Advances in nano- to micro-analytical tools to understand Earth processes

This session is divided into two parts: (1) Defects, interfaces and trace element heterogeneities, and (2) Advances in Raman spectroscopy.
(1) Recent developments in correlative analytical methodologies enable unique observations of physical and chemical complexities in geological materials down to the nanoscale. These observations illustrate complex relationships between trace element segregation and crystal defects that are a nanoscale manifestation of the meso- to tectonic-scale mass transfer processes that govern Earth and planetary systems. This session focuses on the development, integration and application of advanced structural and chemical analysis to investigate of nano- to atomic-scale structural and geochemical processes. Studies involving transmission electron microscopy, high-resolution electron backscatter diffraction, electron channeling contrast imaging, transmission Kikuchi diffraction, laser ablation – inductively coupled plasma – mass spectrometry, secondary ion mass spectrometry and atom probe tomography are particularly welcomed. We encourage contributions that yield new insights into the relationships of defects, interfaces and trace element heterogeneities, including their origin and preservation, as well as the broader implications and applications to geochemistry, geochronology, petrology, mineral physics, economic geology, and structural and metamorphic geology.
(2) Raman spectroscopy is well established in a range of geoscientific disciplines. Geothermometry is one common application, with recent advances in spectral parameterization significantly broadening the range of applicable temperatures. When applied to organic carbon, it has also been shown that Raman spectra can be affected by factors other than temperature, such as strain and starting carbon type. This surge in understanding creates the opportunity to advance Raman spectroscopy as a potential tool across a range of fields. We welcome any contributions that deal with Raman spectroscopy in the context of geoscience, particularly those that shed light on new ways in which Raman can be used to understand Earth systems. We also encourage debate on the opportunities and limitations presented by Raman as an analytical tool.

Convener: Renelle DubosqECSECS | Co-conveners: Lauren KedarECSECS, Steven Reddy, Clare Bond, Dave Muirhead
vPICO presentations
| Wed, 28 Apr, 11:00–12:30 (CEST)

Session assets

Session summary

vPICO presentations: Wed, 28 Apr

Chairpersons: Renelle Dubosq, Lauren Kedar
Defects, interfaces and trace element heterogeneities
Katharina Marquardt, David Dobson, Simon Hunt, and Ulrich Faul

Grain boundaries affect bulk properties of polycrystalline materials, such as electrical conductivity, melting or bulk viscosity. In the past two decades, observations of marked bulk material property changes have been associated with changes in the structure and composition of grain boundaries. This led to the term “grain boundary complexions” to mark the phase-like behaviour of grain boundaries while differing from phases in the sense of Gibbs (Cantwell 2014).

Here we introduce the principles of grain boundary structure to property relations and potent methods to study these. The focus is on the combination of structural, chemical and statistical analysis as obtainable using transmission electron microscopy and electron backscatter diffraction. Data from these complementary methods will be discussed on two systems; garnet and olivine polycrystals.

Past elasticity measurements showed that the Youngs modulus of garnet polycrystals changes as a function of sintering pressure (Hunt et al. 2016). Here we used high resolution transmission electron microscopy to study the structure of grain boundaries from polycrystals synthesized at low (4-8 GPa) and high (8-15) GPa sintering pressure. The HRTEM data were acquired using an image-corrected JEOL ARM 300 to achieve the highest resolution at low electron doses using a OneView camera. Our data indicate a grain boundary structural change occurs from “low-pressure” to “high pressure” grain boundaries, where the grain boundary facets change from >100 nm – 20 nm to 3-7 nm length scale, respectively. We conclude that sintering pressure affects grain-boundary strength and we will evaluate how this may influence anelastic energy loss of seismic waves through elastic or diffusional accommodation of grain-boundary sliding.

Polycrystalline olivine samples show different viscosity related to grain boundary segregation of impurities. To investigate if the distribution of grain boundaries is affected by grain boundary chemistry, we analysed grain orientation data from over 4x104 grains, corresponding to more than 6000 mm grain boundary length per sample. Using stereology, we extract the geometry of the interfacial network. The thus obtained grain boundary character distribution (GBCD) is discussed in relation to bulk viscosity.

How to cite: Marquardt, K., Dobson, D., Hunt, S., and Faul, U.: Grain boundary character information via individual imaging or statistical analyses: complexion transitions and grain boundary segregation, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-14614,, 2021.

Joseph Cukjati, Reid Cooper, Stephen Parman, Ningli Zhao, Austin Akey, and Fernando Laiginhas

Here we report Atom Probe Tomography (APT) analyses of grain and phase boundaries of laboratory-deformed, fine-grained mixtures of clinopyroxene and olivine (Zhao, et al., 2019).  The experiments show that the mixtures deform much more rapidly than either mineral endmember.  This enhanced deformation in the two-phase material is due to stress-driven reactions at the phase boundaries. Lower effective viscosities of phase mixtures may be critical to the initiation of plate tectonics and the formation of mantle shear zones.

The hypothesis presented here is that the ‘bulk rock’ – a wehrlite – deforms rapidly because conversion of one phase to the other occurs at phase boundaries (e.g., Sundberg & Cooper, 2008).  In this model, grain-scale transport of the shared (slowly-diffusing) mineralogical component Si4+ is not required.  The near-boundary gradients of olivine-insoluble ions are presented as evidence of the phase transformation which either dissolves olivine into clinopyroxene or vice versa.  

The resolving power of the APT makes it a promising tool for investigating the microphysics of rock deformation, bridging the atomic scale all the way to the plate-tectonic scale.

