Publications
141 results found
John CM, 2024, Legacy IODP Cores Data in the Era of Big Data
<jats:p>Core data is pivotal for understanding our planet&#8217;s past, present, and future. Despite this richness, extracting meaningful insights from core description poses significant challenges due to the inherent complexity and variability of the data, the amount of existing material, and the subjectivity of the interpreter. IODP (and the preceding programs) offers a rich, well labelled source of core images that can be used in machine learning and deep learning.Focusing largely (but not exclusively) on carbonate rocks, characterized by their heterogeneity at all observational scales, I will discuss how my research group and I have pioneered the application of deep-learning computer vision to geological core interpretation. This technology transcends the traditional, tedious manual interpretations of cores, offering a rapid, and often more accurate, alternative for delineating depositional environments and sequence stratigraphy. Convolutional neural networks (CNNs) form the backbone of our approach, enabling us to process core data with unprecedented efficiency. I will show that these sophisticated models, when correctly trained and fed with substantial datasets, serve as invaluable tools for geologists, outpacing conventional methods in speed without compromising on precision.Our early work was centred on transfer learning, an AI approach that adapts pre-existing models to new data. I will show that this remains one of the best way to train classification algorithms for geological dataset. But we also worked on generative algorithms that fill gaps in our sampling of core imagery: for instance, we use Generative Adversarial Networks (GANs) to transform the resistivity images from formation micro scanners into representations mirroring actual core photographs, thus enhancing the interpretability for geologists irrespective of their background in downhole tools.We tackle the often-limiting factor of dataset size in two ways. First, we recourse to ge
Zheng W, Bell R, John CM, et al., 2024, Deep Learning for Detecting Thrust Faults in Subduction Zones
<jats:p>Subduction plate boundary faults and splay faults in accretionary wedges are capable of generating some of the largest earthquakes and tsunamis on Earth. Owing to the complexity of geological structures and the inherent ambiguity in geophysical data, comprehensively characterizing potential thrust fault systems presents a considerable challenge. Current automated fault detection methods, primarily targeting normal faults, show limited efficacy in complex fault systems of subduction zones. Treating the task of fault detection as a binary image segmentation issue, we propose a supervised end-to-end fully convolutional neural network (U-Net) to automatically and accurately delineate thrust faults from seismic data. To circumvent the labour-intensive and potentially subjective manual labelling process required for model training, we have designed a workflow to efficiently auto-generate more than 10000 training pairs comprising both 2D synthetic seismic images and their corresponding labelled images of the thrust faults simulated in the seismic images. Each synthetic seismic image includes randomly undulating stratigraphic strata and faults with dip angles between 5 and 40 degrees, aiming to simulate realistic and varied geological structures and thrust fault features in subduction zone, which equipped the U-Net model to achieve a 91% accuracy rate in fault detection within the test dataset. The example from the Hikurangi subduction zone, New Zealand demonstrates that the U-Net trained by only synthetic data is superior to conventional automatic methods, such as unsupervised methods or supervised methods trained by normal faults, in delineating more than 70% thrust faults from seismic images. To enhance the U-Net model's adaptation to specific regional fault characteristics and reduce the interference from noise, we incorporated a select set of real 2D seismic images and manually interpreted fault labels into the transfer learning process, which significant
Adlan Q, Kaczmarek SE, John CM, 2023, Clumped Isotope Reordering and Kinetic Differences in Co-Hosted Calcite and Dolomite Minerals throughout Burial Diagenesis and Exhumation, Minerals, Vol: 13
The clumped isotope paleo-thermometer has become a valuable proxy for the burial history reconstruction of carbonate formations. To maximise the accuracy of these reconstructions, post-depositional alterations, such as recrystallisation and Δ47 isotope exchange reactions, must be understood. In this study, we examine the isotopic behaviour of calcites and early dolomite samples from the same stratigraphic intervals, and thus with similar burial history. This approach provides additional constraints on the kinetics of Δ47 reordering in dolomite during exhumation. Clumped isotope measurements were performed on 19 calcites and 15 early dolomites from the Permian, Jurassic, and Cretaceous periods from four locations in Oman spanning different burial regimes. The calcite and dolomite samples were collected from the rock matrix, based on the assumption that fine material was more susceptible to recrystallisation. Our results show that calcites and dolomites record different Δ47 values despite being subjected to the same thermal history. The maximum Δ47 temperature recorded in dolomites (181 ± 13 °C) corresponds to the oldest and most deeply buried Permian rock. This value is approximately 35 °C higher than those measured in the co-located and coeval calcite matrix (145 ± 14 °C). This discrepancy suggests that calcite and dolomite have different kinetic parameters. Our data confirm (1) that dolomite Δ47 values are more resistant to alteration during burial and exhumation than Δ47 calcite values, and (2) that dolomite has a higher Δ47 closing temperature than calcite during cooling. The presence of two mineral phases with distinct kinetic parameters in the same stratigraphic unit provides additional constraints on models of burial and uplift. In addition, mineralogical data coupled with Δ47 and burial depths suggest that the progressive development of dolomite cation ordering is driven by temperature
