An X-ray CT study of miniature clay sample preparation techniques

The quality and reliability of cohesive soil laboratory test data can be significantlyaffected by sample disturbance during sampling or sample preparation. Sample disturbance may affect key design and modelling parameters such as stiffness, preconsolidation stress, compressibility and undrained shear strength, and ultimately determine particle mobilization and shear plane development. The use of X-ray computed tomography (X-CT) in the study of soil is restricted by the inverse relationship of specimen size and obtainable image resolution. This has led to the testing of miniature specimen sizes which are far less than conventional laboratory sample size in a bid to obtain high resolution images and detailed particle-scale soil properties; however, these miniature soil specimens are more prone to sample disturbance. In this work 2% muscovite was mixed with speswhite kaolin clay as a strain marker for use in X-CT. The clay soil sample was prepared from slurry and either consolidated using an oedometer or a gypsum mould. Specimens obtained from a 7 mm tube sampler were compared to lathe trimmed specimens with a diameter (Ø) of 7 mm. Results from X-CT imaging were used to study the influence of sampler type on specimen disturbance, by analysing the muscovite particle orientation of the obtained 3D images. The results show that; for samples subjected to large consolidation stress (>200kpa) lathe trimmed specimens may be subject to lesser disturbance compared to tube sampled specimens.

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The Effect of Image Resolution on Automated Classification of Chest X-rays

10.1101/2021.07.30.21261225 ◽

2021 ◽

Author(s):

Md Inzamam Ul Haque ◽

Abhishek K Dubey ◽

Jacob D Hinkle

Keyword(s):

High Resolution ◽

Automated Analysis ◽

Image Resolution ◽

Free Text ◽

X Rays ◽

Training Time ◽

X Ray ◽

Radiology Reports ◽

Chest X Ray ◽

High Resolution Images

Deep learning models have received much attention lately for their ability to achieve expert-level performance on the accurate automated analysis of chest X-rays. Although publicly available chest X-ray datasets include high resolution images, most models are trained on reduced size images due to limitations on GPU memory and training time. As compute capability continues to advance, it will become feasible to train large convolutional neural networks on high-resolution images. This study is based on the publicly available MIMIC-CXR-JPG dataset, comprising 377,110 high resolution chest X-ray images, and provided with 14 labels to the corresponding free-text radiology reports. We find, interestingly, that tasks that require a large receptive field are better suited to downscaled input images, and we verify this qualitatively by inspecting effective receptive fields and class activation maps of trained models. Finally, we show that stacking an ensemble across resolutions outperforms each individual learner at all input resolutions while providing interpretable scale weights, suggesting that multi-scale features are crucially important to information extraction from high-resolution chest X-rays.

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Relationship of brain imaging with radionuclides and with x-ray computed tomography

10.2172/5896144 ◽

1981 ◽

Author(s):

D.E. Kuhl

Keyword(s):

Computed Tomography ◽

Brain Imaging ◽

X Ray ◽

X Ray Computed ◽

Relationship Of

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A lathe system for micrometre-sized cylindrical sample preparation at room and cryogenic temperatures

Journal of Synchrotron Radiation ◽

10.1107/s1600577519017028 ◽

2020 ◽

Vol 27 (2) ◽

pp. 472-476

Author(s):

Mirko Holler ◽

Johannes Ihli ◽

Esther H. R. Tsai ◽

Fabio Nudelman ◽

Mariana Verezhak ◽

...

Keyword(s):

Sample Preparation ◽

Room Temperature ◽

Focused Ion Beam ◽

Ion Beam ◽

Cylindrical Sample ◽

X Ray ◽

X Ray Computed ◽

Cryogenic Conditions ◽

Cylindrical Samples ◽

Potential Use

A simple two-spindle based lathe system for the preparation of cylindrical samples intended for X-ray tomography is presented. The setup can operate at room temperature as well as under cryogenic conditions, allowing the preparation of samples down to 20 and 50 µm in diameter, respectively, within minutes. Case studies are presented involving the preparation of a brittle biomineral brachiopod shell and cryogenically fixed soft brain tissue, and their examination by means of ptychographic X-ray computed tomography reveals the preparation method to be mainly free from causing artefacts. Since this lathe system easily yields near-cylindrical samples ideal for tomography, a usage for a wide variety of otherwise challenging specimens is anticipated, in addition to potential use as a time- and cost-saving tool prior to focused ion-beam milling. Fast sample preparation becomes especially important in relation to shorter measurement times expected in next-generation synchrotron sources.

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Pore scale imaging and modelling of coal properties

The APPEA Journal ◽

10.1071/aj14103 ◽

2015 ◽

Vol 55 (2) ◽

pp. 468

Author(s):

Hamed Lamei Ramandi ◽

Peyman Mostaghimi ◽

Ryan T. Armstrong ◽

Christoph H. Arns ◽

Mohammad Saadatfar ◽

...

Keyword(s):

Large Scale ◽

Pore Space ◽

Image Resolution ◽

X Ray ◽

Flow Simulations ◽

The Core ◽

Sensitivity Studies ◽

X Ray Computed ◽

3D Image Registration ◽

Stress Dependent

A key parameter in determining the productivity and commercial success of coal seam gas wells is the permeability of individual seams. Laboratory testing of core plugs is commonly used as an indicator of potential seam permeability. The highly heterogeneous and stress-dependent nature of coal makes laboratory measurements difficult to perform and the results difficult to interpret. Consequently, permeability in coal is poorly understood. The permeability of coal at the core scale depends on the geometry, topology, connectivity, mineralisation and spatial distribution of the cleat system, and a better understanding of coal permeability, that and the factors that control this depends on having a better understanding and detailed characterisation of the system. The authors used high resolution micro-focus X-ray computed tomography and 2D-3D image registration techniques to overlay tomograms of the same core plug, with and without X-ray attenuating fluids present in the pore space, with 2D scanning electron microscope images to produce detailed 3D visualisations of the geometry and topology of the cleat systems in the coal plugs. Novel filtering algorithms were used to produce segmentations that preserve cleat aperture dimensions and together with large-scale fluid flow simulations, they performed directly on the images and were used to compute porosities and permeabilities. Image resolution and segmentation sensitivity studies are also described, which show that the core scale permeability is controlled by a small number of well-connected percolating cleats. The results of this study demonstrate the potential of simple image-based analysis techniques to provide rapid estimates of core plug permeabilities.