Sundberg M, Cooper RF (2008) Crystallographic preferred orientation produced by diffusional creep of harzburgite: effects of chemical interactions among phases during plastic flow. J Geophys Res Solid Earth 113(12):B12208.
Zhao N, Hirth G, Cooper RF, Kruckenberg SC, Cukjati J (2019) Low viscosity of mantle rocks linked to phase boundary sliding. Earth Planet Sci Lett 517:83–94.

How to cite: Cukjati, J., Cooper, R., Parman, S., Zhao, N., Akey, A., and Laiginhas, F.: Atom probe as a tool for understanding mineral physics and rock deformation: a case study of deformed wehrlite, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-6581,, 2021.

Ge Bian, Olga Ageeva, Gerlinde Habler, Vladimir Roddatis, and Rainer Abart

Magnetite (Mt) is the foremost carrier of rock natural remanent magnetization (NRM). Needle- and lath shaped Mt micro-inclusions in plagioclase (Pl) from gabbro often have systematic crystallographic- and shape orientation relationships (CORs, SORs) with the Pl host. The SORs of Mt leads to magnetic anisotropy which may bias the NRM of the Mt-Pl inclusion-host assemblage. Thus, the origin of the CORs and SORs between Mt and Pl is important for paleomagnetic reconstructions. In this context, the atomic structures of Mt-Pl interfaces are of particular interest.

The CORs and SORs between Mt and Pl were reported earlier and the underlying systematics was revealed from correlated optical and scanning electron microscopy (SEM) including electron back scattered diffraction (EBSD) analyses [1] (and references therein). The so-called plane normal type Mt micro-inclusions extend parallel to the Mt<111> direction, which is perpendicular to the densely packed Mt{222} oxygen layers that are parallel to one of seven Pl lattice planes with nearly identical d-spacings, namely Pl(112), Pl(-312), Pl(1-50), Pl(150), Pl(100), Pl(31-2) and Pl(1-12). Direct imaging of Mt-Pl interfaces has rarely been reported due to the beam sensitivity of Pl. Here we present the microscopic structure of a Mt-Pl interface along the inclusion elongation direction using high angle annular dark field scanning transmission electron microscopy (HAADF-STEM) and integrated differential phase contrast STEM (iDPC-STEM) techniques.

The TEM foil was prepared using a focused Ga-ion beam (Ga-FIB) from a lath-shaped Mt micro-inclusion of 23 μm x 17 μm x 0.1 μm extending perpendicular to Mt{111}/Pl(-312). The foil is oriented so that the Mt<111>/Pl(-312)-pole are parallel and Mt{110}/Pl(150) planes are perpendicular to the foil.

The STEM images show that the Mt-Pl interface is perfectly straight and parallel to Mt{110}/Pl(150) and that it is devoid of steps. Electron diffraction patterns confirm that the elongation direction of the micro-inclusions is determined by the good fit of oxygen layers across the Pl-Mt interface. A 2.4% difference in the d-spacings between Pl(-312) and Mt{222} is likely accommodated by every about 42'nd Mt{222} plane forming an edge dislocation at the Mt-Pl interface. In addition, elastic strain is indicated by a deviation of d111/d110 of Mt from the strain free reference lattice. Moreover, lattice fringes in iDPC-STEM images reveal coherence between Pl(22-1) and Mt{111} planes without misfit dislocations. This additional coherence may explain the particularly strong alignment of Mt{111} and Pl(-312) reflected by the EBSD data.

In summary, the elongation directions of the Mt inclusions are determined by the alignment of important oxygen layers of both phases across the Mt-Pl interface, which is parallel to oxygen-rich lattice planes in both phases. Misfit dislocations are presumably introduced to compensate the 2.4% lattice misfit along the elongation direction. The well-organized interface structure ensures a low interfacial energy and is a viable explanation for the observed Mt-Pl CORs and SORs.  


Funding by FWF project I 3998-N29 and RFBR project 18-55-14003 is acknowledged.


[1] Ageeva et al (2020) Contrib. Mineral. Petrol. 175(10), 1-16.

How to cite: Bian, G., Ageeva, O., Habler, G., Roddatis, V., and Abart, R.: Atomic scale structure of a plagioclase – magnetite interface, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-2432,, 2021.

Fabian Tramm, Richard Wirth, Bartosz Budzyń, Jiří Sláma, Anja Schreiber, and Łukasz Birski

An intergrowth of zircon and xenotime, formed at ca. 2.09 Ga, was significantly altered after incorporation as a restite into pegmatite at ca. 370 Ma (Piława Górna, Góry Sowie Block, SW Poland; Budzyń et al., 2018). Alteration involved fluid-induced coupled dissolution-reprecipitation processes, which resulted in compositional alteration and development of patchy zoning and porosity in the xenotime and the rim of zircon. Diffusion-reaction processes affected the metamict core of zircon and resulted in nano- to microscale patchy zoning and submicron-scale porosity. This study evaluates the alteration processes with respect to structural and compositional characteristics by using TEM and LA-ICPMS trace element analysis.

Nanoscale observations revealed nanoporosity in the metamict core of zircon and a continuation of patchy zoning on a submicron level, which resulted from heterogeneous metamictization correlating with variation in U and Th contents. The altered xenotime and the zircon rim are dominated by microporosity filled with a variety of secondary phases such as U, Th, Pb and Fe rich oxides and silicates. In rare cases, secondary PbS formed nano inclusions in zircon, occasionally surrounded by amorphous apatite. Aside of known substitution mechanisms in xenotime, such as thorite and cheralite components, a correlation of Zr with LREE and Si contents indicates substitution of the zircon component. Furthermore, the zircon-xenotime interface revealed dissolution pits, filled with secondary zircon that formed at the expense of primary xenotime via coupled dissolution-reprecipitation reactions. This indicates local penetration of the fluid-mineral reaction front into xenotime. Major (Si, Zr and P) and trace elements, including U, Th and Pb, which are geochronologically relevant, have been mobilized in the metamict core of zircon due to alteration induced by an alkali-rich fluid with high activities of F, Na and Ca. The altered xenotime and porous rim of zircon were affected by alteration induced by a fluid containing Fe, which resulted in precipitation of Fe-rich phases, such as Fe-oxides and silicates often accompanied by relevant contents of Pb. In conclusion, nanoscale structural observations and LA-ICP-MS trace element data support the complex geochronological implications of the altered zircon-xenotime intergrowth, emphasising the necessity of understanding alteration processes of zircon and xenotime taking into account element transport and thus the disturbance of their geochronological clock.

