Ex vivo & Liquid/Solution State Protocols

High resolution anatomical imaging

Scan time: Overnight or weekend runs (depending on sample size and required spatial resolution – achievable: 20-50 µm resolution)

Examples: Fixed mouse embryos, zebrafish, organs / tissues, excised mouse aortas
Schneider, Jürgen E., et al. "Identification of cardiac malformations in mice lacking Ptdsr using a novel high-throughput magnetic resonance imaging technique." BMC developmental biology 4.1 (2004): 1.
Allen, Elizabeth R., et al. "MRI Based Localisation and Quantification of Abscesses following Experimental S. aureus Intravenous Challenge: Application to Vaccine Evaluation." PloS one 11.5 (2016): e0154705. 
High res rat
Above: Example slices from a 3D high-resolution image of a perfused rat heart. Imaging resolution was 33 μm isotroptic. Scan time: 16 hours (overnight). 

Structural Imaging (i.e. Diffusion MRI)

Scan time: Overnight or weekend runs (depending on sample size and required resolution; achievable – 80 / 100 / 200µm)

Examples: Fixed mouse, rat and rabbits hearts


Above: Tracks were reconstructed based on v1 and colour-coded by orientation: apico-basal (red), anterior-posterior (green) and lateral-septal (blue).

Tracts in the heart from (a) lateral, (b) anterior, (c) septal, (d) posterior and (e) apical views. Left helical tracks of the LV subepicardium and circumferential tracks of the RV myocardium are seen. Gaps in subepicardial tracks correspond to the left anterior descending artery (LAD). Tracks can be seen to spiral towards the apex. (f) Tracks in the leaflets of the mitral valve (MV) are primarily oriented parallel to the boundary between leaflets (dashed line). (g) Tracks in the vessel wall of the aorta (AA) are aligned primarily in a circumferential direction, while in the cusps of the aortic valve (AV) they are oriented in an equilateral configuration before curving basally into their insertions into the aortic wall. (h) The pulmonary valve (PV) comprises three leaflets, with tracks organised in an equilateral configuration. (i) Tracks in the left and right atria (LA and RA), and left atrial appendage (LAA) viewed from the septal wall. The left coronary artery (LCA) is seen extending from the aorta and tracks in its vessel walls are aligned circumferentially. (j) Tracks in a 13 × 5 × 5 mm section in the LV reveal chordae tendinae (CT), oriented longitudinally between their connections to the mitral valve and papillary muscle (PM). Networks of Purkinje fibres (PF) can be seen towards the apex.

Scan time: 16 hours

This figure may be found at full resolution in "Resolving fine cardiac structures in rats with high-resolution diffusion tensor imaging".

Teh, Irvin, et al. "Resolving fine cardiac structures in rats with high-resolution diffusion tensor imaging." Scientific Reports 6 (2016).

Teh, Irvin, et al. "Mapping cardiac microstructure of rabbit heart in different mechanical states by high resolution diffusion tensor imaging: A proof-of-principle study." Progress in Biophysics and Molecular Biology 121.2 (2016): 85-96.


1H-Relaxation time measurements (T1, T2 & T2*) using MRI

Scan time: Hours

Examples: New contrast agents in solution state or post-mortem

T2 calc small

Above: Measuring the T2 decay in a fixed rat heart. The signal decay with respect to echo time in the yellow square is displayed. Right: A T2-map of the tissue. The resolution is 100 µm isotropic.

Scan time: 1 hour 30 minutes

31P T1 solution state measurements of small volume samples using NMR

Scan time: Hours

Example: 31P T1 measurement of 10 mM phosphocreatine and ATP in PBS.

Above: 31P solution state NMR spectrum of a 100 ul sample of 10 mM PCr/ATP in PBS.  Resonances corresponding to phosphate (blue), PCr (red), g-ATP (green), b-ATP (orange), and a-ATP (teal) are indicated. Inversion recovery measurements of T1 relaxation rates can also made giving the T1 values for each of the resonances in the NMR spectrum. 
(Data with permission of L Tear/S Faulkner)