Electron Microscopy

The imaging team provides a wide range of tools, training, and expertise, with a primary focus on providing access to world-class advanced electron microscopy instrumentation to the CNS community.

Electron Microscopy

The electron microscopy facilities at the Center for Nanoscale Systems (CNS) have been designed to enable cutting edge imaging and analysis research across the physical and biological sciences. The electron microscopy suites were custom-designed to house our sensitive microscopes, with minimal perturbations to imaging from environmental and other external factors. These facilities are supported by dedicated technical staff, with expertise in many aspects of electron microscopy and related techniques.

Several high resolution electron microscopes are available, including aberration corrected instruments, specialized cryo-electron microscopes and advanced analytical detectors. We have focused ion beam tools, which can be used for sample preparation, patterning, milling and in-situ analysis. Our high resolution scanning electron microscopes are equipped with a variety of detectors and are used to study a broad range of specimens. Dedicated spaces, fully equipped with tools for preparing samples, from hard materials and biological specimens, are also provided.

Transmission Electron Microscopy TEM

Transmission Electron Microscopy is one of our core competencies at the Center for Nanoscale Systems. CNS is home to a state-of-the-art collection of high-resolution, aberration-corrected, and cryogenic TEMs. These allow the CNS community, with training and guidance from our knowledgeable staff members, to visualize and analyze their specimens at ultra-high spatial resolution.

High Resolution TEM

High resolution transmission electron microscopy (HRTEM) is a powerful tool for materials analysis. This technique provides visualization of the atomic lattice, providing important information about a materials structure, defects, homogeneity and its composition.

At CNS, we have four HRTEMs available for materials analysis. Each HRTEM is capable of high resolution imaging and diffraction analysis. A dedicated diffraction camera, EDS and/or EELS detectors are available on some instruments. We have a selection of specialized specimen holders available for advanced TEM imaging and analysis.

In-situ electron microscopy allows for real-time visualization and analysis of chemical reactions and other dynamic processes. We have several customized holders available for in-situ TEM/STEM experiments.

Scanning Transmission Electron Microscopy

The technique of Scanning Transmission Electron Microscopy (STEM) is often complimentary to TEM imaging. In this approach, a focused beam of electrons is rastered across the specimen sample, and the transmitted beam is analyzed. Typical STEM analyses include dark field imaging, bright field imaging, and spatially resolved analytical signals such as energy dispersive x-ray spectroscopy (EDS) or electron energy loss spectroscopy (EELS).

The Center for Nanoscale Systems has two STEM instruments, which enable high resolution imaging combined with analytical analysis. One of these instruments is a probe corrected cold FEG system that offers very high spatial and spectral resolution, combined with multiple imaging and analytical detectors.


Cryo electron microscopy (cryo-EM) is a very powerful approach to visualize individual biomolecular systems at an unprecedented resolution and to study their working dynamics in native physiological conditions. At the Center for Nanoscale Systems, researchers are taking advantage of our state-of-the-art cryo-EM equipment to study a variety of soft materials systems in the fields of single particle analysis and structural biology. This research is vital for improving human health and treating diseases, by increasing our understanding of viral membrane fusion machines, ion conducting channels, and protein degradation. We have expertise and equipment available to prepare and image specimens using cryo-TEM and cryo-SEM, enabling analysis of a diverse range of specimens with different specimen preparation methods across many length scales.

Cryo-TEM / Structural Biology / Single Particle Analysis

Cryo-TEM is the analysis of specimens at cryogenic temperatures inside a TEM, enabling imaging of the true integrity of soft materials to be maintained, which is often impossible when standard room temperature protocols are used. As a result, cryo-TEM is of particular importance for applications in single particle analysis and structural biology. In this technique, specimens are rapidly frozen and transferred into the TEM at liquid nitrogen temperatures on a specialized holder, where they are imaged under low beam dose conditions.

We have two dedicated cryo-TEMs available at the Center for Nanoscale Systems. Available facilities include a fully-automated, remotely operated cryo-TEM, designed for structural biologists, with high tilt capacity and a sample autoloader. Our staff are experts at cryo-TEM sample preparation methods and imaging. We also offer rigorous training and guidance on conventional room-temperature sample preparation, including staining, dehydration, fixation, embedding and sectioning protocols, for biological specimens.


The technique of cryo-SEM is a powerful method to study bulk hydrated specimens. These samples are not readily suitable for conventional SEM analysis due to their incompatibility with vacuum conditions. In cryo-SEM, the specimen is rapidly frozen and then imaged at cryogenic temperatures; this allows the integrity of the specimen’s structure to be maintained for imaging without using processing techniques such as dehydration or chemical fixation.

Focused Ion Beam

Focused Ion Beam systems use a finely focused beam of gallium ions to remove nanometers of material or deposit metals and insulators using gaseous precursors. These tools were originally developed for the semiconductor industry but have been readily implemented in the biological sciences, material sciences, applied physics, and geology fields.

At the CNS, we offer three dual beam FIB-SEM systems. These instruments have advanced milling, deposition, imaging and analytical capabilities. Our FIBs are particularly adept at preparing thin TEM specimens, high precision atom probe tips, and performing three dimensional imaging/analysis via the slice-and-view technique.

Scanning Electron Microscopy SEM

Our Scanning Electron Microscopy (SEM) facilities form the backbone of the imaging division. These versatile instruments are used to study wide-ranging specimens including nanofabricated devices, hydrogels, geological specimens and even bugs! Our environmental SEMs capable of imaging biological specimens at variable pressure, hydration experiments and high-resolution field emission SEMs capable of few-nanometer imaging resolution. We can image wet samples, non-conductive materials using variable pressure mode, and conductive samples at the highest resolution using ultra-high vacuum imaging mode. Our knowledgeable technical staff provide training and technical guidance on imaging and analysis to support the broad range of needs of the CNS community.

Field Emission Scanning Electron Microscopy

Field emission scanning electron microscopes (FESEMs) offer high spatial resolution analyses of specimens. At CNS, we have three dedicated FESEMs for high resolution imaging. A range of SEM detectors are available, including Everhart-Thornley, backscatter, STEM, EDS and EBSD.

Our FESEM training procedure comprises three parts: an online course, a hands-on training and a certification. Please see the individual FESEM tool pages for more information about our training program.

Environmental SEM

At the Center for Nanoscale Systems we have specialized SEMs that can perform imaging at variable or extended pressure. These tools enable researchers to compensate for charging effects using an inert gas, and to study specimens under a grater range of conditions, including under hydration.

Biomaterials Facility

The Center for Nanoscale Systems provides a dedicated BL2 laboratory for working with biological materials. This facility is equipped for cell culturing activities and electron microscopy sample preparation. Equipment for cell culturing includes our biohood, mammalian incubator, plate reader, cell counter -20C, -80C and cryo-freezers, a centrifuge and a fluorescence microscope. Equipment for imaging sample preparation includes an ultramicrotome, knife maker, and a biohood for specimen fixation and dehydration.

Imaging Sample Preparation

We have dedicated electron microscopy sample preparation spaces for hard and soft materials specimens. At CNS, we offer specialized training for these facilities, and advise on sample preparation protocols appropriate for the specimen and imaging technique. Our sample preparation facilities include ion mills, cross-section polishers, critical point dryers, a cryoplunge, an ultramicrotome and other systems to facilitate your image acquisition.