Instruments

 

The Advanced Microsocpy Facility houses scanning EM, FIB and other sample preparation instruments. In May 2012 we became home to the highest resolution microscope in the world, the Hitachi HF-3300V scanning transmission electron microscope (STEHM).

Hitachi HF-3300V STEHM


Our HF3300V STEHM in place.  Photo by Adam Schuetze.

Our HF3300V STEHM in place. Photo by Adam Schuetze.



Our HF3300V STEHM in place.  Photo by Adam Schuetze.

Our HF3300V STEHM in place. Photo by Adam Schuetze.



Our HF3300V STEHM in place.  Photo by Adam Schuetze.

Our HF3300V STEHM in place. Photo by Adam Schuetze.


Based on the Hitachi HF-3300 TEM, the HF-3300V scanning transmission electron holography microscope (STEHM) will both achieve a STEM electron probe size and TEM spatial resolution approaching forty picometers. The STEHM assembly and commissioning process is complete, it has been signed off by Hitachi and UVic, and is now in service.

To see images of the installation and assembly, see the history page.

Instrument specifications:

  • Highest brightness (measured as 6x10e13 A/m2 sr), high stability and highest coherence cold-field-emmision electron source.
  • Housed in an extremely quiescent room.
    • The room is mounted on bedrock, mechanically insulated from the building.
    • Thermal insulation maintaining temperature to +/- 0.025 C over 1 hour.
    • Acoustic dampening.
    • Slow diffusion HVAC for room air changes.
    • Stray electromagnetic field reduction using aluminum shielding.
    • Magnetic field reduction using permalloy shielding.
  • 60 keV, 200 keV, and 300 keV acceleration voltage.
  • STEM and TEM mode:
    • First Cs and Cc corrected STEM with ExB Wien filter.
    • First aplanic TEM with Cs and coma correction.
    • Sub angstrom resolution at 60 kV TEM. More resolution details to follow.
  • Dislocated hologram apertures for electron vortex beams.
  • Four electron biprisms for many types of electron holography. One above specimen, and three below the specimen with magnification between lower biprisms equal to one.
  • Detectors:
    • Secondary electron detector in STEM mode.
    • X-ray energy dispersive spectrometer (Bruker).
    • High angle annular dark field for STEM imaging.
    • High angle annular bright field detector for STEM imaging.
    • Electron energy loss spectrometer.
    • Imaging energy filter (Gatan Quantum).
  • High stability single tilt holder (Hitachi).
  • High stability double tilt holder (Hitachi).
  • Low-background analytical holder (Gatan).
  • 360 degree tomography holder (Hitachi Pillar).
  • High temperature (1500 C) holder (Hitachi).
  • LN2 CryoEM holder (Gatan).
  • Farraday cage holder (Gatan).

You can read more technical information about the STEHM in the following two presentation. These presentations cover some of the fundamentals of the STEHM instrument, and what makes the instrument unique.

If you are a member of the press looking for a writeup on the instrument for background, you could start with the following text:


The best resolution microscope ever built

The best resolution microscope ever built

The Scanning Transmission Electron Holography Microscope (STEHM) will be the best high-spatial resolution microscope ever constructed and it will maintain its high position at the forefront of this rapidly moving competitive technology for many years. The STEHM will build upon the fundamentals of a standard electron microscope, which uses electrons rather than light, to give unsurpassed capabilities to see and measure the properties of a hidden world that we know exists.

The electron has a wavelength one million times smaller than light and the spatial resolution of the STEHM will approach its wavelength, i.e., approximately two picometers. The electron also carries a charge and magnetic moment, which can be used by electron holography to interrogate the electronic properties of atoms.

