MR-Microscopy and Preclinical MRI Research Facility

The preclinical MRI research facility provides two dedicated Bruker MR systems; a horizontal bore 7T, and a vertical bore 9.4T.

MR Microscopy and Preclinical MRI Research Facility


MRI introduction

MRI is a technique that uses the properties of the atomic nucleus exposed to magnetic fields to create images. It’s used throughout medicine to detect such things as cancerous growths, diagnose heart function and monitor babies in the womb. Unlike x-rays it does not use ionising radiation to create these images, therefore it is safe for repeated use. Not only can MRI create images, but it can measure dynamic changes such as flow, diffusion and brain function. MRI’s use goes beyond medicine. Its ability to detect a vast range of molecules means it can be used to study the behaviour of different materials such as oils and rock cores. 

NMR is the sister technique to MRI. It uses the same basic science but is applied to the identification of different molecules. It’s commonly used in chemistry to detect molecular structure. Its biological application is in metabolomics. This is the study of how cells convert one molecule to another. NMR can detect these processes to identify which biological processes are important. The information provided by NMR can find biomarkers that can be used in the clinical identification of diseases.

Research Facility

The preclinical MRI research facility at the University of Sheffield (UoS) consists of two scanners. Details of each scanner’s unique capabilities are detailed below. The appropriate choice of scanner depends on the project requirements and research objectives. This would be made on the advice of the facility manager in discussion with the user. The type of experiments that can be performed include structural images, spectroscopy, perfusion, diffusion, and functional MRI. For bespoke requirements, novel imaging protocols can be created in-house alongside any additional hardware developments.

For data analysis, Facility staff can advise the end-user on aspects of this and provide software tools to aid them. Complete analysis of data is available should the user require this.

The facility is available to both internal and external users including industry researchers.

Requests for access can be made by contacting:

7T MRI scanner

The 7T scanner is a horizontal bore system designed to facilitate small animal imaging. The larger bore size means it can image mouse, rat and other animals or objects up to 15 cm breadth. There are a range of rf coils available for detection of 1H or other X-nuclei (e.g. 13C, 31P, 129Xe). The scanner has the latest version of Bruker Paravison 7 imaging software.

7T Bruker MRI scanner
7T MRI scanner

Sited directly next to the magnet room is an equipped surgery. Here, anaesthesia can be provided with animal physiology monitoring (breathing rate, ECG, blood pressure, body temperature). These monitoring methods can be reproduced inside the magnet for animal well-being.

7T surgery / animal preparation room with animal monitoring, mobile anaesthesia and gas delivery system
7T surgery / animal preparation room with animal monitoring, mobile anaesthesia and gas delivery system

The scanner is routinely used in mouse and rat brain imaging at high resolution, typically voxel resolution is 100 μm but can be smaller if required. Images can be enhanced with gadolinium contrast agents, for example to highlight tissue lesions.

Rat and mouse brain images, and rat heart images
Left: rat brain (upper) and mouse brain (lower) images. The facility has dedicated coils for head imaging of both animals at 7T. Right: rat heart dynamic heart images acquired without cardiac gating.

Rapid EPI imaging can be used to estimate cerebral blood flow for the assessment of disease progression. These experiments can be expanded to perfusion, for a marker of blood/brain barrier integrity. EPI imaging is often used in functional imaging (fMRI). Scanning whilst applying shorts period of stimuli can detect regional changes in brain activity.

BOLD effect in a rat brain, and blood flow map in a mouse brain.
Left: (top) Time dependent visual stimuli can be detected by the BOLD effect in the visual cortex of a rat. (bottom) Regular application of light pulses can stimulate the visual cortex. Right: blood flow map in a mouse brain.

Working with the Department of Materials Science & Engineering, we have used the 7T scanner to study the behaviour of flowing fluids under stress. The enhanced sensitivity available at 7T field strength means that high resolution velocity maps can be produced. MRI is well suited to material studies, including biomaterials such as silk.

MR fluid velocity map of oil & a Spin echo image of a silkworm
Left: Fluid velocity map of oil flowing through a restricted orifice. Right: Spin-echo (MSME) imaging of a silkworm (in-plane resolution: 50x50 μm).

9.4T NMR/MRI scanner

The 9.4T scanner is a dual-purpose instrument capable of both magnetic resonance imaging and high-resolution magnetic resonance spectroscopy. Equipped with an automatic sample changer, the scanner can perform high throughput liquid state NMR spectroscopy. It can also analyse biopsy tissue samples. In imaging mode, the combined field strength and gradient strength permits imaging with <50 μm resolution. The facility also houses a hyperpolarisation instrument (HyperSense) that can increase the sensitivity of NMR by many orders of magnitude. This can be used for measuring metabolism and reaction kinetics in real time.

Vertical bore 9.4T scanner (left) and HyperSense (right).
Vertical bore 9.4T scanner (left) and HyperSense (right).