Acknowledgements: This work was supported by the National Science Centre grant no. 2017/27/B/ST10/00813.


BudzyńB., Sláma J., Kozub-Budzyń G.A., Konečný P., HolickýI., RzepaG.,Jastrzębski M. (2018) Lithos 310-311, 65-85.

How to cite: Tramm, F., Wirth, R., Budzyń, B., Sláma, J., Schreiber, A., and Birski, Ł.: TEM and LA-ICP-MS constraints on fluid-induced alteration of a zircon-xenotime intergrowth in pegmatite from Piława Górna (the Góry Sowie Block, SW Poland), EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-124,, 2021.

Rick Verberne, Hugo van Schrojenstein Lantman, Steven Reddy, Matteo Alvaro, David Wallis, Denis Fougerouse, Antonio Langone, Marco Scambelluri, David Saxey, and William Rickard

The trace-element composition of rutile is commonly used to constrain P-T-t conditions for a wide range of metamorphic systems. Recent studies have highlighted the importance of micro- and nanostructures in the redistribution of trace elements in rutile via high-diffusivity pathways and dislocation-impurity associations. In this contribution, we investigate the effect of crystal-plastic deformation of rutile on its composition by combining microstructural and petrological analyses with atom probe tomography. The studied sample is from an omphacite vein of the ultrahigh-pressure metamorphic Lago di Cignana unit, Western Alps, Italy. Zr-in-rutile thermometry and inclusions of quartz in rutile and of coesite in omphacite constrain rutile deformation to around the prograde HP-UHP boundary at 500–550 °C. Crystal-plastic deformation of a large rutile grain resulted in low-angle boundaries that generate a total misorientation of ~25°. Dislocations constituting the low-angle boundary are enriched in common (Fe, Zr) and uncommon trace elements (Ca). The Ca is interpreted to be derived from the grain exterior, suggesting diffusion of trace elements along the dislocation cores. The potential for dislocation microstructures to act as fast diffusion pathways must be evaluated when applying traditional geochemical analyses as compositional disturbances caused by the presence of dislocation might lead to erroneous interpretations.

How to cite: Verberne, R., van Schrojenstein Lantman, H., Reddy, S., Alvaro, M., Wallis, D., Fougerouse, D., Langone, A., Scambelluri, M., Saxey, D., and Rickard, W.: Trace-element migration during crystal-plastic deformation in UHP rutile: dislocations in low-angle boundaries as high-diffusivity pathways., EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-9404,, 2021.

Jasper Huijsmans, Maartje Hamers, Martyn Drury, and Jim Lee

Uranium-lead dating of zircon has been used extensively in geochronological studies based on the widespread occurrence of zircon and its resistance to chemical and physical weathering. Previous research has shown that despite their apparent robustness, many zircons contain evidence for recrystallisation, such as the replacement of the primary oscillatory zoning by unzoned zircon. This replacement is characterised by rims, patches and embayments of unzoned zircon which can either completely replace the primary zoning or preserve faint remnants within the unzoned zircon.  In some samples, the unzoned zircon contains lower U and Pb concentrations, implying that the zircon U-Pb age may be reset during the replacement (Pidgeon, 1992). Interestingly, zircons have also been found in which there is no apparent difference in U-Pb age between the zoned and unzoned zircon (Schaltegger et al., 1999). To better understand the replacement of zoned by unzoned zircon, it is important to study the microstructures present within recrystallised zircon to understand possible mechanisms causing recrystallisation. Multiple mechanisms may explain the trace element distribution within (partially) recrystallised zircon: annealing of radiation damaged (metamict) zircon, annealing of lattice strain imposed by alternating U concentrations in oscillatory zoning, enhanced diffusion along fast-diffusivity pathways (such as low-angle subgrain boundaries or fractures) and coupled dissolution-reprecipitation.  The mechanism(s) by which zircons recrystallise remain poorly understood, as well as the effect of the formation of different microstructures on corresponding zircon U-Pb dates. Understanding these phenomena is therefore of vital importance for correctly interpreting U-Pb ages in zircon.

This work focusses on investigating the microstructures that are present within recrystallised zircons from both metamorphic and igneous environments from the Jack Hills, Australia (Pidgeon, 1992) and the island of Lewis and Harris, Scotland (Van  Breemen  et  al.   1971). Suites of zircons from these areas have been imaged with cathodoluminescence, which is a powerful tool for obtaining high resolution images of the internal structures of zircons. Within these suites, zircons are present which show complex zoning patterns and (partial) recrystallisation; these will be studied in greater detail using EDS, EBSD and SHRIMP. Preliminary results of EDS on the inclusions show that inclusions are composed of feldspars, thorite, quartz and apatite, which were most likely included during the primary crystallisation of the zircon. EBSD measurements will provide additional data on the crystallographic orientation of recrystallized zones and the state of metamictization of the zircons, and may show if zircon has deformed crystal-plastically forming subgrain boundaries.



