NUScon: a community-driven platform for quantitative evaluation of nonuniform sampling in NMR
<p>Although the concepts of nonuniform sampling (NUS) and non-Fourier spectral reconstruction in multidimensional NMR began to emerge 4 decades ago <span class="cit" id="xref_paren.1">(<a href="#bib1.bibx4">Bodenhausen and Ernst</a>, <a...
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Copernicus Publications
2021
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oai:doaj.org-article:37e927b4d2cb48d395d0b5dffc51e56d2021-11-25T14:54:09ZNUScon: a community-driven platform for quantitative evaluation of nonuniform sampling in NMR10.5194/mr-2-843-20212699-0016https://doaj.org/article/37e927b4d2cb48d395d0b5dffc51e56d2021-11-01T00:00:00Zhttps://mr.copernicus.org/articles/2/843/2021/mr-2-843-2021.pdfhttps://doaj.org/toc/2699-0016<p>Although the concepts of nonuniform sampling (NUS) and non-Fourier spectral reconstruction in multidimensional NMR began to emerge 4 decades ago <span class="cit" id="xref_paren.1">(<a href="#bib1.bibx4">Bodenhausen and Ernst</a>, <a href="#bib1.bibx4">1981</a>; <a href="#bib1.bibx2">Barna and Laue</a>, <a href="#bib1.bibx2">1987</a>)</span>, it is only relatively recently that NUS has become more commonplace. Advantages of NUS include the ability to tailor experiments to reduce data collection time and to improve spectral quality, whether through detection<span id="page844"/> of closely spaced peaks (i.e., “resolution”) or peaks of weak intensity (i.e., “sensitivity”). Wider adoption of these methods is the result of improvements in computational performance, a growing abundance and flexibility of software, support from NMR spectrometer vendors, and the increased data sampling demands imposed by higher magnetic fields. However, the identification of best practices still remains a significant and unmet challenge. Unlike the discrete Fourier transform, non-Fourier methods used to reconstruct spectra from NUS data are nonlinear, depend on the complexity and nature of the signals, and lack quantitative or formal theory describing their performance. Seemingly subtle algorithmic differences may lead to significant variabilities in spectral qualities and artifacts. A community-based critical assessment of NUS challenge problems has been initiated, called the “Nonuniform Sampling Contest” (NUScon), with the objective of determining best practices for processing and analyzing NUS experiments. We address this objective by constructing challenges from NMR experiments that we inject with synthetic signals, and we process these challenges using workflows submitted by the community. In the initial rounds of NUScon our aim is to establish objective criteria for evaluating the quality of spectral reconstructions. We present here a software package for performing the quantitative analyses, and we present the results from the first two rounds of NUScon. We discuss the challenges that remain and present a roadmap for continued community-driven development with the ultimate aim of providing best practices in this rapidly evolving field. The NUScon software package and all data from evaluating the challenge problems are hosted on the NMRbox platform.</p>Y. PustovalovaF. DelaglioD. L. CraftH. ArthanariH. ArthanariA. BaxM. BilleterM. J. BostockH. DashtiD. F. HansenS. G. HybertsB. A. JohnsonK. KazimierczukH. LuM. MaciejewskiT. M. MiljenovićM. MobliD. NietlispachV. OrekhovR. PowersX. QuS. A. RobsonD. RovnyakG. WagnerJ. YingM. ZambrelloJ. C. HochD. L. DonohoA. D. SchuylerCopernicus PublicationsarticleElectricity and magnetismQC501-766ENMagnetic Resonance, Vol 2, Pp 843-861 (2021) |
| institution |
DOAJ |
| collection |
DOAJ |
| language |
EN |
| topic |
Electricity and magnetism QC501-766 |
| spellingShingle |
Electricity and magnetism QC501-766 Y. Pustovalova F. Delaglio D. L. Craft H. Arthanari H. Arthanari A. Bax M. Billeter M. J. Bostock H. Dashti D. F. Hansen S. G. Hyberts B. A. Johnson K. Kazimierczuk H. Lu M. Maciejewski T. M. Miljenović M. Mobli D. Nietlispach V. Orekhov R. Powers X. Qu S. A. Robson D. Rovnyak G. Wagner J. Ying M. Zambrello J. C. Hoch D. L. Donoho A. D. Schuyler NUScon: a community-driven platform for quantitative evaluation of nonuniform sampling in NMR |
