A New Straightforward Method for Automated Segmentation of Trabecular Bone from Cortical Bone in Diverse and Challenging Morphologies

AbstractMany physiological, biomechanical, evolutionary and clinical studies that explore skeletal structure and function require successful separation of trabecular from cortical compartments of a bone that has been imaged by X-ray micro-computed tomography (microCT) prior to analysis. Separation is often time-consuming, involves user bias and needs manual sub-division of these two similarly radio-opaque compartments. We have developed an objective, automated protocol which reduces user bias and enables straightforward, user-friendly segmentation of trabecular from cortical bone without requiring sophisticated programming expertise. This method can conveniently be used as a “recipe” in commercial programmes (Avizo herein) and applied to a variety of datasets. Here, we characterise and share this recipe, and demonstrate its application to a range of murine and human bone types, including normal and osteoarthritic specimens, and bones with distinct embryonic origins and spanning a range of ages. We validate the method by testing inter-user bias during the scan preparation steps and confirm utility in the architecturally challenging analysis of growing murine epiphyses. We also report details of the recipe, so that other groups can readily re-create a similar method in open access programs. Our aim is that this method will be adopted widely to create a more standardized and time efficient method of segmenting trabecular and cortical bone.

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A new straightforward method for semi-automated segmentation of trabecular bone from cortical bone in diverse and challenging morphologies

Royal Society Open Science ◽

10.1098/rsos.210408 ◽

2021 ◽

Vol 8 (8) ◽

pp. 210408

Author(s):

Eva C. Herbst ◽

Alessandro A. Felder ◽

Lucinda A. E. Evans ◽

Sara Ajami ◽

Behzad Javaheri ◽

...

Keyword(s):

Cortical Bone ◽

Skeletal Structure ◽

Micro Ct ◽

Micro Computed Tomography ◽

X Ray ◽

Straightforward Method ◽

Successful Separation ◽

And Function ◽

Automated Protocol ◽

User Friendly

Many physiological, biomechanical, evolutionary and clinical studies that explore skeletal structure and function require successful separation of trabecular from cortical compartments of a bone that has been imaged by X-ray micro-computed tomography (micro-CT) prior to analysis. Separation often involves manual subdivision of these two similarly radio-opaque compartments, which can be time-consuming and subjective. We have developed an objective, semi-automated protocol which reduces user bias and enables straightforward, user-friendly segmentation of trabecular from the cortical bone without requiring sophisticated programming expertise. This method can conveniently be used as a ‘recipe’ in commercial programmes (Avizo herein) and applied to a variety of datasets. Here, we characterize and share this recipe, and demonstrate its application to a range of murine and human bone types, including normal and osteoarthritic specimens, and bones with distinct embryonic origins and spanning a range of ages. We validate the method by testing inter-user bias during the scan preparation steps and confirm utility in the architecturally challenging analysis of growing murine epiphyses. We also report details of the recipe, so that other groups can readily re-create a similar method in open access programmes. Our aim is that this method will be adopted widely to create a reproducible and time-efficient method of segmenting trabecular and cortical bone.

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Three-dimensional analysis of cortical bone structure using X-ray micro-computed tomography

Physica A Statistical Mechanics and its Applications ◽

10.1016/j.physa.2004.03.046 ◽

2004 ◽

Vol 339 (1-2) ◽

pp. 125-130 ◽

Cited By ~ 23

Author(s):

A.C. Jones ◽

A.P. Sheppard ◽

R.M. Sok ◽

C.H. Arns ◽

A. Limaye ◽

...

Keyword(s):

Computed Tomography ◽

Cortical Bone ◽

Dimensional Analysis ◽

Bone Structure ◽

Three Dimensional ◽

Micro Computed Tomography ◽

X Ray

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Automated Protein Crystallization Trials Using the Thermo Scientific Matrix Hydra II eDrop

JALA Journal of the Association for Laboratory Automation ◽

10.1016/j.jala.2007.04.001 ◽

2007 ◽

Vol 12 (4) ◽

pp. 213-218 ◽

Cited By ~ 4

Author(s):

Tal Murthy ◽

Yongcheng Wang ◽

Colin Reynolds ◽

Titus J. Boggon

Keyword(s):

Single Channel ◽

Protein Crystallization ◽

X Ray Diffraction ◽

X Ray ◽

Screening Experiments ◽

Macromolecular Crystallization ◽

Automated Protocol ◽

User Friendly ◽

Rate Limiting ◽

Liquid Handling Robot

Obtaining suitable crystals for X-ray diffraction experiments is one of the rate-limiting steps in macromolecular crystallography. Robotic platforms that can increase throughput are highly desirable for crystal screening operations. The Thermo Scientific Matrix Hydra II eDrop is a liquid handling robot capable of dispensing sub-microliter and microliter volumes of solutions. Equipped with single-channel noncontact microdispenser, 96-channel syringe-based contact microdispenser and user-friendly ControlMate software, the Thermo Scientific Matrix Hydra II eDrop is appropriately designed for crystal screening experiments. The microdispensers are used in a single operational process to rapidly dispense sub-microliter volumes of liquids for automated crystallization plate setup. In this report, we discuss the design of the Thermo Scientific Matrix Hydra II eDrop. We also discuss an automated protocol for macromolecular crystallization trials that has successfully been used to produce crystals of a membrane protein, the rhomboid family intramembrane protease, GlpG. (JALA 2007;12:213–8)

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A Method for Evaluation the Fatigue Microcrack Propagation in Human Cortical Bone Using Differential X-ray Computed Tomography

Materials ◽

10.3390/ma14061370 ◽

2021 ◽

Vol 14 (6) ◽

pp. 1370

Author(s):

Petr Koudelka ◽

Daniel Kytyr ◽

Tomas Fila ◽

Jan Sleichrt ◽

Vaclav Rada ◽

...

