David Brink-Roby1, Brian L.McIntyre2

University of Rochester 1.Department of Earth Science, 2.The Institute of Optics

OPT407: Practical Electron Microscopy
Spring 2015

Final Project


  1. Introduction
  2. Geologic Background
  1. Light Microscopy
  2. ImageJ Analysis
  3. Evaporative Carbon Coating
  4. Secondary Electron Imaging
  5. Backscater Electron Imaging
  6. EDS Spectra & Elemental Mapping
  1. Light Microscopy
  2. ImageJ Analysis
  3. Evaporative Carbon Coating
  4. Secondary Electron Imaging
  5. Backscater Electron Imaging
  6. EDS Spectra & Elemental Mapping
  7. Electron Flight Simulation
  8. 3D Imaging & Colorization

Conclusions and Acknowledgements

  1. Conclusion
  2. Acknowledgements



The large-scale geologic fluid migrations that occur within the foreland of mountain belts are responsible for transporting substantial heat, minerals, and hydrocarbons, and are known to be integral to tectonic deformation. However, the causal mechanisms that link tectonic deformation and fluid migration remain unclear. Hypothesized causes of fluid migrations within fold-thrust belts include (1) gravity-driven flow resulting from hydraulic head (caused by topographic relief between the thickened, elevated internal portion and the lower foreland) and (2) in situ pressure increases (thermally and/or chemically generated during heating, dehydration, pressure solution, or hydrocarbon maturation, or mechanically generated during compaction related to tectonic thickening and synorogenic sedimentation). These proposed mechanisms and the possible paths of such migrations lack data driven support. This study aims to determine the spatial and temporal patterns of fluid-flow systems in a well characterized fold-thrust belt to test models of fluid migration. A robust model of fluid migration will allow us to better predict the location of resulting geothermal, hydrocarbon, and ore deposits and to better understand fault propagation.

Cartoon diagram of hypothesized drivers and sources for fluid migration.

Geologic Background

The Sevier fold-thrust belt is a well-characterized belt whose tectonic evolution has been carefully constrained in previous work. The Idaho-Utah-Wyoming section of the Sevier fold-and-thrust belt forms a broad salient that is convex toward the east. The faults themselves dip westward and include, from west to east, the Paris-Willard, Meade-Crawford, Absaroka, Darby-Hogsback, and Prospect faults. These six or seven major thrust faults, as well as numerous minor ones, have transported Paleozoic and Mesozoic sediments eastward. The thrust sheets themselves were then eroded, producing Cretaceous synorogenic sediments, with later faults transporting sediments derived from earlier faults. Thrust faults cut up from a regional decollement at the Precambrian-Cambrian boundary in the Gros Ventre Formation, through Paleozoic and lower Mesozoic sedimentary units.

Regional geologic map and cross sections of the Sevier fold and thrust belt (Yonkee, 2015, personal communication).

Systematic suites of mesoscopic structures, including vein/fracture sets, spaced cleavage, and minor faults accommodated internal strain and provided pathways and barriers to local fluid flow within different hydrostratigrphic units. This project focused on analysis of oolitic and micritic limestone units in the Jurassic Twin Creek Formation. The Twin Creek Formation displays multiple vein sets, spaced cleavage, and multiple minor fault sets. Cleavage is typically at high angles to bedding and perpendicular to the shortening direction. Microscopically, cleavage is represented by seams enriched in clay that formed mostly by dissolution of calcite and minor quartz. Calcite was partly re-precipitated in veins, some of which show complex fibrous fillings, but limestone underwent net volume loss as fluids transported dissolved material over large distances. Veins are widely developed, with a dominant set sub perpendicular to structural trend (cross-strike set) that accommodated tangential extension and provided cross-strike fluid pathways. Other veins sets include a set parallel to bedding and a set parallel to structural the trend.

Outcrop photos and photomicrographs showing the dominant structures and their relations (S1 is the primary cleavage, TS is the shortening direction)



In order to characterize vein sets, their relation to each other, and their morphological and chemical variations I employed several methods. These include light microscopy (including image analysis), backscatter electron (BSD) and secondary electron (SE) scanning electron microscopy (SEM), and energy dispersive X-ray spectroscopy. Samples upon which analysis were performed were a combination of ultra-thin petrographic sections were prepared by Gerry Kloc at the University of Rochester EES department and artificially fractured rock and vein material.


Light Microscopy

Ultra-thin sections were first scanned at a very high resolution using a Nikon Coolscan 5000. These images were then analyzed using image analysis software to determine vein orientation, intensity, area, length, and aperture. This process involves thresholding an image, manually cutting veins at their termination, and running a particle analysis on the resultant image. Ultra-thins, were then inspected under a petrographic microscope to characterize vein morphology and determine cross cutting relationships.


Petrographic light microscope, UofR structural geology. 


Scanning Electron Microscopy (SEM) and Energy Dispersive X-RAY Spectroscopy (EDS)

Ultra-thin sections were prepared for SEM analysis by evaporative carbon coating. Coated samples were then loaded into the SEM, where they were imaged using backscatter and secondary electron detectors. Microgeochemical analysis was completed using energy dispersive X-ray spectroscopy and recording EDS spectra as well as chemical maps.

