Magnetic Resonance Imaging (and Spectroscopy)


Magnetic Resonance Imaging (MRI) is based on the resonance response from magnetic atomic nuclei to radiofrequency excitation. Proton MRI utilizes 1H nuclei in water and other compounds to produce images that yield unique information about the local distribution and relaxation properties of water in tissues and samples. With its highly adaptable, proton-property dependent signal, MRI is able to produce exceptional image contrast in soft, moist tissues and biological samples.

In addition to its high-resolution structural imaging capabilities MRI is also capable to assess a wide variety of biomarkers that provide in-depth physiological and molecular information about tissue viability, function and therapy effects. MRI Methods for physiological and molecular imaging include, tissue vascularization imaging (e.g. perfusion, blood flow, vessel size), oxygenation mapping, localized metabolite assessment using spectroscopy, diffusion imaging, etc. Apart from protons, MRI can also use other nuclei to extend the spectrum of available physiological information. Examples are 3-He/129-Xe imaging, for lung ventilation studies, 31-P/13-C MRI/MRS for the assessment of metabolic pathways and 19-F imaging to assess local tissue oxygenation or cell tracking and targeted imaging.

UNSW BRIL runs a Bruker high-field pre-clinical MRI which is especially optimized for  high-resolution imaging and assessment of physiological and molecular biomarkers in small samples and animals.


The Method – General Overview

Magnetic Resonance Imaging (MRI) is an imaging technology that is based on the resonance response from certain, spinning atomic nuclei to radiofrequency irradiation. Although a wide variety of atomic nuclei can be utilized to obtain information from experimental objects, in the vast majority of cases the response of protons (in water and certain metabolites) is used to produce images of tissues or samples. Proton MRI yields unique information about the local distribution of tissue/sample water and is able to deliver the best contrast for soft tissues of any imaging modality. Modern pre-clinical high field scanners are able to deliver high-resolution anatomical information that is useful for a wide range of applications [1].

Besides high-resolution, high-contrast anatomical imaging of soft-tissues, there is also a wide variety of MRI methods that are able to provide in-depth physiological information about the viability and function of tissues, organs and diseases.

Some examples of current physiological proton MRI methods and applications are:

·   Diffusion of water in samples and tissue: Diffusion weighted MRI is able to give information about diffusion in living tissues. This can yield information about structure sizes in certain regions of interest as well as main anisotropy and directions of structures. This can be utilized to measure integrity of brain white matter axons, etc. [2]

·   Tissue Vascularization: MRI can be used to gather a variety of information about the vascular system. Either contrast agent based or non-contrast agent based methods can be used to measure local blood supply, blood flow, blood volume or perfusion. Also vessel sizes and vessel permeability can be assessed with appropriate MRI methods.

·   Flow imaging: MRI can be used to assess information about general flowing systems. Flow and flow velocities can be quantified over time [3].

·   Fat imaging: Certain contrasts in MRI can be used to assess local fat distribution in tissue. Either contiguous fat pads can be assessed in size, or the local distribution of fat relative to water/muscle can be assessed on a pixel by pixel basis.

·   Spectroscopy/CSI: MRI can be used to gather localized information about a wide variety of metabolites that contain protons with certain shifted resonances. Examples of metabolites that can be identified and quantified by proton MRI are NAA, Creatine, Choline,  Glutamate, Glutamine, myo-inositol, etc. With so called spectroscopic imaging methods (also called chemical shift imaging, CSI) it is also possible to produce images of the distribution of single metabolite concentrations.

·   Tissue oxygenation and oxygen supply can be assessed by exploiting specific magnetic properties of blood for MR Imaging. As blood iron changes its state from a paramagnetic to a diamagnetic state upon oxygenation information can be extracted about current oxygenation status of organs. This so-called BOLD (blood oxygenation level dependent) effect is used in neurofunctional MRI to map neuronal activity and can also deliver information about oxygen supply, e.g. in tumors [4].

·   Magnetic properties of tissues and magnetization transfer can be exploited to collect information about local tissue integrity, e.g. in white matter myelin [5].

·   Novel chemical exchange transfer saturation (CEST) imaging methods can be used to generate novel contrast agents to obtain information about further physiological parameters, such as local tissue pH [6].


Apart from protons, MRI can also use other nuclei that show nuclear resonances to extend the spectrum of available information. E.g. the following Isotopes can be used if special hardware is available (not generally the case for the UNSW facility): Phosphourous P, 3-He, 13-C, 129-Xe, 19F

These so called X-nuclei can open the field to interesting novel experiments and make additional information available, which is not otherwise accessible. Possible applications/examples of X-nuclei Imaging can be: Lung studies ventilation with noble gases as 3-He or 129-Xe, spectroscopy and imaging of metabolic pathways using 31-P od 13-C as “tracers”, oxygenation imaging, cell tracking and targeted imaging with 19-F nuclei, etc. Some examples may be found in the references [7], [8].



1.         Benveniste, H. and S.J. Blackband, Translational neuroscience and magnetic-resonance microscopy. The Lancet Neurology, 2006. 5(6): p. 536-544.