Herlambang A, John CM, 2023, Fluid flow evolution revealed by carbonate clumped isotope thermometry along the fractures in a complex salt dome setting: Study case (Jebel Madar, Oman), MARINE AND PETROLEUM GEOLOGY, Vol: 152, ISSN: 0264-8172
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- Citations: 1
Herlambang A, John CM, Drake H, 2023, Physicochemical Conditions of the Devonian-Jurassic Continental Deep Biosphere Tracked by Carbonate Clumped Isotope Temperatures of Granite-Hosted Carbonate Veins, GEOFLUIDS, Vol: 2023, ISSN: 1468-8115
Dawson HL, Dubrule O, John CM, 2023, Impact of dataset size and convolutional neural network architecture on transfer learning for carbonate rock classification, Computers and Geosciences, Vol: 171, Pages: 1-11, ISSN: 0098-3004
Modern geological practices, in both industry and academia, rely largely on a legacy of observational data at a range of scales. However, widespread ambiguities in the petrographic description of rock facies reduce the reliability of descriptive data. Previous studies have demonstrated a great potential for the use of convolutional neural networks (CNNs) in the classification of facies from digital images; however, it remains to be determined which of the available CNN architectures performs best for a geological classification task. We evaluate the ability of top-performing CNNs to classify carbonate core images using transfer learning, systematically developing a performance comparison between these architectures on a complex geological dataset. Three datasets with orders of magnitude difference in data quantity (7000–104,000 samples) were created that contain images across seven classes from the modified Dunham Classification for carbonate rocks. Following training of nine different CNNs of four architectures on these datasets, we find the Inception-v3 architecture to be most suited to this classification task, achieving 92% accuracy when trained on the larger dataset. Furthermore, we show that even when using transfer learning the size of the dataset plays a key role in the performance of the models, with those trained on the smaller datasets showing a strong tendency to overfit. This has direct implications for the application of deep learning in geosciences as many papers currently published use very small datasets of less than 5000 samples. Application of the framework developed in this research could aid the future of deep learning based carbonate classification, with further potential to be easily modified to suit the classification of cores originating from different formations and lithologies.
Nathwani CL, Wilkinson JJ, Brownscombe W, et al., 2023, Mineral texture classification using deep convolutional neural networks: An application to zircons from porphyry copper deposits, Journal of Geophysical Research: Solid Earth, Vol: 128, Pages: 1-19, ISSN: 2169-9313
The texture and morphology of igneous zircon indicates magmatic conditions during zircon crystallization and can be used to constrain provenance. Zircons from porphyry copper deposits are typically prismatic, euhedral, and strongly oscillatory zoned which may differentiate them from zircons associated with unmineralized igneous systems. Here, cathodoluminescence images of zircons from the Quellaveco porphyry copper district, Southern Peru, were collected to compare zircon textures between the premineralization Yarabamba Batholith and the Quellaveco porphyry copper deposit. Quellaveco porphyry zircons are prismatic, euhedral, and strongly oscillatory zoned, whereas the batholith zircons are subhedral-anhedral with weaker zoning. We adopt a deep convolutional neural network (CNN) approach to demonstrate that a CNN can classify Quellaveco porphyry zircons with high success. We trial several CNN architectures to classify zircon images: LeNet-5, AlexNet and VGG, including a transfer learning approach where we used the weights of a VGG model pretrained on the ImageNet data set. The VGG model with transfer learning is the most effective approach, with accuracy and receiver operating characteristic-area under curve (ROC-AUC) scores of 0.86 and 0.93, indicating that a Quellaveco porphyry zircon CL image can be ranked higher than a batholith zircon with 93% probability. Visualizing model layer outputs demonstrates that the CNN models can recognize crystal edges, zoning, and mineral inclusions. We trial implementing trained CNN models as unsupervised feature extractors, which can empirically quantify crystal textures and morphology. Therefore, deep learning provides a tool for the extraction of information from large, imaged-based petrographic data sets which can facilitate petrologic and provenance studies.
Adlan Q, John CM, 2023, Clumped isotope record of individual limestone fabrics: A potential method to constrain the timing of oil migration, Chemical Geology, Vol: 616, Pages: 1-12, ISSN: 0009-2541
This study applied clumped isotope analyses to investigate how different limestone components (larger skeletal grains and enclosing matrix) and cements may have varying degrees of susceptibility to recrystallization during progressive burial. The results also provide new constraints on the temperatures of recrystallization and cementation, the nature of the waters involved, the timing of the diagenetic events, and the effect of oil emplacement on inhibiting diagenetic processes. We used clumped isotope measurements from core samples in two giant oilfields, together with petrography and well-constrained thermal histories, to study the reactivity of different limestone fabrics and whether the displacement of pore water by oil affected the recrystallization processes. We recognize seafloor micritization, cementation, and recrystallization as distinct diagenetic processes. The results indicate that skeletal grains record burial temperatures of 60 °C to72°C and enclosing coarse-blocky calcite cements record temperatures of 85 °C to 86 °C. Oxygen isotopes suggest that both processes involve high water/rock ratios. Burial histories together with carbonate Δ47 values are used to estimate that the skeletal grains recrystallized from 99 to 70 Ma and the cements formed at around 54 Ma. By contrast, the matrix shows temperatures of 68 °C to 90 °C, consistent with continuous recrystallization at low water/rock ratios from 90 to 50 Ma. The large skeletal grains thus tend to recrystallize early, but are less reactive during subsequent burial because of larger crystal size, whereas the more finely crystalline and reactive matrix more faithfully records maximum burial conditions. The lower temperature recorded in the matrix relative to the present reservoir temperatures is interpreted as reflecting stoppage or inhibition of recrystallization by oil emplacement.
Holdsworth C, MacDonald J, John C, 2022, Non-Linear Clumped Isotopes from DIC Endmember Mixing and Kinetic Isotope Fractionation in High pH Anthropogenic Tufa, Minerals, Vol: 12
Clumped isotope values (Δ47) of carbonates forming in high pH conditions do not correspond to mineral precipitation temperatures due to certain effects including kinetic isotope fractionation and dissolved inorganic carbon (DIC) endmember mixing. Field-based archives of these carbonate environments are needed to evaluate and quantify these effects accurately. In this study, we measure the clumped isotope values of anthropogenic carbonates for the first time. Tufa layers were analyzed from samples precipitating in a high pH (>10) stream that drains a major slag heap in north east England. Δ47 values are 0.044‰–0.183‰ higher than expected equilibrium values. Non-linear distribution of clumped isotope data is diagnostic of DIC endmember mixing, rather than partial equilibration of DIC. Episodic dilution of hydroxide-rich stream waters by equilibrated rainfall surface runoff provides the mechanism by which mixing occurs. Δ47 values are ~0.010‰–0.145‰ higher than linear clumped isotope mixing profiles, suggesting that the majority of Δ47 increase results from a combination of endmember non-linear mixing effects and an atmosphere-hydroxide sourcing of DIC. The diagnostic trends and variation in clumped isotope values present in these results demonstrates the potential of anthropogenic carbonate systems as a useful archive for studying and quantifying kinetic effects in clumped isotopes.
El-Yamani MS, John CM, Bell R, 2022, Stratigraphic evolution and karstification of a Cretaceous Mid-Pacific atoll (Resolution Guyot) resolved from core-log-seismic integration and comparison with modern and ancient analogues, Basin Research, Vol: 34, Pages: 1536-1566, ISSN: 0950-091X
Atolls are faithful recorders helping us understand eustatic variations, the evolution of carbonate production through time, and changes in magmatic hotspots activity. Several early Cretaceous Mid-Pacific atolls were previously investigated through ocean drilling, but due to the low quality of vintage seismic data available, few spatial constraints exist on their stratigraphic evolution and large-scale diagenesis. Here, we present results from an integrated core-log-seismic study at Resolution Guyot and comparison with modern and ancient analogues. We identify six seismic-stratigraphic units: (1) platform initiation with aggradation and backstepping through the Hauterivian which ended by platform emersion; (2) reflooding of the platform with progradation and aggradation through the Barremian till the early-Aptian when ocean anoxic event 1a resulted in incipient drowning; (3) platform backstepping till the mid-Aptian when the platform shifted to progradation and aggradation till the mid-Albian; (4) platform emersion; (5) reflooding with backstepping ending at the latest-Albian by platform emersion; and (6) final drowning. The stratigraphic surfaces bounding these units are coeval with some of the Cretaceous eustatic events, which suggest an eustatic control on the evolution of this atoll and confirm that several previously reported sea-level variations in the early Cretaceous are driven by eustasy. Changes in subsidence and carbonate production rates and suspected later magmatism have also impacted the stratigraphic evolution. The suspected later magmatism could lead to environmental perturbations and potentially platform demise. Contrary to previous studies, we identify two emersion events during the mid- and late-Albian which resulted in intensive meteoric dissolution and karstification. The platform margin syndepositional fractures interacted with the subaerial exposure events by focusing the dissolution which formed vertically stacked flank-margin fracture-cave s
Sun X, Gomez-Rivas E, Alcalde J, et al., 2022, Origin and distribution of calcite cements in a folded fluvial succession: The Puig-reig anticline (south-eastern Pyrenees), SEDIMENTOLOGY, Vol: 69, Pages: 2319-2347, ISSN: 0037-0746
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- Citations: 8
Robinson AS, Dale A, Adatte T, et al., 2022, Cenozoic sediment bypass versus Laramide exhumation and erosion of the Eagle Ford Group: Perspective from modelling of organic and inorganic proxy data (Maverick Basin, Texas, USA), GEOLOGY, Vol: 50, Pages: 817-821, ISSN: 0091-7613
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- Citations: 4
Al-Wazzan HA, Hawie N, John CM, 2022, Predicting marine organic-rich deposits using forward stratigraphic modelling: The Jurassic Najmah source rock-Case study, MARINE AND PETROLEUM GEOLOGY, Vol: 140, ISSN: 0264-8172
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- Citations: 2
Ho SL, Wang J-K, Lin Y-J, et al., 2022, Changing surface ocean circulation caused the local demise of echinoid <i>Scaphechinus mirabilis</i> in Taiwan during the Pleistocene-Holocene transition, SCIENTIFIC REPORTS, Vol: 12, ISSN: 2045-2322
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- Citations: 1
Garfi G, John CM, Rucker M, et al., 2022, Determination of the spatial distribution of wetting in the pore networks of rocks, JOURNAL OF COLLOID AND INTERFACE SCIENCE, Vol: 613, Pages: 786-795, ISSN: 0021-9797
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- Citations: 9
Marchegiano M, John CM, 2022, Disentangling the Impact of Global and Regional Climate Changes During the Middle Eocene in the Hampshire Basin: New Insights From Carbonate Clumped Isotopes and Ostracod Assemblages, PALEOCEANOGRAPHY AND PALEOCLIMATOLOGY, Vol: 37, ISSN: 2572-4517
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- Citations: 2
Garfi G, John C, Rücker M, et al., 2022, Determination of the spatial distribution of wetting in the pore networks of rocks
<jats:p>The macroscopic movement of subsurface fluids involved in CO2 storage, groundwater, and petroleum engineering applications is controlled by interfacial forces in the pores of rocks, micrometre to millimetre in length scale. Recent advances in physics based models of these systems has arisen from approaches simulating flow through a digital representation of the complex pore structure. However, further progress is limited by a lack of approaches to characterising the spatial distribution of the wetting state within the pore structure. In this work, we show how observations of the fluid coverage of mineral surfaces within the pores of rocks can be used as the basis for a quantitative 3D characterisation of heterogeneous wetting states throughout rock pore structures. We demonstrate the approach with water-oil fluid pairs on rocks with distinct lithologies (sandstone and carbonate) and wetting states (hydrophilic, intermediate wetting, or heterogeneously wetting). The resulting 3D maps can be used as a deterministic input to pore scale modelling workflows and applied to all multiphase flow problems in porous media ranging from soil science to fuel cells.</jats:p>
