Cryo-FIB-SEM-CT: a 'three-in-one' imaging facility for opaque soft matter

Lead Research Organisation: University of Edinburgh
Department Name: Sch of Physics and Astronomy


The University of Edinburgh (UoE) is an international centre for soft matter research. Soft matter scientists study complex liquids in which there are structures intermediate in size between the small molecules making up the solvent and the macroscopic world of structures visible to the naked eye. The structures may be pigment particles in paint (colloids), self-assembled aggregates of soap molecules in washing-up liquid (surfactant micelles), bubbles (say, in whipped cream) or long-chain molecules (polymers) such as DNA (as used in gene transfection). The field is of fundamental interest because the properties of these materials are controlled by many competing length and time scales, and can change dramatically under everyday conditions. Such materials are also ubiquitous in formulations of all kinds, such as medicines (CALPOL is a suspension of colloidal paracetamol) and personal care products (a shampoo is a surfactant-polymer mixture). They are also key intermediates in many sectors: all ceramics, for example, begin as soft pastes (think potter's clay) that are pumped into moulds or extruded before they are sintered at high temperatures to form the final hard products.

A fundamental challenge in soft matter is to figure out the way these intermediate structural elements are organised, and how such organisation changes in response to external forces. Most of such materials are opaque to light, so that optical microscopies of all kinds are not useful except to give surface information. As a result, scientists sometimes resort to various kinds of electron microscopy, which, however, operate in a vacuum, so that wet samples are desiccated and their native structures destroyed.

A major development in the last decades is cryogenic scanning electron microscopy (cryo-SEM). A native, wet soft sample is frozen in liquid nitrogen, using special techniques to ensure rapidity of cooling to preserve intricate microstructures. Then these frozen samples are fractured, exposing internal structures to be imaged by SEM. (One disadvantage is that samples fracture more or less randomly, so that what is exposed to view is haphazard.) A single cryo-SEM instrument exists at UoE. This decade-old instrument is limited in both resolution (ten times worse than the best instruments today) and in access for soft matter scientists, as it requires laborious conversion of the system to cryogenic mode. We propose to purchase a state-of-the-art cryo-SEM to enable this cutting-edge technique to become routinely available for day-to-day work.

This purchase is timely, because cryo-SEM has recently been revolutionised for soft matter researchers by the addition of focussed ion beam (FIB). This powerful technique uses a focused beam of charged atoms (ions) to cut and section specimens very accurately inside the SEM. This not only allows the user to expose desired sections at will, but also to build up a complete 3D picture (literally) by imaging the sample section by section to a resolution of 10 nm (100 times the size of atoms). We propose to purchase a cryo-FIB SEM. The technique is so new that we know of only two current instruments in the UK, neither of which is dedicated to the study of soft matter. We propose to add X-ray tomography capability to our cryo-FIB SEM. This allows us to build up a 3D picture non-destructively to 350 nm resolution, much like the way X-ray CT scanners build up 3D images of the body in hospitals. The availability of this combined suite of instruments will transform the ability of soft matter scientists to see inside their samples routinely. A host of exciting applications immediately follow. One example is 'designer electrodes' based on novel soft materials that minimise expansion/shrinkage during charge/discharge cycles. A programme of outreach and training will make this facility available to academic and industrial researchers UK-wide.

Planned Impact

The equipment will contribute to four areas with national societal and economic significance, which are also EPSRC priorities:
1) Formulations: industrial formulations include complex fluids as the final product (e.g. shampoos, foods), or products with complex-fluid stages during their processing and manufacturing (e.g. polymer composites and nanocomposites). Formulations contribute £180bn mark value in the UK, but their production to date is largely based on empirical formulas and past experience. Innovation and creation of new markets require a radical change to predictive models for new formulations. Obtaining an accurate picture of nano/microscale structures is of paramount importance in transitioning formulations 'from art to science' (terminology used by the UK's National Formulation Centre), because it is the response of these structures to external forcing that underpin all applications of soft matter. Our instrument allows scientists to probe the 3D structure of soft samples at the 10 nm to 10 micrometre scale, which is the most relevant for applications. By making this technique routinely available, it will therefore transform our understanding of many industrial products and processes, and therefore contribute directly to reaching to goal of 'predictive formulations' by validating models and simulations.
2) Energy: the instrument will enable new work by our hard-matter scientists studying hydrogen under extreme conditions, creating improved solar energy solutions and synthesising novel solid-state hydrides. Our soft matter scientists are using a new material they patented, bijels, as novel solid electrolytes with improved safety, and as new-generation electrodes minimising cracking and therefore improved lifetime. The new instrument will transform their work in collaboration with some of the top battery scientists in the country (e.g. Peter Bruce, Oxford). For example, it will enable them to survey cracks non-destructively (CT), and then study sections near the crack at high resolution (FIB).
3) Health: living cells are 'soft matter come alive'; synthetic soft matter also finds many applications as biomedical materials (catheters, implants, etc.). Again, detailed structural information underpins all advances in these fields. Thus, e.g., UoE scientists will use the new instrumentation to help find new ways of synthesizing organic-inorganic composites that may be useful for enamel repair. Separately, SoPA hosts one of the biggest bacterial biophysics research efforts in the UK, where the new instrument will enable researchers to study the structure of bacterial colonies and biofilms at a new level of detail. The information obtained should give insights in the continued effort to find new ways of stopping bacterial adhesion, which offer a different pathway to impact on the global problem of antimicrobial resistance (by reducing the need for antibiotics).
4) Food security: As many foods are soft matter systems, the new instrument will have the capacity to be used in this key area of societal and economic importance. UoE scientists will use it to help in the discovery of new ingredients, e.g. to modify ice melting, which can significantly decrease food spoilage and therefore wastage. Discovering the nano/microstructure of food ingredients can also lead to more efficient ways of enabling one industry to use wastes from another, from animal-skin-derived collagens to cellulose from plant materials (fruit peels, etc.).


