A spark of 3D revisualization: new method for re-exploring segmented data

Hu, Yuzhi; Limaye, Ajay; Lü, Jing

doi:10.1101/2020.08.01.222869

Cited by 3 publications

(2 citation statements)

References 28 publications

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“…Greyscale is a proxy for relative X‐ray attenuation, where brighter areas have a relatively higher attenuation value, which in turn reflects atomic number and density. Image stacks were initially modified using a non‐linear greyscale stretch to enhance contrast between phases of interest, performed using the Drishti 2.7 software package (Y. Hu et al., 2020a, Hu et al., 2019; Limaye, 2012). A Tschumperle‐Deriche anisotropic filter (Tschumperlé & Deriche, 2007) was applied to each.tiff image using ImageJ v2.3.0 (Abràmoff et al., 2004; Schneider et al., 2012) to reduce noise.…”

Section: Methodsmentioning

confidence: 99%

A 3D Petrofabric Examination of Martian Breccia NWA 11220 via X‐Ray Computed Microtomography: Evidence for an Impact Lithology

Goodwin,

Tartèse,

Garwood

et al. 2023

JGR Planets

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The Martian regolith breccia Northwest Africa (NWA) 11220 and paired stones represent the only known meteorites that sample a clastic sub‐surface lithology from Mars. By applying X‐ray computed microtomography to monomineralic clasts, we identify three phases that can be automatically segmented by thresholding X‐ray attenuation greyscale values: (A) feldspars, (B) pyroxene and apatite, and (C) iron‐rich oxides and sulfides, confirmed via scanning electron microscopy and Raman spectroscopy. For these three phases, we demonstrate scale invariance in size and shape for sand‐sized clasts and smaller, a characteristic commonly observed for clast populations generated by fragmentation without further sorting from sedimentary transport (e.g., Aeolian or fluvial processes). Additionally, by assessing the preferred orientation of fitted ellipses and ellipsoids to manually segmented proto‐breccia clasts in two and three dimensions, we identified a weak planar fabric that likely resulted from compaction rather than impact transport. Combining clast size distribution with evidence for nested textures inside proto‐breccia clasts, we propose that NWA 11220 has experienced a minimum of two hypervelocity impact events and should be considered a lithified impact ejecta lithology with little to no reworking via surface regolith processes.

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Section: Methodsmentioning

confidence: 99%

A 3D Petrofabric Examination of Martian Breccia NWA 11220 via X‐Ray Computed Microtomography: Evidence for an Impact Lithology

Goodwin,

Tartèse,

Garwood

et al. 2023

JGR Planets

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show abstract

“…For the two-and three-dimensional visualisation of the tomographic datasets we used the open source image processing packages Fiji [23] and Drishti [24]- [26] respectively.…”

Section: Image Visualisation Toolsmentioning

confidence: 99%

Monitoring tissue engineered constructs and protocols with laboratory-based x-ray phase contrast tomography

et al. 2022

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Advanced three-dimensional X-ray imaging unravels structural development of the human thymus compartments

Savvidis,

Ragazzini,

de Rafael

et al. 2024

Commun Med

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Background The thymus, responsible for T cell-mediated adaptive immune system, has a structural and functional complexity that is not yet fully understood. Until now, thymic anatomy has been studied using histological thin sections or confocal microscopy 3D reconstruction, necessarily for limited volumes. Methods We used Phase Contrast X-Ray Computed Tomography to address the lack of whole-organ volumetric information on the microarchitecture of its structural components. We scanned 15 human thymi (9 foetal and 6 postnatal) with synchrotron radiation, and repeated scans using a conventional laboratory x-ray system. We used histology, immunofluorescence and flow cytometry to validate the x-ray findings. Results Application to human thymi at pre- and post-natal stages allowed reliable tracking and quantification of the evolution of parameters such as size and distribution of Hassall’s Bodies and medulla-to-cortex ratio, whose changes reflect adaptation of thymic activity. We show that Hassall’s bodies can occupy 25% of the medulla volume, indicating they should be considered a third thymic compartment with possible implications on their role. Moreover, we demonstrate compatible results can be obtained with standard laboratory-based x-ray equipment, making this research tool accessible to a wider community. Conclusions Our study allows overcoming the resolution and/or volumetric limitations of existing approaches for the study of thymic disfunction in congenital and acquired disorders affecting the adaptive immune system.

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A spark of 3D revisualization: new method for re-exploring segmented data

Cited by 3 publications

References 28 publications

A 3D Petrofabric Examination of Martian Breccia NWA 11220 via X‐Ray Computed Microtomography: Evidence for an Impact Lithology

A 3D Petrofabric Examination of Martian Breccia NWA 11220 via X‐Ray Computed Microtomography: Evidence for an Impact Lithology

Monitoring tissue engineered constructs and protocols with laboratory-based x-ray phase contrast tomography

Advanced three-dimensional X-ray imaging unravels structural development of the human thymus compartments

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