Opening new worlds

Opening new worlds

At the time of van Leeuwenhoek in the 1600’s, the light microscope using finely ground lenses was considered to be the highest level of technology made as it was able to resolve living cells. The STEHM is in the same league, relateively speaking, as its lenses will give direct observation of hitherto unobservable quantum phenomena by using electrons [1]. Electron holography is a special method of microscopy measuring both the amplitude and phase of a material. A hologram is created by the interference of two or more beams giving three-dimensional information at the atomic level. The phase is additional information not provided by other forms of microscopy. The phase measures the refractive index or more precisely for electrons, the mean inner potential of the specimen, which can be used to determine the specimen’s absolute composition, internal strain, electrostatic fields, magnetic fields and temperature.

A little bit about technology

A little bit about technology

Recent developments in the modularity of electron microscopes allow this first-of-a-kind microscope to be constructed. These developments, which significantly increase the STEHM’s capabilities, include:

  • A cold-field emitting electron source to increase its coherence (like a laser) and to decrease the energy spread of the electron beam
  • Spherical (Cs), chromatic (Cc) and coma aberration correctors to increase the microscope’s information capability
  • Multiple electron biprisms to enhance the spatial resolution and to enable the creation of new forms of microscopy for new capabilities
  • A large CCD detector to better measure the gray scale of fringes produced in holograms and a fine-movement specimen stage to help invent confocal electron holography

The Cs + Cc correctors improve the spatial resolution to picometers, substantially better than angstroms, which is the recent state-of-the art. The Cs corrector localizes the information in lattice images so the contrast of a lattice position in the image has a one-to-one correspondence with an atomic position, whereas without these correctors this is not possible. A Cs + Cc corrector reduces the point spread function to the dimensions of the electron probe enabling the sampling of the specimen at sub-atomic dimensions. Both aberration correctors will make it possible to see atomic columns that don’t have to be interpreted and previously hidden positions of atoms, and, when used by electron holography, measure the electron density between the atoms.

Multiple electron biprisms substantially improve the spatial resolution of holograms by separating the contrast of the fringes from the interference width of the holograms. The use of three biprisms placed below the specimen permits flexible control of all of the interference parameters, ie., the interference region, fringe spacing and fringe angle, involved in electron holography [2]. Scanning-beam electron holography is made possible by placing an additional biprism above the specimen. Multiple biprisms enable many forms of electron holography to be possible, as envisioned by Cowley [3]. For example, holography typically reconstructs its holograms outside of the microscope using Fourier transform methods. Two electron biprisms enable the hologram to be reconstructed inside the microscope so a phase image of the specimen can be directly observed during the experiment. Multiple electron biprisms also enable the creation of confocal electron holography, which will be used to make three-dimensional measurements of the physical, electrostatic and magnetic properties of a specimen.

The cold-field emission source will make it possible to see the bandgap electrons, holes, excitons, phonons and plasmons of materials used in electronic, photonic and magnetic devices so their properties can be measured by energy-filtered electron holography. These measurements will answer many fundamental questions of science and engineering. The phase measurements of the electrostatic field strength existing between atoms provide a direct insight into the basic bonding configurations, which is information currently lacking by science.

Measuring material properties

Measuring material properties

Energy-filtered electron holography, which combines electron holography with the imaging energy filter (GIF) will make it possible to characterize the coherence properties of surface plasmons and surface phonons (two energy filters used) of carbon nanotubes (CNT) that are responsible for the observed ballistic electron mobility and excellent heat conduction.

Researchers will also use the STEHM to measure the physical properties (strength) of carbon nanotubes using a modified specimen holder. This information will help the implementation of CNTs as field emitters, heat conductors and in structural components.

Also, this configuration of the STEHM will make it possible to measure the coherence of phonons on the B planes in MgB2 and possibly Cu-O planes in high temperature superconductors that are a possible source of their superconducting properties.

Electron holography is the only means possible to measure the dimension of the electrostatic field between the source and drain of field emission transistors.

Similarly, high-resolution electron holography should be able to measure the orientation of the spinning electron’s magnetic field to characterize spintronic devices.

