Thin-section Images Research Articles

Effect of 2D Image Resolution on 3D Stochastic Reconstruction and Developing Petrophysical Trend

Multi-resolution digital rock physics (DRP) makes it possible to up-scale petrophysical properties from micron size to core sample size using two-dimensional (2D) thin section images. Resolution of 3D images and sample size are challenging problems in DRP where high-resolution images are acquired from small samples using inefficient and expensive micro-CT facilities. Three-dimensional stochastic reconstruction is an alternative approach to overcome these challenges. In this paper, we use multi-resolution images and investigate effect of 2D image resolution on 3D stochastic reconstruction and development of petrophysical trends for our two sandstone and carbonate original representative volume elements (RVEs). The proposed method includes three steps. In the first step, the spatial resolution of our original RVEs is decreased synthetically. In the second step, stochastic RVEs are realized for each resolution using two perpendicular images, correlation functions, and phase recovery algorithm. In the reconstruction method, a full set of two-point correlation functions (TPCFs) is extracted from two perpendicular 2D images. Then TPCF vectors are decomposed and averaged to realize 3D stochastic RVEs. In the third step, petrophysical properties like relative and absolute permeability as well as porosity and formation factor are computed. The output is used to develop trends for petrophysical properties in different resolutions. Experimental results illustrate that the proposed method can be used to predict petrophysical properties and reconstruct 3D RVEs for resolutions unavailable in the acquired 2D or 3D data.

Effect of Wettability Changes on Evaporation Rate and the Permeability Impairment due to Salt Deposition

Pore-scale visualization was employed to investigate evaporative drying of brine and associated salt deposition at different wetting conditions, using a 2.5D etched-silicon/glass micromodel based on a thin section image of a carbonate rock. We also compared air drying with CO2 drying, with the latter having important applications in CO2 sequestration processes. The resulting permeability impairment was also measured. For deionized water in a water-wet model, we observed the three classical periods of evaporation: the constant rate period (CRP), the falling rate period (FRP), and the receding front period (RFP). The length of the deionized water CRP was much shorter for a uniformly oil-wet model, but mixed wettability made little difference to the drying process. For brine systems at all wetting conditions, the dry area became linear with the square root of time after a short CRP. This is due to the deposited salt acting as a physical barrier to hydraulic connectivity, unlike the case of deionized water, w...

Multi-radial LBP Features as a Tool for Rapid Glomerular Detection and Assessment in Whole Slide Histopathology Images

We demonstrate a simple and effective automated method for the localization of glomeruli in large (~1 gigapixel) histopathological whole-slide images (WSIs) of thin renal tissue sections and biopsies, using an adaptation of the well-known local binary patterns (LBP) image feature vector to train a support vector machine (SVM) model. Our method offers high precision (>90%) and reasonable recall (>70%) for glomeruli from WSIs, is readily adaptable to glomeruli from multiple species, including mouse, rat, and human, and is robust to diverse slide staining methods. Using 5 Intel(R) Core(TM) i7-4790 CPUs with 40 GB RAM, our method typically requires ~15 sec for training and ~2 min to extract glomeruli reproducibly from a WSI. Deploying a deep convolutional neural network trained for glomerular recognition in tandem with the SVM suffices to reduce false positives to below 3%. We also apply our LBP-based descriptor to successfully detect pathologic changes in a mouse model of diabetic nephropathy. We envision potential clinical and laboratory applications for this approach in the study and diagnosis of glomerular disease, and as a means of greatly accelerating the construction of feature sets to fuel deep learning studies into tissue structure and pathology.