High Resolution Spectroscopy 

For high resolution NMR spectroscopy, the scanner is equipped with a multinuclear probe capable of observing all of the standard nuclei, e.g. 1H, 13C, 31P and many more (frequency range 1H–15N). It has been used extensively to perform metabolomics studies of cells and biofluids. An automatic sample changer allows 16 samples to be scan without user input for high throughput scanning and overnight/weekend data acquisition. The scanner also has a high-resolution MAS probe that can be used to analyse tissue samples and biopsies.

High-resolution NMR spectra of a biofluid and biopsy tissue sample
High resolution 1H-NMR spectroscopy can be performed on either biofluids (top: example of cervicovaginal fluid) of biopsy tissue (bottom).


The ultra-shield 9.4T magnet allows the scanner to produce high quality images with improved signal to noise ratio (SNR). This can shorten scanning time to reduce the duration of animal experiments. The system is equipped with a powerful gradient set (1500 mT/m) allowing micrometre resolution imaging as small 15 μm in plane voxel size. 

Images of excised mouse brain and foetal heart
Left: Spin-echo (RARE) imaging of excised mouse brain ( Right: Foetal heart 58x58x58 mm (

Zebrafish have become a ubiquitous animal model for studying a range of diseases and conditions. Typically, these studies are conducted in transparent juvenal fish where optical imaging techniques can be used. However, this is more difficult in adult zebrafish, restricting their use in longitudinal studies. Developed within the preclinical MRI facility, we have the capability to image live zebrafish. The animal can be scanned at high resolution (In plane, 50x50 μm, 200 μm slice thickness) with easy loading and full recovery to facilitate longitudinal studies.

MRI scan of a live zebrafish at 9.4T. The animal was fully recovered after imaging. In plane resolution 50x50 um, 200 um slice thickness, TE/TR 14/1500 ms, NEX 64. Animal age at scanning was 10 months old.


The HyperSense instrument uses dissolution dynamic nuclear polarisation (dDNP) to increase the sensitivity of magnetic resonance spectroscopy (see our Hyperpolarisation webpage for the physics behind the technique).

To date the method has been extensively used in studying pyruvate metabolism, a key molecule in cellular energy generation. The experiment involves administering a bolus of hyperpolarised pyruvate to an animal or cells and rapidly measuring the 13C MRS spectrum in real time. As pyruvate is metabolised, daughter products such as lactate and bicarbonate can be detected. The rate of formation of these products can inform on the relative importance of glycolytic metabolism (lactate) and oxidative phosphorylation (bicarbonate). High levels of lactate are a marker of cancer, and when combined with imaging DNP can detect tumour cells and their response to response to treatment. The technique has been applied to other target organs, including the heart, kidney and brain.

Kinetics of 13C pyruvate to lactate conversion
Rapid sequential acquisition of MR spectra shows the time evolution of peaks representing hyperpolarised pyruvate and its metabolic products, lactate & bicarbonate (left). The size of the peaks can be fitted to model metabolic conversion rates (right).


The equipment the facility has available is listed below.


(Alfred Denny Building G Floor)

Horizontal Bore  Bruker Biospec (70/30S)

  • Dedicated imaging gradient inserts (660mT/m) and (1000mT/m)
  • RF coils, including quadrature 1H volume coils (156, 86, & 35mm inner diameter), single loop 1H surface coils, and two 4-channel phased array coils (mouse & rat). Dual nuclei surface RF coils ( 13C/1H,  31P/1H)
  • Designated surgical theatre, recovery room
  • Mobile anaesthesia and gas delivery system
  • Physiology monitoring equipment (Respiration rate, and ECG)
  • Zoovent artificial respiration control system
  • Blood gas analyser
  • Dedicated electronics lab space and equipment

9.4T MRI/S

(Jessop Wing, Level 4)

Imaging: Vertical Bore  Bruker MRI/S system

  • Imaging gradient insert (1500 mT/m)
  • Imaging probes
    • 1H detection, 5, 25 mm, volume coil
    • 1H/13C detection, 10, 25 mm, volume coil
    • 1H/31P detection, microscope slides
  • MR elastography transducer and driver
  • Live animal physiology maintenance and monitoring (temperature, breathing, ECG). Live zebrafish maintenance and recovery
  • Full anaesthetic via dedicated isoflurane vaporiser and nose cone system
  • Separate room for animal preparation


  • Broadband 5 mm high-resolution liquid spectroscopy probe for 1H and broadband nuclei detection (e.g. 13C, 15N, 19F). This is used extensively to perform metabolomics studies of cells and biofluids
  • Automatic sample changer for high throughput scanning and overnight/weekend data acquisition
  • High-resolution Magic Angle Spinning multinuclear probe (1H, 13C, 31P), used to obtain MR spectra of solid-state samples including powders, cells and biopsy tissue

13C Hyperpolarisation - HyperSense:

  • The 9.4T facility possesses a HyperSense polarizer for in vivo/ex vivo real time detection of cellular metabolism using non-radioactive isotope tracers, e.g 13C-pyruvate for cancer metabolism

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