTATE knob to rotate stage to appropriate position. X/Y button and black toggle allow control in those directions.

4. Remove glove, and wipe black door seal with your finger to remove dust, then close and latch door.

5. Push EVAC button for a long second. Monitor pumping progress on LCD:

  • a. "Pre evac" is roughing (rotary) pump (takes pressure to ~10&endash;3 torr).
  • b. "Evac" is diffusion pump (takes pressure to ~10&endash;6 torr).

6. When operating pressure has been achieved, the SEM will beep and the LCD will read "HT READY" (High Tension ready). This should take 5-6 minutes.

Saturating the filament:

Note: Do not saturate filament using computer assisted mode, as this shortens the life of the filament considerably (it happens too fast and at too high a voltage).

1. Below Polaroid camera is a hidden control panel. Push on panel to open.

2. Push white LSP1 button (screen acts like oscilloscope). Line on screen will move up and down as brightness is adjusted; amplitude increases with filament voltage.

3. Set AUTO BEAM toggle to OFF position. For normal SEM operation, set DETECTOR toggle to SEI and FILAMENT toggle to W.

4. Push red HT button. Since there is no current at this point, the FILA display light will blink. LCD will show a LC which should be a small fraction of the accelerating voltage even before filament is saturated, e.g. LC = 25 A at 25 kV.

5. Turn FILAMENT knob slowly clockwise to increase voltage. Oscilloscope line peaks should increase in amplitude. If line goes off screen, adjust brightness knob to lower position. To increase the line amplitude, increase contrast. (The contrast and brightness knobs are multipurpose; make sure brightness/contrast functions are selected by pushing the TONE button to the right of the knobs, etc.)

6. As voltage is increased, the amplitude of the oscilloscope line will increase, then dip (usually once or twice) before increasing again to a maximum where it will level off. Voltage should be adjusted to the beginning point of this maximum. This position is illustrated schematically below:

Note: Do not oversaturate filament. by turning past this point. This causes filament whiskering and greatly shortens the life of the filament.

7. If, after reaching the maximum, the amplitude drops gradually instead of leveling off (see below), then the beam is off center. Center the beam using GUN Tilt X, Y controls to maximize oscilloscope amplitude. Repeat until oscilloscope amplitude is maximized for both X and Y controls. Re-saturate filament using FILAMENT knob again to make sure at maximum with no drop off.

GUN Shift: Adjust only if LCD shows not X, Y centered. If you need to adjust, simply set in center of X, Y scales in LCD when SHIFT button is selected. If adjusted, then readjust GUN Tilt (same controls, but SHIFT not selected).

8. If, before reaching the maximum, the amplitude drops instantaneously, the filament is probably "whiskering" and shorting out. The Wehnelt/filament assembly needs to be removed and especially the hole through which the filament protrudes cleaned out (see "Changing the filament").

9. If FILA light next to HT button has not stopped blinking, then the filament is burned out. After saturation, LC should have increased (e.g., 70-100 A at 25 kV).

Note: Filament saturation current decreases over the life of the filament (100 hr is average for HV work). Why? As a filament is used, it evaporates, usually from one point. That point becomes thinner, and resistance at that point thus increases. Since voltage is constant, current decreases (Ohm's Law).

Other factors which shorten filament life:

  • Frequent sample exchange (pump and vent)
  • Samples which outgas
  • LV work (orifice only protects slightly against pressure in column and gun)
  • Improper filament saturation (e.g., overheating that leads to whiskering)

Scanning a specimen:

1. Reduce magnification and select a scanning speed :








Fastest scan speed and low magnification are best settings to get your bearings on sample stage. Slow scan speeds (SL) give analog images; fast speeds (TV) give digital images.

2. Push COARSE button and begin to focus. Focus range is adjusted using the COARSE button. Move stage using black toggle and appropriate buttons (note the rate of movement is always geared to your magnification).

T/Z: adjusts tilt, height (Z). Move toggle front and back to control Z, left and right to control T. (Z = WD only when sample surface is even with top of sample holder.) To avoid collision between sample and objective lens/BEI detector, choose Z (or WD) > 8 mm.

X/Y: adjusts left/right, back/front position of sample holder

FINE SHIFT: shifts beam, not sample stage, and operates over a limited range.

3. Adjust contrast and brightness (make sure TONE is selected).

4. If necessary, adjust stigmation (necessary if, at magnification is >1000x, the image stretches while you are focusing). To adjust, first center focus between stretch directions. Then select STIG and adjust STIG X and STIG Y control knobs for best focus. Check focus and repeat until image no longer stretches during high magnification focusing. More detailed directions appended in the hard copy of these directions.