Other unique capabilities include the measurement of the composition and defect density of self-assembled nanodots for nanotechnology, the domain structures of magnetic materials, which when combined with the Cs + Cc correctors may be able to measure the dimension and properties of the domain boundaries and their triple points, which is now not possible by any means.

Useful to many research areas

Useful to many research areas

The new capabilities of the STEHM will make measurements to be used by researchers in engineering, physics, chemistry, materials science, biology and medical sciences. The STEHM will push the boundaries of research in nanotechnology: nanoelectronics, nanochemistry, bionanotechnology, nanophotonics, molecular devices, and diagnostics, for example.

[1] A. Tonomura, Direct observation of hitherto unobservable quantum phenomena by using electrons, Proceedings of the National Academy of Sciences of the USA, volume 102, number 42, pg 14952, 2005.

[2] K. Harada, T. Natsuda, A. Tonomura, T. Akashi, and Y. Togawa, Triple Biprism Electron Interferometry, Journal of Applied Physics, submitted.

[3] J.M. Cowley, Twenty forms of electron holography, Ultramicroscopy, volume 41, pg 335, 1992.

Hitachi S-4800 FESEM

With a cold field emission electron source for high resolution, ExB in-lens filter and a host of other features, our Hitachi S-4800 field emission scanning electron microscope is an extremely powerful and flexible tool.


Our S-4800 SEM in place

Our S-4800 SEM in place



Specifications

Specifications

  • 0.5 kV to 30 kV accelerating voltage
  • 1 nm resolution at 15 kV, 1.4 nm at 1 kV
  • Magnification from 30x to 800,000x
  • Maximum specimen size = 100 mm
  • Super ExB filter technology
  • Dry vacuum system
  • X+Y motorized eucentric stage with trackball interface (tilt and Z by manual control)
  • Ring-type YAG backscatter detector
  • Bruker Quantax EDS System for X-ray spectroscopy.

Instrument instructions

Instrument instructions

Sample images

Sample images

Other resources

Other resources

  • Online articles, papers, and other online resources on scanning electron microscopy are here

Hitachi FB-2100 FIB

The Hitachi FB-2100 Focused Ion Beam system is used for making TEM specimens of hard and soft materials and their combination, useful for engineers, physical scientists and life scientists, and for making TEM specimens containing different types of tissue, for example tissue growing on implants.


Our FB-2100 FIB in place

Our FB-2100 FIB in place



Specifications

Specifications

  • 10 to 40 kV accelerating voltage
  • 6 nm or better resolution
  • Magnification range from 700x to 90,000x
  • Maximum current of 40 nA at 40 kV
  • Liquid gallium metal ion source
  • 100 mm specimen diameter
  • Actuated TEM holder stage
  • Actuated SEM holder stage
  • Actuated pick/place probe
  • Tungsten deposition system

Samples can be cut using layouts created on the instrument's control computer, by importing a vector file via ftp, or by importing a bitmap image via ftp.

Hitachi High-Technologies Europe has a FB-2100 brochure, which contains a very good description of the instrument's capabilities.

Software and technical information on particle interactions with matter.

Beam current values

The following tables show beam current at the sample, in nA, as a function of acceleration voltage and aperture diameter. The first table is for the condensor lens off, the second table is for the condensor lens on.

Beam current in nA, Condensor lens off
  5 um 15 um 30 um 80 um 150 um 300 um 520 um
10 kV 0.00010 0.00027 0.00133
15 kV
20 kV 0.00305
25 kV
30 kV 0.00143 0.00674 0.03946
35 kV
40 kV 0.00130 0.00335 0.01583 0.09280
Beam current in nA, Condensor lens on
  5 um 15 um 30 um 80 um 150 um 300 um 520 um
10 kV
15 kV
20 kV 0.00588 0.26861
25 kV
30 kV 0.00882 0.05195 0.44652 2.1265
35 kV
40 kV 0.00303 0.01064 0.06540 0.64103 3.0318 15.0243 43.892

