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Optical and SEM-Based Microscopy

Integration for Optimisation of
Geometallurgical Modelling and Ore
Deposit Characterisation
R Hartner1, S G Walters2 and R Berry3

ABSTRACT
Digital optical microscopy (DOM) and automated SEM-based (ASEM) mineralogy systems (MLA,
QEMSCAN) have experienced significant developments within the last decade. However these
developments have been independent from each other and the two mineralogical techniques
have so far not yet been integrated to combine the strengths and technical benefits of both
analytical platforms. This detailed comprehensive mineralogical information is critical support
for geometallurgy.
Major hardware and software advances in DOM in the last few years have provided important
new capabilities with potential applications to automated mineralogy. These technological
advances have been largely driven by sectors outside mining (eg medical pathology) and have
not yet been widely adopted within the minerals industry. The advent of DOM offers significantly
more automated mineralogy capabilities than traditional expert-mineralogist driven optical
microscopy. This is based on advances in automated image acquisition, high resolution cameras
for digital imaging, imaging of large areas through mosaic options, integration of multiple layers
and application of advanced image analysis techniques.
Ongoing research involves combining the outputs of DOM and ASEM-based microscopy to create
new capabilities for integrated microscopy based on development of advanced cross-platform
image fusion and data integration between DOM and ASEM (exploiting the benefits of both
analytical platforms). This requires non-linear image registration and transfer of mineralogical
identification from ASEM to DOM systems using sophisticated image manipulation and data
analysis software.
Examples will be given of image fusion and data registration for a range of different ore types.
Image fusion techniques are demonstrated using a porphyry copper deposit sample where sulfides
and precious metals are classified using the MLA and gangue mineralogy obtained from DOM
images. Data integration enables creation of a library containing optical property variability
information for minerals identified by the MLA; thus reducing the reliance on skilled mineral
identification by supplementing human interpretation.

INTRODUCTION
Within the field of quantitative ore characterisation there is
increasing demand for efficient automated mineral mapping
at different scales and resolutions. Since the 1990s, there have
been significant advances in applied mineralogy driven by
automated SEM-based (ASEM) systems (MLA and QEMSCAN).
These mineralogy platforms are capable of automatically
providing quantitative mineralogical assessment and textural
mapping (Gu and Sugden, 1995; Gottlieb and Wilkie, 2000).
Several ASEM measurement modes have been developed
varying from back scattered electron (BSE) based mapping
techniques to detailed energy dispersive (EDS) x-ray analysis
based techniques to address different needs and resolution
(Gu, 2003).
Digital Optical Microscopy (DOM) can take a similar
direction as a reliable platform for quantitative mineralogical
assessment supported by technology advances and expanding
needs for mineralogical ore characterisation. DOM technology
advances have been largely developed in response to sectors
outside mining, eg medical pathology and biology (Baatz and
Schäpe, 2000; Katz et al, 2011) and have not yet been widely
adopted within the minerals industry. The advent of DOM
offers significantly more automated mineralogy capabilities

1. PhD Candidate, Julius Kruttschnitt Mineral Research Centre (JKMRC), The University of Queensland, 40 Isles Road, Indooroopilly Qld 4068. Email: R.Hartner@uq.edu.au
2. Professor, Julius Kruttschnitt Mineral Research Centre (JKMRC), The University of Queensland, 40 Isles Road, Indooroopilly Qld 4068. Email: S.Walters2@uq.edu.au
3. Associate Professor, CODES ARC Centre of Excellence in Ore Deposits, University of Tasmania, Private Bag 79, Hobart Tas 7001. Email: Ron.Berry@utas.edu.au

