Shale fabric and organic nanoporosity in lower Palaeozoic shales, Bornholm, Denmark

In organic-rich shales, pores form during oil and gas genesis within organic matter (OM) domains. The porosity thus differs markedly from that of conventional reservoir lithologies. Here we present the first description of shale fabric and pore types in the lower Palaeozoic shales on Bornholm, Denmark. The pores have been studied using the focused ion beam scanning electron microscope (FIB-SEM) technique, which allows for high resolution SEM images of ion polished surfaces. Shale porosity is influenced by many factors including depositional fabric, mineralogical composition, diagenesis and oil and gas generation (Schieber 2013). Here we discuss some of these factors based on a study of lower Palaeozoic shale samples from the Billegrav-2 borehole on Bornholm (Fig. 1) undertaken by Henningsen & Jensen (2017). The shales are dry gas-mature (2.3% graptolite reflectance; Petersen et al. 2013) and have been extensively used as analogies for the deeply buried Palaeozoic shales elsewhere in Denmark (Schovsbo et al. 2011; Gautier et al. 2014). The Danish lower Palaeozoic shale gas play was tested by the Vendsyssel-1 well drilled in northern Jylland in 2015. Gas was discovered within a c. 70 m thick gas-mature, organicrich succession (Ferrand et al. 2016). However, the licence was subsequently relinquished, due to a too low gas content. The present study confirms a close similarity of pore development between the shales on Bornholm and in the Vendsys sel-1 indicating a high porosity within this stratigraphic level throughout the subsurface of Denmark. However, the rather different development of porosity in the different shale units presents a hitherto neglected aspect of the Palaeozoic gas play in Denmark.

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Rendering Semisynthetic FIB-SEM Images of Rock Samples

10.20948/graphicon-2021-3027-855-863 ◽

2021 ◽

Author(s):

Ilia Safonov ◽

Anton Kornilov ◽

Iryna Reimers

Keyword(s):

Focused Ion Beam ◽

Oil And Gas ◽

Rock Sample ◽

Pore Space ◽

Ion Beam ◽

Ground Truth ◽

Fine Tuning ◽

Back Side ◽

Sem Images ◽

Rock Samples

Digital rock analysis is a prospective approach to estimate properties of oil and gas reservoirs. This concept implies constructing a 3D digital twin of a rock sample. Focused Ion Beam - Scanning Electron Microscope (FIB-SEM) allows to obtain a 3D image of a sample at nanoscale. One of the main specific features of FIB-SEM images in case of porous media is pore-back (or shine-through) effect. Since pores are transparent, their back side is visible in the current slice, whereas, in fact, it locates in the following ones. A precise segmentation of pores is a challenging problem. Absence of annotated ground truth complicates fine-tuning the algorithms for processing of FIB-SEM data and prevents successful application of machine- learning-based methods, which require a huge training set. Recently, several synthetic FIB- SEM images based on stochastic structures were created. However, those images strongly differ from images of real samples. We propose fast approaches to render semisynthetic FIB- SEM images, which imply that intensities of voxels of mineral matrix in a milling plane, as well as geometry of pore space, are borrowed from an image of rock sample saturated by epoxy. Intensities of voxels in pores depend on the distance from milling plane to the given voxel along a ray directed at an angle equal to the angle between FIB and SEM columns. The proposed method allows to create very realistic FIB-SEM images of rock samples with precise ground truth. Also, it opens the door for numerical estimation of plenty of algorithms for processing FIB-SEM data.

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In Situ Delineation Etch Reveals Subtle Detail in SEM Images of Ion Milled Cross Sections Enabling In-Fab 3-D Metrology and Characterization

Microscopy Today ◽

10.1017/s1551929500057497 ◽

2000 ◽

Vol 8 (2) ◽

pp. 36-39

Author(s):

Clive Chandler

Keyword(s):

Sample Preparation ◽

Cross Sections ◽

Focused Ion Beam ◽

Ion Beam ◽

Automated System ◽

Sem Images ◽

Difficult Time ◽

Device Structures ◽

Wet Etch ◽

Conventional Sample

Control of layer thickness is critically important in the manufacture of semiconductor devices. Cross-sectioning exposes device structures for direct examination but conventional sample preparation procedures are difficult, time consuming, and grossly destructive. Cross sections created by focused ion beam (FIB) milling are easier, faster, and less destructive but have not offered the clear layer delineation provided by etching in the conventional sample preparation process. A new gas etch capability (Delineation Etch™ from FEI Company) offers results that are equivalent to conventional wet-etch preparations in a fraction of the time from a single, automated system in the fab without destroying the wafer. The new etch process also has application in milling high-aspect-ratio holes to create contacts to buried metal layers, and in deprocessing devices to reveal silicon and polysilicon structures.