5. If necessary, center objective aperture (necessary if image moves as focus is adjusted). To adjust, select WOBB, which will automatically focus and blur the image rapidly (the image appears to wobble). Adjust both aperture knobs until wobble has been eliminated. The image should no longer move while being focused. (Note: the instrument should be set to aperture #2 for general use. #1 is slightly smaller than #2, #3 is larger than #2 and used only when X-ray analysis is being performed.) More detailed directions appended in the hard copy of these directions.

6. Uses of other controls:

SPOT: Changes the diameter of the electron beam (= spot). This changes the resolution but also changes the signal/noise ratio. For highest resolution, want a small spot size. To change size, select SPOT and use control knobs to increase or decrease. LCD gives spot size as a percentage of maximum size possible (shows range). Note: if spot size is changed, stigmation and aperture alignment will need to be readjusted. Note: If, at high spot size, signal becomes greatly diminished, try larger objective aperture. Then re-center aperture, If that doesn't solve the problem, then use GUN Shift and adjust for maximum brightness.

BLANK: Blanks screen (minimally useful)

RESET: sends high signal through lens systems to clear of scrambled fields. Select repeatedly and re-focus until selecting doesn't alter focus appreciably (usually 2-3 times).

DFU: Dynamic focusing unit. Corrects for focusing changes when SEM is scanning a tilted image, but only if stage is tilted toward the detector (to the right)

YMD: Gives a brightness "relief" image if photo taken (minimally useful)

D-MAG: Direct magnification (1:1). Gives true magnification (and actual size of Polaroid photo). Note: the normal display screen actually doubles the image size by 2x.

VIEW: Used for rapidly decreasing magnification to 85x to search field of view (minimally useful).

AUTO IMAGE: Will automatically adjust conditions for best focus, etc. Disengaged on this instrument.

REFLECTED toggle setting in small control panel: "Poor man's BEI detector". When selected, SEI detector remains on, but 10 kV accelerating voltage needed to see SE is turned off. The high energy BE are still detected, however. Image is poor quality, with lots of artifacts (e.g., shadowing), which is why a separate BEI detector is provided. Useful only when trying to resolve surface topography of very smooth sample.

Under SET-UP menu (the non-obvious controls):

TV2 continually averages most recent 255 scans; TV1 averages a variable number, which can be set (175 is typical)

Photograph resolution: HR (high resolution) is normal, unless many photos needed and you want to save time

ACB adjustment: useful if you know how it needs to change to take a picture. Or adjust to center, then remember monitor brightness (pencil marks on dial?) to match micrograph brightness.

Automatic: ignore most of the time (no real benefit over manual control).

To disengage AUTO IMAGE control button: in this menu, turn off all three buttons


For best resolution, use a short WD (~15), a high accelerating voltage (~25 kV), and a small spot size. Make sure objective aperture and stigmator are optimized. Clear lens systems frequently using RESET button and re-focusing. A more detailed table of settings and their effect on resolution, etc., is appended.

At a very low accelerating voltage, try a larger objective aperture (#3) for more signal, though some resolution can be lost, especially at high magnification.

Backscattered electron imaging (BEI):

Detailed directions appended to hard copy of SEM instructions. Note the following additional comments:

1. COMPO mode minimizes topography, maximizes atomic number effects

TOPO: emphasizes topography

Shadow: Allows you to see both in COMPO mode, but atomic number contrast is maximized when Shadow is turned off. If shadow is selected, topography is more emphasized because an additional detector is activated, however as shadow feature is enhanced, signal to one of the original BEI detectors is reduced, so image becomes darker. Use of shadow feature only useful in LV work, where COMPO mode is used. In LV, SEI is disengaged automatically, and thus BEI is the only source of topographic information.

2. In BEI, contrast and brightness controls are more sensitive than they are in SEI, because the E range of electrons hitting the detector is greater. If the controls seem coupled (which they should not be), it probably means contrast is too high. Use LSP1 to reset controls to more normal appearance, then resume imaging.

Low Vacuum (LV):

Detailed directions appended to hard copy of SEM instructions. Note the following additional comments:

1. IR chamber camera must be turned off for any BEI work (required for LV work).

2. If charging is apparent, increase leak pressure (although signal will decrease as a result).

3. If, at low magnification, a shadow obliterates part of scanning area, it's probably due to the OL. Adjust aperture to remove shadow.

Saving an image electronically:

Use program "Archive 5800" or "Arc 58" on PC. Manipulate by importing into "Micrografx."