| description |
<p>Although the concepts of nonuniform sampling (NUS) and non-Fourier spectral reconstruction in multidimensional NMR began to emerge 4 decades ago <span class="cit" id="xref_paren.1">(<a href="#bib1.bibx4">Bodenhausen and Ernst</a>, <a href="#bib1.bibx4">1981</a>; <a href="#bib1.bibx2">Barna and Laue</a>, <a href="#bib1.bibx2">1987</a>)</span>, it is only relatively recently that NUS has become more commonplace. Advantages of NUS include the ability to tailor experiments to reduce data collection time and to improve spectral quality, whether through detection<span id="page844"/> of closely spaced peaks (i.e., “resolution”) or peaks of weak intensity (i.e., “sensitivity”). Wider adoption of these methods is the result of improvements in computational performance, a growing abundance and flexibility of software, support from NMR spectrometer vendors, and the increased data sampling demands imposed by higher magnetic fields. However, the identification of best practices still remains a significant and unmet challenge. Unlike the discrete Fourier transform, non-Fourier methods used to reconstruct spectra from NUS data are nonlinear, depend on the complexity and nature of the signals, and lack quantitative or formal theory describing their performance. Seemingly subtle algorithmic differences may lead to significant variabilities in spectral qualities and artifacts. A community-based critical assessment of NUS challenge problems has been initiated, called the “Nonuniform Sampling Contest” (NUScon), with the objective of determining best practices for processing and analyzing NUS experiments. We address this objective by constructing challenges from NMR experiments that we inject with synthetic signals, and we process these challenges using workflows submitted by the community. In the initial rounds of NUScon our aim is to establish objective criteria for evaluating the quality of spectral reconstructions. We present here a software package for performing the quantitative analyses, and we present the results from the first two rounds of NUScon. We discuss the challenges that remain and present a roadmap for continued community-driven development with the ultimate aim of providing best practices in this rapidly evolving field. The NUScon software package and all data from evaluating the challenge problems are hosted on the NMRbox platform.</p> |
| format |
article |
| author |
Y. Pustovalova F. Delaglio D. L. Craft H. Arthanari H. Arthanari A. Bax M. Billeter M. J. Bostock H. Dashti D. F. Hansen S. G. Hyberts B. A. Johnson K. Kazimierczuk H. Lu M. Maciejewski T. M. Miljenović M. Mobli D. Nietlispach V. Orekhov R. Powers X. Qu S. A. Robson D. Rovnyak G. Wagner J. Ying M. Zambrello J. C. Hoch D. L. Donoho A. D. Schuyler |
| author_facet |
Y. Pustovalova F. Delaglio D. L. Craft H. Arthanari H. Arthanari A. Bax M. Billeter M. J. Bostock H. Dashti D. F. Hansen S. G. Hyberts B. A. Johnson K. Kazimierczuk H. Lu M. Maciejewski T. M. Miljenović M. Mobli D. Nietlispach V. Orekhov R. Powers X. Qu S. A. Robson D. Rovnyak G. Wagner J. Ying M. Zambrello J. C. Hoch D. L. Donoho A. D. Schuyler |
| author_sort |
Y. Pustovalova |
| title |
NUScon: a community-driven platform for quantitative evaluation of nonuniform sampling in NMR |
| title_short |
NUScon: a community-driven platform for quantitative evaluation of nonuniform sampling in NMR |
| title_full |
NUScon: a community-driven platform for quantitative evaluation of nonuniform sampling in NMR |
| title_fullStr |
NUScon: a community-driven platform for quantitative evaluation of nonuniform sampling in NMR |
| title_full_unstemmed |
NUScon: a community-driven platform for quantitative evaluation of nonuniform sampling in NMR |
| title_sort |
nuscon: a community-driven platform for quantitative evaluation of nonuniform sampling in nmr |
| publisher |
Copernicus Publications |
| publishDate |
2021 |
| url |
https://doaj.org/article/37e927b4d2cb48d395d0b5dffc51e56d |
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