Recent sedimentation in three adjacent fjord-lakes on the Québec North Shore (eastern Canada): facies analysis, laminae preservation, and potential for varve formation

This paper analyzes short gravity cores sampled along transects in three adjacent deep fjord-lakes (lakes Pentecôte, Walker, and Pasteur) on the Québec North Shore, eastern Canada, to evaluate the distribution of laminated sediments and potential for varve formation. Facies analysis based on lithological description, digital photos, CT-scan images, and bathymetric data allowed for the identification of four main sediment facies, namely laminated sediments, partially laminated sediments, bioturbated sediments, and massive sediments. Direct evidence that Lake Walker undergoes thermal stratification was monitored from 2014 to 2016. Mean sedimentation rates and sedimentation fluxes of postglacial sediments in the distal basin of the three studied lakes are ≤0.12 cm a−1 and 0.03–0.16 g cm−2 a−1, respectively, based on 210Pb, 137Cs, and AMS radiocarbon dating. On the basis of thin section image analysis and 210Pb (CIC) chronology model, Lake Pentecôte contains mainly massive, partially laminated sediments, while Lake Pasteur contains partially laminated sediments and non-annual varve-like sediments. However, Lake Walker contains laminated sediments that are likely varves. The increased potential for laminae preservation observed in Lake Walker compared to lakes Pentecôte and Pasteur is associated with more favourable morphological characteristics including higher relative depth, mean depth, maximum depth, and topographic exposure.

Prediction of shell content from thin sections using hybrid image process techniques

Shell content is an important indicator to evaluate the accumulation capability of carbonate reservoirs, but still needs to be estimated artificially. As such, some techniques that can automatically predict shell content only from stained thin section image are proposed. The processing procedures of those techniques include four steps: binarizing color thin section image; detecting edges of objects; using a special technique to extract shell areas; finally adjusting appearances of those extracted shells by dilating and eroding. Six thin sections used for validating techniques derive from the Lower Jurassic formations of the Sichuan Basin. For these six validated cases, the error between the expected and calculated shell content is 0.51%, 2.59%, 0.93%, 2.31%, 2.14% and 2.75% respectively. Moreover, within each thin section image, the main lithology predicted in accordance with the calculated shell content is consistent with that deduced from the expected shell content. The small errors and exact judgments of the lithology manifest that the proposed techniques are capable to provide the reliable shell content data, and compared to the conventional observation and analysis methods they are cost-efficient when dealing with a large amount of thin section images. Therefore, the proposed techniques have practical value and can be used as the handy tool for geologists in the work of observing and identifying thin section.

Investigation of cadmium accumulation mechanism in hepatopancreas of Patinopecten yessoensis by synchrotron radiation X‐ray absorption fine structure and synchrotron radiation X‐ray fluorescence analyses

Chemical state of cadmium in a hepatopancreas of a scallop (Patinopecten yessoensis) was studied by means of synchrotron radiation‐based X‐ray analytical techniques. X‐ray absorption fine structure (XAFS) and X‐ray fluorescence (XRF) imaging were used to identify the chemical state and the distribution of cadmium in the hepatopancreas, respectively. The results of in vivo Cd K‐edge XAFS suggested that the neighboring atoms of the cadmium in the hepatopancreas are of sulfur. Therefore, we propose that cadmium was accumulated by a metalloprotein with sulfur. Micro XRF imaging of thin sections of the hepatopancreas showed that cadmium is distributed on the surface of intestinal epithelia and concentrated in the internal tissue of the hepatopancreas. These results indicated that scallops accumulate cadmium inside the hepatopancreas through the intestinal epithelium.

Controlling factors and physical property cutoffs of the tight reservoir in the Liuhe Basin

Tight gas sandstone reservoirs of the Lower Cretaceous Xiahuapidianzi Formation are the main exploration target in the Liuhe Basin in China. Petrology characteristics, reservoir space (pore space), controlling factors and physical property cutoffs of the tight sandstone reservoir in the Liuhe Basin were determined through the integrated analysis of several methods including: casting thin section, field emission scanning electron microscopy (FE-SEM), X-ray diffraction (XRD), mercury intrusion porosimetry (MIP), nuclear magnetic resonance (NMR) and nitrogen gas adsorption (N2GA). The sandstones dominated by lithic arkoses and feldspathic litharenites are characterized by low porosity, low permeability and strong microscopic heterogeneity. The porosity has a range between 0.48% and 4.80%, with an average of 2.26%. Intercrystalline pores, intergranular pores, dissolved pores and microfractures can be observed through the casting thin section and FE-SEM images. Compaction and carbonate cementation are the two primary mechanisms resulting in the low porosity of the Liuhe sandstones. Microfractures improve the permeability of the tight sandstones and provide pathways for fluid migration and the storage of hydrocarbon accumulations. Moreover, the theoretical cutoff of the porosity in the Xiahuapidianzi Formation tight sandstones is 3.3%.