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Description Using the cryo-FIB/SEM we were able to characterise ionogels and determine that their pores are filled by imaging in cross-section using the SEM and EDS ( These ionogels are of interest as novel materials that can be used to help with dealing with waste heat, turning previously wasted heat that would have been dumped into a river (for example) to something more productive such as desalination.

The cryo-FIB/SEM was also used to produce a TEM sample of novel ZnO nanowires using the liftout method. The site-specific nature of this method was used to gain information on the grain structure at the interface of the seed layer used during growth of these one dimensional materials, leading to a better understanding of the process (

The EDS detector has been used to help with characterisation of novel superconducting materials by confirming the ratio of elements present after crystal growth (

The use of Cryo-SEM was also used to characterise the effect of different cross-linkers on the morphology of hydrogels, with clear changes to the pore size observed.(

We have also been involved in several industrial collaborations, where we have used the microscope to reveal something important to the companies about their product. These range from 'house-hold name' food products to engine oils. These findings are covered by NDAs so full details can't be included here.
Exploitation Route Various findings are reported in publications and disclosed back to collaborating industrial partners.
Sectors Aerospace, Defence and Marine,Agriculture, Food and Drink,Chemicals,Electronics,Energy,Environment,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology

Description So far images taken using the microscope have been used by two industrial food companies as part of a larger research project. The exact findings are confidential but we know that they were interested and pleased with the findings and are in the process of finding further funding for another research project. We expect these findings to contribute to changes in their food products in the next few years. In 2020 and 2021 we have also been involved in several industrial collaborations, where we have used the microscope to reveal something important to the companies about their product. Again, the findings are covered by NDAs but we know that both collaborators were pleased with the findings and they should contribute to product improvements in the future. One collaborator plans to use the facility again in the near future.
Sector Aerospace, Defence and Marine,Agriculture, Food and Drink,Chemicals,Electronics,Energy,Environment
Impact Types Economic

Description Rosetrees Trust Seedcorn Grant
Amount £17,684 (GBP)
Funding ID Ref m847 
Organisation Rosetrees Trust 
Sector Charity/Non Profit
Country United Kingdom
Start 05/2019 
End 06/2020
Description Afton project 
Organisation Afton Chemical
Country United States 
Sector Private 
PI Contribution Cryo FIB/SEM was used to image various engine oil mixtures (or samples derived from constituent parts) in cross-section. No other technique is able to view the structures of these mixtures at high resolution.
Collaborator Contribution Afton supplied the samples and materials for us to make our own samples. They also provided expertise in the samples that made interpretation of the images easier.
Impact No direct outcomes yet, project is ongoing. Multi-disciplinary collaboration with Physics and Chemistry involved.
Start Year 2020
Description Project Bisto 
Organisation Premier Foods Group Ltd
Country United Kingdom 
Sector Private 
PI Contribution The Cyro-FIB-SEM was used to get high magnification images of food samples in the wet state and frozen fast to reduce ice crystal size. The FIB enabled imaging of the cross-section and therefore a closer look at the interface between different parts of the sample. EDS was also used for elemental analysis.
Collaborator Contribution A 6 week secondment of a member of their research team. During this time the researcher used the Cyo-FIB-SEM facility on numerous occasions, with assistance from Univeristy of Edinburgh staff. They also provided the samples and research questions.
Impact Possible further future collaboration with Premier Foods - still under discussion.
Start Year 2019
Description Quorn Study 
Organisation Quorn Foods Limited
Country United Kingdom 
Sector Private 
PI Contribution Cryo-SEM was used to image and measure ice crystals in frozen Quorn products.
Collaborator Contribution Our partners provided the sample and scientific questions.
Impact Further investigations are currently being planned.
Start Year 2019
Description STEM sample 
Organisation MCS Group
Country United Kingdom 
Sector Private 
PI Contribution Use of the FIB to make a thin sample for TEM or STEM imaging. STEM imaging in the Cryo-FIB-SEM.
Collaborator Contribution Provided the sample.
Impact We are not sure about the outcomes and impact the work had as the partner was doing the work for another client.
Start Year 2019
Description Microscope demonstration 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Undergraduate students
Results and Impact ~30 undergraduates from China toured the University. They were shown the Cryo-FIB/SEM working during a demo and introduction. The intended purpose is to advertise the university and increase postgraduate attendance here.
Year(s) Of Engagement Activity 2019,2020
Description Virtual microscope demonstration for teaching 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Undergraduate students
Results and Impact Microscope demonstration was held virtually for undergraduate teaching purposes. Students responsed well with interest and enthusiasm.
Year(s) Of Engagement Activity 2021