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Electron microscopy

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Allan Mitchell
Allan Mitchell

Electron microscopy uses a beam of accelerated electrons to visualise specimens. This can create high resolution images that reveal the fine structures of cells, microorganisms, molecules, metals, crystals and many other specimens.

Read more about:

Your project

To start a project, please contact a staff member to discuss options, normally this contact will be Allan Mitchell. If appropriate, we will then ask you to register your intention to use the facility so that we have your details.

If you are new to electron microscopy, discussing your plans before you start collecting specimens, especially biological specimens, is strongly advised. The staff will help you with specimen preparation and, where appropriate, train you to use the equipment.

Depending on your needs and the scale of your project, you may choose to use the facility in a fairly independent manner (subject to appropriate training and staff approval), or have the staff do the bulk of your work.

Initial advice and consultation

Contact for initial advice:

For advice on the latest academic advances contact:
Dr Mihnea Bostina
Director, Electron Microscopy

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Services and techniques

Our electron microscopy facility accommodates a broad range of techniques.

Electron microscopy staff expertise

Visit Scanning electron microscopy (SEM) techniques  to read more about:

  • Array Tomography
  • Backscattered Electron Imaging
  • Cathodoluminescence
  • Cryo-SEM
  • Electron Backscatter Diffraction Imaging
  • Energy-Dispersive X-ray Spectroscopy
  • High Resolution SEM
  • Secondary Electron Imaging
  • Variable Pressure SEM

Visit Transmission electron microscopy (TEM) techniques  to read more about:

  • Conventional TEM
  • Correlative TEM
  • Cryo-TEM
  • Cryoultramicrotomy
  • Electron Tomography
  • Freeze-Fracture TEM
  • Heating and Cooling TEM
  • High Pressure Freezing (HPF)
  • Immunocytochemistry
  • Metal Shadowing
  • Negative Staining
  • Scanning Transmission Electron Microscopy (STEM)
  • Single Particle Reconstruction

Other services

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Charges for Electron Microscope use from 1 July 2021

Users can choose to be charged at the casual hourly rate or to prepay for a Tiered Fee (see table below). From 1 July to 31 December 2021 the Tiered Fee rates will be half of these.

Full year charges for microscope use:

Tier Number of hours Division of Health Sciences users Other users
Casual 1 $60 $240
Tier 1 up to 40 $1,500 $6,000
Tier 2 40 to 80 $2,500 $10,000
Tier 3 80 to 150 $4,500 $18,000
Tier 4 more than 150 $7,000 $28,000

OMNI Electron Microscopy charges (PDF)

Electron Microscopy sample processing charges from 1 July 2021:

Health SciencesNon-Health SciencesExternal
TEM sample preparation with resin embedding
Price per sample vial35.0035.0035.00
Price for staff processing time (1 to 10 vials)30.00120.00240.00
High pressure freezing (HPF) (includes LN2*)
HPF run – up to half day of freezing130.00280.00400.00
HPF run - full day of freezing200.00350.00500.00
Plus per-sample cost7.507.507.50
Automatic freeze substitution (AFS) (includes LN2*)
AFS run (up to 30 samples) – Epoxy resin230.00330.00450.00
AFS run (up to 30 samples) – Acrylic resin350.00450.00570.00
Vitrobot run (up to 4 grids) – by EM staff35.0070.00110.00
Vitrobot run (up to 4 grids) – by user25.0030.0030.00
Plus per-sample cost of grids:
Quantifoil/C-Flat carbon10.0010.0010.00
Quantifoil Gold20.0020.0020.00
Ultramicrotomy and staining (per block)
Semi-thin sections (includes trimming block) – by EM staff10.0025.0045.00
Ultra-thin sections (~3 grids) and staining – by EM staff15.0035.0055.00
Semi-thin sections (includes trimming block) – by user5.008.00
Ultra-thin sections (~3 grids) and staining – by user5.0010.00
SEM preparation
Fixation, CPD and mounting per sample/vial – by EM staff40.0090.00160.00
Mounting only per sample – by EM staff5.0010.0020.00
Sputter coating per run – by EM staff30.0035.0040.00
Carbon coating per run – by EM staff15.0020.0025.00
Fixation, CPD and mounting per sample/vial – by user25.0025.00
Mounting only per sample – by user3.003.00
Sputter coating per run – by user25.0025.00
Carbon coating per run – by user10.0010.00
Microscopy operation by EM staff for users (per hour)10.0040.0080.00
Training in sample preparation or EM use by EM staffFreeFreeFree

*LN2 = liquid nitrogen

Good preparation helps minimise your costs:

  • Good planning (knowing what to expect before starting the investigation)
  • Knowing your sample (the time taken to find the information you are looking for—often under-estimated)
  • The number of samples you prepare at any one time (very important)
  • Consider if new questions may emerge as your investigation proceeds

Email for further advice.

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Student Research Award

The OMNI Electron Microscopy Student Research Award is open to applications twice a year. It provides students with up to 15 hours of free microscopy time. Consult with your supervisor and check out your eligibility.

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Discussing your Electron Microscopy needs with staff is essential prior to registration and training in the use of equipment. Access to booking calendars is given only after users demonstrate competence on the relevant equipment.

Visit Microscope specifications and sample preparation equipment for more information about:

  • JEOL 2200FS Cryo-TEM
  • JEOL 6700F FE-SEM
  • Philips CM100 TEM
  • Zeiss Sigma VP FEG SEM
  • SEM and TEM sample preparation equipment

For more about our equipment's capabilities visit:


To begin a new project please read the User Policy and complete a Project Registration form. This includes projects involving transmission electron microscopy (TEM), scanning electron microscopy (SEM), ultramicrotomy sectioning, specimen preparation, or supply of liquid nitrogen.

User Group

The User Group consists of members that represent University of Otago departments that use the Electron Microscopy unit and it advises the OMNI Academic Advisory Group on direction and strategy.

Visit About us for information about how our user groups work and how to make contact.

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Training and online resources

Technique training resources and support

Email if you need help or advice.

Data analysis resources and support

The Electron Microscopy unit has various computer hardware running OS X and Linux for data processing and analysis. These computers are available for registered users. Please discuss your data processing needs with the staff.

Electron microscopy data and archiving provides advice on protecting your data.