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JEOL 3200 training

Cryogen fill

Chuck dewar

  • Fill in morning and last thing at night
  • Keep cold all the time - no need for any bake-out or cryo-cycle

N2 outer tank

  • turn on heater switch (warms exhaust)
  • cover energy filter and electronics to protect from condensation
  • connect rubber hose to port
  • open fill valve, close vent valve, open pressure valve until 0.02-0.03 on gauge
  • monitor -> temperature. After temperature of outer tank reaches <80K, look for LN2 spilling out of exhaust site glass
  • turn off heater switch (could melt exhaust site glass eventually)

He inner tank

  • turn on heater switch
  • fit He tank with balloon
  • vent valve closed, balloon valve open, top valve open, vent valve closed
  • slide collar down on wand to start - loosen lock ring
  • place wand into He tank
  • lower slowly and once connection made, shove rod down until contacts He
    • (supposed to push to bottom of tank and raise slightly, but maybe difficult)
    • monitor balloon size and release pressure from vent valve if necessary
  • allow He gas to thoroughly purge line - wait until see condensation in exhausting gas
  • tighten lock ring on wand when reach required depth of wand in He tank
  • open valve and insert rod into He port
  • monitor tension on balloon - lower rod if necessary - press balloon to disturb surface of He and speed evaporation if pressure falls too low
  • once temp of He tank reduces to 4K, check level with He level meter
    • only turn on briefly as it puts energy into the tank
  • once full, take balloon off tank to relieve pressure
  • remove wand, close main valve
  • turn off He heater
  • 2 hr drift time after filling with He
    • after 1 hr, maybe ok with use of piezo drift compensation

He inner tank with N2

  • He level meter will not work with N2
  • similar procedure, but listen to cracking of N2 exhaust to judge if tank is full. If cracking is not present, look at the exhaust line for condensation (it is especially useful to look in the adjacent room, the one with the roughing pumps)
  • turn on exhaust heater
  • attach wand to end of rubber hose
  • fill with pressure regulated to 0.04
  • warm up valve with hair dryer before withdrawing wand
  • turn off exhaust heater

Expected Temperatures

He cooled

  • specimen: 18
  • He shield: 8.3
  • He tank: 4.3
  • N2 tank: 77-78
  • Chuck : 88.3 K (note - takes ~2h to cool)

N2 cooled

  • specimen: 97.4 (uncooled); 84.1 (cooled N2 tank)
  • He shield: 80.8 (uncooled) ; 77.7 (cooled N2 tank)
  • He tank: 77.9 (uncooled); 77.4 (cooled N2 tank)
  • N2 tank: 258(uncooled) ; 77.6 (cooled N2 tank)

Expected Vacuum level (PEG1)

  • Inner and out tanks cooled with N2 : 1.5 - 1.6 X 10^-5 Pa (Aug 2007)
  • Only inner tank cooled with N2: 1.9 - 2.0 X 10^-5 Pa (Aug 2007)

Relevant cryogen info

  • outer tank: 2.1L capacity
  • inner tank: 2.5L capacity
  • To switch from He -> LN2, wait until inner tank reaches 77K
  • To switch from LN2 -> He, wait until inner tank reaches 100K
  • Hold times
    • chuck dewar with N2: 14h
    • inner tank with He: 4.5h
    • inner tank with N2:
      • 4-5 days with outer tank cooled
      • 2 days with outer tank warm
    • outer tank with N2: 4-6h

Specimen loading

  • Neutralize stage
  • Load grid in cartridge
    • place cartridge onto block with square end at beveled end of the block
    • don't touch end of cartridge with leaf spring
      • when spring gets deformed, call for maintenance
      • will not engage properly with stage once deformed
  • put grid in cartridge
  • put spacer/washer in cartridge
  • cylindrical tool has two ends to adjust tines on screw pickup tool
  • flat side of screw goes down
  • align tines with grooves in screw
  • DO NOT OVER-TIGHTEN

Load cartridge into transfer rod

  • pick up square end of cartridge with forceps and push leaf spring end of cartridge into transfer cup
  • withdraw rod into chamber and insert cover
  • make sure cartridge triangle (notch) faces outwards (to the back wall) when mounting:

IMG-20111212-00114.jpg

Load cartridge into chuck chamber

  • check chuck to make sure it is empty, also column
  • push SPC2AIR to vent airlock
  • remove plug
  • push SPC2AIR to arm airlock
  • engage 3 pins of transfer rod with airlock, rotate
  • remove white cover
  • push transfer rod chamber in to initiate pumping
  • wait for ready light (left side - SP2)
  • open MV2 valve (rotate up, pull out, rotate further up to vertical)
  • rotate transfer rod 90º counterclockwise, lift spring over stop and insert
  • bring chuck forward in pickup position
  • pull chuck back while checking mirror for cartridge movement
  • pull transfer rod back and lift spring over stop
  • close MV2
  • push SPC2AIR to vent
  • remove transfer rod
  • push SPC2AIR and replace plug - push switch to initiate vacuum for 10 sec

Load cartridge into column

  • make sure stage has been neutralized
  • check ready light for chuck vacuum (right side)
  • open MV1 (turn up, pull out - turn up to vertical)
  • bring chuck forward, slowly into column while observing through site glass
  • lock chuck
  • pull end screw and rotate up to release position
  • withdraw chuck while carefully observing for cartridge movement inside column
    • should be no movement at all - otherwise retrieve cartridge and consider using a different one
    • score side of cartridge at left edge of grid for better visibility
  • return end screw (knob 1) to pickup position

Initial setup/alignments

  • Press STD FOCUS before doing any alignments
  • Degauss energy filter (on Filter Tuning page - hit FILTER)
  • Gun to Condenser alignment
    • C2 aperture 1
    • spot 5 - wobble C2 lens rapidly with brightness knob (eliminate hysteresis), go to beam crossover, center beam with bright shift
    • spot 1 - wobble C2 lens, go to beam crossover, center beam with gun shift
    • repeat until beam stays in place (not as good as in J2100)
  • To activate gun shift, hit gun align button
    • shift knob -> gun shift
    • defstg knob -> gun tilt
    • To activate bright shift, hit any other button and use shift knob
  • Gun alignment
    • spot 1 -> crossover
    • JEOLS -> Alignment -> anode wobbler
    • adjust gun tilt to make beam expand symmetrically
  • Z height
    • focus beam
    • adjust Z height until rings disappear and see only clean spot in the center
      • probably good enough, but can check with STD FOCUS
  • Condenser to objective (Current Center)
    • 50kx or less
    • STD FOCUS
    • center object
    • focus beam, expand to size of large screen (eliminate hysteresis)
    • change focus (15 course clicks over or under focus)
    • recenter obj with bright tilt
    • return to *STD FOCUS step and repeat until satisfied
    • can also use obj wobbler (maybe adjust step size) and minimize movement (but this is annoying)
  • C2 apertures: 150, 70, 50, 20
  • 50kx - current density in pA/cm2 = dose at sample in electrons/Å2/sec

  • Pivot Points
    • Tilt:
      1. Go to mag mode, condense beam
      2. Under Alignment panel, Choose TiltX wobbler and choose Tilt Compensator
      3. Using Def/Stig X, minimize beam movement
      4. Unselect TiltX wobbler and select TiltY wobbler
      5. Using Def/Stig Y, minimize beam movement
    • Shift (only staff should do this)
      1. In mag mode, fully expand beam, then go to SA DIFF
      2. Condense beam to caustic spot using Diff Focus
      3. Under Alignment panel, choose ShiftX and select Shift compensator
      4. Using Def/Stig X, minimize movement of spot
      5. Repeat for ShiftY

MDS

This is no longer relevant: we are using iMDS

  • software shutter: use 16000 (decimal) for whatever coil you choose
    • if use max, then introduce hysteresis into system
    • Gatan goes in one direction, if use the same coil as Gatan, must go in the same direction because they are additive

  • hardware shutter
    • standard = gun shift
    • high speed = electrostatic
    • standard hardware is equally fast to software

  • C2 aperture 1, spot size 5: 18-20 pA/cm2 at 50kx (corresponds to 18-20 electrons/A2/sec)
  • C2 aperture 2, spot size 1: 18-20 "
  • C2 aperture 3, spot size 1: 10 pA/cm2

Energy filter

  • normally, use HT control to center spectrum
    • 3000V total shift range
    • FL not functional on this microscope
  • SPCTR button to see spectrum on screen
  • DeGauss energy filter every day
  • Filter lens (FL) same as Diff Focus
    • moves spectrum normal to energy spread axis
  • Dispersion spreads spectrum out

