3.099 5.

Article

Geospatial Management and

Analysis of Microstructural Data
from San Andreas Fault
Observatory at Depth (SAFOD)
Core Samples

Elliott M. Holmes, Andrea E. Gaughan, Donald J. Biddle, Forrest R. Stevens and Jafar Hadizadeh

Special Issue
Application of Geology and GIS
Edited by
Dr. Peter Blišťan

https://doi.org/10.3390/ijgi10050332
 International Journal of
Geo-Information

Article
Geospatial Management and Analysis of Microstructural Data
from San Andreas Fault Observatory at Depth (SAFOD)
Core Samples
Elliott M. Holmes *, Andrea E. Gaughan , Donald J. Biddle, Forrest R. Stevens and Jafar Hadizadeh

Department of Geography and Geosciences, University of Louisville, Louisville, KY 40208, USA;

[email protected] (A.E.G.); [email protected] (D.J.B.); [email protected] (F.R.S.);
[email protected] (J.H.)
* Correspondence: [email protected]; Tel.: +1-502-718-3862

Abstract: Core samples obtained from scientific drilling could provide large volumes of direct mi-
crostructural and compositional data, but generating results via the traditional treatment of such data
is often time-consuming and inefficient. Unifying microstructural data within a spatially referenced
Geographic Information System (GIS) environment provides an opportunity to readily locate, visual-
ize, correlate, and apply remote sensing techniques to the data. Using 26 core billet samples from
the San Andreas Fault Observatory at Depth (SAFOD), this study developed GIS-based procedures
for: 1. Spatially referenced visualization and storage of various microstructural data from core billets;
2. 3D modeling of billets and thin section positions within each billet, which serve as a digital record





 after irreversible fragmentation of the physical billets; and 3. Vector feature creation and unsuper-
vised classification of a multi-generation calcite vein network from cathodluminescence (CL) imagery.
Citation: Holmes, E.M.; Gaughan,
Building on existing work which is predominantly limited to the 2D space of single thin sections, our
A.E.; Biddle, D.J.; Stevens, F.R.;
results indicate that a GIS can facilitate spatial treatment of data even at centimeter to nanometer
Hadizadeh, J. Geospatial Management
and Analysis of Microstructural Data
scales, but also revealed challenges involving intensive 3D representations and complex matrix
from San Andreas Fault Observatory transformations required to create geographically translated forms of the within-billet coordinate
at Depth (SAFOD) Core Samples. systems, which are suggested for consideration in future studies.
ISPRS Int. J. Geo-Inf. 2021, 10, 332.
https://doi.org/10.3390/ijgi10050332 Keywords: Geographic Information Systems (GIS); remote sensing; structural geology; 3D visualiza-
tion; spatial analyses
Academic Editors: Peter Blišt’an and
Wolfgang Kainz

Received: 24 March 2021 1. Introduction

Accepted: 8 May 2021
In recent decades, scientific drilling activities aimed at solid earth research such as
Published: 14 May 2021
tectonic deformation, heat flow, and earthquakes have been on the increase. By examining
geophysical logs recorded during drilling and cored rock exhumed from the boreholes
Publisher’s Note: MDPI stays neutral
thereafter, the scientific community has gained new insight on Earth’s subsurface processes
with regard to jurisdictional claims in
published maps and institutional affil-
and structures. Active fault zone drilling has informed critical advancements in our under-
iations.
standing of fault system dynamics and composition, and how those factors then coalesce
to influence seismic hazards experienced by humans at the surface. Structural geologists
often utilize traditional analytical techniques such as X-ray diffraction (XRD), cathodo-
luminescence (CL or SEM-CL), electron backscatter diffraction (EBSD), and optical and
electron microscope imaging to gather data from drill cores [1]. Many applications require
Copyright: © 2021 by the authors.
a combination of several approaches and, though these established techniques generate
Licensee MDPI, Basel, Switzerland.
large volumes of reliable measurements, deriving results via the traditional, piecemeal
This article is an open access article
treatment of the data is often a time-consuming and inefficient process. Geophysical instru-
distributed under the terms and
conditions of the Creative Commons
mentation and core samples thus allow direct access and observation of the fault zones that
Attribution (CC BY) license (https://
is unattainable solely through exhumed fault rocks or historical analysis of seismic events,
creativecommons.org/licenses/by/ but the ability to examine spatial relationships and understand multi-scalar subsurface
4.0/).