2.         Jiang, Y. and G.A. Johnson, Microscopic diffusion tensor imaging of the mouse brain. Neuroimage, 2010. 50(2): p. 465-471.

3.         Lotz, J., et al., Cardiovascular flow measurement with Phase-Contrast MR imaging: Basic facts and implementation1. Radiographics, 2002. 22(3): p. 651-671.

4.         He, X. and D.A. Yablonskiy, Quantitative BOLD: mapping of human cerebral deoxygenated blood volume and oxygen extraction fraction: default state. Magnetic Resonance in Medicine, 2007. 57(1): p. 115-126.

5.         Liu, C., et al., High-field (9.4 T) MRI of brain dysmyelination by quantitative mapping of magnetic susceptibility. Neuroimage, 2011. 56(3): p. 930-938.

6.         van Zijl, P. and N.N. Yadav, Chemical exchange saturation transfer (CEST): what is in a name and what isn't? Magnetic Resonance in Medicine, 2011. 65(4): p. 927-948.

7.         Lilburn, D.M., G.E. Pavlovskaya, and T. Meersmann, Perspectives of Hyperpolarized Noble Gas MRI beyond< sup> 3</sup> He. Journal of Magnetic Resonance, 2012.

8.         Ruiz‐Cabello, J., et al., Fluorine (19F) MRS and MRI in biomedicine. NMR in Biomedicine, 2011. 24(2): p. 114-129.


Bioluminescence and Fluorescence Imaging

Fluorescence Imaging

Fluorescence detection of GFR680 fluorescent dye in various organs over time with the SpectrumCT


Fluorescently labelled siRNA detection ex vivo in an orthotopic pancreatic cancer model (Images provided by  Ms Joann Teo, Dr. Phoebe Phillips, Dr. Joshua McCarroll)


3D Multimodal Tomographic

Multimodal contrast imaging- The spectrum-CT system is capable of performing Fluorescence/Bioluminescence and CT imaging and provide a good indication of the location of the tumour (C). Normally, the tumour cells will have a bioluminescent reporter and the CT scan can image the bones to provide an anatomical outline of the mouse. However, as soft tissue cannot be imaged well with the CT it is hard to identify which soft tissue the metastatic tumour is developing in. These images show a mouse with tumour cells developing right under the ribs, which can be the spleen, intestines or liver. Without contrast, we could not discern the different organs within that area (A1 and A2). We injected the mouse with a CT contrast agent Exitron 12000 (Miltenyi Biotec) and imaged the mouse further after 25 mins and found that we could better visualise the spleen, liver and even the heart (B1 and B2). This allows us to pinpoint exactly where the tumour is developing. 

Micro PET-CT

Bone Imaging

Scan of the skull of a Juvenile Capybara. (Image provided by Dr. Laura Wilson)


Implant Imaging

Cochlear implant in guinea pig (Image provided by Mr. Jeremy Pinyon, Prof. Gary Housley, UNSW). Scan of a rabbit heart with and without a pace maker (Image provided by Dr Andrew Woolley, UNSW).


Soft Tissue Contrast Imaging


Contrast imaging with CT scanner- CT scans can be used easily for imaging bony structures, however soft tissues and organs and not immediately visible in a CT scan. By using contrast agents, we can better visualise soft tissue and the vascular structure, and with the higher resolution scans, microvasculature. We imaged a mouse using the normal setting we would use for low dose longitudinal studies (A1 and A2) and another mouse was injected with a CT contrast agent (B1 and B2, Exitron 12000) prior to imaging under the same settings. Only the outline of the organs a slightly visible in the normal scan without the contrast (A1 &A2) while with the contrast agent, the heart, liver, spleen and kidneys can be clearly seen (B1 & B2). Contrast imaging with the CT at high resolution also allows imaging of the microvasculature in the tumour. A tumour bearing mouse was imaged without contrast (C) and with CT contrast agent (D) and imaged with the Inveon microCT scanner. The vasculature of the tumour can be clearly visualised and can be subsequently used for quantification of changes in tumour vasculature.


PET Imaging

18-FDG imaging of a mouse with a subcutaneous tumour. Accumulation of radioisotope in the tumour post injection  (labelled with the arrow).

High Frequency Ultrasound


Embryo imaging

Embryos are detectable as early as E5.5 and can be well visualised at E7. The heart is visible and heart rate of the fetus can be measured at about E10. 



B-mode cardiological imaging of the left ventricle on the (a) long axis allowing measurement of heart muscle  thickness, ejection fraction and strain analysis.



Aortic arch can be visualised and the velocity of blood flow can be measured with the doppler.



3D volumetric quantification of tumours

Optoacoustic (Photoacoustic) Imaging

Multispectral imaging of haemoglobin, oxygenated haemoglobin and indocyanine green (ICG) with the MSOT InVision256-TF (Ithera-Medical). Oxygenated blood (red) and deoxygenated blood (blue) can be quantified in different tissues and organs and the clearance of ICG (green) from the renal cortex into the renal pelvis over time.


Oxygenated and deoxygenated blood imaged through the skull of a mouse.