Instrument instructions

Instrument instructions

Fabrication examples

Fabrication examples

Other resources

Other resources

Downloads

Downloads

Generating bitmaps with Illustrator and Javascript

Previously we suggested that our users utilize Matlab to generate bitmaps of grids of elements, or do it by hand with Illustrator. MATLAB had the benefit of speed, and Illustrator produced cleaner bitmap files. Now, you can download Javascript scripts to automate the procedure in Illustrator. There are three sample files, one for making an array of circles, one for making an array of rectangles, and one for making an array of arbitrary structures.

Use the following steps to build a bitmap file:

  1. Download the appropriate file linked above, and edit the approriate variables to select: pitch, number of elements in the array, and diameter for circles or width and height for rectangles. The "arbitrary stuctures" example is currently written to make an array of double nanoholes, but it can be modified to make an array of any type of structure.
  2. Open Adobe Illustrator.
  3. Control-F12 will open a dialog box for selecting the script file. Select the appropriate script file, and click Open. This will execute the script.
  4. File -> Saveas Illustrator EPS, this saves the file as encapsulated postscript.
  5. Open this encapsulated postscript file in Photoshop. When you open it, make the height and width 2000 pixels (or, if the bitmap is not square, make the largest dimension 2000 pixels), use Grayscale mode, and turn off anti-aliasing.
  6. Layer -> Flatten
  7. File -> Saveas BMP

To learn more about Javascript and Illustrator, refer to the following:

The following are some relevant notes for modifying the script for arbitrary structures:

  • When you create an element such as a circle or a square, its "origin" is at the top left corner of the element.
  • The sample script uses two nested for loops to move in the array area in X and Y. At each step, you can call an arbitrary function to create an arbitrary shape or set of shapes. Inside this function, you have to make sure that you have properly shifted the position of the elements making up your arbitrary shape, keeping the above point in mind.
Finding the center point of a rotated square

For available for download, an Excel spreadsheet for calculating the center of a rotated square. Useful for finding the centerpoint of a SiN window. Simply use the FIB to navigate to the four corners of the square, record the coordinates, and enter them into the spreadsheet. The center coordinates are then computed.

Computing focus as a function of position on a plane

Now available for download, an Excel spreadsheet for calculating focus values as a function of position, on a plane. If you are fabricating on a gold-coated glass slide, it is useful to be able to move to a position or a number of positions that are distant from each other, and cut your structure without first looking at the sample to check the focus. This maintains the pristine condition of the gold coating at your structure position.

Since the glass slide is flat, but possibly tilted in three axes, it is necessary to compute the equation of the plane, where x and y are the coordinates, and z is the focus value F. To do this, go to three positions on the glass slide, and record the x, y, and focus values. Put these values into the spreadsheet as Point 1, Point 2, and Point 3. The spreadsheet will calculate the plane equation coefficients A, B, C, and D. Then enter your x and y coordinates of the point in question, and the spreadsheet will tell you the focus value at that point. Simply go into calibration mode, change the focus value to that number, register the beam, and then switch back to fabrication mode. Move the stage to the desired x and y coordinates, and then you can cut the pattern blind without looking at the sample first.

Font bitmap files

Now available for download, font bitmap files for use on the FIB. Create indicator marks, write notes on your sample, and more. Contains numerals 0 to 9, and capital letters A to Z.

Generating bitmaps with Matlab

To generate bitmap images of grids of elements (such as circles, squares, rectangles, or other more complicated features) for use on the FIB, use the Matlab function makegrid.m, along with one of the helper functions plotcircle.m, plotsquare.m, plotrectangle.m, or plotantenna.m. The helper functions are provided as working samples, you can create arbitrary ones. To generate the bitmap, do the following:

  1. Use makegrid.m and one of the helper functions to make a figure containing the grid of elements. The function templates are:

    makegrid(function_name,element_params,num_elements_x,spacing_x,num_elements_y,spacing_y)

    plotcircle(X,Y,element_params) [all the helper functions have the same template]

    element_params is an arbitrary length vector containing [width, height, ... ] where [...] are parameters you can use to define some arbitrary element.