Cystic pancreatic lesions; CT characterization and pathological evaluation

ObjectiveThe aim of this study was to assess the ability of CT to predict the pathological nature of pancreatic cystic lesions if it is benign, malignant or premalignant. MethodsThis is a retrospective study from the database of our hospital EMR (electronic medical records) for pancreatic lesions from patients who proven to be of pathological cystic nature. The diagnosis and characterization of pancreatic cysts were done by multislice 32 CT examination. We reviewed the data from the radiology, surgery and pathology departments from the period of November 2012 until January 2015. We compared between operative and pathological data and findings of MDCT using chi square test. ResultsWe reviewed the data from the radiology, surgery and pathology departments from the period of November 2012 until January 2015. The study was done on 66 patients. Our results showed that CT features for benign cystic lesions are lobulated shape and a thin wall (≤1 mm) while the round or oval shape or a complex cystic shape with tubular cyst and a thick wall (>1 mm) are more frequently seen in pancreatic premalignant and malignant macrocytic lesions. ConclusionCT with thin section images allows adequate morphological characterization of macrocytic pancreatic masses that could predict its pathological nature if benign or malignant.

The Small Bowel: An Imaging Guide

Background: This article reviews the latest radiological advances in the evaluation of small bowel disease. MRI and CT have been optimized in recent years for small bowel imaging including the development of enteric agents to distend the bowel, multiplanar thin-section imaging, advanced imaging applications, and radiation dose optimization techniques. Discussion: MR enterography, with the absence of ionizing radiation exposure, excellent tissue contrast, ultrafast breath-holding pulse sequences, and the ability to perform real-time functional imaging, has become the first-line imaging modality for the evaluation of the majority of small bowel disorders. Advanced MR applications including diffusion-weighted imaging, dynamic contrast-enhanced MRI, and motility imaging are becoming central in the imaging evaluation of small bowel disease. Conclusion: CT enterography is the preferred modality in patients with known or suspected inflammatory bowel disease in the acute setting to assess for extra-luminal complications. The enteroclysis technique is of use in selected cases in which adequate small bowel distention is not achieved with oral enteral contrast administration. Capsule endoscopy is reserved for patients in whom the clinical suspicion of small bowel disease remains high despite negative evaluations with endoscopy and imaging. Keywords: Small bowel, MR enterography, CT enterography, enteroclysis, dose optimization, Crohn's disease.

Inverse estimation of rock thermal conductivity based on numerical microscale modeling from sandstone thin sections

The effective thermal conductivity (ETC) of porous rocks is primarily controlled by the matrix thermal conductivity (MTC) and the thermal conductivity of the pore fluid as a function of porosity. Rock ETC has been investigated widely, however, information on MTC is rather sparse. This study proposes a new approach using a numerical model to determine the MTC of porous rocks by parameter fitting to the measured ETC. The model represents realistic rock textures as detailed information on grain and pore geometries was obtained from microscopic images of thin sections. MTC fitted from water saturated condition (water as pore fluid) showed plausible values between 4.9 and 7.6W/(m∙K), while MTC values from dry condition (air as pore fluid) were disproportionate, except for one model with consistent MTC for both conditions. This supports the idea that at constant temperature and pressure, MTC is an intrinsic property independent of fluid saturation. For this reason, MTC from water saturated condition was used to calculate dry ETC. The model showed lower dry ETC than the lab measurements, but within a reasonable range for dry sandstones. Investigation of ETC regarding saturation degree revealed that the samples may contain 12%–45% residual moisture, which explained the higher measured dry ETC. Additionally, the models allowed observation of textural influences, showing that grain size, distribution, and connectivity affected the heat conduction of porous rocks.