ISPRS Int. J. Geo-Inf. 2021, 10, 332. https://doi.org/10.3390/ijgi10050332 https://www.mdpi.com/journal/ijgi

ISPRS Int. J. Geo-Inf. 2021, 10, 332 2 of 16

processes is potentially limited without novel geospatial techniques for integrating various
2D and 3D data sources [2–4].
Unifying core-based data in a Geographic Information System (GIS) allows researchers
to locate, visualize, correlate, and explore microstructural characteristics in a streamlined
interface. While GIS is most often utilized to manage georeferenced data that span scales
of meters to kilometers, it provides robust database management and analysis structures
that facilitate spatially explicit treatment of data regardless of its type or scale [5]. As such,
in situ microstructural data collected at the nanometer-millimeter scale also fundamentally
contain spatial information that can be efficiently managed and analyzed with GIS and
remote sensing techniques. Recognizing the value of applying geospatial techniques to
microstructural geology allows researchers to maximize the potential of their data, reduce
the time needed for spatial analyses of data collected via traditional analytical techniques,
and address interdisciplinary questions that were previously challenging.
In the ‘traditional’ literature, GIS and remote sensing techniques are commonly lever-
aged in support of community- to global-scale inquiries about anthropogenic climate
change, socio-economic conditions, crime distribution, transportation networks, or ecologi-
cal systems dynamics [6–9]. Studies typically span scales of meters to kilometers and may
integrate multiple sources of remotely sensed aerial imagery and vector data acquired with
GNSS-enabled devices. One unifying aspect among these applications is the importance
of the coordinate space that defines the study area; in other terms, the spatial context of
research results is often of equal importance to, or inseparable from, the research itself. In
studies involving the remote sensing of land cover, for example, both questions and an-
swers regarding dynamic land systems processes are strongly informed by the geophysical
context of the study area, the spatial and temporal resolution of available data, and the
computational resources available to process the data. The spatial distribution of patterns
and features at the micro-scale has also prompted geologists to explore contemporary GIS
techniques for managing microstructural data.
More recently, there is a growing number of studies in the geologic literature regard-
ing the potential applications of GIS frameworks to visualize and analyze microstructural
data. Previous work demonstrates the viability of GIS for multi-source data management
and integration [10–12], while others have utilized built-in remote sensing tools to ex-
tract spatial information from microscopic image data [13–18]. Additional studies have
developed methods for linking and reorientation of petrographic thin sections to real-
world geographic coordinates [4,19,20]. In this respect, the work of Linzmeier et al. [21] is
particularly informative, creating a framework for spatial registration of multi-source mi-
crostructural data from within a single thin section in arbitrary, two-dimensional space. By
using GIS software to integrate raster images from optical and electron microscopes, along
with vector point data from secondary ion mass spectrometry (SIMS) and electron probe
microanalysis (EPMA), the authors mapped the distribution of structural and chemical
characteristics across various crystal grains [21]. Another study that our method expands
upon is that of Basil Tikoff et al. [4]. They propose a robust framework for defining the
orientation of thin sections relative to sampled billets and the entire drill core, providing a
tractable spatial registration method for use with both local and geographic coordinate
systems. An application of the GIS-based remote sensing to Cathodoluminescence images
of calcite vein networks, particularly using image classification techniques, is apparently
absent from the geospatial discourse and stands as a novel technique in our study.
Cathodoluminescence (CL) image data analysis presents a useful application of the
micro-GIS framework because, like land cover analysis with optical satellite images, one
objective of CL is to quantify the vein network patterns by processing the changes in
spectral values assigned to certain luminescing features. Structure from Motion (SFM)
photogrammetry is an additional remote sensing technique that may be applied in mi-
crostructural analyses [22]. SFM is a low-cost and automated modeling approach based
on the aggregation of multiple overlapping images from varying perspectives of an object
or terrain. Though well established in the remote sensing literature as a viable technique
ISPRS Int. J. Geo-Inf. 2021, 10, 332 3 of 16

for UAS image analysis, recent studies demonstrate that SFM is also capable of accurately
modeling surfaces at laboratory or microscopic scales [23].
The methods described in this study leverage geospatial tools to integrate various
multi-scalar and -dimensional data layers, including tabular, graphical, and visual infor-
mation, to produce spatially referenced results and accessible digital models of sample
billets extracted from drill cores (Figure 1). Utilizing ESRI’s ArcGIS software suite [24],
this study establishes and evaluates micro-GIS procedures for compiling, managing, and
analyzing those data using core samples from the San Andreas Fault Observatory at Depth
(SAFOD). Our main objectives are three-fold: 1. Develop GIS-based methods for spatially
referenced visualization and storage of various microstructural data from drill core billet
samples; 2. Produce 3D models of sample billets and thin section positions within each
billet, which serve as a digital record after irreversible material loss and fragmentation of
the physical billets; and 3. Further examine the viability of the micro-GIS framework via
creation of a semi-automated model for unsupervised classification of a multi-generation
calcite vein network from CL imagery. Building upon previous innovative work in the field
of ‘micro-GIS’, we address boundaries that constrain the spatially explicit examination
of microstructural data and consider the challenges that persist high on the agenda of
future studies.