    Examples of use would be:

    • makegrid('plotcircle',[50],5,400,10,600)
      This makes a grid of 50 nm diameter circles, 5 in the horizontal direction with 400 nm center spacing, and 10 in the vertical direction with 600 nm center spacing.
    • makegrid('plotsquare',[50],5,400,10,600)
      This makes a grid of 50 nm x 50 nm squares, 5 in the horizontal direction with 400 nm center spacing, and 10 in the vertical direction with 600 nm center spacing.
    • makegrid('plotrectangle',[50,100],5,400,10,600)
      This makes a grid of 50 nm wide x 100 nm high rectangles, 5 in the horizontal direction with 400 nm center spacing, and 10 in the vertical direction with 600 nm center spacing.
    • makegrid('plotantenna',[300,200,30,30],5,400,10,600)
      This makes a structures that consist of an outer box and two nested interior boxes, 5 in the horizontal direction with 400 nm center spacing, and 10 in the vertical direction with 600 nm center spacing.

    See documentation in the files. This makes a figure with units in nanometers.

  2. On the figure window, use file -> saveas and save as encapsulated postscript.
  3. Open this file with Photoshop. When you open it, make the height so that 1 pixel = 1 nanometer. This ensures the image is large enough so circle resolution is fairly decent. So for a 10x10 grid of 200 nm circles with 400 nm center spacing, the image size would be (10-1)*400 + 200 = 3800 px high.
  4. Make the image grayscale: Image -> Mode -> Grayscale.
  5. Make it a 1 bit image, use the Posterize function: Image -> Adjustments -> Posterize, set value to 2.
  6. Depending on how you write your subfunction, you may or may not have to invert the image so the elements are black and the background is white. The provided plotcircle(), plotsquare(), and plotrectangle() build arrays of filled elements on a white background. plotantenna() does not. If your subfunction makes filled elements you don't need to do anything, otherwise:
    • Use paint bucket tool, and fill the space between the circles with black.
    • Use: Image -> Adjustments -> Invert.
  7. Use the crop tool, and crop to 2000 px by 2000 px.
  8. Save as .bmp file format.

Fischione 1010 Ion Mill

Fischione 1010 Ion Mill

The Fischione 1010 Ion Mill is a precision ion mill and polishing system for TEM specimens.










Specifications

Specifications

  • PC-controlled table top system
  • Fully programmable and easy to use
  • Includes liquid nitrogen specimen cooling option, and chemical etching option

Fischione 1020 Plasma Cleaner

Fischione 1020 Plasma Cleaner

The Fischione 1020 Plasma Cleaner is used to clean TEM and SEM specimens and specimen holders.









Specifications

Specifications

  • A low energy reactive gas plasma cleans without changing the specimen's elemental composition or structural characteristics
  • Removes hydrocarbons from surfaces such as electron microscopy specimens and specimen holders
  • Easy to use front panel controls

Instrument use instructions

Instrument use instructions

These instructions are also available for download in pdf format.

Operating instructions:

  1. Open the main gas supply tank valve.
  2. Adjust the regulator knob so the gauge reads 10 psig.
  3. Note: failure to turn on the supply gas at the required pressure will result in damage to the plasma cleaner.

