Stride: a flexible software platform for high-performance ultrasound computed tomography
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Published version
Author(s)
Type
Journal Article
Abstract
BACKGROUND AND OBJECTIVE: Advanced ultrasound computed tomography techniques like full-waveform inversion are mathematically complex and orders of magnitude more computationally expensive than conventional ultrasound imaging methods. This computational and algorithmic complexity, and a lack of open-source libraries in this field, represent a barrier preventing the generalised adoption of these techniques, slowing the pace of research, and hindering reproducibility. Consequently, we have developed Stride, an open-source Python library for the solution of large-scale ultrasound tomography problems. METHODS: On one hand, Stride provides high-level interfaces and tools for expressing the types of optimisation problems encountered in medical ultrasound tomography. On the other, these high-level abstractions seamlessly integrate with high-performance wave-equation solvers and with scalable parallelisation routines. The wave-equation solvers are generated automatically using Devito, a domain-specific language, and the parallelisation routines are provided through the custom actor-based library Mosaic. RESULTS: We demonstrate the modelling accuracy achieved by our wave-equation solvers through a comparison (1) with analytical solutions for a homogeneous medium, and (2) with state-of-the-art modelling software applied to a high-contrast, complex skull section. Additionally, we show through a series of examples how Stride can handle realistic numerical and experimental tomographic problems, in 2D and 3D, and how it can scale robustly from a local multi-processing environment to a multi-node high-performance cluster. CONCLUSIONS: Stride enables researchers to rapidly and intuitively develop new imaging algorithms and to explore novel physics without sacrificing performance and scalability. This will lead to faster scientific progress in this field and will significantly ease clinical translation.
Date Issued
2022-06-01
Date Acceptance
2022-05-03
Citation
Computer Methods and Programs in Biomedicine, 2022, 221
ISSN
0169-2607
Publisher
Elsevier
Journal / Book Title
Computer Methods and Programs in Biomedicine
Volume
221
Copyright Statement
© 2022 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/)
License URL
Sponsor
Engineering & Physical Science Research Council (EPSRC)
Engineering & Physical Science Research Council (E
Identifier
https://www.ncbi.nlm.nih.gov/pubmed/35588663
PII: S0169-2607(22)00237-1
Grant Number
EP/V001493/1
EP/W007789/1
Subjects
Algorithms
Reproducibility of Results
Software
Tomography
Ultrasonography
Publication Status
Published
Coverage Spatial
Ireland
Article Number
ARTN 106855
Date Publish Online
2022-05-04