Figure 1. Workflow diagram of in situ data collection, processes, and resulting outputs under a GIS-based
framework. Starred items indicate procedures carried out by third parties (see Acknowledgements).
ISPRS Int. J. Geo-Inf. 2021, 10, 332 4 of 16

2. Materials and Methods

2.1. The SAFOD Core Samples
The method for spatialized archival of core-based data in a micro-GIS environment is
applied with 26 billets from the San Andreas Fault Observatory at Depth (SAFOD), which
were sampled from select areas in an approximately 40 m core length during the SAFOD
Phase III drilling (Figure 2). The SAFOD is located near Parkfield, California, and was
–
drilled jointly by the National Science Foundation and the US Geological Survey beginning
in 2002. Intersecting the San Andreas Fault at depths of 2–3km, the observatory provides
geophysical data as well as core samples, gas, and pore-fluid samples recovered from the
borehole for laboratory analysis [25].

Figure 2. (A) General lithological characteristics of SAFOD core sections with a legend for units
(measured depth-MD-meters). Black and white circles represent the distribution of sample billets
(adapted from [26]). (B) Color photo of Hole E, Run 1, Section 1 including red and black core
orientation lines (adapted from [27]).

The SAFOD phase III core consists of 3 intervals—Hole E, Hole G (Runs 1–3), and
Hole G (Runs 4–6)—which are further subdivided into runs and sections. As in most
SAFOD-related studies, numbering of the samples in this paper reflects —these designations;
for example, a billet – — from Hole E, Run 1, Section 1 will be referred to as sample
extracted
‘E11′ . Each physical billet was marked with an arrow indicating up-borehole direction and
orientation lines which establish billet rotation with respect to the core axis. Sectioning
lines indicating where the billet is to be cut for thin section extraction and a 2cm scale-bar
sample
were added‘Eafter
1′ the core billets were received by our laboratory.

2.2. Data Collection

2.2.1. D Billet Models
From each billet we extracted 3D solid surface models from RGB digital camera
imaging, 3D internal structure models from CT scans, and mineral composition tables
from X-ray diffraction (XRD) analysis. The 3D solid surface models retain detailed surface
morphology and spatial orientation markings that allow for the creation of an arbitrary
local coordinate system within each billet, both of which are lost on the physical sample
due to irreversible fragmentation and material loss. A Canon Powershot G1X Mark II
camera with a stabilizing tripod was used to capture imagery at 12.8-megapixel resolution.
The camera was placed in aperture priority (AV) mode with a wide aperture setting of F16,
allowing the entire field of view to be focused. A low ISO of 200 reduced the shutter speed
ISPRS Int. J. Geo-Inf. 2021, 10, 332 5 of 16

and maximized the signal-to-noise ratio in the images, in turn mitigating the potential for
distinct features (i.e., prominent grains and fractures) to exhibit spectral variability from
one image to the next. The billets were imaged on a rotating mount inside of a controlled
lighting environment.
To process the images, we used a structure for motion (SFM) photogrammetry method
from the Agisoft Metashape software [28]. This procedure constructs a 3D model using
the series of systematically captured, overlapping images of each billet. The slight shift in
perspective between each image is exploited with an automated image alignment process
that generates a 3D cloud of discrete image tie points containing color data. Ultimately,
the colorized point cloud serves as the vertices from which a triangulated model surface
is interpolated (Figure 3). The SFM output can then be considered as a multi-resolution
olutionsurface
‘solid ‘solid model’
surfaceconsisting
model’ consisting of a 3D
of a 3D object object
mesh boundmesh
by abound by a photo
photo-realistic image
texture [29,30].

Figure 3. Procedure for processing 2D images to generate 3D billet models depicting: (A) camera
positions; (B) initial tie points; (C) dense tie points cloud; and (D) processed 3D billet model.

The internal 3D structure models provided additional information regarding the billet
interiors which were then used to identify orientation of individual billet thin sections. To
extract internal 3D structures, billets were processed through a ImTek MicroCAT II CT
scanner. Raw data comprises a cubic stack of DICOM images (1024 pixels2 × 1024 images).

2.2.2. Thin Section-Based Imagery

From individual thin sections, we produced mosaics of whole sections from optical
microscope images, which serve as base map layers in the GIS. Additional data include
the cathodoluminescence (CL) data as well as additional image layers from the scanning
electron microscope (SEM). Base maps from the thin sections were imaged using the Zeiss
Axioplan optical microscope and a Scion Corporation CFW-1312C digital camera. We
ensured a 30% overlap between images to ensure adequate overlap in images. Processing
of the basemaps was done in the Microsoft Image Composite Editor (ICE) software [31].