Pidgeon, R. T. (1992). Recrystallisation of oscillatory zoned zircon: some geochronological and petrological implications. Contributions to Mineralogy and Petrology, 110(4), 463-472.

Schaltegger, U., Fanning, C. M., Günther, D., Maurin, J. C., Schulmann, K., & Gebauer, D. (1999). Growth, annealing and recrystallization of zircon and preservation of monazite in high-grade metamorphism: conventional and in-situ U-Pb isotope, cathodoluminescence and microchemical evidence. Contributions to Mineralogy and Petrology, 134(2-3), 186-201.

Van Breemen, O., Aftalion, M., & Pidgeon, R. (1971). The age of the granitic injection complex of harris,outer hebrides.Scottish Journal of Geology,7(2), 139–152.

How to cite: Huijsmans, J., Hamers, M., Drury, M., and Lee, J.: Zircon recrystallisation microstructures andthe implications for U-Pb dating, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-3100,, 2021.

Nicholas Udy and Michael Stearns

The U-Pb system in titanite has been shown to be reset during a variety of high-temperature processes including high-temperature deformation, but post-deformation modification and recovery of crystal-lattice strain have so far made U-Pb equilibration mechanism from deformed titanites equivocal. Microstructures, including mechanical twinning and subgrain rotation recrystallization are more likely to be preserved at low-temperatures, but the systematics of chemical equilibration have not been established for these conditions. This study identifies progressive crystallographic misorientation and deformation twins in titanite porphyroclasts from the Wasatch Fault Zone, Utah, USA. The microstructures, mapped using electron backscatter diffraction (EBSD), developed at ~11 km depth during 300–400 ºC crystal-plastic deformation within the ductile fault zone. These microstructural maps were used to guide laser ablation-split stream ICP-MS analysis: U-Pb isotopes measured in tandem with major and trace element contents. Despite the low temperature, U-Pb and trace element contents in titanite equilibrated, at least partially, during deformation. Both major and trace elements in titanite also likely partitioned with a fluid and in response to the (re)crystallization of other mineral phases in the fault zone. Chemical zoning and crystal lattice recovery suggestive of fluid-aided recrystallization are absent, and the main mechanism for this resetting may instead be an enhancement of element mobility along microstructure dislocations. These processes are interpreted to record complex open-system behavior of titanite caused by crystal-plastic deformation during the initiation of the WFZ. This presentation will summarize the comparative analysis of microstructure by EBSD and titanite chemistry by LASS-ICP-MS, and how it bears on the understanding of elemental mobility in titanite during low-temperature crystal-plastic deformation.

How to cite: Udy, N. and Stearns, M.: Insights into chemical mobility in titanite driven by low-temperature crystal-plastic deformation, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-7327,, 2021.

Zuzanna Kabacińska, Alida Timar-Gabor, and Benny Guralnik

Thermally activated processes can be described mathematically by the Arrhenius equation. The Meyer-Neldel Rule (MNR), or compensation law, linearly relates the pre-exponent term to the logarithm of the excitation enthalpy for processes that are thermally driven in an Arrhenian manner. This empirical rule was observed in many areas of materials science, in physics, chemistry, and biology. In geosciences it was found to uphold in hydrogen diffusion (Jones 2014a) and proton conduction (Jones 2014b) in minerals.

Trapped charge dating methods that use electron spin resonance (ESR) or optically or thermally stimulated luminescence (OSL and TL) are based on the dose-dependent accumulation of defects in minerals such as quartz and feldspar. The thermal stability of these defects in the age range investigated is a major prerequisite for accurate dating, while the accurate determination of the values of the trap depths and frequency factors play a major role in thermochronometry applications. 

The correlation of kinetic parameters for diffusion has been very recently established for irradiated oxides (Kotomin et al. 2018). A correlation between the activation energy and the frequency factor that satisfied the Meyer–Neldel rule was reported when the thermal stability of [AlO4/h+]0 and [TiO4/M+]0 ESR signals in quartz was studied as function of dose (Benzid and Timar-Gabor 2020). Here we compiled the optically stimulated luminescence (OSL) data published so far in this regard, and investigated experimentally the thermal stability of OSL signals for doses ranging from 10 to 10000 Gy in sedimentary quartz samples. We report a linear relationship between the natural logarithm of the preexponent term (the frequency factor) and the activation energy E, corresponding to a Meyer-Neldel energy of 45 meV, and a deviation from first order kinetics in the high dose range accompanied by an apparent decrease in thermal stability. The implications of these observations and the atomic and physical mechanisms are currently studied.



Benzid, K., Timar Gabor, A. 2020. The compensation effect (Meyer–Neldel rule) on [AlO4/h+]0 and [TiO4/M+]0 paramagnetic centers in irradiated sedimentary quartz. AIP Advances 10, 075114.

Kotomin, E., Kuzovkov, V., Popov, A. I., Maier, J., and Vila, R. 2018. Anomalous kinetics of diffusion-controlled defect annealing in irradiated ionic solids. J. Phys. Chem. A 122(1), 28–32

Jones, A. G. (2014a), Compensation of the Meyer-Neldel Compensation Law for H diffusion in minerals, Geochem. Geophys. Geosyst., 15, 2616–2631

Jones, A. G. (2014b), Reconciling different equations for proton conduction using the Meyer-Neldel compensation rule, Geochem. Geophys. Geosyst., 15, 337–349

How to cite: Kabacińska, Z., Timar-Gabor, A., and Guralnik, B.: Meyer-Neldel Rule on thermal stability parameters (trap depth and frequency factor) of luminescence signals in quartz, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-10775,, 2021.