Center slit

  • Degauss the filter
  • IMAGE mode: 20kx
    • this is where slit was centered and beam comes through filter at different positions depending on magnification
  • focus beam and center accurately
  • SPCTR mode
  • center spectrum with Filter Lens accurately on small screen
  • insert slit (20 eV)
  • adjust center mechanically (this is approximate)
  • IMAGE mode
  • center slit until dark spot just disappears
    • now slit is mechanically centered in middle of Filter Lens
    • do not change mechanical center at other mags
    • use Filter Lens
  • go up 1 mag at a time, adjust Filter Lens to eliminate dark shadow for each
  • continue until reach target magnification
  • Isochromaticity adjusted for each magnification
    • minimize size of black annulus in image (should be in center)
    • readjust slit center until annulus disappears
    • this annulus is the shadow of the slit
  • Apertures
    • small entrance aperture improves EELS spectrum resolution
      • but lose intensity in spectrum as a result
    • SA aperture also effective, usually use at lower mag
  • DigitalMicrograph Filter menu (alt-menu item -> setup
    • filter calibration ~once per month
    • energy shift - use Carbon peak at 284 eV
    • illumination compensation
      • slit calibration
      • just follow directions
  • Thickness map (Filter menu)
    • t/lambda = ln (Io/It)
      • t=thickness
      • lambda=mean free path
      • Io = zero loss intensity
      • It = total electrons intensity
      • from t/lambda, could figure out lambda for amorphous carbon, which is published at 120kV, and extrapolate to 300kV
    • EELS menus, can measure absolute thickness (uses carbon edge)
      • collection angle = angle of diffraction at obj aperture (not exactly at back focal plane so using focal length would be a rough approximation - calibrate with diffraction sample better)
      • convergence angle (Toshi Aoki will send info on this)
      • effective atomic number (if have heterogeneous material, then take some kind of average (ask Toshi)
  • Collection angle
    • from diffraction pattern, measured diameter of gold 2.3 A diffraction rings to be 788 pixels
      • measured 2nd obj aperture to be 962 pixels
      • d * sin(theta/2) = lambda => 110mrad for semiangle for aperture #2

Collect spectrum

  • dispersion 100um/eV, obj#3 or #4, mag 30k
  • center spectrum first * FL initially, PLA for fine adjustment
    • filter-> spectrum setup
      • acquire corrected mode .04 s
      • display raw image - center zero loss peak
        • make two diagonal lines to define center of image
        • center of CCD is below and to left of central black dot on focus screen
        • ~ one diameter away from central black dot
        • Acquire spectrum - then run thickness calculation in EELS menu
        • will fail if image is saturated - can check min/max values in image - reduce exp time if necessary
      • acquire thickness map - 10eV slit used by this routine

Performance

He temp N2 temp lattice resolution 300kx single xtal gold 0º tilt 2.0 Å 2.0 Å +/- 70º tilt 3.4 Å 3.4 Å Scherzer focus 300 kx carbon film 2.7 Å 2.7 Å info limit 300 kx carbon film 2.1 Å 1.8 Å info limit 250kx gold on carbon unfiltered 2.3 Å gold + Thon rings filtered 2.3 Å gold + Thon rings drift piezo off (nm/min) 0º tilt 1.2264 1.0 +70º tilt 1.748 - -70º tilt 0.66 0.812 drift piezo on (nm/min) 0º tilt 0.669 0.31 +70º tilt 0.56 0.9 -70º tilt 0.2768 0.746 beam current 70um C2 ap spot size 2 5.2 pA/cm2 on big screen 200 cm^2 1 nA img shift 8kx => 10um for big screen x/y shift: 12 um S distortion waffle grid 0.6% spot scan LHC crystal spot 5 C2 ap 3 (50um) C1 currnt A4B0 50kx, 1um df 100nm spots no apparent displacements shutter speed 0.1 sec exp spot diam 1 cm gun shift => blurred edges electrostatic coil => sharp

Software Issues

KVM switch

  • June 2007: KVM stopped working after reboot. Fiddling with several reboots made it work again
  • June 2007: KVM stopped working after turning on Windows Firewall. Turned off and rebooted -- worked again
  • July 2007: KVM stopped working after Norton Internet Security installed. Uninstalled - still did not work
    • Finally fixed after changing configuration in KVM client from "default" to actual IP of Broadcom card
  • note that Broadcom card has same IP address as Jeol3200 microscope -- should look into this
  • Aug 28 2007 - Stopped working again after reboot of camera PC.
    • Could only get to work again by quitting and restarting server and client on microscope pc. Same settings as before

SerialEM

  • June 2007 - When using SerialEM in low mag mode for montage, DO NOT attempt to correct eucentricity. In the 3200 this caused the goniometer to move out of range and the specimen could not be retrieved, even after rebooting the goniometer. Service had to be called.
  • July 2007 - SerialEM stopped working - complained that it could not communicate with GATAN camera
    • Turned out that Gatan DM software had been reinstalled, so the SerialEM plug-ins needed to be reinstalled as well. Doing this solved the problem.