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The Release of Incidental Nanoparticles During the Weathering of Gunshot Residue in Soils of a Shooting Range in Ontario, Canada

The Canadian Mineralogist ◽

10.3749/canmin.1900092 ◽

2020 ◽

Author(s):

Michael Schindler ◽

Keegan Weatherhead ◽

Haley Mantha

Keyword(s):

Electron Microscopy ◽

Inductively Coupled Plasma ◽

Focused Ion Beam ◽

Ion Beam ◽

Fine Particulate Matter ◽

Mineralogical Composition ◽

Gunshot Residue ◽

Detailed Knowledge ◽

Shooting Range ◽

Colloidal Fraction

Abstract Gunshot residue is emitted as fine particulate matter upon the ignition of percussion-sensitive explosives among other additives in a firearm barrel. The particulates condense from a vapor phase and contain material from the Pb-Sb-Ba-bearing primer, S-bearing gunpowder, and the Pb-bearing bullet fragments. Shooters can inhale or ingest the fine particulates which also attach to their hands, clothing, and other surfaces. Estimation of the bioavailability of the emitted toxic Pb- and Sb-bearing particulates requires detailed knowledge of their mineralogical composition and those of their weathering products. For this purpose, gunshot residue particulates have been collected from soils in front of a firing line of a shooting range in Ontario, Canada. Bulk mineralogical and chemical features of the soils have been characterized using X-ray powder diffraction, inductively coupled plasma-mass spectrometry, and scanning electron microscopy. The focused ion-beam technique has been used to extract a section containing numerous altered gunshot residue particulates from a soil grain. Subsequent transmission electron microscopy shows for the first time that gunshot residue particulates are composed of metallic δ-Pb, α-Sb, galena (PbS), and an unidentified Ba-bearing phase. Weathering of the gunshot residue particulates results in the formation of incidental nanoparticles (i.e., not purposely engineered to occur at the nanometer scale) in the form of δ-Pb, massicot, PbO, and galena. The formation and mobilization of some of these nanoparticles within the soil grain suggest that their release during the weathering of bullets and gunshot residue contributes to the release of Pb into the environment. Hydrocerussite, Pb3(CO3)2(OH)2, cerussite, PbCO3, and massicot and anglesite, PbSO4, are the major secondary Pb-phases in and around altered GSR particulates. These phases form during the weathering of metallic Pb, massicot, and galena nanoparticles in a Ca-carbonate rich environment. Secondary Sb-bearing phases are valentinite, Sb2O3, and amorphous Sb-Pb phases (Sb:Pb ratio = 2:1–4:1). The latter phases have partially replaced large proportions of the Ca-carbonates surrounding the gunshot residue particulates. The larger abundance of the amorphous Sb-Pb phases relative to valentinite suggests that their solubility most likely controls the release of Sb into the bulk soil. The SEM and TEM characterizations and chemical analyses of mineral surface coatings and the colloidal fraction of a leachate from the collected surficial soils indicate that Pb occurs predominantly in the colloidal fraction, is often associated with sulfate-bearing colloids, and is sequestered in sulfate and carbonate/hydroxide coatings.

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APPLICATION OF ONE-DIMENSIONAL PALEOTEMPERATURE MODELING TO ESTIMATE THE HYDROCARBON POTENTIAL OF CRETACEOUS SEDIMENTS OF THE MIDDLE AMUR SEDIMENTARY BASIN

Tikhookeanskaya Geologiya ◽

10.30911/0207-4028-2021-40-4-87-98 ◽

2021 ◽

Vol 40 (4) ◽

pp. 87-98

Author(s):

P.N. Prokhorova ◽

◽

E.P. Razvozzhaeva ◽

V.I. Isaev ◽

◽

...