In vitro Validation of Quantitative Light-Induced Fluorescence for the Diagnosis of Enamel Fluorosis in Permanent Teeth

This study aimed to validate quantitative light-induced fluorescence (QLF) as a diagnostic tool for mild and moderate enamel fluorosis in permanent teeth, comparing it to visual diagnosis and histological assessment completed using polarized light microscopy (PLM). The buccal surfaces of 139 teeth were visually classified using the Thylstrup and Fejerskov Index (TFI) into sound (TFI 0; n = 17), mild (TFI 1-2; n = 69), and moderate (TFI 3-4; n = 43) fluorosis. Fluorosis was then assessed with QLF (variables ΔF, A, and ΔQ at 5-, 15-, and 30-radiance thresholds) using as reference areas the entire surface and a region of interest (ROI), identified as the most representative region of a fluorosis lesion. PLM images of longitudinal thin sections including the ROI were assessed for histological changes. Correlations among TFI, PLM, and QLF were determined. A receiver-operating characteristic curve was conducted to determine QLF's diagnostic accuracy when compared to the TFI and PLM assessments. This was used to assess the probability that the images were correctly ranked according to severity as determined by PLM and TFI. A positive correlation was found between QLF and PLM, and between QLF and TFI. QLF showed the highest sensitivity and specificity for the diagnosis of mild fluorosis. There was also a strong agreement between TFI and PLM. The selection of a ROI resulted in a stronger correlation with TFI and PLM than when the entire surface was used. The study results indicate that defining an ROI for QLF assessments is a valid method for the diagnosis of mild and moderate enamel fluorosis.

Using Resin-Based 3D Printing to Build Geometrically Accurate Proxies of Porous Sedimentary Rocks.

Three-dimensional (3D) printing is capable of transforming intricate digital models into tangible objects, allowing geoscientists to replicate the geometry of 3D pore networks of sedimentary rocks. We provide a refined method for building scalable pore-network models ("proxies") using stereolithography 3D printing that can be used in repeated flow experiments (e.g., core flooding, permeametry, porosimetry). Typically, this workflow involves two steps, model design and 3D printing. In this study, we explore how the addition of post-processing and validation can reduce uncertainty in the 3D-printed proxy accuracy (difference of proxy geometry from the digital model). Post-processing is a multi-step cleaning of porous proxies involving pressurized ethanol flushing and oven drying. Proxies are validated by: (1) helium porosimetry and (2) digital measurements of porosity from thin-section images of 3D-printed proxies. 3D printer resolution was determined by measuring the smallest open channel in 3D-printed "gap test" wafers. This resolution (400µm) was insufficient to build porosity of Fontainebleau sandstone (∼13%) from computed tomography data at the sample's natural scale, so proxies were printed at 15-, 23-, and 30-fold magnifications to validate the workflow. Helium porosities of the 3D-printed proxies differed from digital calculations by up to 7% points. Results improved after pressurized flushing with ethanol (e.g., porosity difference reduced to ∼1% point), though uncertainties remain regarding the nature of sub-micron "artifact" pores imparted by the 3D printing process. This study shows the benefits of including post-processing and validation in any workflow to produce porous rock proxies.

An improved model for permeability estimation in low permeable porous media based on fractal geometry and modified Hagen-Poiseuille flow

Permeability is a crucial macroscopic parameter in characterizing fluid flow and mass transfer behavior in porous media. A great theoretical basis for permeability estimation has been provided by many traditional and recently presented fractal models. However, since the influence of overlying sediments, the low-permeability porous media such as natural rock and coal generally have lower permeability and porosity with abundant pores which have more complex structure and rougher surface. The fluid located at surface tends to be bound to form irreducible state. Generally, this natural phenomenon is often ignored in the conventional fractal permeability model. In this study, the improved model was theoretically deduced based on the fractal geometry theory with considering the irreducible water saturation. 133 total sandstone samples from a gas reservoir were used to verify the validity of the developed model. The mercury injection experiment and the conventional physical property test were carried out, and the thin section image of each sample was crafted. The pores were segmented by the proposed color extracted algorithm for calculating pore fractal dimension. The results show that the available fractal model overestimates permeability values. A new form of the classical Kozeny-Carman equation was also developed to accurately estimate permeability. In the low permeable porous media, the empirical Kozeny-Carman constant needs to take 3.5, instead of 5. However, no longer is typical superiority found at very low permeability (<0.5mD) in the improved fractal model and corresponding reasons are analyzed and discussed.