Maja Milošević and Bojan Kostić

Inclusions in garnets from the river Lešnica alluvion (Cer mountain area, Serbia),  were investigated in an effort to study their distribution within the garnet host and to estimate the mechanism of their origin. Garnets are often occurring in the Lešnica alluvion in a form of loosely separated crystals with preserved crystalline forms and as mildly rounded broken grains [1]. Their mineralogical determination was previously published by Milošević et al, [1]. Crystals, that have been extracted and separated from the sandy fraction, have exhibited the presence of various types of inclusions in their structure. Single and multiphase inclusions in the garnets were examined optically by petrographic methods followed by SEM-EDS method, applied for the chemical analyses of the individual inclusion, and LA-ICP-MS applied to determine distribution and content of trace elements in the host garnet.

Results from SEM-EDS method show that garnets are of the spessartine-almandine type with the incorporation of irregular inclusions determined as rare earth elements (REE) minerals (monazite, xenotime, columbite-tantalite) and accessory minerals that usually incorporate REE (titanite, apatite, and zircon) together with uranium oxide minerals. Other single-phase inclusions are often quartz and rutile. Size of inclusion varieties from grain to grain, between 5 and 40 µm, while their distribution doesn’t follow any pattern, random distribution. It has been noted that zircon and uranium oxide minerals are often found coupled and as multiphase inclusions while monazite, xenotime and columbite-tantalite minerals are observed as separate, single, inclusions. Chondrite normalized REE in the host garnets plotted on spider diagram show extreme depletions of large ion lithophile elements (LILE) and enrichment in high field strength elements (HFSE), with negative Ce, Nd and Eu anomaly. Single-phase and multiphase inclusions that are occurring in the same garnet host with a random distribution are suggesting different genetic relations.

[1] Milošević M., Kostić B., Vulić P., Jelić I. 2019. Garnets from river Lešnica alluvion, mountain Cer. II Kongres Geologa Bosne i Hercegovine sa medjunarodnim učešćem, Pp. 306-311

How to cite: Milošević, M. and Kostić, B.: Single and multi-phase inclusions in garnets from the Lešnica alluvion in the Internal Dinarides, Serbia, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-2423,, 2021.

Rich Taylor

The proliferation of modern techniques available for petrologists has resulted in an explosion of detailed information on mineral compositions and processes over the last decade. One area of research that is undergoing dramatic advances is the non-destructive interrogation of samples in three dimensions through X-ray microscopy (XRM). Techniques such as ZEISS Versa and Ultra XRM can be performed at a variety of scales and resolutions, resulting in micro-to-nano scale information on geological samples. Such techniques can be correlated with each other i.e. expanding nanoscale resolution to a large sample or internal calibration of X-ray intensity to identify mineral assemblages, or even correlation with other techniques such as electron microscopy (EM). X-ray techniques are also particularly adaptable to digital resolution enhancements through software processes such as machine learning algorithms.

Collecting 3D information for petrological investigations can often require ground truthing of mineralogical and compositional interpretations. The more developed the 3D microscopy becomes, the more we are increasingly interested in features that are deeply buried within our samples. This means the corresponding techniques for excavating a region of interest also need to advance in both speed and accuracy.

The ZEISS Crossbeam-Laser (XBL) system provides a unique capability of rapidly excavating to a point of interest within a 3D sample volume. The XBL is already seeing use in material sciences, with a standard XB chamber with focussed Ion Beam (FIB) and Electron Microscopy (EM), and a correlated femtosecond laser chamber for rapid material removal. Sample data collected through XRM can be correlated to the XBL stage so that any internal features located by XRM have their coordinates automatically available in three dimensions. The femtosecond laser can excavate to a region of interest (RoI) within the sample within seconds or minutes, dramatically reducing preparation time compared to standard FIB/PFIB. The laser cut surface can be used for analysis techniques such as energy dispersive spectroscopy (EDS) and electron backscatter diffraction (EBSD), even prior to final polishing with the focussed ion beam (FIB).

Here we show the XRM-XBL workflow in high grade metamorphic rocks for identifying minerals in context for geochronology and micro-to-nano scale textures.

How to cite: Taylor, R.: Advances in 3D characterisation for correlative microscopy in geosciences, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-9597,, 2021.

Advances in Raman Spectroscopy
Aaron Jubb, Justin Birdwell, and Paul Hackley

Geochemical, petrographic, and spectroscopic indices that vary with compositional changes in petroliferous organic matter (OM) during thermal maturation are key petroleum system parameters used to understand petroleum generation. In unconventional shale source-rock reservoirs, where multiple, highly dispersed OM types may be present in intimate contact with surrounding mineral phases, OM molecular composition (e.g., aromaticity) is especially useful for informing structure-reactivity relationships representative of different OM types. Here, we employ microscale, in situ, and correlative Raman and reflectance approaches to evaluate aromaticity evolution for a suite of OM types (i.e., liptinite, micrinite, solid bitumen, vitrinite, and inertinite) at the single particle level across an artificial thermal gradient. Our samples include a marginally mature (vitrinite reflectance ~0.5%) Late Cretaceous Boquillas Shale from south Texas, United States, and two hydrous pyrolysis (HP) residues following reaction of the raw Boquillas Shale sample at 300°C and 330°C for 72 hours. Our data indicate that: (i) liptinite, micrinite, solid bitumen, vitrinite, and inertinite particles exhibit different aromatic signatures in the raw shale sample and (ii) these OM types, with the exception of inertinite, effectively experience similar changes in aromatic structure with thermal advance. Data also reinforce the concept that reservoir temperature may be a secondary factor in controlling the molecular composition of inertinite. These findings inform a broader understanding of how different petroliferous OM types evolve throughout thermal reactions and further demonstrate that correlative Raman spectroscopy and reflection analyses, combined with careful organic petrography, can provide complimentary estimates of OM molecular composition and thermal maturity.

