DAMARIS — a flexible and open software platform for NMR spectrometer control (original) (raw)
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IEEE Transactions on Nuclear Science, 1989
We describe a software environment created to s u p port real-time instrument control, signal acquisition and array-processor based signal and image processing in up to five dimensions. The environment is configured for NMR imaging and in vivo spectroscopy.' It is designed to provide flexible tools for implementing novel NMR experiments in the research laboratory. Data acquisition and processing operations are programmed in macros that are loaded in assembled form to minimize instruction overhead. Data arrays are dynamically allocated for efficient use of memory and can be mapped directly into disk files. The command set includes primitives for real-time control of data acquisition, scalar arithmetic, string manip ulation, branching, a file system, and vector operations carried out by an array processor.
A low–cost Arduino–based NMR console
Journal of Physics: Conference Series, 2019
Time domain nuclear magnetic resonance (TD–NMR) is a non-destructive technique to investigate a samples’ physical properties, such as fat and water contents, porosity, viscosity and water states in cell compartments etc., by analysis of the samples’ proton relaxations. However, commercial NMR consoles are still expensive, closed–source and unable to be customized for various applications. In this work, we demonstrate a low–cost, easy–to–build and customizable Arduino–based NMR console. The Arduino Due was chosen due to being easy–to–program while delivering high performance. The Arduino conducts four important functions i.e. controlling an RF synthesizer, timing control, data acquisition and PC interface. The NMR console is equipped with a quadrature modulator for RF phase control and a demodulator for signal phase detection. A low–cost HF power amplifier is used to amplify the transmitting signal, while a low noise amplifier TB–411–6+ is combined with an adjustable gain amplifier A...
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Journal of Magnetic Resonance, 2000
We have developed a "virtual NMR facility" (VNMRF) to enhance access to the NMR spectrometers in Pacific Northwest National Laboratory's Environmental Molecular Sciences Laboratory (EMSL). We use the term virtual facility to describe a real NMR facility made accessible via the Internet. The VNMRF combines secure remote operation of the EMSL's NMR spectrometers over the Internet with real-time videoconferencing, remotely controlled laboratory cameras, real-time computer display sharing, a Web-based electronic laboratory notebook, and other capabilities. Remote VNMRF users can see and converse with EMSL researchers, directly and securely control the EMSL spectrometers, and collaboratively analyze results. A customized Electronic Laboratory Notebook allows interactive Web-based access to group notes, experimental parameters, proposed molecular structures, and other aspects of a research project. This paper describes our experience developing a VNMRF and details the specific capabilities available through the EMSL VNMRF. We show how the VNMRF has evolved during a test project and present an evaluation of its impact in the EMSL and its potential as a model for other scientific facilities. All Collaboratory software used in the VNMRF is freely available from www.emsl.pnl.gov:2080/ docs/collab.
Modeling of NMR processing, toward efficient unattended processing of NMR experiments
Journal of Magnetic Resonance, 2007
Many alternative processing techniques have recently been proposed in the literature. Most of these techniques rely on specific acquisition protocols as well as on specific data processing techniques, the need for an efficient versatile and expandable NMR processing tool would be a particularly timely addition to the modern NMR spectroscopy laboratory. The work presented here consists in a modeling of the various possible NMR data processing approaches. This modeling presents a common working frame for most of the modern acquisition/processing protocols. Two different data modeling approaches are presented, strong modeling and weak modeling, depending whether the system under study or the measurement is modeled. The emphasis is placed on the weak modeling approach. This modeling is implemented in a computer program developed in python and called NPK standing (standing for NMR Processing Kernel), organized in four logical layers (i) mathematical kernel; (ii) elementary actions; (iii) processing phases; (iv) processing strategies. This organisation, along with default values for most processing parameters allows the use of the program in an unattended manner, producing close to optimal spectra. Examples are shown for 1D and 2D processing, and liquid and solid NMR spectroscopy. NPK is available from the site: http://abcis.cbs.cnrs.fr/NPK Ó
A personal computer-based nuclear magnetic resonance spectrometer
Review of Scientific Instruments, 1994
Nuclear magnetic resonance (NMR) spectroscopy using personal computer-based hardware has the potential of enabling the application of NMR methods to fields where conventional state of the art equipment is either impractical or too costly. With such a strategy for data acquisition and processing, disciplines including civil engineering, agriculture, geology, archaeology, and others have the possibility of utilizing magnetic resonance techniques within the laboratory or conducting applications directly in the field. Another aspect is the possibility of utilizing existing NMR magnets which may be in good condition but unused because of outdated or nonrepairable electronics. Moreover, NMR applications based on personal computer technology may open up teaching possibilities at the college or even secondary school level. The goal of developing such a personal computer (PC)-based NMR standard is facilitated by existing technologies including logic cell arrays, direct digital frequency synthesis, use of PC-based electrical engineering software tools to fabricate electronic circuits, and the use of permanent magnets based on neodymium-iron-boron alloy. Utilizing such an approach, we have been able to place essentially an entire NMR spectrometer console on two printed circuit boards, with the exception of the receiver and radio frequency power amplifier. Future upgrades to include the deuterium lock and the decoupler unit are readily envisioned. The continued development of such PC-based NMR spectrometers is expected to benefit from the fast growing, practical, and low cost personal computer market.