  4. Ensure the unit is plugged into the wall socket.
  5. Turn on the unit with the small on-off switch located on the back of the instrument beside the power cable connection.
  6. If a sample holder or blank is installed in the plasma cleaner chamber port and the HIGH VACUUM indicator is lit, the instrument will need to be vented prior to loading your specimen:
    1. Press the VENT button on the front panel, wait until the ATMOSPHERE indicator is lit.
    2. Gently remove the specimen holder or blank from the plasma cleaner chamber port.
  7. Load your specimens (TEM or SEM) on the appropriate holder, re-install holder in plasma cleaner chamber port.
  8. Press the PUMP button on the front panel, wait until the HIGH VACUUM indicator is lit.
  9. Enter cleaning time in minutes:seconds using the numerical buttons on the front panel.
  10. Press SET to begin plasma cleaning. The minutes:seconds display will flash for a short while as the instrument starts up. Once cleaning begins the time will count down and the purple plasma glow will be visible through the glass window on the side of the instrument tower.
  11. Once the timer hits zero, press VENT to vent the chamber to atmospheric pressure, wait until the ATMOSPHERE indicator is lit.
  12. Gently remove specimen holder.
  13. When finished cleaning, place a specimen holder or blank into the plasma cleaner chamber port, press PUMP button on the front panel.
  14. Once the HIGH VACUUM indicator is lit, turn off the instrument with the small on-off switch located on the back of the instrument beside the power cable connection. The instrument will remain at high vacuum until the next use.
  15. Turn off the main gas supply tank valve.

Hitachi Zone cleaner

Hitachi ZoneSEM

Hitachi ZoneTEM

The Hitachi ZoneSEM and ZoneTEM desktop sample cleaners use UV light to remove hydrocarbon contamination from specimens, in a very gentle manner. Learn more about these instruments from the Hitachi High Technologies Canada web site.

Hitachi has a few PDF documents on the Zone cleaners:

Anatech Hummer VI metal sputter coater

Anatech Hummer VI

The Anatech Hummer VI is a metal sputter coater currently setup with a Gold-Palladium target. It is used to apply a metal coating to non-conductive samples for imaging in the SEM.




Specifications

Specifications

  • Continuous and pulse modes
  • Degauss function to remove static charge from samples
  • Gold-Palladium alloy target

Coating rate

Coating rate

To better understand the coating rate (we do not have a thickness monitor attached), two samples were made.

Method:

  1. A piece of polished Gallium Arsenide was used as a substrate.
  2. Layers of Carbon were deposited with the Cressington 208 between different thickness layers of Au-Pd to clearly separate the Au-Pd layers from each other and from the substrate. Hummer VI parameters were 75 mTorr Argon and 10 mA current, with 1 minute, 2 minute, and 3 minute run times.
  3. A Tungsten protective pad was laid down and a TEM section was lifted out of this bulk sample and attached to a half-grid in the FB-2100, and thinned sligthly to reveal the layers of Carbon and Au-Pd with the capping layer of Tungsten.
  4. This grid was mounted to an SEM stub and carbon coated for conduction, and then imaged in the S-4800 SEM to determine Au-Pd layer thicknesses.

The two samples were made separately, to determine level of consistency in the coating runs. Each sample A and B were imaged in three locations, and thicknesses measured.

The average thickness of the depositions were:

Sample A:

  • 1 minute runtime: 9.76 nm
  • 2 minute runtime: 14.55 nm
  • 3 minute runtime: 19.18 nm

Sample B:

  • 1 minute runtime: 11.58 nm
  • 2 minute runtime: 15.54 nm
  • 3 minute runtime: 21.17 nm

This is a completely scientific study with statistical significance, but the results seem mostly consistent. For simplicity the thicknesses can be approximated as:

  • 1 minute runtime: 10 nm
  • 2 minute runtime: 15 nm
  • 3 minute runtime: 20 nm

Instrument use instructions

Instrument use instructions

These instructions are also available for download in pdf format.