2.3. Micro-GIS Framework

ESRI’s ArcGIS v10.7.1 software served as the primary environment for integration
and visualization of microstructural, compositional, and surface feature data. Its database
ESRI’s ArcGIS
management v10.7.1
architecture andsoftware served
geospatial tools as the primary
facilitated environment
the creation of two- for
andintegration
three-
dimensional representations of digital billet models with respect to their positions in the
SAFOD core, as well as the position (or superposition) of the various layers of thin section
data within the billets.

a custom arbitrary coordinate system was created and defined as geodatabase’s spatial
ISPRS Int. J. Geo-Inf. 2021, 10, 332 6 of 16

First, a new file geodatabase was created to house the data, relational information,
and custom geoprocessing tool kits required for the project. Prior to importing any files,
a custom arbitrary coordinate system was created and defined as geodatabase’s spatial
reference grid. This was a crucial step to ensure that data were archived correctly within
one shared digital space. Additionally, attribute field domains and topological rules were
established to enforce data integrity when importing, displaying, and editing features.
Because future micro-GIS studies will encompass a multitude of approaches and data
requirements, some database settings (i.e., spatial units, precision, display, and hardware
utilization) utilized in this study are not reviewed in exhaustive detail.
The second step involved compiling the data into the geodatabase. This process was
facilitated by initially creating an empty feature dataset corresponding to each of the data
sources described throughout the paper, allowing them to be imported in batch and with
respect to the defined workspace settings. The 3D solid surface models were loaded into a
single ‘multipatch’ feature dataset. The ArcGIS-supported multipatch format reads the vertex,
edge, face, and color data contained within the input COLLADA files and reconstructs an
identical version of the model. 2D imagery from petrographic thin sections and sliced CT
data were stored as raster datasets.
Depending on their nature and purpose, tabulated data were either imported into the
geodatabase as stand-alone tables that could be graphically displayed or associated with
other features via relationship classes or joined to the attributes of existing map layers if
they contained direct spatial information. The XRD mineral composition plots, for example,
were uploaded as stand-alone figures because their spatiality is tied to the whole extent of
the corresponding billet, while the CL data table discussed later is tied directly to precise X,
Y image coordinates and was joined to point features at those locations.
Using arbitrary local coordinate systems defined within individual samples, the digital
billet models and corresponding thin section-based data could be stored and displayed
in 3D space. Given that a reliable measured depth within a core section and the core-top
direction for each sample billet is known, it was possible to define the spatial relationships
of different samples in a core section using both foliation and distance. This procedure
entailed assigning the centroids of the solid surface models to the corresponding placement
point at the correct measured depth in local coordinates. Proceeding initial placement,
the digital models were scaled using the 2 cm reference marked on the physical billet
prior to imaging. The additional arrow markings were used to establish each billet’s
unique rotational orientation with respect to the long axis of the borehole. The up-borehole
direction indicated by the arrows is, in other terms, the direction along the long axis in
which measured depth in the borehole decreases.
Subsequently, the 3D surface models allowed the planar orientation of the petrographic
thin sections to be defined within the local coordinates of each billet through a visual
identification procedure. The planes from which the thin sections were extracted are
identifiable in the ‘intact’ surface models by reference lines labeled on the physical billets
prior to sectioning. These sectioning lines appear in photo-realistic color in the solid surface
models and are made apparent in the internal structure models by placing elastic bands
around the physical billets prior to CT-scanning. Because the physical cut line was visible in
both models, the location of the thin section base maps and the corresponding slice of CT
data could be approximated.

2.4. Cathodoluminescence (CL) Analysis

CL is commonly applied in solid earth science for investigations of growth and disso-
lution features in ore minerals, growth structures in fossils, cementation and diagenesis
processes in sedimentary rocks, and the chemical and mechanical conditions of mineralized
systems as they evolve through time [32]. Calcite veins are the cemented remnants of fluids
introduced through repeated fracture-seal episodes within the host rock, each episode
producing a new generation due to varying levels of trace impurities in the source fluid [33].
With well-established spectral proxies, CL allows identification of vein generations and the
ISPRS Int. J. Geo-Inf. 2021, 10, 332 7 of 16

relative time, depth, and fluid conditions in which they formed [34–38]. For the cathodo-
luminescence analysis, we utilized a GIS-based workflow to 1. archive CL imagery and
create point features containing spectral data and additional attribute information; and
2. extract spatially referenced information layers from raw spectral data via unsupervised
classification of calcite vein generations within a thin section from the SAFOD core.

Spectral Data Identification

The first component of our analysis involves spatialized color sampling and wavelength
determination of RGB pixels from luminescent areas in the CL image. Though CL records
light emission from the visible portion of the electromagnetic spectrum (350–750 nm), it
is not possible to quantitatively derive a spectral wavelength from a combination of RGB
values because several RGB combinations exist per each unit wavelength in the 400 nm
spectral range [39]. Spectral data acquisition from the pixel samples thus required a manual
color matching procedure using the CIE 1931 RGB color space standard [40]. The image
contains two distinct generations of calcite growth, which were visually distinguished by
surveying the image for regions with pronounced contrast in apparent brightness and
superimposing relationships between growth features. Figure 4 contains the CL image
and provides an example of a region containing two calcite generations. Within each area
of interest, the pixels in each generation with the greatest and least apparent brightness
were marked with corresponding point features and then populated with their manually
determined wavelengths.

Figure 4. CL image containing two visually distinct generations of calcite vein growth and predefined
regions of interest for spectral sampling and vector data creation. Because of significant spectral variation
and superimposition among growth features, we infer that there are two distinct generations of calcite
and that generation 1 (G1) is relatively younger than G2.2.4.2. CL Image Classification and Assessment.