Reservoir Characterization of Tight Sandstones Using Nuclear Magnetic Resonance and Incremental Pressure Mercury Injection Experiments: Implication for Tight Sand Gas Reservoir Quality

A series of experiments including porosity and permeability measurements, thin section and scanning electron microscopy (SEM) observations, incremental pressure mercury injection (IPMI), and nuclear magnetic resonance (NMR) were conducted to systematically characterize the pore structure of tight sandstone from the Lower Shihezi Formation of Permian (P2x) in the northeastern Ordos Basin, China. The influences of pore types, pore size distribution, and fractal characteristics on reservoir quality of tight sandstones are also investigated. Results show that the studied tight sandstones generally possess poor quality and complex pore structure. The porosity and permeability range from 4.08% to 17.56% (average 9.22%) and from 0.05 to 16.66 mD (average 2.49 mD), respectively. Five pore types were observed in thin section and SEM images: primary intergranular pores, intergranular dissolution pores, intragranular dissolution pores, micropores within clay aggregates, and microfractures. The pore throats are mainly hairy/fibrous, inhibiting the connectivity between pores. Three types of pore structures were identified in the mercury-injection curves and pore size distribution curves from the IPMI experiment and in the T2 relaxation time spectrum obtained by NMR. Both experiments yielded consistent classifications, and their combination was necessary to analyze the pore structure effectively. In general, permeability and porosity are positively related and depend on pore types. Large numbers of small pores confer high storage capacity, whereas small numbers of larger pores improve the flow capability. In the high porosity–permeability zone, larger pores also determine the storage capacity. The P2x tight sandstone is fractal, and macropores are more heterogeneous while micropores are more homogeneous. The fractal dimensions of macropores are good indicators of the reservoir quality of the P2x tight sandstone as larger fractal dimension values of macropores reflect poor reservoir quality.

Construction of Recombinant Pdu Metabolosome Shells for Small Molecule Production in Corynebacterium glutamicum.

Bacterial microcompartments have significant potential in the area of industrial biotechnology for the production of small molecules, especially involving metabolic pathways with toxic or volatile intermediates. Corynebacterium glutamicum is an established industrial workhorse for the production of amino acids and has been investigated for the production of diamines, dicarboxylic acids, polymers and biobased fuels. Herein, we describe components for the establishment of bacterial microcompartments as production chambers in C.glutamicum. Within this study, we optimized genetic clusters for the expression of the shell components of the Citrobacter freundii propanediol utilization (Pdu) bacterial compartment, thereby facilitating heterologous compartment production in C.glutamicum. Upon induction, transmission electron microscopy images of thin sections from these strains revealed microcompartment-like structures within the cytosol. Furthermore, we demonstrate that it is possible to target eYFP to the empty microcompartments through C-terminal fusions with synthetic scaffold interaction partners (PDZ, SH3 and GBD) as well as with a non-native C-terminal targeting peptide from AdhDH (Klebsiella pneumonia). Thus, we show that it is possible to target proteins to compartments where N-terminal targeting is not possible. The overproduction of PduA alone leads to the construction of filamentous structures within the cytosol and eYFP molecules are localized to these structures when they are N-terminally fused to the P18 and D18 encapsulation peptides from PduP and PduD, respectively. In the future, these nanotube-like structures might be used as scaffolds for directed cellular organization and pathway enhancement.

GrainAutLine: an Environment for Semi-Automatic Processing of Marble Thin Section Images

GrainAutLine is an interdisciplinary microscopy image analysis tool with domain specific smart functions to partially automate the processing of marble thin section images. It allows the user to create a clean grain boundary image which is a starting point of several archaeometric and geologic analyses. The semi-automatic tools minimize the need for carefully drawing the grain boundaries manually, even in cases where twin crystals prohibit the use of classic edge detection based boundary detection. Due to the semi-automatic approach, the user has full control over the process and can modify the automatic results before finalizing a specific step. This approach guarantees high quality results both in cases where the process is easy to automate, and also if it needs more help from the user. This paper presents the basic operation of the system and details about the provided tools as a case study for an interdisciplinary, semi-automatic image processing application.

