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pH using APT-MRI

Amide Proton Transfer is a form of Chemical Exchange Saturation Transfer MRI that exploits endogenous amide groups to measure cellular information such as pH normally only available from spectroscopy methods but with higher resolution.

Images from CEST research


Paula Croal, Yunus Mysaib, Robert Brand (FMRIB Centre), Kevin Ray (FMRIB/Oncology), Yee Kai Tee (Alumnus)


Nic Blockley, Peter Jezzard (FMRIB Centre)
George Harston, James Kennedy (OxAVIC)
Nicola Sibson (Oncology)


The signal that generates an MR image can be destroyed using saturation pulses tuned to the resonant frequency of water in the magnetic field. If the saturation is applied off resonance the effect is reduced. However, some extra saturation can be seen in particular frequency ranges, where the saturation hits the resonances of protons attached to other molecules. Where these protons are in chemical exchange with water, for example in amide groups, the saturation can be transferred from from these molecules to water where it can be observed. This mechanism called Chemical Exchange Saturation Transfer (CEST) can be exploited to measure information about these molecules even where their concentrations are relatively low.

For amide groups the saturation effect depends both upon the number of these groups and also the rate at which the proton exchange occurs. The latter depends on pH and thus CEST in the form of Amide Proton Transfer (APT) MRI provides a measure that is sensitive to changes in pH that might arise for example in ischaemic tissue using only endogenous amide bearing molecules.


The size of the APT effect is confounded by the direct saturation of water as well as other exchange mechanisms present that also modulate the MR image intensity. We have been investigating model-based approaches to APT quantification that attempts to isolate the pH based effect from other sources of signal change.


We are working with Peter Jezzard (FMRIB Centre) and James Kennedy (OxAVIC) on the use of APT pH measurements for treatment decision support in acute ischaemic stroke and with Nicola Sibson (Oncology) to use CEST measures to identify pH changes in tumours.


Both model-based inference and model-free methods for CEST quantification for CEST MRI are available as a widget in Quantiphyse (included in the full academic package). Software for the model-based analysis of CEST data is also available as the command line tool BayCEST as part of the FMRIB Software Library.

Selected Publications

Harston, G. W. J., Tee, Y. K., Blockley, N., Okell, T. W., Thandeswaran, S., Shaya, G., Sheerin,F., Cellerini, M., Payne, S.J., Jezzard, P., Chappell, M.A., Kennedy, J.
Identifying the ischaemic penumbra using pH-weighted magnetic resonance imaging.
Brain, 138(Pt 1), 36–42. doi:10.1093/brain/awu374

Chappell, M. A., Donahue, M. J., Tee, Y. K., Khrapitchev, A. A., Sibson, N. R., Jezzard, P., & Payne, S. J.
Quantitative Bayesian model-based analysis of amide proton transfer MRI.
Magnetic resonance in medicine, doi:10.1002/mrm.24474

Tee, Y. K., Khrapitchev, A. A., Sibson, N. R., Payne, S. J., & Chappell, M. A.
Evaluating the use of a continuous approximation for model-based quantification of pulsed chemical exchange saturation transfer (CEST).

Journal of Magnetic Resonance, 222(C), 88–95. doi:10.1016/j.jmr.2012.07.003