THE FIRST AUSIMM INTERNATIONAL GEOMETALLURGY CONFERENCE / BRISBANE, QLD, 5 - 7 SEPTEMBER 2011 157
R HARTNER, S G WALTERS AND R BERRY
than traditional expert-mineralogist driven optical micro-
scopy. This is based on advances in automated image
acquisition, high resolution cameras for digital imaging,
integration of multiple optical image layers and application of
advanced image analysis techniques.
The advent of modern petrographic microscopy using thin
sections was pioneered by Henry Clifton Sorby in the mid-
nineteenth century (Humphries, 1967). Traditional optical
microscopy requires manual mineral identification typically
involving expert mineralogists (eg Ramdohr, 1980; Ixer, 1990;
Schouten, 1962, Criddle and Stanley, 1993; Pirard, 2004;
Pirard, Lebichot and Krier, 2007). For the current study,
automated mineral identification and mapping using DOM
has been introduced for the characterisation of both opaque
minerals and gangue phases using multi-layered object based
image analysis with mineral identification based on ASEM
(Berry, Walters and McMahon, 2008).
Currently there is minimal integration between ASEM
and DOM techniques which means the inherent limitations
and advantages of these different analysis systems are not
optimised. An integrated approach, combining the latest
advances in state-of-the-art DOM and the strengths of the
ASEM mineralogy systems, can provide significantly more
appropriate and holistic mineralogical ore characterisation
than can be obtained from either analytical platform alone.
Integrating DOM and ASEM combines the advantages of
both analytical instruments and addresses their inherent
limitations.
INTEGRATING DIGITAL OPTICAL MICROSCOPY
AND AUTOMATED SEM-BASED MINERALOGY
SYSTEMS
The two mineralogy systems DOM and ASEM
The novel digital optical microscopy (DOM) approach
employed in the current study supports an increased demand
for automated mineral mapping (at different scales and
resolution) related to orebody characterisation. Important
tools and methodologies which have been used in the current
study involve:
 State-of-the-art digital optical microscopy using multiple
layers for imaging (currently up to 12 layers). The
different layers can be achieved through combinations of
transmitted light, polarisers, filters, incident light and tint
plates (Berry, Walters and McMahon, 2008).
 Sophisticated image segmentation and mineral
classification with multiple layers is provided by Object
Based Image Analysis (eCognition® Developer version 8
– Trimble, 2011). This major advance in image analysis is
already applied in remote sensing (REF) and biomedical
applications (REF). The software has been adapted to the
TABLE 1
Comparison of Digital Optical Microscopy and ASEM-based mineralogy systems.
Digital optical microscope (DOM)
Traditional technique with recent major technological advances
Fast and simple image acquisition
Comparably low overhead and maintenance costs
Capable of differentiating gangue phases and iron oxides
Appropriate for characterising macerals in coal analysis
158 THE FIRST AUSIMM INTERNATIONAL GEOMETALLURGY CONFERENCE / BRISBANE, QLD, 5 - 7 SEPTEMBER 2011
requirements of microscopic ore characterisation within
this research.
The primary objective of DOM integration in the current
study is acquisition of automated mineralogy using a platform
with lower capital and operational costs as well as faster image
capture compared to ASEM. DOM techniques can also be used
to differentiate minerals with similar chemical composition
but different crystal systems which can be difficult to
differentiate using ASEM. This includes phases such as pyrite
versus marcasite, different iron oxides (Donskoi et al, 2007)
and organic substances, eg macerals in coal analysis (Jenkins
and Kwan, 2003).
ASEM mineralogy systems provide strengths in fully
automated mineralogical ore characterisation and high
resolution. Table 1 compares important aspects of Digital
Optical Microscopy and ASEM-based mineralogy systems.
Integrating the two mineralogy systems –
digital optical microscopy and automated
SEM-based
General aspects for automated integrated
microscopy
Efficient DOM and ASEM integration is a challenge because
data from two different microscopy systems have to be
combined. The images in both microscopes are typically
captured at different resolutions, different pixel sizes and
different image orientations. In addition DOM and ASEM
images have distortions due to the optical/electromagnetic
lens systems and different stage movements and precision,
requiring non-linear image registration. Successful new
image registration techniques and novel methodologies for
data integration and image fusion have been developed to
overcome these challenges.
The first machine-driven integrative approach, data
integration between ASEM and DOM, provides a library
of optical parameter variability for minerals identified
using ASEM, thus reducing the reliance on skilled manual
mineralogical identification and supplementing human
optical microscopy interpretation. Automated data inte-
gration between ASEM and DOM is a significant machine-
driven support. In the future these libraries will enable less
experienced operators to set up the rules for automated DOM
mineral characterisation.
The second integrative approach, image fusion for
DOM and MLA, is designed to facilitate the extraction
of selective information from both systems to create an
optimised mineral map by combining customised mineral
discrimination capabilities from both microscopy platforms.
For example, characterising sulfides and precious metals by
ASEM and identifying gangue phases by DOM to produce a
comprehensive hybrid mineral map.
ASEM-based mineralogy systems
Fully automated mineralogy system
Longer time for data acquisition necessary
High capital and operational costs
Optimised for identifying sulfides and precious metals
Ideal for characterising minerals in coal analysis
 OPTICAL AND SEM-BASED MICROSCOPY INTEGRATION FOR OPTIMISATION OF GEOMETALLURGICAL MODELLING
TABLE 2
Schematic workflow for the image manipulation techniques.
Image data acquisition (DOM and ASEM)
Linear image registration technique
Nonlinear image registration for pixel by pixel coherence
Superimposed image stack with DOM and ASEM images
Segmentation of the image stack into objects
Object based image analysis for mineral classification
Data integration: leading to a library Image fusion, eg gangue phases from
showing optical parameter variability for DOM and sulfides from ASEM in a
minerals identified by the ASEM classified hybrid mineral map
Developing image manipulation techniques for
integrating the two systems
Table 2 shows the schematic workflow for image manipulation
techniques for data integration and image fusion used in the
current study. Mosaiced images from a polished block or
polished thin section are acquired using DOM and ASEM.
Linear image registration roughly aligns the ASEM image(s)
to the DOM image followed by nonlinear image registration
to correct for frame by frame lens distortions in the mosaiced
images and to enable a pixel by pixel coherence between the
DOM and ASEM images (see next section). Fully registered
images from two different mineralogy systems can now be
loaded together and superimposed as an image stack ready
for classification. The segmentation algorithm in eCognition®
(Trimble, 2011) is used to produce small objects based on
homogeneity across all bands (Berry, Walters and McMahon,
2008). Object based image analysis is used to extract
information from DOM and ASEM images and provide the
results of data integration or image fusion.
Image registration
Before classification algorithms involving data integration
and image fusion can be applied, DOM and ASEM images
have to be registered into congruent images with a pixel by
pixel coherence. Manual or automated image registration
techniques have been described in literature (Zitova and
Flusser, 2003). The following criteria are important for
successful image registration:
FIG 1 - Warping intensity and arrow diagram for the non-linear image registration, dislocation pattern of 0 - 2 pixels (blue to red) in order to make
the frames align correctly.
THE FIRST AUSIMM INTERNATIONAL GEOMETALLURGY CONFERENCE / BRISBANE, QLD, 5 - 7 SEPTEMBER 2011
 automatic detection of features which can be used to
control registration;
 congruency of registered images so that they can be loaded
in an image stack for further image segmentation and
mineral classification. A pixel to pixel correspondence
between DOM and ASEM images is required for this novel
approach to work correctly;
 correction of frame by frame distortions evident in
combined mosaiced microscopy images; and
 quality assurance/quality control of registration.
Effective linear and nonlinear image registration techniques
for pixel by pixel coherence between DOM and MLA images
have been established and applied in this research. Existing
public domain registration algorithms based on Scale
Invariant Feature Transform (Lowe, 2004) for automated
affine image aligning for the first linear registration step
followed by non-linear elastic transformations (Klein
et al, 2010) for automatically correcting frame by frame
distortions have been combined, optimised and refined
enabling production of accurately registered mineral images.
Different parameter settings and combinations of registration
components facilitated the design of a hybrid linear and non-
linear registration algorithm system.
Figure 1 illustrates the typical non-linear distortions that
require correction in an image created by mosaicing several
frames together (Ibáñez et al, 2005). Up to two pixels
dislocation (red colour) is necessary in this example (one pixel
= 4.73 μm) in order to make the frames align correctly. The
dislocation pattern and vector field illustrates the extent of
non-linear image registration distortion. This can also be used
as a quality control for SEM acquisition where images which
require excessive dislocation in the non-linear registration
step can be rejected and rerun under improved SEM frame
calibration.
RESULTS
Data integration
Data integration can be illustrated using the following
workflow (Figure 2):
 Reflected light and reflected light crossed polarised
images for a selected sample are captured using DOM.
For the current study images are typically captured using

