<i>TomocuPy</i> – efficient GPU-based tomographic reconstruction with asynchronous data processing

Никитин, В. В.

doi:10.1107/s1600577522010311

Cited by 24 publications

(19 citation statements)

References 41 publications

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“…Scan rates were between 0.5 and 1 s per angle, covering approximately 175°. Data were reconstructed using Tomopy, 52 which has now been replaced with Tomocupy, 53 and visualized using ImageJ. The voxel resolution of the resulting 3D tomographic images was 56 nm.…”

Section: Methodsmentioning

confidence: 99%

Carbonate Coprecipitation for Cd and Zn Treatment and Evaluation of Heavy Metal Stability Under Acidic Conditions

Kim

Lee

Fenter

et al. 2023

Environ. Sci. Technol.

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Mining wastes or combustion ash are materials of high carbon sequestration potential but are also known for their toxicity in terms of heavy metal content. To utilize such waste materials for engineered carbon mineralization purposes, there is a need to investigate the fate and mobility of toxic metals. This is a study of the coprecipitation of metals with calcium carbonate for environmental heavy metal mitigation. The study also examines the stability of precipitated phases under environmentally relevant acid conditions. For a wide range of cadmium (Cd) and zinc (Zn) concentrations (10 to 5000 mg/L), induced coprecipitation led to greater than 99% uptake from water. The calcium carbonate phases were found to contain amounts as high as 9.9 wt % (Cd) and 17 wt % (Zn), as determined by novel synchrotron techniques, including X-ray fluorescence element mapping and three-dimensional (3D) nanotransmission X-ray microscopy (TXM). TXM imaging revealed first-of-a-kind observations of chemical gradients and internal nanoporosity within particles. These observations provided new insights into the mechanisms leading to the retention of coprecipitated heavy metals during the dissolution of calcite in acidic (pH 4) solutions. These observations highlight the feasibility of utilizing carbonate coprecipitation as an engineered approach to the durable sequestration of toxic metals.

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Section: Methodsmentioning

confidence: 99%

Carbonate Coprecipitation for Cd and Zn Treatment and Evaluation of Heavy Metal Stability Under Acidic Conditions

Kim

Lee

Fenter

et al. 2023

Environ. Sci. Technol.

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“…To obtain qualitative tomographic reconstructions, we used the TomocuPy package (Nikitin, 2023) to organize a reconstruction pipeline. The reconstruction pipeline included common processing functions such as ring removal, phase retrieval filtering, and filtered backprojection implemented via the log-polar-based method (Andersson et al, 2016).…”

Section: Data Description and Low-contrast Problem Definitionmentioning

confidence: 99%

A hybrid machine-learning approach for analysis of methane hydrate formation dynamics in porous media with synchrotron CT imaging

Fokin

Никитин

Duchkov

2023

J Synchrotron Radiat

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Fast multi-phase processes in methane hydrate bearing samples pose a challenge for quantitative micro-computed tomography study and experiment steering due to complex tomographic data analysis involving time-consuming segmentation procedures. This is because of the sample's multi-scale structure, which changes over time, low contrast between solid and fluid materials, and the large amount of data acquired during dynamic processes. Here, a hybrid approach is proposed for the automatic segmentation of tomographic data from time-resolved imaging of methane gas-hydrate formation in sandy granular media, which includes a deep-learning 3D U-Net model. To prepare a training dataset for the 3D U-Net, a technique to automate data labeling based on sample-specific information about the mineral matrix immobility and occasional fluid movement in pores is proposed. Automatic segmentation allowed for studying properties of the hydrate growth in pores, as well as dynamic processes such as incremental flow and redistribution of pore brine. Results of the quantitative analysis showed that for typical gas-hydrate stability parameters (100 bar methane pressure, 7°C temperature) the rate of formation is slow (less than 1% per hour), after which the surface area of contact between brine and gas increases, resulting in faster formation (2.5% per hour). Hydrate growth reaches the saturation point after 11 h of the experiment. Finally, the efficacy of the proposed segmentation scheme in on-the-fly automatic data analysis and experiment steering with zooming to regions of interest is demonstrated.

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“…Each resulting HDF5 file containing dark, flat, and projection data is structured as a standard Data Exchange file (De Carlo et al, 2014) and can be read using the read_dx() function from the DXchange toolbox (De Carlo, 2022a). These files can be reconstructed offline using tomoPy (Gu ¨rsoy et al, 2014b) via its command-line interface tomopyCLI (De Carlo, 2019), or using a GPU-based reconstruction with tomocupyCLI (Nikitin, 2022).…”

Section: Streaming Data Acquisition Modelmentioning

confidence: 99%

Real-time streaming tomographic reconstruction with on-demand data capturing and 3D zooming to regions of interest

Никитин¹,

Tekawade²,

Duchkov³

et al. 2022

J Synchrotron Radiat

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Complex dynamic tomographic experiments at brilliant X-ray light sources require real-time feedback on the sample changes with respect to environmental conditions, selecting representative regions of interest for high-resolution scanning, and on-demand data saving mechanisms for storing only relevant projections acquired by fast area detectors and reducing data volumes. Here the implementation details of a 3D real-time imaging monitoring instrument, with zooming to a volume of interest with easy-to-use visualization via ImageJ, a tool familiar to most beamline users, is presented. The instrument relies on optimized data flow between the detector and processing machines and is implemented on commodity computers. The instrument has been developed at beamline 2-BM of the Advanced Photon Source, where the automatic lens changing mechanism for zooming is implemented with an Optique Peter microscope. Performance tests demonstrate the ability to process more than 3 GB of projection data per second and generate real-time 3D zooming with different magnification. These new capabilities are essential for new APS Upgrade instruments such as the projection microscope under development at beamline 32-ID. The efficacy of the proposed instrument was demonstrated during an in situ tomographic experiment on ice and gas hydrate formation in porous samples.

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TomocuPy – efficient GPU-based tomographic reconstruction with asynchronous data processing

Cited by 24 publications

References 41 publications

Carbonate Coprecipitation for Cd and Zn Treatment and Evaluation of Heavy Metal Stability Under Acidic Conditions

Carbonate Coprecipitation for Cd and Zn Treatment and Evaluation of Heavy Metal Stability Under Acidic Conditions

A hybrid machine-learning approach for analysis of methane hydrate formation dynamics in porous media with synchrotron CT imaging

Real-time streaming tomographic reconstruction with on-demand data capturing and 3D zooming to regions of interest

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