How to cite: Jubb, A., Birdwell, J., and Hackley, P.: Evaluating aromaticity changes with thermal stress at the single particle level for a suite of organic matter types from the Boquillas Shale (Texas, United States) via correlative Raman and reflection analyses, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-259,, 2021.

Ekaterina Fomina, Evgeniy Kozlov, Mikhail Sidorov, and Vladimir Bocharov

Along with some other Na-minerals, carbonophosphates indicate a high initial Na activity in carbonatite and kimberlite melts, which is beneficial for petrological reconstructions. Because carbonophosphates are capable of incorporating large-ion lithophile and rare earth elements (REEs) in their structure, they can participate in the transport of these elements. Moreover, due to the presence of both [PO4]3− and [CO3]2− groups in carbonophosphates, these mineral phases play an important role in the Earth's global carbon and phosphate cycles. With all these properties, carbonophosphates have long attracted the attention of geologists. Raman spectroscopy appears to be one of the most suitable tools for their diagnosis, since they commonly present in rocks as small inclusions in other mineral grains. Despite this profit, only a few publications contain Raman characteristics of either natural or synthetic carbonophosphates.

We studied and compared Raman spectra of three natural carbonophosphate phases (sidorenkite, bonshtedtite, and bradleyite) with the general formula Na3MCO3PO4 (M = Mn, Fe, and Mg, correspondingly). These spectra showed from 21 to 24 vibrational bands, of which the two most intense (963±5 cm-1 и 1074±3 cm-1) correspond to the ν1(P–O) and ν1(C–O) modes. These two bands split due to the occurrence of isomorphic impurities. It was found that the crystallographic orientation of the sample influences the intensity of most bands. A natural increase in the Raman shift was observed for most bands assigned to the same vibrations (the smallest shift in the spectrum is characteristic of sidorenkite, an intermediate - of bonshtedtite, and the largest - of bradleyite).

We propose the following algorithm for the diagnosis of carbonophosphates:

  • Checking minerals for belonging to the group of carbonophosphates by the main bands and the characteristic profile of the spectrum;
  • Testing the hypothesis that the mineral of question is bradleyite based on the analysis of the estimated shift of the main bands;
  • Diagnosis of a mineral species by peaks located between the main bands;
  • Validation of the diagnostics by considering the position of the bands at 185±9 cm-1, 208±7 cm-1, 255±5 cm-1, and 725±6 cm-1.

The proposed algorithm allows one to perform Raman diagnostics of carbonophosphates in inclusions even in the absence of EPMA data. In the study of carbonatites, kimberlites, and other rocks, the diagnostics of the mineral species of the carbonophosphate group can be important in the petrological aspect.

This research was funded by the Russian Science Foundation, grant number 19-77-10039.

How to cite: Fomina, E., Kozlov, E., Sidorov, M., and Bocharov, V.: A Raman spectroscopic study of the natural carbonophosphates Na3MCO3PO4 (M = Mn, Fe, and Mg), EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-1528,, 2021.

Thomas Theurer, David Muirhead, David Jolley, and Dmitri Mauquoy

Raman spectroscopy represents a novel methodology of characterising plant-fire interactions through geological history, with enormous potential. Applications of Raman spectroscopy to charcoal have shown that this is an effective method of understanding intensity changes across palaeofire regimes. Such analyses have relied on the determination of appropriate Raman parameters, given their relationship with temperature of formation and microstructural changes in reference charcoals. Quantitative assessments of charcoal microstructure have also been successfully applied to the assessment of carbonaceous maturation under alternate thermal regimes, such as pyroclastic volcanism. Palaeowildfire systems in association with volcanism may present a complex history of thermal maturation, given interactions between detrital charcoals and volcanogenic deposition. However, whilst palaeofire and volcanic maturation of carbonaceous material are well understood individually, their interaction has yet to be characterised. Here we present the first analysis of palaeofire charcoals derived from volcanic ignition utilising Raman spectroscopy. Our results indicate that complex interactions between volcanism and palaeofire systems may be better understood by the characterisation of charcoal microstructure, alongside palaeobotanical and ecosystem studies. Understanding the unique relationship between wildfires and volcanism, and the impact that this has on the fossil record, may better assist our understanding of wildfire systems in deep history. Further still, this highlights the potential for better understanding the socioecological impacts of modern and future wildfire systems closely associated with volcanic centres. 

How to cite: Theurer, T., Muirhead, D., Jolley, D., and Mauquoy, D.: The Potential Applications of Raman Spectroscopy in Unravelling Complex Palaeowildfire Ecosystems, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-2626,, 2021.