Journal of Magnetic Resonance, 2000
This paper presents a software program, the Virtual NMR Spectrometer, for computer simulation of multichannel, multidimensional NMR experiments on user-defined spin systems. The program is capable of reproducing most features of the modern NMR experiment, including homo-and heteronuclear pulse sequences, phase cycling, pulsed field gradients, and shaped pulses. Two different approaches are implemented to simulate the effect of pulsed field gradients on coherence selection, an explicit calculation of all coherence transfer pathways, and an effective approximate method using integration over multiple positions in the sample. The applications of the Virtual NMR Spectrometer are illustrated using homonuclear COSY and DQF COSY experiments with gradient selection, heteronuclear HSQC, and TROSY. The program uses an intuitive graphical user interface, which resembles the appearance and operation of a real spectrometer. A translator is used to allow the user to design pulse sequences with the same programming language used in the actual experiment on a real spectrometer. The Virtual NMR Spectrometer is designed as a useful tool for developing new NMR experiments and for tuning and adjusting the experimental setup for existing ones prior to running costly NMR experiments, in order to reduce the setup time on a real spectrometer. It will also be a useful aid for learning the general principles of magnetic resonance and contemporary innovations in NMR pulse sequence design.
Digitally Based Precision Time-Domain Spectrometer for NMR Relaxation and NMR Cryoporometry
Micro, 2023
first_pagesettingsOrder Article Reprints Open AccessArticle Digitally Based Precision Time-Domain Spectrometer for NMR Relaxation and NMR Cryoporometry by John Beausire Wyatt Webber *ORCID andPavel Demin Lab-Tools Ltd., Marlowe Innovation Centre, Marlowe Way, Ramsgate CT12 6FA, UK * Author to whom correspondence should be addressed. Micro 2023, 3(2), 404-433; https://doi.org/10.3390/micro3020028 Received: 14 February 2023 / Revised: 16 March 2023 / Accepted: 19 March 2023 / Published: 3 April 2023 (This article belongs to the Section Analysis Methods and Instruments) Download Browse Figures Review Reports Versions Notes Abstract NMR Relaxation (NMRR) is an extremely useful quantitative technique for material science, particularly for studying polymers and porous materials. NMR Cryoporometry (NMRC) is a powerful technique for the measurement of pore-size distributions and total porosities. This paper discusses the use, capabilities and application of a newly developed compact NMR time-domain relaxation spectrometer suitable for studying both solid and liquid samples (Mk3 NMR Relaxation spectrometer & Cryoporometer, Lab-Tools (nano-science), Ramsgate, Kent, UK. (2019)). This highly compact precision NMR Spectrometer is based on a Field Programmable Gate array (FPGA) module and custom surface mount low-noise NMR receiver and NMR linear transmitter. A high proportion of the RF circuitry is in a digital form, implemented as firmware in the FPGA, which gives the instrument an excellent long-term stability. It also includes an on-chip Linux computer. The FPGA module is credit-card sized, and both the NMR receiver and NMR transmitter are even smaller. The software, including the top-level NMR pulse sequence definitions, are written in an array processing language, Apl. The spectrometer comes complete with a Graphical User Interface (GUI) for control and on- and offline curve fitting and data analysis. The recent development of the Lab-Tools Peltier thermo-electrically cooled NMR variable-temperature (V-T) probe that cools the sample below −60 °C is also discussed. This Peltier cooling gives the precision temperature control and smoothness needed by NMR Cryoporometry (10 mK near the probe liquid bulk melting point). This enables the NMRC measurement of pore-size distributions in porous materials, for the unusually wide pore-size range of sub-nano to over 1 micron-sized pores. The NMR Spectrometer’s unusually small size, ability to measure solids, low noise and high performance make it particularly suitable for material science studies both in the field and in university, research institute, company and even school laboratories. A human portable version now exists. Use of the controlling GUI is described, and results from example NMR Relaxation and NMR Cryoporometric measurements are given. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY