sisterlonger/nmrtool

MRI

These programs are used for research in Magnetic Resonance Imaging.

Nuclear Magnetic Resonance (NMR) simulation and analysis tools

Extract and analyze experimental parameters; generate experimental notes from NMR datasets; simulate NMR signal under chemical exchange, spin relaxation and electromagnetic wave; generate publishable figures using matplot, numpy and scipy; code in pythonand MatLab. This tool was used by dozens of scholars in this area for experiments design and validation, leading to 3 co-authored paper published in top journals including Journal of American Chemical Society.

• X. Xu, N.N. Yadav, H. Zeng, C.K. Jones, J. Zhou, P.C. van Zijl, J. Xu,"Magnetization transfer contrast-suppressed imaging of amide protontransfer and relayed nuclear overhauser enhancement chemical exchange saturation transfer effects in the human brain at 7T", Magn. Reson.Med. 2016;75 (1): 88-96. [link]
• H. Zeng, J. Xu, N.N. Yadav, M.T. McMahon, B. Harden, D. Frueh, P.C. van Zijl, "(15)N Heteronuclear Chemical Exchange Saturation Transfer MRI", J. Am. Chem. Soc. 2016;138 (35): 11136-11139. [link]
• H. Zeng, J. Xu, J. Gillen, M.T. McMahon, J.A. Lohman, P.C. van Zijl, "Achieving 1% NMR polarization in water in less than 1min using SABRE", J. Magn. Reson. 2014;246 119-121. [link]

Control System of a chemical reactor

Control the reaction of hydrogen gas with drug solutions; regulate the pressure of the gas and the magnetic field of the reactor; synchronize the valves for transportation of the product solution; monitor the status of the instrument in real time; achieve 1400 times NMR signal enhancement through polarization; program in C.

• H. Zeng, J. Xu, J. Gillen, M.T. McMahon, J.A. Lohman, P.C. van Zijl, "Achieving 1% NMR polarization in water in less than 1min using SABRE", J. Magn. Reson. 2014;246 119-121. [link]
• H. Zeng, J. Xu, J. Gillen, M.T. McMahon, D. Artemov, J.M. Tyburn, J.A. Lohman, R.E. Mewis, K.D. Atkinson, G.G. Green, S.B. Duckett, P.C. van Zijl, "Optimization of SABRE for polarization of the tuberculosis drugs pyrazinamide and isoniazid", J. Magn. Reson. 2013;237 73-78. [link]

MRI database management

Integrate various source data into relational databases via ETL, and interact with NoSQL, HDFS databases; provide service recommendations using data analytics tools such as Python anaconda, and using machine-learning techniques such as Random Forests, SVM, Logistic Regression;

Compressed Sensing MRI

Algorithm for under-sampling MRI acquisition and reconstruction using information theory; reduce acquisition time to 25% of standard procedure while keeping all the diagnostic information.