An ISODATA unsupervised classification [41] was performed on the CL image to

identify and classify calcite vein formations on the image. Input for the classification
consisted of the clipped RGB raster containing only calcite, as well the FM raster (the
0–1 membership values were rescaled to the 0–255 value range of the 8-bit RGB pixels),
for a total of four image bands. The classification was then run with a specified output of
10 spectral classes, which were combined as needed to achieve the final product with two
apparent calcite vein generations classified. –
As calcite vein generations were the sole target of classification, a fuzzy membership
(FM) function was first used to isolate and extract the calcite network and remove all
other image pixels from consideration. The FM function calculated the strength of pixel
ISPRS Int. J. Geo-Inf. 2021, 10, 332 8 of 16

membership based on the mean and standard deviation of the input RGB values (large
values were specified as having high membership because luminescing calcite contains
the brightest pixels in the image), generating a new raster image indicating strength of
membership values ranked from 0 to 1. The membership raster was then used for two
distinct purposes: (1) creating a binary dataset indicating if pixels are calcite/not calcite via
a simple thresholding procedure, providing a mask for clipping the raw CL image data;
and (2) input as an additional image band in the unsupervised classification algorithm
(Figure 5).

Figure 5. Intermediate data from the classification procedure including: (A) the raw CL image; (B) the
raster band generated via the FM function, with pixel values indication strength of membership;
(C) the binary mask band produced by thresholding the original FM image; and (D) the clipped
raster containing RGB pixel values only within the calcite region defined by the mask band. Images
B and D serve as the input for the unsupervised classification.

Accuracy assessment was conducted using 50 random points within each class
(n = 100). Because a classified validation image was not available, the points were gener-
ated within the clipped raster containing only calcite and then manually assigned to the
correct reference class. To reduce the potential for sampling bias, 200 points were initially
produced and then reordered using randomly generated numbers. The points were then
hand-classified in random order until the desired 50 points per class were obtained. A con-
fusion matrix allowed us to quantitatively evaluate the classification performance and
provided the following metrics: overall accuracy, producer’s accuracy, user’s accuracy,
provided the following metrics: overall accuracy, producer’s accuracy, user’s accuracy, and
the Kappa coefficient. Overall accuracy refers to the number of correctly classified pixels
pixels divided by the total number of pixels. Producer’s accuracy is a measure of how
divided by the total number of pixels. Producer’s accuracy is a measure of how often any
often any one class is omitted or misclassified, while user’s accuracy refers to how often
one class is omitted or misclassified, while user’s accuracy refers to how often within a
reference class that pixels from other classes are misclassified. The Kappa coefficient is
a measure of agreement between classified and reference samples and compensated for
chance agreement [42]. The described workflow was implemented using the ArcGIS Mod-
elBuilder visual programming interface, which provides a classification model framework
that can be readily applied to different CL images using adjusted parameters, as needed.
ISPRS Int. J. Geo-Inf. 2021, 10, 332 9 of 16

3. Results
3.1. The Micro-GIS Framework
Once imported, all data could be navigated via a catalog and examined individually
using the available visualization and spatial analytical tools. ArcGIS also lent many
beneficial tools for establishing relationships within and between each type of data and
producing visual representations that effectively conveyed meaningful information. In this
study, several of such representations were produced not only to display data but also to
provide means for interactive navigation throughout the available information content for
all billets.
Navigation begins at the top-most spatial level of the database with a SAFOD core
overview map. This map represents the core sections as polygon features and identifies each
billet sample location with corresponding points, providing a simplified menu from which
additional information can be explored and basic spatial inferences can be made. Arbitrary
coordinates for these features were established by adopting their known measured depths
as the y-axis (the x-axis was only used to define the width of the core polygons). When a
point feature corresponding to a given billet is selected, the user is presented with an HTML
pop-up window containing basic attribute information. The pop-up window also directly
tioning planes
displays in the composition
the mineral billets’ internal CTderived
plots data, and CL images
through XRDfrom SEM.which
analysis, The base
can mosaics
simply
be viewed in the window or downloaded if required. Additionally, any data associated
with a given billet may be accessed through hyperlinks in the pop-up (Figure 6a,b).

Figure 6. Flow diagram illustrating how project microstructural data are structured, visualized,
and explored interactively within the micro-GIS. The figure depicts (A) the SAFOD core overview
map showing sample billet locations and attributes; (B) An example of the HTML pop-up window
containing attribute information, results from XRD analysis, and links to additional data associated
4′
with sample billet G24; (C) the ArcScene workspace containing billet G24′ s 3D solid surface model;
and (D) the spatially referenced 2D image data from a thin section extracted from the XY plane
in G24.