Reinstallation of Gatan Digital Microgaph software

  • was done June 27 2007 for training purposes, and again on Aug 7 2007
  • Steps are as follows:
  1. Back up the three preferences files, located in c:/Program Files/Gatan/Digital Micrograph/Pefs
  2. Back up reference images, located in c:/Program Files/Gatan/Digital Micrograph/Reference Images/
  3. Uninstall everything -- Run Setup.exe. Choose to remove licenses as well
  4. Install licenses from CD
  5. Install GMS using setup.exe (current version is 1.6.2)
    1. Be sure to select that hardware is connected
    2. System configuration should be as follows:
    3. Then accept all defaults

reinstall_screen_shot.JPG

Using EM Menu 3 to take CCD images

  • Need to have Digital Micrograph running
  • Does not communicate directly with scope -- need to manually enter mag if accurate scale bar is desired
  • Saves a maximum of 24 full-size images at a time (greater than 24 causes software lockup)

Flatfielding in EM Menu 3

  • Should have hot pixel correction on, as many are created with a 300 kv beam
  • Dark field images are not collected properly - beam is not blanked during dark field collection
  • To make a new flatfield, need to manually blank the beam
  • Press Beam blank button, then collect flatfield
  • Monitor progress of collection (appears as message at bottom of EM Menu window)
  • After final dark image is collected, manually unblank beam
  • After collection, verify that flat field is ok:
    • a) look at dark images - intensity should be ~ 1000 (NOT binning dependant!)
    • b) look at flat image
    • c) Take corrected image and look at power spectrum
    • d) Compare uncorrected and corrected intensities in both EM Menu and Digital Micrograph - counts should be the same

Electrostatic Shutter

  • Jan 2009 - new power supply for electrostatic shutter installed
    • With old power supply, not enough power to fully move beam off of sample
  • Currently set up with electrostatic shutter as shutter 2, gun-tilt shutter as shutter 1
  • To use mechanical shutter, unplug "electrostatic shutter" cable from back of Gatan box and plug in "PL shutter" cable
  • Note that mechanical shutter is POST SPECIMEN
  • DigitalMicrograph software:
    • Gun tilt shutter is called "pre-specimen"
    • Electostatic is called "post-specimen" (even though it is really a pre-specimen)
  • NOTE: For electrostatic shutter to work, "START" button on Spot-Scan control panel should be on
    • Note also that turning it on causes a small (negligible) amount of electrical interference

Bake Out

  • Make sure temperature in all tanks is RT (289K)
  • Go to HT tab
    • Select Turn Off
    • A window will open that says "Do not Touch Conditioning Knob" or something to that effect. You can ignore.
  • Go to Maintenance ACD & Bake/Bake out tab
    • Cooling time should read 4 hours.
    • Select end date
    • Start
  • Turn off water flow to lenses
    • Red handled valves labeled CL, OL and IL mounted on wall in ancillary equipment hallway

Relighting the tip

  • Turn off lens power supply
  • Turn on water flow to lenses
  • Turn on lens power supply
  • DC condition
  • Light the tip

Other Issues

Lens Currents

  • 12-2-11
    • Saw only a very tiny beam, mag changes had no effect, brightness changes had no effect, degauss had no effect
    • Open Lens Voltage on Status Monitor: all voltages -10.24 --> seems lenses were turned off
    • Open panel next to camera chamber. Toggle Lens off then on. Lens currents then went back to normal values

Removing a sample from chuck

  • 12-12-11
    • problem:
      • Sample was inserted backwards (notch facing front)
      • Was visibly tilted when observed through small window; impossible to make eucentric
      • Could remove from column, but loading tool would not pick up from chuck
    • solution
      • Warm up chuck dewar(let warm naturally over weekend)
      • Vent chuck as follows:
      1. insert loading tool as normal, wait to pump down
      2. when pumped down, open mv2 valve
      3. now close V104
      4. press SPEC2 AIR -- chuck will be purged with N2 to vent
      5. remove loading tool -- now have access to inside of chuck
      6. Remove cartridge using tweezers and double sided tape -- be careful not lose it!
      • Re-pump chuck as follows:
      1. Place loading tool in chuck and pump down (MV2 still open)
      2. press SPEC2 AIR
      3. close MV2 valve
      4. close V104

-- KdDerr - 17 May 2007