Notes:
  • Do not over tighten the nitrogen supply needle valve, or it will be damaged. When closing this valve, once you feel resistance, STOP IMMEDIATELY.
  • Do not touch anything inside the chamber without first wearing gloves.
Operating instructions:
  1. Ensure power switches are off.
  2. Put on gloves.
  3. Lift open chamber lid, do not shake or move top suddenly to prevent target from detaching.
  4. Lift off glass cylinder, place on it's side on the stand provided on top of the sputter coater.
  5. Place sample stub(s) inside chamber. Sample stub should be 1.5 inches from the target. If sample height needs adjusting, please consult staff.
  6. Replace glass cylinder, and lower chamber lid into place.
  7. Gently apply pressure to the chamber lid, and turn on the power switch. Once the vacuum pump starts and vacuum gauge shows vacuum, you can release pressure on the chamber lid.
  8. Adjust needle valve to closed position (DO NOT OVERTIGHTEN), and allow chamber to pump down to approximately 30 mTorr.
  9. Turn on the Argon gas valve at the top of the tank.
  10. Open needle valve wide to flush chamber with Argon, allow vacuum gauge to read 500 mTorr or higher. Close needle valve, and wait for chamber to pump down to approximately 30 mTorr.
  11. Repeat flushing of chamber once more.
  12. Adjust needle valve so there is between 55 mTorr to 70 mTorr of Argon in the chamber.
  13. Turn on high voltage control switch, and adjust voltage control knob until plasma discharge current reads 10 mA.
  14. It may be necessary to make slight adjustments to needle valve and voltage dial to maintain a plasma discharge current of 10 mA.
  15. Start your timer as soon as you see the plasma glow.
  16. Once your desired timer has expired, turn off the high voltage control switch, and open the needle valve wide open to flood the chamber back to atmospheric pressure.
  17. Lift the lid, extract your sample(s). Return lid to closed position.
  18. Turn off Argon gas supply valve at the top of the tank, unplug sputter coater.

Cressington 208 carbon coater

Cressington 208carbon

The Cressington 208carbon is used to apply a thin carbon layer to non-conductive samples prior to SEM imaging, and is suitable for imaging at higher magnifications where metal sputter coating particles become visible.




Specifications

Specifications

  • Microprocessor controlled automatic mode, plus manual mode
  • Continuous and pulsed mode
  • Manual tilt, motorized rotating stage
  • Thickness monitor

Instrument use instructions

Instrument use instructions

These instructions are also available for download in pdf format.

Notes:
  • Do not touch anything inside the chamber without first wearing gloves.
  • Each sharpened carbon rod will typically yield three to four runs of six seconds each. If you start the coating run and it stops before the predermined time, the rod must be replaced.
Operating instructions:
  1. Put on gloves.
  2. Lift open top of chamber.
  3. Remove glass cylinder, and clean it with Kimwipes and aecetone, followed by Kimwipes and ethanol to remove carbon film, and place it on its side on clean aluminum foil.
  4. Install carbon feed rods. Be sure to sand smooth the ride side rod, and install a rod with sharpened tip on the left side.
  5. Install samples on stage and ensure they stay in place when stage is spinning.
  6. Tilt stage if you need to coat the sides of your specimen.
  7. Reinstall glass cylinder.
  8. Close top of chamber.
  9. Turn on stage rotation (use speed 4 out of 5).
  10. Press power switch to ON.
  11. When vacuum reaches better than 10-4 mbar (takes about 4 minutes), ensure auto/manual switch is set to auto, and press Start. Instrument will run for six seconds, which yields approximately 1.5 nm thick film.
  12. Wait at least two minutes for the carbon rods to cool, and vacuum to reach better than 10-4 mbar, and repeat step 11 until required thickness obtained.
  13. When finished coating, press Power to turn off the instrument. WAIT FOR TURBO PUMP TO GO COMPLETELY SILENT BEFORE OPENING CHAMBER OR YOU WILL DAMAGE THE PUMP.
  14. Remove glass as before and remove samples.
  15. Clean glass as before and reinstall on instrument, and close the lid.
  16. Sign log book.

Gatan Cryoplunge 3

Gatan Cryoplunge 3

The Gatan Cryoplunge 3 is a semi-automatic plunge freezing instrument for preparing frozen hydrated samples.