The 3D solid surface models are also accessible via hyperlink in the pop-up menu or
opened from direct access in the database catalog. Doing so opens an ArcScene workspace
with the pre-loaded billet model, where the model may be viewed, edited, or subjected
to various spatial analyses (Figure 6c). Though the whole 3D internal structure models
could not be integrated directly into the database management framework, they could
be accessed using hyperlinks within the GIS by providing the path to their 3DSlicer
program workspace.
ISPRS Int. J. Geo-Inf. 2021, 10, 332 10 of 16

Pop-up windows were also enabled for the 3D billet models, allowing rapid navigation
to the 2D thin section-based data acquired from within each billet (though this review
follows a top-down sequence, note that links were established so that users can explore
the interactive menu in any order). Organized on a per-sample basis, the thin section
maps contain spatially referenced optical base mosaics, raster slices extracted from along
sectioning planes in the billets’ internal CT data, and CL images from SEM. The base
mosaics establish primary local coordinate systems in which the other map layers are
spatially registered.

3.2. CL Image Analysis

The results of the CL image analysis are discussed in two distinct components: (1) cre-
ating and editing of vector point features to facilitate spatialized acquisition of spectral
samples; and (2) leveraging geoprocessing tools to develop a streamlined approach for cal-
cite feature extraction, unsupervised classification of vein generations within the extracted
calcite, and the presentation of accuracy metrics for f the classified output. We produced
spatial features containing spectral data and their corresponding point locations in the local
coordinates of the CL image. The new point features contain XY information, indication
sample’s associated calcite vein generation,
of if the sample pertains to calcite or a different luminescent mineral phase, the sample’s
associated calcite vein generation, and the wavelength derived by matching pixel color
swatches to the CIE 1931 color standard (Figure 7). All listed attributes are of significant
interest in various facets of CL-based research but primarily serve in this paper as a valida-
tion dataset for accuracy assessment of the unsupervised classification output. Nonetheless,
the procedures outlined for spatial color sampling encompassed many important aspects
of creating, editing, and displaying vector data in the micro-GIS environment.

Figure 7. ArcGIS map view of sample points within the local coordinates of the CL image, labeled
with custom symbology and relevant attribute information regarding spectral wavelength and calcite
generation association.

The unsupervised classification process generated two products: the classified image
indicatingeach
indicating each pixel’s
pixel’s membership
membership in generation
in generation 1, 2, or1,neither
2, or neither
and the and the transferrabl
transferrable
model developed within ArcGIS ModelBuilder to accomplish the procedures. The proce-
dure also generated an additional classification image band derived via the fuzzy member-
ship (FM) function, a binary mask created by thresholding the FM raster, and the image
containing only the calcite extracted by applying the mask.
ISPRS Int. J. Geo-Inf. 2021, 10, 332 11 of 16

The FM-derived mask preliminarily classified a total of 318,156 pixels, or approximately

6.5% of the total image, as calcite. By masking the remainder of the image, a significant
amount of noise was removed from consideration by the spectral clustering algorithm,
resulting in better model performance. Using both the FM raster and the clipped RGB CL
image as input bands in the ISODATA classification was also found to produce more desir-
able spectral classes. The output of this procedure is a classified raster image that defines
each pixel as either calcite generation 1, calcite generation 2, or background (Figure 8).

(A) (B)

Figure 8. Results of unsupervised classification showing (A) the input CL image, randomly generated accuracy assessment
points (n = 100), and (B) the classified output with counts of pixels assigned as either calcite generation 1 or 2.

The results of accuracy assessment of the classified output were derived from 100 points
(50 points per class) that were randomly generated within the masked calcite and assigned
to the correct class. The confusion matrix indicated that overall accuracy was 85% with a
85% with
Kappa a Kappa
coefficient ofcoefficient of 70%. producer’s
70%. The highest The highestaccuracy
producer’s
wasaccuracy was
observed in observ
the generation
the generation 2 class (90%), while the highest user’s accuracy (89%) was reported
2 class (90%), while the highest user’s accuracy (89%) was reported in the generation in 1the
class.
These statistics indicate that of the 100 reference points, 85 were classified correctly. Of the
50 points from the generation 1 class, 20% were mis-classified as generation 2. Likewise,
′
10% of generation 2′ s points were erroneously classified as generation 1.

4. Discussion
Microstructural studies of fault rocks use numerous analytical and imaging techniques
to conduct research, many of which produce data that contain spatially dependent informa-
tion. Utilizing GIS to process these various data is beneficial because it allows them to be
integrated with respect to their spatiality (1) within petrographic thin sections, (2) within
core billets, and (3) within the arbitrary coordinates of the drill site and borehole. The
procedures described in this paper present a universal framework for a spatially explicit
management and visualization of 2D and 3D microstructural data obtained from drill
core samples. Each of the various stages were ultimately marked with successes, but also
identified key challenges that should be addressed in future micro-GIS efforts.
In the micro-GIS database, each 3D billet model is referenced by a corresponding
placement point in a 2D overview of the SAFOD core. When a billet is selected from the
overview, the user can navigate directly to the billet model and any associated microstruc-
tural data (refer to Figure 6 for an example from billet G24). Using this structure means
onlythe
that only themodels’
models’ centroids
centroids are
arespatially
spatiallyregistered
registeredand
andthat billet
that rotation
billet with
rotation respect
with respect
to other billets and the core itself is not explicitly defined. In this case the exact distance
between billet
between billet A’s
A’s centroid
centroid and
and billet
billet B’s
B’scentroid
centroid(equivalent
(equivalentto to
thethe difference in their
measured depths) can be measured, but angles or distances between any vertices in billet
ISPRS Int. J. Geo-Inf. 2021, 10, 332 12 of 16

