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FEI Magellan 400 XHR Scanning Electron Microscope (SEM)


The instrument is an FEI Magellan 400 XHR Scanning Electron Microscope (SEM) with FEG source, located in the basement of the Spilker Building, Room 008A. The microscope is equipped with a retractable backscatter detector, retractable STEM detector, beam deceleration capabilities, and a Thermo Fisher Scientific Pathfinder EDS UltraDry 60M with Pinnacle software.

Principles of operation: In a SEM, a fine beam of electrons is scanned across the surface of a specimen in synchronism with a spot on the display screen. A detector monitors the intensity of a chosen secondary signal from the specimen (for example, secondary electrons) and the brightness of the display spots controlled by an amplified version of the detected signal. If, for any reason, the intensity of the emitted secondary signal changes across the specimen then contrast will be seen in the image on the display screen. The resulting image is strikingly similar to what would be seen through an optical microscope; the illumination and shadowing show a natural-seeming topography. It is important to remember that the image formed in an SEM is not necessarily that of the surface. As the electron beam penetrates the sample, the interaction causes excitation of secondary, backscatter, and Auger electrons; characteristic and Bremsstrahlung x-rays; and photons. It is possible, by choosing the electron energy, to control the depth to which the electrons penetrate and the type of emitted signal used to form the image. While this gives the microscopist a great deal of control over the nature of the final image, an understanding of how the image is formed is required to interpret it sensibly.

Restrictions on samples: The sample material must be able to withstand a high vacuum environment without outgassing. It must be clean. It may be attached to the sample holder using high-vacuum-compatible silver paint or clean clips. The sample should be electrically grounded to the sample holder to minimize charging. If the sample is nonconductive, the sample may be coated with a conductive layer (we can provide Pd coating upon request). Note that rough surfaces should be conformally coated. The workstation can accommodate up to 100 mm (4”) wafers.

For Au/Pd (60:40 ratio) coating on your samples, please do the following:

  • Bring your mounted sample(s) in a case (labeled with your contact info, any non-standard parameters, and the time of your scheduled microscope session) to the Sample Mounting Lab in McCullough 101.  The overhead cabinet to the right of the coater is labeled with one side where you will drop off your sample (“Samples to be coated”), and the other for where we will place the coated samples.
  • Email “” to let us know that you have dropped off your sample(s) - similarly indicate when your microscope session will be.  Please remember that we may not be able to get to it immediately, so last-second requests will be difficult.
  • When we are finished coating, we will put it back in the “Coated samples” side of the cabinet and you can pick it up.

Electron beam resolution:

At optimum working distance (SE mode)
15 kV 0.8 nm
2 kV 0.8 nm
1 kV 0.9 nm
200 V 1.5 nm


Advanced techniques:

  • Energy Dispersive Spectroscopy (EDS)

Contact Information

Richard Chin
office: (650) 723-8142

Ann Marshall
office: (650) 723-3572

Spilker 008A
lab: (650) 725-2278


Research Examples

Crystals of Indium Tin Oxide (ITO). Image courtesy of Arnold Forman (Jaramillo Group, Stanford).

Silica Nanoshells. See Stanford News for more details on this research. Image courtesy of Yan Yao (Cui Group, Stanford)


Getting Started

In order to become a qualified user on the FEI Magellan SEM, you need to follow these steps:

Our normal mode of operation is to train users to perform the characterization experiments themselves. Service requests will be considered on a case-by basis.


Training Information

Before being considered for training on the FEI Magellan SEM, you must first be a fully qualified user of either the Thermo Fisher Scientific Apreo SEM.  You will need at least two Magellan training sessions (one orientation with the Magellan interface, the second as a final) to be authorized as a beginner user.  Training sessions occur at routine times and dates on the calendar.  Please contact a trainer if you cannot make existing training sessions.
In order to begin Magellan training, you need to follow each of these steps in the order as listed here:

  • Complete the Magellan Project Proposal Form
  • Arrange a time with one of the staff scientists (Rich Chin, Juliet Jamtgaard) to discuss the completed form.  The login and password for the Magellan sign up calendar will be given at that time.
  • Sign up for training slots on the Magellan sign up calendar.  If final training, you will be expected to provide your own sample, properly and cleanly mounted.

Our normal mode of operation is to train users to perform the characterization experiments themselves. Service requests will be considered on a case-by basis.


Other information