Artificially fractured samples were also prepared and coated for SEM secondary electron imaging. These samples were fractured orthogonal to the vein orientation, in order to show the crystal morphology of the vein. This allowed for imaging of the crystal structure of the veins in three dimensions. In order to highlight the crystal structure, 3D images were created by taking 2 images of the same subject, rotating the stage 3-4 degrees between image captures.


Zeiss Auriga SEM/FIB with EDAX, UofR Optics. 


Light Microscopy

Petrographic analysis of vein and host rock reveals the majority of the samples carbonates to fine grained micritic or oolitic material. Vein material varies in morphology, with most veins having a blocky texture, although fibrous vein growth was also found. Crack seal vein textures were commonplace and indicate that veins were opened and reactivate multiple times, and were conduits to fluid flow over an extended period. All veins showed pervasive twinning, indicating deformation continued post precipitation. Analysis of cross-cutting relationships show that deformation progresses predictably, with cross structure vein sets (E-W) forming first, followed by strike parallel cleavage (N-S), and finally strike parallel veining (N-S) that often propagate along cleavage seams.

Petrographic images of typical veins cound within the Twin Creek. Left image shows blacky texture and strong twinning. Right image shows the crack seal texture common to many veins.

Image Analysis (ImageJ)

Image analysis using ImageJ is a method I adopted from this class and allowed for an entirely new data set to be developed. Using this technique, vein prevalence and importance to fluid flow can easily be determined, and rough estimates on secondary permeability can be calculated. An example of an image, its threshold image, and resulting particle outlines can be seen below. The resulting data produced by the analysis can also be seen below.

Left image shows how image analysis is performed, starting with a high resolution scan, thresholding it, and finally performing a particle analysis on it. Right image shows the data that results. Results are ploted against the vein rake, or the angle of the rake from horizontal. It is clearly evident from the data that the E-W set dominates, while a N-S set also exists.

SEM Imaging

BSD imaging of ultra-thin petrographic samples proved incredibly useful in showing vein relations that were indiscernible with light microscopy. A common theme seen in the interaction between veins was for a later crosscutting vein to propagate along previous veins. Under light microscopy this is often indiscernible. BSD imaging along with EDS also shows multiple fluid phases, with some closely matching the carbonate composition of the host rock, and some later veins being chemically quite different. SE detection imaging on polished sections showed very little, but worked very well for imaging the crystal structure of artificially fractured samples. Examples of these images and their 3D renderings can be seen below.


Colorized image of a blocky texured vein (blue), against a micritic host rock(dark brown)

A photomicrograph at 615x showing the interface between the blocky vein and the micritic limestone host. Note the low porosity of the host rock.

Some veins show fiberous morphology, as can be seen in this photmicrograph of a vein fractured along crytal faces.

Vein fibers can be seen in 3D if you have red and cyan tinted glasses.

For those without 3D glasses, some find that these GIF images apear 3D (look towards the center), all others just find them annoying.

Energy Dispersive X-RAY Spectroscopy

EDS spectra and chemical maps showed the chemistry of the host rock to be dominantly Ca, with lesser amounts of Si, Mg, Al, and Fe, indicating a dirty carbonate. Some host rocks contained enough Mg to be classified as primarily dolomite. Vein material contained Ca and in some cases Mg. Mg levels in the veins varied from low to roughly equal to Ca, which indicates a dolomite vein fill rather that calcite.


Images showing an example vein intersection and the resulting imagery. From top left clockwise: petrographic photomicrograph of the intersection in cross polarized light; BSD image of the intersection, notice ~E-W vein with dolomitic composition similar to the host rock and later vein of very different fluid composition, indicating an exogenous fluid source. Also note the second veins partial reactivation of the first; spectrograph of the composition of the examined area; Ca map of the area (note high concentration in the second vein); Si map of area (note only the host rock contains Si); Mg map of the area (note that most of the first vein is dolomite, closely reflecting the host rock composition, while none of the second is.

Electron flight similation of electron beam interaction with pure calcite sample. Model was run fro 2000 interactions; blue paths are electron paths, red are produced X-rays taht escape the sample, and green are X-rays trapped within the sample.



The long term goal of this project is to characterize vein formation and composition, relate it to fluid sources and paths, and produce a refined model for fluid migration and interaction with its host rock. In order to achieve this, microstructural and microgeochemical analyses are needed to constrain kinematics and relative timing of the vein/fracture sets and to distinguish incremental filling histories. By paring light microscopy, SEM imaging, and EDS spectroscopy and mapping we have proven this detailed characterization is possible. Future work involves incorporating this data into regionally collected mesoscopic geologic data, C-O stable isotopic data, and fluid inclusion data. I would also like to apply some of the same techniques to both large and small scale faults, as they also are likely to record complex cracking and cementation histories, and may provide late stage fluid pathways.


This project was part of an ongoing research project Advised by Gautam Mitra (University of Rochester), Adolph Yonkee (Weber State), and Mark Evans (Central Connecticut State University). Funding has been provided by the National Science Foundation (NSF), the Geologic Society of America (GSA), and the American Association of Petroleum Geologist (AAPG). A special thanks to Brian McIntyre, who answered many “stupid” questions for me and taught a great class.


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