A and B cannot. In future core-based GIS mapping, this study recommends that a unique
spatial position for individual billets be defined within the geographic coordinates of the
drill site by making full use of the trajectories recorded during drilling. Doing so would
enable geometric transformations that account for the compass bearing of the core segment
and the clockwise angular relationship between the billet and core orientation line. This
operation would be most accurate for billets that include a portion of core’s circumference;
This operation
otherwise, thewould be angle
clockwise most must
accurate for billets
be estimated thatoninclude
based the dip aangle
portion of core’s
of foliation circum-
in the
billet’s respective section of the core (Figure 9).
tion in the billet’s respective section of the core (Figure 9).

(A) (B)
Figure 9. (A) Map view of SAF bearing 137◦ SE through California, core sections G123 and G456 cutting across the SAF
with compass bearings of 027◦ NE (plunge of 67◦ ) and 035◦ NE (plunge of 68◦ ), respectively. (B) Schematic depiction of
borehole depicting billet clockwise angle with respect to red and black core orientation lines.

The results of this study indicate that instead of tentative placement of the thin
section base maps inside the models, data from thin sections could be mapped within
the local 3D coordinate space of the billet model with greater precision. Each pixel in
the base maps would then contain a unique XYZ position within both the billet and the
borehole at-large. A recent study [4] prescribes a universal system for defining the spatial
orientation of petrographic thin sections that is primarily based on a robust notching
procedure that provides all information required for geometric transformation into 3D
billet space (Figure 10). Though the authors did not focus on GIS-based implementation
of the framework, they have suggested procedures that would complement spatially
explicit map visualizations of 3D billet models and 2D thin section-based data from optical,
SEM, and CL image analyses. Notably, the management of micro-structural data within a
spatially referenced micro-GIS framework affords more opportunities to leverage the robust
range of geospatial techniques of GIS and remote sensing. Object-based Image Analysis
(OBIA) [43,44] of CL and other thin section image data represents one exciting possibility.
In this study, we employ ‘traditional’ pixel-based geospatial techniques of classification
and raster analysis to derive meaningful information layers from the raw pixel values.
‘ by the GIS’ database architecture, where the model could
This effort was greatly facilitated
be effectively developed, tested, and modified using the ModelBuilder GUI and readily
available geoprocessing tools. Furthermore, the outputs generated from the classification
procedures could be seamlessly ingested as new, spatially referenced information content
in the micro-GIS. As an alternative approach to the pixel-based approach in classifying the
calcite vein generations, OBIA image segmentation techniques could be used to identify
image objects within CL image data, and subsequent classification methods used to extract
classes of features such as multiple generations of calcite veins to be stored as vector
features within the micro-GIS. These vector features could then be interrogated similarly
ISPRS Int. J. Geo-Inf. 2021, 10, 332 13 of 16

with the micro-GIS spatial analysis techniques to characterize spatial patterns, such as
trends in size, shape, density, or directional orientation.

(A) (B)
Figure 10. Schematic representation of thin section orientation framework depicting: (A) Definition of billet sectioning
planes XY, XZ, and YZ with respect to within-billet foliation plane; and (B) Suggested markings to be placed on physical
thin sections for spatial referencing within the local coordinates of billet models (2D section markings in B were adapted
after Tickoff et al. [4]).

Lastly, though spatial relationships were established to some extent between all data in
this study (i.e., the measured depth of the corresponding billet), the use of multiple arbitrary
coordinate systems constrained the ability to achieve high spatial precision between billets
and also between data products from two or more thin sections within individual billets.
Initial efforts were made to establish all billet models within a single local coordinate
system representing the dimensions of the SAFOD core, but were hindered by the complex
transformations involved in establishing proper billet orientation with respect to the core.
Similar complexities were encountered in attempts to transform planar thin section data
into the 3D coordinate space of the solid surface models. The potential extensions to the
spatial registration framework discussed here could possibly enhance efforts to create
geographically translated forms of within-billet and -thin section coordinate systems.
As such, this study suggests that improved affine transformation matrices should be
developed in future research, with emphasis placed on how they might be more seamlessly
integrated into the database schema to better facilitate spatial data conversion from local to
geographic coordinates.