Rock images classification by using deep convolution neural network

Granularity analysis is one of the most essential issues in authenticate under microscope. To improve the efficiency and accuracy of traditional manual work, an convolutional neural network based method is proposed for granularity analysis from thin section image, which chooses and extracts features from image samples while build classifier to recognize granularity of input image samples. 4800 samples from Ordos basin are used for experiments under colour spaces of HSV, YCbCr and RGB respectively. On the test dataset, the correct rate in RGB colour space is 98.5%, and it is believable in HSV and YCbCr colour space. The results show that the convolution neural network can classify the rock images with high reliability.

Stress‐dependent permeability and wave dispersion in tight cracked rocks: Experimental validation of simple effective medium models

AbstractWe experimentally assess the impact of microstructure, pore fluid, and frequency on wave velocity, wave dispersion, and permeability in thermally cracked Carrara marble under effective pressure up to 50 MPa. The cracked rock is isotropic, and we observe that (1) P and S wave velocities at 500 kHz and the low‐strain (&lt;10−5) mechanical moduli at 0.01 Hz are pressure‐dependent, (2) permeability decreases asymptotically toward a small value with increasing pressure, (3) wave dispersion between 0.01 Hz and 500 MHz in the water‐saturated rock reaches a maximum of ~26% for S waves and ~9% for P waves at 1 MPa, and (4) wave dispersion virtually vanishes above ~30 MPa. Assuming no interactions between the cracks, effective medium theory is used to model the rock's elastic response and its permeability. P and S wave velocity data are jointly inverted to recover the crack density and effective aspect ratio. The permeability data are inverted to recover the cracks' effective radius. These parameters lead to a good agreement between predicted and measured wave velocities, dispersion and permeability up to 50 MPa, and up to a crack density of ~0.5. The evolution of the crack parameters suggests that three deformation regimes exist: (1) contact between cracks' surface asperities up to ~10 MPa, (2) progressive crack closure between ~10 and 30 MPa, and (3) crack closure effectively complete above ~30 MPa. The derived crack parameters differ significantly from those obtained by analysis of 2‐D electron microscope images of thin sections or 3‐D X‐ray microtomographic images of millimeter‐size specimens.

Improved Image Quality in SEM Imaging of Thin Tissue Sections

Improved Image Quality in SEM Imaging of Thin Tissue Sections

Quality of Computed Tomography Pulmonary Embolism and Aortic Phase Images Acquired with Power Injection via an Arm Port

BackgroundThe safety of power-injectable implanted arm ports is well established, but there is insufficient data to conclude that image quality of computed tomography resulting from contrast introduced via the port is of equal quality to images derived from contrast introduced via traditional peripheral access. The objective of this study was to determine whether the image quality of computed tomography pulmonary embolism and computed tomography aorta studies would differ when injecting contrast via an implanted arm port vs a peripheral intravenous site. We hypothesized that injecting via an implanted arm port would produce better-quality images, the result of more appropriate timing and less streak artifact. MethodsScans from a provincial database search for patients who underwent a computed tomography pulmonary embolism or aorta study with contrast injection via the implanted arm port and thin section images available, were reviewed (pulmonary embolism studies n = 3, aorta studies n = 3). Only a limited number of patients were available for review because there are currently few patients with these ports in place and we limited evaluation to thin section images. Comparison was made with 6 control patients who did not have a port and had received a peripheral arm intravenous contrast injection for these study types. Objective measurements included signal-to-noise ratio and contrast-to-noise ratio of the pulmonary arteries (4 sites) and aorta (2 sites) as appropriate for scan type. Subjective analysis of image quality was performed by 2 radiologists. ResultsAlthough sample size was limited, the implanted arm port group had similar or higher mean signal-to-noise ratio and contrast-to-noise ratio values at all sites. Subjective assessments showed the implanted arm port group to have similar or better opacification and diagnostic confidence; similar or less streak artifact was also observed at each of the sites. ConclusionsThese exploratory results suggest that studies with implanted arm port injection can generate high-quality images on both objective and subjective assessment, similar to, or possibly better than, images generated from usual peripheral intravenous access for contrast injection.