Using thermal printer to print an SEM micrograph:

Push PRINT button on either the printer itself or on the control panel lid under the camera. Note: Images can be printed in both directions and in a variety of sizes (see settings on front panel of thermal printer).

Making a Polaroid micrograph:

1. Push any scan speed button twice to see exposure marker. Adjust contrast and brightness. Camera speed is controlled automatically during exposure.

2. Make sure camera lever is in L position (to the right). Insert film. Pull out until it stops.

3. For an analog photo, push green PHOTO button on the control panel lid under the camera.

4. For a digital photo of the image on either monitor, freeze the image on the monitor, then select the appropriate orange monitor button (L or R) and push the orange PHOTO button.

5. After exposure, push film in, move lever on camera to P (left), remove film, and return lever to L.

6. Follow directions on film


If you need to reset the SEM during operation, turn the key to START and release to ON. This resets the microprocessor. If you feel the controls are not responding, restart the PC. Upon SEM restart, connection to the PC must be re-established. Hit the F1 key, then type EXT ON, using the SEM keyboard. Repeat sequence.

Shutting down:

1. If filament was manually saturated: turn FILAMENT knob to zero, then turn HT off. If filament was automatically saturated: turn HT off.

2. Wait ~5 minutes for filament to cool to less than white-hotness before venting sample compartment

3. Vent sample compartment, open door, and remove sample holder (gloves!).

4. Re-evacuate chamber (should be under vacuum when not in use).

5. Turn off camera monitor.

6. Leave computer on and SEM running. Turn down monitor brightness. PC has a screen saver.

7. Turn scan speed to SL3 and put magnification on 300,000x.

8. Record usage information in SEM log.

Changing the filament:

1. Vent sample chamber. Wear gloves for all steps below.

2. Open top of column (gun assembly). Cover opening with Al foil to prevent dust falling in while working. Better: close column and keep under HV while cleaning Wehnelt.

3. Remove Wehnelt (hot!) using black cylindrical tool. (Wehnelt contains filament inside the Wehnelt cap.) Tighten screws and pull off.

4. Remove tool and loosen 3 outer set screws and one alignment screw to remove filament from metal cap. Porcelain and its outer steel holder should still be attached to one another.

5. Remove filament and ring.

6. Clean metal cap with metal polish as follows:

  • a. Use wooden swab with polish to clean out all holes, paying special attention to carbon buildup around central hole.
  • b. Use 2" x 2" piece of lint-free cloth with polish to scour the inside of the cap and the ring. Q-tips can be used to clean the larger holes.

7. Repeat (6), using acetone.

8. Put whole cap and ring in beaker with high purity acetone and ultrasonicate 3-5 minutes. Dry with hair dryer.

9. Put cap and ring in beaker with high purity methanol, ethanol, or isopropanol and ultrasonicate 3-5 minutes. Dry with hair dryer. Repeat.

10. Replace ring in cap and insert new filament. If filament is not centered in tiny hole in cap, adjust using screws which attach the ceramic part to its metal holder.

11. Replace Wehnelt on gun assembly. Use compressed air to blow off last minute dust from Wehnelt and assembly. Clean O-ring. Close and evacuate.

12. If possible, wait 30 minutes after installing new Wehnelt before saturating for the first time (allows for degassing).

Differential pumping apertures:

Three orifices can be used, depending on scanning conditions. The orifice in use is located within the OL.

800 m HV work or most LV work (<1 torr). OL aperture = "2"

150 m Higher pressure LV work (>1 torr). OL aperture = "0"

No orifice HV work. OL aperture = "2"

Sample stubs:

Teflon stubs are used primarily for backscattered electron work, since they have low atomic weight.

Automatic Scanning Instructions:

1. Choose STAGE menu on computer. When the stage is in a position where it can be changed, a red line will appear across the top:

The computer has a setting for default load position. Under menu for STAGE, choose LOAD SAMPLE and click on START button. Stage will automatically return to loading position.

If actual position and computerized drawing of position do not agree, hit the F1 key, then type STAGE_-O. This will reset all five axes. If just one axis needs to be reset (e.g., x-axis), command would be modified as STAGE_-OX.

2. Computer control of SEM operations (upper case letter are typed):

All commands are preceded with F1 (command key) and followed by RETURN.

( * ) Indicates a numeric value.

( _ ) Indicates a space.

Accelerating Voltage


(KV may be omitted)


10 KV - 30 KV


01 KV - 09 KV (0 is required)


0.3 KV - 2.9 KV

Stage Control


Rotate stage by ***.**


Tilt stage by **.**