Olivier Beyssac

Over the last two decades, Raman microspectroscopy has known a spectacular development in various research fields of petrology opening new avenues for studies in sedimentology, metamorphism or magmatism and cosmochemistry. This has been made possible thanks to major technological improvements (e.g., Raman hyperspectral mapping) and a better theoretical approach (e.g., data processing and interpretation). Raman spectra are actually sensitive to even minor (chemical or structural) perturbations within chemical bonds in (even amorphous) solids, liquids, and gases. They can, thus, help identify, characterize, and differentiate between individual minerals, fluid inclusions, glasses, carbonaceous materials, solid solution phases, strain in minerals, and dissolved species in multi-component solutions. Such sensitivity and versatility make Raman a unique tool for petrology. Yet, it relies on a weak and subtle signal and a cautious approach is required to avoid pitfalls during the analysis and/or the interpretation of data. Some recent scientific milestones will be presented and discussed in various fields like geothermobarometry of metamorphic rocks, geochemistry of meteorites, speciation of deep fluids involved in fluid-rock interactions or the characterization of organic/mineral assemblages of astrobiological interest. For the particular c       ase of petrology, Raman microspectroscopy has the immense advantage that it requires minimal sample preparation, thus it can be performed in situ preserving the original microtexture of the sample with a rather high spatial resolution for analysis, typically 1 mm at 532 nm for modern systems. Therefore, this technique is now increasingly used to study poorly crystalline and chemically heterogeneous materials involved for instance in geochemical processes occuring at Earth surface. But it faces numerous challenges due to the reactivity of such phases making them fragile under the laser beam, or due to the quasi-systematic presence of intense backgrounds in the spectra overwhelming the Raman signal. The source of this background can be multiple as it can be observed with fine-grained samples and/or it can be generated by the presence of luminescence/fluorescence emission centers. More generally such background is not well understood although it is a major issue for Raman spectroscopy in many petrological applications. However, there too, recent technological developments, sometimes based on old ideas, offer new possibilities to investigate safely and accurately such materials : time-resolved spectroscopy and surface-enhanced Raman spectroscopy (SERS) will be presented as well as some applications for petrology of complex samples.

How to cite: Beyssac, O.: Raman spectroscopy for petrology : recent scientific milestones, technological trends and challenges, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-3416,, 2021.

Christoph Moeller, Christian Schmidt, Francois Guyot, and Max Wilke

In recent decades increasing evidence was found for life under extreme conditions, e.g., near black smokers on the ocean floor. The synthesis and stability of vital molecules like adenosine triphosphate (ATP) and adenosine diphosphate (ADP) are essential to maintain the metabolism of all known organisms. The lifetime of these molecules in water is limited by the non-enzymatic hydrolysis reaction that becomes dominant at elevated temperatures. A better understanding of this mechanism will provide us insights of life at extreme conditions.

Previous studies determined the hydrolysis rate constants of ATP for several compositions, temperatures and pressures using quench experiments and subsequent analysis. So far, it was not tested whether quench artefacts might have affected those results. Therefore, the current study was performed to develop a method to follow the reaction in-situ with a high sampling rate at elevated temperatures. A confocal micro-Raman spectrometer and a hydrothermal diamond anvil cell were used to perform experiments at elevated temperatures and vapour pressure. Spectra were obtained in the range of 660 cm-1 to 1157 cm-1 as a function of time. Different solutions of ATP and ADP were measured at 353 K, 373 K, and 393 K, at starting pH values of 3 and 7. First findings are consistent with previous studies and show that with decreasing pH value the hydrolysis rate increases. The data indicate hydrolysis rate constants in the magnitude of 10-3 s-1 by 393 K, 10-4 s-1 by 373 K and 10-5 s-1 by 353 K. These initial observations show that this technique produces reliable kinetic data on this reaction. It also provides much better sampling statistics than quench experiments. 

The high reaction rates suggest that a mechanism exists to regulate this reaction at higher temperatures, which is necessary to allow metabolism under extreme conditions. Moreover, it is commonly known that ATP interacts with various metal ions with different effects on the reaction rate. An application of this method would be the quantification of the hydrolysis rate constant in chemically more complex systems.

How to cite: Moeller, C., Schmidt, C., Guyot, F., and Wilke, M.: A new in-situ method to determine the hydrolysis rate constant of adenosine triphosphate (ATP) by application of Raman spectroscopy in a hydrothermal diamond anvil cell, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-3419,, 2021.

Andrea Schito, Achraf Atouabat, Rocco Calcagni, Sveva Corrado, David Muirhead, Claudia Romano, Alessandro Pozzi, Roberto Galimberti, and Amalia Spina

The correct assessment of maximum temperatures experienced by rocks is an essential tool to unravel the evolution of the thermal structure of the crust during the main phases of an orogenesis. Given to broad P-T stability field of classical metamorphic mineralogical indicators, maximum temperatures derived from the analyses of carbonaceous material dispersed in rocks by means of Raman spectroscopy has shown to be a suitable alternative to classical geothermometer. Initially developed for high metamorphic rocks the use of this tools has recently been extended also at lower metamorphic degree and diagenesis. This allowed us to extend the analyses of paleotemperatures experienced by rocks from Ghomarides and Sebtides from the Internal Rif in North Morocco with respect to previous works. Ghomaride and Sebtides in this portion of the Rif-Betic-Tell chain, represent respectively the upper and lower plates of a metamorphic core complex  and are composed, the first, by Paleozoic rocks with a partially preserved Mesozoic-Cenozoic cover and the second by lower Paleozoic to Triassic deep-crustal mica-schists, migmatites and granulites associated with peridotites (Beni Bousera complex).

Our data suggest that the uppermost Tiszgarine Unit of the Upper Sebtides experienced warmer condition than previously observed. Moreover, we calculate the maximum temperatures experienced by the Ghomarides  during both the Eo and Late Variscan cycles showing that differences in temperature exist among the vary units that compose the complex. Finally, in the southern area our data suggest a less severe alpine heating related to the emplacement of the Beni Bousera peridotite, than previously calculated.

How to cite: Schito, A., Atouabat, A., Calcagni, R., Corrado, S., Muirhead, D., Romano, C., Pozzi, A., Galimberti, R., and Spina, A.: An insight on the polyphase thermal history of the Ghomarides and Upper Sebtides in the Internal Rif (North Morocco) by means of Raman spectroscopy on organic matter, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-7459,, 2021.

Nadezda Chertkova, Anna Spivak, Egor Zakharchenko, Yuriy Litvin, Oleg Safonov, and Anastasiia Burova

Rapid development of in situ experimental techniques provides researchers with new opportunities to model geological processes, which take place deep in the Earth’s interior. Raman spectroscopy is considered a powerful analytical tool for investigation of the samples subjected to high pressures in a diamond anvil cell, since in such experiments phase assemblages can be determined in real time using measured Raman spectra.