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An improved sample preparation method for imaging microstructures of fine-grained marine sediment using microfocus X-ray computed tomography and scanning electron microscopy

Limnology and Oceanography Methods ◽

10.4319/lom.2014.12.469 ◽

2014 ◽

Vol 12 (7) ◽

pp. 469-483 ◽

Cited By ~ 7

Author(s):

Go-Ichiro Uramoto ◽

Yuki Morono ◽

Katsuyuki Uematsu ◽

Fumio Inagaki

Keyword(s):

Electron Microscopy ◽

Computed Tomography ◽

Scanning Electron Microscopy ◽

Sample Preparation ◽

Preparation Method ◽

Sample Preparation Method ◽

X Ray ◽

Fine Grained ◽

X Ray Computed ◽

Scanning Electron

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An improved method for the segmentation of roots from X-Ray computed tomography 3D images: Rootine v.2

10.5194/egusphere-egu2020-5225 ◽

2020 ◽

Author(s):

Maxime Phalempin ◽

Eva Lippold ◽

Doris Vetterlein ◽

Steffen Schlueter

Keyword(s):

Computed Tomography ◽

Root System ◽

Root System Architecture ◽

Root Diameter ◽

Image Resolution ◽

Absolute Difference ◽

Improved Method ◽

3D Images ◽

X Ray ◽

X Ray Computed

<p>X-ray computed tomography (CT) is acknowledged as a powerful tool for the study of root system architecture (RSA) of plants grown in soil. The study of the root system properties is however only possible after performing root segmentation, i.e. the binarization of all root voxels. Root segmentation is often regarded as a tedious and difficult task as its success depends on several factors such as the image resolution, the signal to noise during image acquisition and the gray value contrast between the roots and all other surrounding features. Here, we present an improved method for the segmentation of roots from X-Ray computed tomography 3D images. The algorithm Rootine (Gao et al. 2019) does not detect roots by their gray values but by their characteristic tubular shape. This algorithm was further developed in order to improve the root recovery rate and to reduce the number of parameters involved during the segmentation process. This was achieved by adding two key steps: (1) an absolute difference transform and (2) an automatic calculation of the parameters used during the Gaussian smoothing. The first step allows for targeting specific features based on a gray value criteria contained within a user-defined gray value range in order to better distinguish roots from pores whereas the second step allows for targeting root segments of specific diameters. On the benchmark dataset of Gao et al. 2019, the newly called &#8220;Rootine v.2&#8221; was able to recover 34 % more roots as compared to its preceding version. Moreover, the number of parameters was reduced from 10 down to 5 which allows for a faster calibration and an overall better usability of the algorithm. The presented method also allows for a more reliable estimation of root diameter derived from X-Ray CT images. This work was carried out in the framework of the priority programme 2089 &#8220;Rhizosphere spatiotemporal organization - a key to rhizosphere functions&#8221; funded by DFG (project number 403640293).</p>

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Recent applications of TEM to the study of interfaces

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100174679 ◽

1990 ◽

Vol 48 (4) ◽

pp. 308-309

Author(s):

C. Barry Carter

Keyword(s):

High Resolution ◽

Sample Preparation ◽

Grain Boundaries ◽

Diffuse Scattering ◽

Imaging Techniques ◽

Amorphous Material ◽

Contrast Imaging ◽

Current State ◽

Actual Nature ◽

High Resolution Images

This paper will review the current state of understanding of interface structure and highlight some of the future needs and problems which must be overcome. The study of this subject can be separated into three different topics: 1) the fundamental electron microscopy aspects, 2) material-specific features of the study and 3) the characteristics of the particular interfaces. The two topics which are relevant to most studies are the choice of imaging techniques and sample preparation. The techniques used to study interfaces in the TEM include high-resolution imaging, conventional diffraction-contrast imaging, and phase-contrast imaging (Fresnel fringe images, diffuse scattering). The material studied affects not only the characteristics of the interfaces (through changes in bonding, etc.) but also the method used for sample preparation which may in turn have a significant affect on the resulting image. Finally, the actual nature and geometry of the interface must be considered. For example, it has become increasingly clear that the plane of the interface is particularly important whenever at least one of the adjoining grains is crystalline.A particularly productive approach to the study of interfaces is to combine different imaging techniques as illustrated in the study of grain boundaries in alumina. In this case, the conventional imaging approach showed that most grain boundaries in ion-thinned samples are grooved at the grain boundary although the extent of this grooving clearly depends on the crystallography of the surface. The use of diffuse scattering (from amorphous regions) gives invaluable information here since it can be used to confirm directly that surface grooving does occur and that the grooves can fill with amorphous material during sample preparation (see Fig. 1). Extensive use of image simulation has shown that, although information concerning the interface can be obtained from Fresnel-fringe images, the introduction of artifacts through sample preparation cannot be lightly ignored. The Fresnel-fringe simulation has been carried out using a commercial multislice program (TEMPAS) which was intended for simulation of high-resolution images.

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