Keyword(s):

Oil And Gas ◽

Sedimentary Basin ◽

Gas Content ◽

Hydrocarbon Potential ◽

Hydrocarbon Generation ◽

Gas Generation ◽

One Dimensional ◽

Middle Amur Sedimentary Basin ◽

History Of ◽

History Of Formation

The prospects of oil and gas content of the Cretaceous-Paleogene deposits of the Middle Amur sedimentary basin within the Pereyaslavsky graben are clarified on the basis of updated data on the tectonic-stratigraphic complexes of the basin using the method of one-dimensional paleotemperature modeling. It is established that throughout the history of formation of the studied part of Pereyaslavsky graben hydrocarbon generation could occur in lower Cretaceous sediments of the Assikaevsky and Alchansky/Strelnikovsky suites. The gas generation conditions for the Assykaevsky formation are still maintained.

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New insights in the mechanisms of the reaction 3.65 Å phase = clinoenstatite + water down to nanoscales

European Journal of Mineralogy ◽

10.5194/ejm-33-675-2021 ◽

2021 ◽

Vol 33 (6) ◽

pp. 675-686

Author(s):

Monika Koch-Müller ◽

Oona Appelt ◽

Bernd Wunder ◽

Richard Wirth

Keyword(s):

Grain Size ◽

High Resolution ◽

Focused Ion Beam ◽

Ion Beam ◽

High Water ◽

High Water Content ◽

High Porosity ◽

Ambient Conditions ◽

Double Peaks ◽

Diffraction Patterns

Abstract. The reaction of 3.65 Å phase <=> clinoenstatite + water was investigated in five experiments at 10 GPa, 470–600 ∘C, using a rotating multi-anvil press. Under these P/T conditions, clinoenstatite exists in its high-pressure modification, which, however, is not quenchable to ambient conditions but transforms back to low-pressure clinoenstatite. The quenched run products were characterized by electron microprobe analyses (EMPA), powder X-ray diffraction (XRD), Raman spectroscopy and by high-resolution transmission electron microscopy (HRTEM) on focused ion beam (FIB)-cut foils. We bracketed the reaction in the T range 470 to 510 ∘C (at 10 GPa). The hydration of clinoenstatite to the 3.65 Å phase at 470 ∘C was very sluggish and incomplete even after 96 h. Clinoenstatites range in size from less than 1 to up to 50 µm. Usually clinoenstatite has a very small grain size and shows many cracks. In sub-micron-sized broken clinoenstatite, an amorphous phase (0.91Mg:1.04Si, with about 20 wt % H2O) was observed, which further transformed with increasing reaction time into the 3.65 Å phase (1Mg:1Si, with 34 wt % H2O). Thus, the sub-micron-sized fractured clinoenstatite transformed via an amorphous water-bearing precursor phase to the 3.65 Å phase. The dehydration to clinoenstatite was faster but still incomplete after 72 h at 600 ∘C. From the backscattered electron images of the recovered sample of the dehydration experiment, it is obvious that there is a high porosity due to dehydration of the 3.65 Å phase. Again, the grain size of clinoenstatite ranges from less than 1 up to 50 µm. There are still some clinoenstatite crystals from the starting material present, which can clearly be distinguished from newly formed sub-micron-sized clinoenstatite. Additionally, we observe a water-rich crystalline phase, which does not represent the 3.65 Å phase. Its Raman spectra show the double peaks around 700 and 1000 cm−1 characteristic for enstatite and strong water bands at 3700 and 3680 cm−1. The Mg:Si ratio of 0.90:1.04 was determined by EMPA, totalling to 81 wt %, in accordance with its high water content. Diffraction patterns from high-resolution images (fast Fourier transform – FFT) are in agreement with an orthoenstatite crystal structure (Pbca). The surprising observation of this study is that, in both directions of the investigated simple reaction, additional metastable phases occur which are amorphous in the hydration and crystalline in the dehydration reaction. Both additional phases are water rich and slightly deviate in composition from the stable products 3.65 Å phase and clinoenstatite, respectively. Thus, as a general remark, conventional investigations on reaction progress should be complemented by nanoscale investigations of the experimental products because these might reveal unpredicted findings relevant for the understanding of mantle processes. The extreme reduction in grain size observed in the dehydration experiments due to the formation of nanocrystalline clinoenstatite rather than the slowly released fluids might cause mechanical instabilities in the Earth's mantle and, finally, induce earthquakes.