5. Conclusions
Utilizing ESRI’s ArcGIS software suite, this study establishes micro-GIS procedures
Utilizing ESRI’s ArcGIS software suite, this study establishes micro
and tests the data management process with core samples from the San Andreas Fault
Observatory at Depth (SAFOD). In addition to applying spatial analytical techniques on in-
dividual data layers extracted from the SAFOD thin sections, the use of a GIS framework in
a microspatial context allows even further insights to be drawn. Specifically, the micro-GIS
serves as an ideal repository and analytical workspace for drill core-based microstructural
data that are traditionally compartmentalized. The various microstructural data (recounted
below) could be imported and then managed within an optimized environment with pre-
defined attribute domains, topological constraints, and custom coordinate systems suited
for analyses in arbitrary space at centimeter to sub-millimeter scales. These are as follows:
1. 3D solid surface models, which provide a geometrically accurate, photorealistic
representation of the physical billets;
2. Image slices from 3D internal structure models, which consist of gridded CT data that
identify internal characteristics along the sectioning planes of the billets;
ISPRS Int. J. Geo-Inf. 2021, 10, 332 14 of 16

3. X-ray diffraction (XRD) histogram plots that characterize the mineralogical composi-
tion of the billets;
4. Thin section optical mosaics that serve as a base map layer from which the spatial
positions of other thin section-based data can be registered; and
5. SEM-CL image data which contain high-resolution spectral information from areas of
interest within the thin sections.
This study sought to probe the potential for treatment of those data with the geospatial
framework in a study involving 26 sample billets from the SAFOD. Multiple forms of 3D
and 2D data were integrated in a geodatabase that archived not only the input data, but
also their later-defined spatial relationships and outputs derived from spatial analyses.
By-products of the method included interactive map visualizations, a hierarchical data
catalog based on spatial relationships, and ModelBuilder workflows for accomplishing the
various database management and analysis tasks.
The overarching concept inherent to GIS is that of relating different, spatially overlap-
ping data to interrogate associations between data types. If data are adequately spatially
referenced, it has the potential to assess relationships between data sources that may mo-
tivate further research and methods development focused on the micro-GIS framework.
Novelty may be found specific to micro-GIS analyses for characterizing a host of deforma-
tion microstructures including complex, multi-generation networks of calcite and quartz
veins, as preliminarily explored in the CL analysis of this paper.
To this end, future structural geology studies should continue prioritizing the spatial
relationships within and between the different sources of microstructural data, but also
work toward a more standardized vernacular around spatially explicit handling of those
data in a GIS framework. For example, civil engineers benefit from tailored analytical
toolkits such as ‘CityEngine’ for 3D modeling and ‘Network Analyst’ for studies involving
infrastructure and transportation data, while hydrologists have access to specific tools
for delineating watersheds, estimating the flow and accumulation of surface water, and
modeling the path of groundwater contaminants [24]. In a similar fashion, custom geo-
processing tools and workspace templates should also be developed to better facilitate
structural geologists working at the micro-scale.
Our study confronted the procedural and conceptual challenges associated with
spatial integration of core-based microstructural data, built on recent advances to develop
universal micro-GIS procedures, and demonstrated the usefulness of GIS within the broader
context of structural geology as a whole. With continued advances on both disciplinary
fronts, the novel approaches discussed in this study are well-positioned to inform, and
simultaneously be informed by, innovations in the future.

Author Contributions: Conceptualization: Elliott M. Holmes, Andrea E. Gaughan, Donald J. Biddle,

Forrest R. Stevens, and Jafar Hadizadeh; Methodology: Elliott M. Holmes, Andrea E. Gaughan,
Donald J. Biddle, and Forrest R. Stevens; Data Curation: Elliott M. Holmes and Jafar Hadizadeh;
Writing—Original Draft Preparation: Elliott M. Holmes; Writing—Review and Editing: Elliott M.
Holmes, Andrea E. Gaughan, Donald J. Biddle, Forrest R. Stevens, and Jafar Hadizadeh; Figure Edit-
ing: Elliott M. Holmes; Supervision: Andrea E. Gaughan and Jafar Hadizadeh; Funding Acquisition:
Jafar Hadizadeh, Andrea E. Gaughan, and Donald J. Biddle. All authors have read and agreed to the
published version of the manuscript.
Funding: This research was partially supported by the U.S. National Science Foundation grant NSF-
EAR-1800933 to J. Hadizadeh, A.E. Gaughan, and D.J. Biddle.
Institutional Review Board Statement: Not applicable.
Informed Consent Statement: Not applicable.
Data Availability Statement: The data presented in this study are available on request from the
corresponding author. The data are primarily derived from microstructural and geospatial analyses
and are not publicly available due to large file dimensions.
ISPRS Int. J. Geo-Inf. 2021, 10, 332 15 of 16

Acknowledgments: The authors express our appreciation for the data curation efforts of Huaiyu
Zheng, Aryan Ghazipour, and Grace Embree (CT scans), in addition to Alan Boyle (CL imaging).
We thank Judith Chester, Texas A&M University, chair of the NSF SAFOD sample committee for
providing the core samples.
Conflicts of Interest: The authors declare no conflict of interest.

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