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:
To start a project, please contact a staff member to discuss options, normally this contact will be Richard Easingwood. 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.
Contact for initial advice:
Our electron microscopy facility accommodates a broad range of techniques.
Visit Scanning electron microscopy (SEM) techniques to read more about:
- Array Tomography
- Backscattered Electron Imaging
- 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
- Electron Tomography
- Freeze-Fracture TEM
- Heating and Cooling TEM
- High Pressure Freezing (HPF)
- Metal Shadowing
- Negative Staining
- Scanning Transmission Electron Microscopy (STEM)
- Single Particle Reconstruction
- Consumables for Electron Microscopy
- Liquid nitrogen supply
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|
|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|
Electron Microscopy sample processing charges from 1 July 2021:
|Health Sciences||Non-Health Sciences||External|
|TEM sample preparation with resin embedding|
|Price per sample vial||35.00||35.00||35.00|
|Price for staff processing time (1 to 10 vials)||30.00||120.00||240.00|
|High pressure freezing (HPF) (includes LN2*)|
|HPF run – up to half day of freezing||130.00||280.00||400.00|
|HPF run - full day of freezing||200.00||350.00||500.00|
|Plus per-sample cost||7.50||7.50||7.50|
|Automatic freeze substitution (AFS) (includes LN2*)|
|AFS run (up to 30 samples) – Epoxy resin||230.00||330.00||450.00|
|AFS run (up to 30 samples) – Acrylic resin||350.00||450.00||570.00|
|Vitrobot run – by EM staff||35.00||70.00||110.00|
|Vitrobot run – by user||25.00||30.00||30.00|
|Plus per-sample cost of grids:|
|Ultramicrotomy and staining (per block)|
|Semi-thin sections (includes trimming block) – by EM staff||10.00||25.00||45.00|
|Ultra-thin sections (~3 grids) and staining – by EM staff||15.00||35.00||55.00|
|Semi-thin sections (includes trimming block) – by user||5.00||8.00|
|Ultra-thin sections (~3 grids) and staining – by user||5.00||10.00|
|Fixation, CPD and mounting per sample/vial – by EM staff||40.00||90.00||160.00|
|Mounting only per sample – by EM staff||5.00||10.00||20.00|
|Sputter coating per run – by EM staff||30.00||35.00||40.00|
|Carbon coating per run – by EM staff||15.00||20.00||25.00|
|Fixation, CPD and mounting per sample/vial – by user||25.00||25.00|
|Mounting only per sample – by user||3.00||3.00|
|Sputter coating per run – by user||25.00||25.00|
|Carbon coating per run – by user||10.00||10.00|
|Microscope operation by EM staff for users (per hour)||10.00||40.00||80.00|
|Training in sample preparation or EM use by EM staff||Free||Free||Free|
*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 email@example.com for further advice.
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.
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 Serial Block Face SEM
- 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.
- Electron Microscopy User Policy
- OMNI Electron Microscopy Project Registration - internal users
- OMNI Electron Microscopy Project Registration - external users
- OMNI Equipment Use Policy (PDF)
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.
Technique training resources and support
Email firstname.lastname@example.org if you need help or advice.
- Visit My Scope for advanced instrumentation and techniques (AMMRF website)
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.