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Two-Stage Alignment of FIB-SEM Images of Rock Samples

Journal of Imaging ◽

10.3390/jimaging6100107 ◽

2020 ◽

Vol 6 (10) ◽

pp. 107

Author(s):

Iryna Reimers ◽

Ilia Safonov ◽

Anton Kornilov ◽

Ivan Yakimchuk

Keyword(s):

High Frequency ◽

Focused Ion Beam ◽

Pore Space ◽

Ion Beam ◽

Affine Transformations ◽

Sem Images ◽

Alignment Procedure ◽

Natural Rock ◽

Alignment Algorithms ◽

Frequency Components

Focused Ion Beam Scanning Electron Microscopy (FIB-SEM) tomography provides a stack of images that represent serial slices of the sample. These images are displaced relatively to each other, and an alignment procedure is required. Traditional methods for alignment of a 3D image are based on a comparison of two adjacent slices. However, such algorithms are easily confused by anisotropy in the sample structure or even experiment geometry in the case of porous media. This may lead to significant distortions in the pore space geometry, if there are no stable fiducial marks in the frame. In this paper, we propose a new method, which meaningfully extends existing alignment procedures. Our technique allows the correction of random misalignments between slices and, at the same time, preserves the overall geometrical structure of the specimen. We consider displacements produced by existing alignment algorithms as a signal and decompose it into low and high-frequency components. Final transformations exclude slow variations and contain only high frequency variations that represent random shifts that need to be corrected. The proposed algorithm can operate with not only translations but also with arbitrary affine transformations. We demonstrate the performance of our approach on a synthetic dataset and two real FIB-SEM images of natural rock.

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FIB Micro-Pillar Sampling of Si Devices and its 3D Observation

ISTFA 2003: Conference Proceedings from the 29th International Symposium for Testing and Failure Analysis ◽

10.31399/asm.cp.istfa2003p0282 ◽

2003 ◽

Author(s):

T. Yaguchi ◽

T. Kamino ◽

T. Ohnishi ◽

T. Hashimoto ◽

K. Umemura ◽

...

Keyword(s):

Focused Ion Beam ◽

Ion Beam ◽

Three Dimensional ◽

Sampling Technique ◽

Scanning Transmission Electron Microscope ◽

Dark Field ◽

Limiting Factor ◽

Sem Images ◽

Cross Sectional ◽

Scanning Transmission

Abstract A novel technique for three-dimensional structural and elemental analyses using a dedicated focused ion beam (FIB) and scanning transmission electron microscope (STEM) has been developed. The system employs an FIB-STEM compatible sample holder with sample stage rotation mechanism. A piece of sample (micro sample) is extracted from the area to be characterized by the micro-sampling technique [1-3]. The micro sample is then transferred onto the tip of the stage (needle stage) and bonded by FIB assisted metal deposition. STEM observation of the micro sample is carried out after trimming the sample into a micro-pillar 2-5 micron squared in cross-section and 10 -15 micron in length (micro-pillar sample). High angle annular dark field (HAADF) STEM, bright field STEM and secondary electron microscopy (SEM) images are obtained at 200kV resulting in threedimensional and cross sectional representations of the microsample. The geometry of the sample and the needle stage allows observation of the sample from all directions. The specific site can be located for further FIB milling whenever it is required. Since the operator can choose materials for the needle stage, the geometry of the original specimen is not a limiting factor for quantitative energy dispersive X-ray (EDX) analysis.

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Scanning Electron Microscopy Observation of Interface Between Single Neurons and Conductive Surfaces

Journal of Nanoscience and Nanotechnology ◽

10.1166/jnn.2016.12311 ◽

2016 ◽

Vol 16 (4) ◽

pp. 3383-3387 ◽

Cited By ~ 3

Author(s):

Toichiro Goto ◽

Nahoko Kasai ◽

Rick Lu ◽

Roxana Filip ◽

Koji Sumitomo

Keyword(s):

Electron Microscopy ◽

Scanning Electron Microscopy ◽

Indium Tin Oxide ◽

Focused Ion Beam ◽

Ion Beam ◽

Single Neurons ◽

Sem Images ◽

Cross Sectional ◽

Integrated Devices ◽

Scanning Electron

Interfaces between single neurons and conductive substrates were investigated using focused ion beam (FIB) milling and subsequent scanning electron microscopy (SEM) observation. The interfaces play an important role in controlling neuronal growth when we fabricate neuron-nanostructure integrated devices. Cross sectional images of cultivated neurons obtained with an FIB/SEM dual system show the clear affinity of the neurons for the substrates. Very few neurons attached themselves to indium tin oxide (ITO) and this repulsion yielded a wide interspace at the neuron-ITO interface. A neuron-gold interface exhibited partial adhesion. On the other hand, a neuron-titanium interface showed good adhesion and small interspaces were observed. These results are consistent with an assessment made using fluorescence microscopy. We expect the much higher spatial resolution of SEM images to provide us with more detailed information. Our study shows that the interface between a single neuron and a substrate offers useful information as regards improving surface properties and establishing neuron-nanostructure integrated devices.

