Synchrotron X-ray biosample imaging: opportunities and challenges

Sena, Gabriela; Fidalgo, Gabriel; Paiva, Katrine; Barcelos, Renan; Nogueira, Liebert Parreiras; Colaço, Marcos V.; Gonzalez, Marcelo S.; Azambuja, Patrícia; Colaço, Gustavo; Silva, Hélio Ricardo; Meneses, Anderson Alvarenga de Moura; Barroso, R.C.

doi:10.1007/s12551-022-00964-4

Cited by 3 publications

(3 citation statements)

References 59 publications

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“…Although the theoretical minimum is four sets of SB-PCXI data, the numerical stability of the solutions can be improved by utilising SB-PCXI data from more mask positions. Namely, for N mask positions, we can generate an over-determined system of N linear equations following the form of equation (5). The system generated can then be solved in a least-squares sense using pixel-wise QR decomposition 59 .…”

Section: Stabilising the Sb-pcxi Multimodal Inverse Problemmentioning

confidence: 99%

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Multimodal intrinsic speckle-tracking (MIST) to extract images of rapidly-varying diffuse X-ray dark-field

Alloo

Morgan

Paganin

et al. 2023

Sci Rep

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Speckle-based phase-contrast X-ray imaging (SB-PCXI) can reconstruct high-resolution images of weakly-attenuating materials that would otherwise be indistinguishable in conventional attenuation-based X-ray imaging. The experimental setup of SB-PCXI requires only a sufficiently coherent X-ray source and spatially random mask, positioned between the source and detector. The technique can extract sample information at length scales smaller than the imaging system’s spatial resolution; this enables multimodal signal reconstruction. “Multimodal Intrinsic Speckle-Tracking” (MIST) is a rapid and deterministic formalism derived from the paraxial-optics form of the Fokker–Planck equation. MIST simultaneously extracts attenuation, refraction, and small-angle scattering (diffusive dark-field) signals from a sample and is more computationally efficient compared to alternative speckle-tracking approaches. Hitherto, variants of MIST have assumed the diffusive dark-field signal to be spatially slowly varying. Although successful, these approaches have been unable to well-describe unresolved sample microstructure whose statistical form is not spatially slowly varying. Here, we extend the MIST formalism such that this restriction is removed, in terms of a sample’s rotationally-isotropic diffusive dark-field signal. We reconstruct multimodal signals of two samples, each with distinct X-ray attenuation and scattering properties. The reconstructed diffusive dark-field signals have superior image quality—as measured by the naturalness image quality evaluator, signal-to-noise ratio, and azimuthally averaged power-spectrum—compared to our previous approaches which assume the diffusive dark-field to be a slowly varying function of transverse position. Our generalisation may assist increased adoption of SB-PCXI in applications such as engineering and biomedical disciplines, forestry, and palaeontology, and is anticipated to aid the development of speckle-based diffusive dark-field tensor tomography.

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Section: Stabilising the Sb-pcxi Multimodal Inverse Problemmentioning

confidence: 99%

“…already been proven in multiple disciplines. Such studies have been performed using synchrotron and conventional laboratory X-ray sources for applications in several fields, including biomedical [3][4][5][6] , agricultural and food sciences 7 , palaeontology 8,9 , and materials science 10,11 .…”

mentioning

confidence: 99%

Multimodal intrinsic speckle-tracking (MIST) to extract images of rapidly-varying diffuse X-ray dark-field

Alloo

Morgan

Paganin

et al. 2023

Sci Rep

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“…The superiority of PCXI techniques over attenuation-based imaging has already been proven in multiple disciplines. Such studies have been performed using synchrotron and conventional laboratory X-ray sources for applications in several fields, including biomedical [9,10,11,12], agricultural and food sciences [13], palaeontology [14,15], and materials science [16,17].…”

Section: Introductionmentioning

confidence: 99%

Multimodal Intrinsic Speckle-Tracking (MIST) to extract rapidly-varying diffuse X-ray scatter

Alloo¹,

Morgan²,

Paganin³

et al. 2023

Preprint

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Speckle-based phase-contrast X-ray imaging (SB-PCXI) can reconstruct high-resolution images of weakly-attenuating materials that would otherwise be indistinguishable in conventional attenuationbased imaging. The experimental setup of SB-PCXI requires only a sufficiently coherent source and spatially random mask, positioned between the source and detector. The technique can extract sample information at length scales smaller than the imaging system's spatial resolution; this enables multimodal signal reconstruction. "Multimodal Intrinsic Speckle-Tracking" (MIST) is a rapid and deterministic formalism derived from the paraxial-optics form of the Fokker-Planck equation. MIST simultaneously extracts attenuation, refraction, and small-angle scattering (diffusive-dark-field) signals from a sample and is more computationally efficient compared to alternative speckle-tracking approaches. Hitherto, variants of MIST have assumed the diffusive-dark-field signal to be spatially slowly varying. Although successful, these approaches have been unable to well-describe unresolved sample microstructure whose statistical form is not spatially slowly varying. Here, we extend the MIST formalism such that there is no such restriction, in terms of a sample's rotationally-isotropic diffusive-dark-field signal. We reconstruct multimodal signals of two samples, each with distinct Xray attenuation and scattering properties. The reconstructed diffusive-dark-field signals have superior image quality compared to our previous approaches which assume the diffusive-dark-field to be a slowly varying function of transverse position. Our generalisation may assist increased adoption of SB-PCXI in applications such as engineering and biomedical disciplines, forestry, and palaeontology, and is anticipated to aid the development of speckle-based diffusive-dark-field tensor tomography.

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Biophysical reviews: call for nominations for the 2023 Michèle Auger Award

Hall

2022

Biophys Rev

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This Editorial for Issue 3 (Vol. 14 2022) of Biophysical Reviews first describes the Issue’s contents (five commentaries/editorials within the front matter and seven review/letter articles appearing within the main body) before going on to discuss a number of matters of potential importance to the journal and its readers. Amongst this second tranche of content is the opening of the call for nominations for the 2023 Michèle Auger Award for Young Scientists’ Independent Research.

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Synchrotron X-ray biosample imaging: opportunities and challenges

Cited by 3 publications

References 59 publications

Multimodal intrinsic speckle-tracking (MIST) to extract images of rapidly-varying diffuse X-ray dark-field

Multimodal intrinsic speckle-tracking (MIST) to extract images of rapidly-varying diffuse X-ray dark-field

Multimodal Intrinsic Speckle-Tracking (MIST) to extract rapidly-varying diffuse X-ray scatter

Biophysical reviews: call for nominations for the 2023 Michèle Auger Award

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Synchrotron X-ray biosample imaging: opportunities and challenges

Cited by 3 publications

References 59 publications

M﻿ultimodal intrinsic speckle-tracking (MIST) to extract images of rapidly-varying diffuse X-ray dark-field

M﻿ultimodal intrinsic speckle-tracking (MIST) to extract images of rapidly-varying diffuse X-ray dark-field

Multimodal Intrinsic Speckle-Tracking (MIST) to extract rapidly-varying diffuse X-ray scatter

Biophysical reviews: call for nominations for the 2023 Michèle Auger Award

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Product

Resources

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Multimodal intrinsic speckle-tracking (MIST) to extract images of rapidly-varying diffuse X-ray dark-field

Multimodal intrinsic speckle-tracking (MIST) to extract images of rapidly-varying diffuse X-ray dark-field