The instrument has been delivered and our staff trained in its use. It is ready for use, but will have to be moved to a lab with a working fume hood, until our fume hoods are plumbed.






Instrument instrutions

The following PDF files are available for download:

General resources

Finding the center of a circle

Finding the center of a circle

There are situations where one might want to navigate to the center of a circle that is too large to see at the lowest available magnification. In these situations, record three points along the perimeter of the circle, and use the following Matlab function to compute the center of the circle:

Coordinate transformations

Coordinate transformations

There are situations where one might want to translate coordinates between systems:

  • Moving a specimen from the FIB to SEM, to take high resolution images of fabrications.
  • Finding the same location on a specimen on the SEM or FIB, some time later, when the specimen is assembled differently on the holder.

The following two downloads discuss the method (Helmert Transformation in two dimensions), and provide a Matlab function to compute coordinates of a point of interest P, between coordinate systems.

Two reference points are needed on the specimen. Typically a fine point Sharpie is used to make these marks, and the FIB used to fabricate cross hairs on the Sharpie dots. The coordinates of those two reference points must be known in both instruments, and the coordinates of the point of interest P must be known in one coordinate system (typically on the FIB, where the structure was fabricated). The Matlab function then computes the new coordinates of P based on the location of the reference marks in both coordinate systems.

Critical Information

Please review these items before booking your instrument or planning your project.



  • Adam will be away next Tuesday and Wednesday, October 28 and 29.
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  • Hitachi S-4800 SEM users will no longer pay an additional fee to use EDS, as of April 1st. See http://t.co/44xClI4ICg
    Posted 6 months ago
  • Hitachi S-4800 SEM user fees have increased for inside and academic users as of April 1st. See http://t.co/ZXK9HQM45L
    Posted 6 months ago
  • Want to book sessions past 4:45 PM? Contact Adam about becoming approved for after hours access.
    Posted 9 months ago
  • Want to get trained on the STEHM? Fill out the application form, and we'll notify you when the next session will be. http://t.co/FBND5ZHPGC
    Posted 1 year ago

Workshop News

See below for the next available workshop and workshop related news.


  • The first day of the next SEM workshop has been moved from October 29th to October 30th.
    Posted 19 mins ago
  • The next SEM workshop has been moved by several days. New dates: October 29th and November 4th, 2014.
    Posted 20 days ago
  • The next FIB workshop is Nov 3 & 5, 9:30 AM to 12:30 PM. Sign up online: http://t.co/iRkXOeXgKg
    Posted 24 days ago
  • Just posted -- four SEM training videos: astigmatism correction, beam align, aperture align, and stigma align. http://t.co/ieIudpP3YT
    Posted 1 month ago
  • Training videos on inserting and removing specimens with Hitachi S-4800 SEM have been posted. http://t.co/ieIudpP3YT
    Posted 11 months ago
  • The fee structure has been posted for SEM EDX training. http://t.co/PsGRc7y4k0
    Posted 11 months ago
  • Want to get trained on the STEHM? Fill out the application form, and we'll notify you when the next session will be. http://t.co/FBND5ZHPGC
    Posted 1 year ago

In The News

When the AMF is featured in the news, you will find it here.


Full Feed

This is the complete feed of every posted item. Click on the icons below for archive of older items.


  • Adam will be away next Tuesday and Wednesday, October 28 and 29.
    Posted 10 mins ago
  • The first day of the next SEM workshop has been moved from October 29th to October 30th.
    Posted 19 mins ago
  • There is now a study area with table and chairs at the end of the lab hallway.
    Posted 43 mins ago
  • Food and drink is no longer allowed in the lab. Please leave it on the table outside the main lab door.
    Posted 44 mins ago
  • Adam has resigned his position at the lab, and will be leaving UVic in several weeks.
    Posted yesterday