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Morphological Processes of Foot Process Effacement in Puromycin Aminonucleoside Nephrosis Revealed by FIB/SEM Tomography

Journal of the American Society of Nephrology ◽

10.1681/asn.2018020139 ◽

2018 ◽

Vol 30 (1) ◽

pp. 96-108 ◽

Cited By ~ 10

Author(s):

Koichiro Ichimura ◽

Takayuki Miyaki ◽

Yuto Kawasaki ◽

Mui Kinoshita ◽

Soichiro Kakuta ◽

...

Keyword(s):

Cell Body ◽

Focused Ion Beam ◽

Developmental Process ◽

Ion Beam ◽

Primary Process ◽

Puromycin Aminonucleoside ◽

Sem Images ◽

Foot Process Effacement ◽

Foot Process ◽

Morphologic Changes

BackgroundFoot process effacement is one of the pathologic indicators of podocyte injury. However, the morphologic changes associated with it remain unclear.MethodsTo clarify the developmental process, we analyzed puromycin nephrotic podocytes reconstructed from serial focused-ion beam/scanning electron microscopy (FIB/SEM) images.ResultsIntact podocytes consisted of four subcellular compartments: cell body, primary process, ridge-like prominence (RLP), and foot process. The RLP, a longitudinal protrusion from the basal surface of the cell body and primary process, served as an adhesive apparatus for the cell body and primary process to attach to the glomerular basement membrane. Foot processes protruded from both sides of the RLP. In puromycin nephrotic podocytes, foot process effacement occurred in two ways: by type-1 retraction, where the foot processes retracted while maintaining their rounded tips; or type-2 retraction, where they narrowed across their entire lengths, tapering toward the tips. Puromycin nephrotic podocytes also exhibited several alterations associated with foot process effacement, such as deformation of the cell body, retraction of RLPs, and cytoplasmic fragmentation. Finally, podocytes were reorganized into a broad, flattened shape.ConclusionsThe three-dimensional reconstruction of podocytes by serial FIB/SEM images revealed the morphologic changes involved in foot process effacement in greater detail than previously described.

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Super High-Quality SEM/FIB Imaging of Dentine Structures Without Collagen Fiber Loss Through a Metal Staining Process

10.21203/rs.3.rs-716957/v1 ◽

2021 ◽

Author(s):

Shiyou Xu ◽

Michael Stranick ◽

Deon Hines ◽

Ke Du ◽

Long Pan

Keyword(s):

Collagen Fiber ◽

Focused Ion Beam ◽

Ion Beam ◽

Milling Process ◽

Collagen Fibers ◽

Real Sample ◽

Acquisition Time ◽

High Quality ◽

Sem Images ◽

The Real

Abstract Scanning Electron Microscope/Focused Ion Beam (SEM/FIB) system has become a valuable and popular tool for the analysis of biological materials such as dentine structures. According to physiological and anatomical studies, dentine structures are a complicated system containing collagen fibers, nanocrystalline hydroxyapatite, and numerous networks of tubular pores. During a routine FIB milling process, collagen fibers and other organic structures are vaporized, while the number of tubular pores remaining is increased. This causes the final cross-section to be more porous than the real sample. Unfortunately, little attention has been paid to the collagen fiber loss and how to preserve them during a FIB milling process. In this work, we present a novel and simple approach to preserve the organic portions of the dentine structure through metal staining. By using this method, the porosity of the dentine structure after the FIB milling process is significantly reduced similar to the real sample. This indicates that the organic portion of the dentine structure is well protected by the metal staining. This approach enables the SEM/FIB system to generate super-high quality SEM images with less ion beam damage; and the SEM images can better reflect the original condition of the dentine structure. Further, serial energy-dispersive X-ray spectroscopy (EDS) mapping of the stained dentine structure is achieved without an additional metal coating; and three-dimensional (3-D) elemental mapping of an occluded dentine is achieved with a significantly reduced data acquisition time.

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