Keyword(s):

Computed Tomography ◽

Cortical Bone ◽

Imaging System ◽

Fatigue Loading ◽

Micro Computed Tomography ◽

Damage Development ◽

Internal Damage ◽

Time Resolved ◽

X Ray ◽

Microcrack Propagation

Fatigue initiation and the propagation of microcracks in a cortical bone is an initial phase of damage development that may ultimately lead to the formation of macroscopic fractures and failure of the bone. In this work, a time-resolved high-resolution X-ray micro-computed tomography (CT) was performed to investigate the system of microcracks in a bone sample loaded by a simulated gait cycle. A low-cycle (1000 cycles) fatigue loading in compression with a 900 N peak amplitude and a 0.4 Hz frequency simulating the slow walk for the initialization of the internal damage of the bone was used. An in-house developed laboratory X-ray micro-CT imaging system coupled with a compact loading device were employed for the in situ uni-axial fatigue experiments reaching a μ2μm effective voxel size. To reach a comparable quality of the reconstructed 3D images with the SEM microscopy, projection-level corrections and focal spot drift correction were performed prior to the digital volume correlation and evaluation using differential tomography for the identification of the individual microcracks in the microstructure. The microcracks in the intact bone, the crack formation after loading, and the changes in the topology of the microcracks were identified on a volumetric basis in the microstructure of the bone.

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Identification of Fibrotic Thickening as Early Marker of Aortic Valve Stenosis Using X-Ray Micro Computed Tomography and Optical Coherence Tomography

The Thoracic and Cardiovascular Surgeon ◽

10.1055/s-0036-1571661 ◽

2016 ◽

Vol 64 (S 01) ◽

Author(s):

A. Jannasch ◽

C. Schnabel ◽

M. Santini ◽

S. Fest-Santini ◽

M. Lorenzi ◽

...

Keyword(s):

Computed Tomography ◽

Optical Coherence Tomography ◽

Aortic Valve ◽

Aortic Valve Stenosis ◽

Optical Coherence ◽

Micro Computed Tomography ◽

X Ray ◽

Early Marker

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Crystal Structures of Fragments D and Double-D from Fibrinogen and Fibrin

Thrombosis and Haemostasis ◽

10.1055/s-0037-1615842 ◽

1999 ◽

Vol 82 (08) ◽

pp. 271-276 ◽

Cited By ~ 8

Author(s):

Glen Spraggon ◽

Stephen Everse ◽

Russell Doolittle

Keyword(s):

Electron Microscopy ◽

High Resolution ◽

Crystal Structures ◽

Structure And Function ◽

X Ray ◽

Long Period ◽

And Function

IntroductionAfter a long period of anticipation,1 the last two years have witnessed the first high-resolution x-ray structures of fragments from fibrinogen and fibrin.2-7 The results confirmed many aspects of fibrinogen structure and function that had previously been inferred from electron microscopy and biochemistry and revealed some unexpected features. Several matters have remained stubbornly unsettled, however, and much more work remains to be done. Here, we review several of the most significant findings that have accompanied the new x-ray structures and discuss some of the problems of the fibrinogen-fibrin conversion that remain unresolved. * Abbreviations: GPR—Gly-Pro-Arg-derivatives; GPRPam—Gly-Pro-Arg-Pro-amide; GHRPam—Gly-His-Arg-Pro-amide

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Morphology and Affinities of Ampelocissites Seeds (Vitaceae: Ampelopsis clade) from the Paleogene of Texas, USA

Systematic Botany ◽

10.1600/036364420x15935294613400 ◽

2020 ◽

Vol 45 (3) ◽

pp. 478-482

Author(s):

Steven R. Manchester

Keyword(s):

Computed Tomography ◽

Cross Sections ◽

Seed Coat ◽

Ct Scanning ◽

Seed Morphology ◽

Early Eocene ◽

Micro Computed Tomography ◽

X Ray ◽

Fossil Seeds ◽

Fossil Genus

Abstract—The type material on which the fossil genus name Ampelocissites was established in 1929 has been reexamined with the aid of X-ray micro-computed tomography (μ-CT) scanning and compared with seeds of extant taxa to assess the relationships of these fossils within the grape family, Vitaceae. The specimens were collected from a sandstone of late Paleocene or early Eocene age. Although originally inferred by Berry to be intermediate in morphology between Ampelocissus and Vitis, the newly revealed details of seed morphology indicate that these seeds represent instead the Ampelopsis clade. Digital cross sections show that the seed coat maintains its thickness over the external surfaces, but diminishes quickly in the ventral infolds. This feature, along with the elliptical chalaza and lack of an apical groove, indicate that Ampelocissites lytlensis Berry probably represents Ampelopsis or Nekemias (rather than Ampelocissus or Vitis) and that the generic name Ampelocissites may be useful for fossil seeds with morphology consistent with the Ampelopsis clade that lack sufficient characters to specify placement within one of these extant genera.

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