Fiordalisi E, Marchegiano M, John CM, et al., 2021, Late Cretaceous volcanism and fluid circulation in the South Atlantic: Insights from continental carbonates in the onshore Namibe Basin (Angola), MARINE AND PETROLEUM GEOLOGY, Vol: 134, ISSN: 0264-8172
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- Citations: 3
Cruset D, Verges J, Benedicto A, et al., 2021, Multiple fluid flow events from salt-related rifting to basin inversion (Upper Pedraforca thrust sheet, SE Pyrenees), BASIN RESEARCH, Vol: 33, Pages: 3102-3136, ISSN: 0950-091X
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- Citations: 8
Davies AJ, Davis S, John CM, 2021, Evidence of taxonomic non-equilibrium effects in the clumped isotope composition of modern cephalopod carbonate, CHEMICAL GEOLOGY, Vol: 578, ISSN: 0009-2541
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- Citations: 5
Cai C, Li K, Liu D, et al., 2021, Anaerobic oxidation of methane by Mn oxides in sulfate-poor environments, GEOLOGY, Vol: 49, Pages: 761-766, ISSN: 0091-7613
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- Citations: 15
Bernasconi SM, Daeron M, Bergmann KD, et al., 2021, InterCarb: A Community Effort to Improve Interlaboratory Standardization of the Carbonate Clumped Isotope Thermometer Using Carbonate Standards, GEOCHEMISTRY GEOPHYSICS GEOSYSTEMS, Vol: 22
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- Citations: 73
Anderson NT, Kelson JR, Kele S, et al., 2021, A Unified Clumped Isotope Thermometer Calibration (0.5-1,100°C) Using Carbonate-Based Standardization, GEOPHYSICAL RESEARCH LETTERS, Vol: 48, ISSN: 0094-8276
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- Citations: 67
Herlambang A, John CM, 2021, Combining clumped isotope and trace element analysis to constrain potential kinetic effects in calcite, GEOCHIMICA ET COSMOCHIMICA ACTA, Vol: 296, Pages: 117-130, ISSN: 0016-7037
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- Citations: 3
Tagliavento M, John CM, Anderskouv K, et al., 2021, Towards a new understanding of the genesis of chalk: Diagenetic origin of micarbs confirmed by clumped isotope analysis, SEDIMENTOLOGY, Vol: 68, Pages: 513-530, ISSN: 0037-0746
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- Citations: 9
John CM, Kussanov I, Hawie N, 2021, Constraining stratal architecture and pressure barriers in the subsalt Karachaganak Carboniferous carbonate platforms using forward stratigraphic modelling, MARINE AND PETROLEUM GEOLOGY, Vol: 124, ISSN: 0264-8172
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- Citations: 4
Elyamani M, John CM, Bell RE, 2021, SENSITIVITY ANALYSIS OF THE AMPLITUDE OF EARLY CRETACEOUS EUSTATIC CHANGES USING FORWARD STRATIGRAPHIC MODELLING (RESOLUTION GUYOT), Pages: 2332-2336
Multiple studies focused on eustatic changes during the Cretaceous as an example of greenhouse world. Most of these studies were performed in local areas. These sea level estimates might be derived from localised effects and therefore reflect relative sea level changes rather than eustasy. Based on that, sensitivity analysis to test the applicability of using the Cretaceous ESL curves of Rohl & ogg (1996), Sahagian et al. (1996), Hardenbol et al. (1998), and Haq (2014) is crucial to validate or refute them. To do that, forward stratigraphic modelling of one of the Mid-Pacific mountain guyots, Resolution Guyot, is performed. The study area is unique as it represents deposition of Cretaceous carbonates (growing at sea-level) on an isolated volcanic island away from the influence of continents and tectonic activity. The initial results show that Haq (2014) ESL curve wasn’t perfectly fitting some of our constraints, and some of the cycles need finer subdivision. The outcomes of this study will constrain the fluctuations of ESL in the Cretaceous and serve as a test to whether the amplitude and timing of regionally-derived eustatic curves are valid for other locations, or whether these curves are too influenced by specific local conditions in the areas.
Munoz-Lopez D, Alias G, Cruset D, et al., 2020, Influence of basement rocks on fluid evolution during multiphase deformation: the example of the Estamariu thrust in the Pyrenean Axial Zone, SOLID EARTH, Vol: 11, Pages: 2257-2281, ISSN: 1869-9510
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- Citations: 5
Cruset D, Cantarero I, Benedicto A, et al., 2020, From hydroplastic to brittle deformation: Controls on fluid flow in fold and thrust belts. Insights from the Lower Pedraforca thrust sheet (SE Pyrenees), MARINE AND PETROLEUM GEOLOGY, Vol: 120, ISSN: 0264-8172
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- Citations: 15
Munoz-Lopez D, Cruset D, Cantarero I, et al., 2020, Fluid Dynamics in a Thrust Fault Inferred from Petrology and Geochemistry of Calcite Veins: An Example from the Southern Pyrenees, GEOFLUIDS, Vol: 2020, ISSN: 1468-8115
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- Citations: 13
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