In this study, we describe experimental methods for in situ observation and spectroscopic analysis of fluids and minerals, which constitute environment for diamond growth, at the upper mantle pressure conditions. Experiments were conducted in the externally heated, “piston-cylinder” type diamond anvil cell at pressures exceeding 6 GPa and temperatures up to 600 degree C. Phase relationships and fluid speciation were monitored during experiments to reconstruct the environment and mechanism of inclusions formation. Compared to other analytical tools, commonly used in combination with diamond anvil cell apparatus, Raman spectroscopy offers several advantages, such as short sample preparation time, non-destructive characterization of the phases observed in the sample chamber and relatively short measurement time.

This work was supported by grant No. 20-77-00079 from the Russian Science Foundation.

How to cite: Chertkova, N., Spivak, A., Zakharchenko, E., Litvin, Y., Safonov, O., and Burova, A.: In situ Raman spectroscopic technique for high-pressure studies of mineral and fluid inclusions formation , EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-7530,, 2021.

David Muirhead

Amorphous carbonaceous materials are typically those that would be considered immature, at temperatures below 300°C, in a typical sedimentary basin burial setting. Only recently has there been much discussion on the efficacy of Raman spectroscopy on amorphous carbon at temperatures below 300°C. Here we present data from a variety of published sources alongside our own data reviewing the apparent trends in amorphous carbon with some discussion related to thermal regime (intensity, duration), with case studies including intruded host rocks, fold and thrust belts and wildfires. We conclude that Raman spectroscopy can be applied successfully to ‘low-temperature’ carbonaceous material whilst noting the challenges faced to fully understand the physio-chemical mechanisms at these temperature ranges.

How to cite: Muirhead, D.: Raman Spectral Trends in ‘low-temperature’ Carbonaceous Materials., EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-7939,, 2021.

Alexander O'Donnell

Carotenoid compounds such as β-carotene are some of the most prevalent organic molecules on Earth and are key biomarkers as there is no known abiogenic source. During diagenesis and thermal alteration, carbon undergoes well-documented changes in Raman spectra.

There has been little research into the transitional degradation of carotenoid spectra to where they are fully replaced by the carbon spectra as the main identifier of thermal maturity under Raman spectroscopy. This is an overlooked regime when discussing the search for life, terrestrial and extra-terrestrial, where current research (using Raman spectroscopy) either focuses on finding living organisms displaying common organic molecules, or looks for the elemental carbon evidence of extinct fossil life. The real world is not usually so polarised, so covering the transition between these modes of life detection will improve any detection analysis.

For this study the volcanic thermal spring system in Viterbo, Italy was used as a field-based laboratory. The high rate of carbonate precipitation in these thermal springs, the wide range of thermal regimes (58°C to 25°C), and the prevalence of fast-growing algae in the run-off streams, give excellent preservation of a range of organic matter states at directly measurable temperatures.

The results demonstrate how the Raman spectra of the carotenoid compounds change with hydration, death of the organism, and thermal alteration of the organic material. The relationship between the spectra of the carotenoid compound and the elemental carbon spectra in the transition zone is also shown.

This study expands on the use of Raman spectroscopy of carbon as a low-temperature geothermometer, and provides a framework for the spectral response of organic matter in an often-overlooked geological regime. It is anticipated that the fields of geothermal energy, climatology, geobiology and astrogeobiology, could all benefit from this study, incorporating this enhanced thermal alteration data into existing and future work.

How to cite: O'Donnell, A.: Searching for life in volcanic carbonate systems and the effect of temperature on organic molecules, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-9659,, 2021.

Lauren Kedar, Clare Bond, and David Muirhead

Organic carbon in rocks undergoes nanostructural changes when exposed to increased temperatures or strain. These changes can be identified using Raman spectroscopy, giving information about thermal maturity and strain conditions. However, it is well documented that in a heterogeneous rock, strain can be highly localised, evident in microstructural variations such as strain shadows, sub-grain development, twinning, and the rotation and alignment of crystal axes. In this study we map microstructural textures in deformed calcite through optical microscopy and EBSD of calcite crystal axes. This textural map is compared to mapped Raman spectral parameters of organic carbon particles in the same thin section. A comparison of the maps allows assessment of the extent to which Raman spectral parameters and hence carbon nanostructure is influenced by strain at a sub-mm scale. The study highlights the sensitivity of organic carbon nanostructure to sub-mm scale changes in strain localisation within a single deformed carbonate sample.

How to cite: Kedar, L., Bond, C., and Muirhead, D.: Strain-related carbon ordering on a sub-mm scale: a comparison of carbonate microfabrics and organic carbon nanostructure within a single sample., EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-9921,, 2021.

Clare Bond, Lauren Kedar, and David Muirhead

Raman Spectroscopy is increasingly being used to better understand a range of Earth Science processes. Notable recently is the application of Raman Spectroscopy to carbonaceous material in strained rocks. Here we investigate the changes in Raman Spectral response in strained material relative to an unstrained equivalent, drawing on examples from the published literature and our own work. We consider inconsistencies in the relative changes in Raman Spectral parameters of strained material and their potential causes. In doing so we look at some of the current methods for determining Raman Spectral parameters in rocks and what they might tell us about the strain state of carbon in a single rock sample. Finally, we consider the implications for use of Raman Spectroscopy of carbonaceous material as a geothermometer as well as a future potential strain gauge. 

How to cite: Bond, C., Kedar, L., and Muirhead, D.: Raman Spectroscopy as a potential strain gauge, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-11092,, 2021.