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R HARTNER, S G WALTERS AND R BERRY

FIG 2 - Schematic illustration of data integration for a polished block.

a pixel size of 4.73 μm/pixel, which is a good compromise
between field of view and resolution.
 After carbon coating the sample an XMOD acquisition
routine (an MLA point counting mode resulting in a grid
of identified mineral points - Gu, 2003) is undertaken.
In order to develop libraries for the current study XMOD
acquisition covering a mineral area of 12 × 12 mm is used
in this study involving 22 000 mineralogy measurement
points at a step size of 32 × 32 pixels (1 pixel = 3.52 μm).
 Linear and nonlinear registration is required for coherence
between the XMOD mineral points and the DOM image.
The BSE image is congruent with the XMOD mineral point
grid and thus used as a carrier of the registration for the
XMOD image. This is a crucial step for registering the
XMOD data.
 The accurately registered data produce a stack of congruent
DOM and XMOD images which are loaded together and
superimposed in eCognition® (Trimble, 2011).
 The XMOD mineral classification point and the
segmented objects in the DOM images are linked in
eCognition® (Trimble, 2011).
 A database library with optical parameter variability (eg
brightness in reflected light - Ibright, blue intensity in
reflected light - Iblue - Berry, Walters and McMahon,
2008) for each mineral identified by the XMOD analysis
can be set up. Figure 3 illustrates this parameter variability

FIG 3 - Blue intensity in reflected light Iblue (in per cent) versus brightness in reflected light (Ibright) for sphalerite.

160 THE FIRST AUSIMM INTERNATIONAL GEOMETALLURGY CONFERENCE / BRISBANE, QLD, 5 - 7 SEPTEMBER 2011
 OPTICAL AND SEM-BASED MICROSCOPY INTEGRATION FOR OPTIMISATION OF GEOMETALLURGICAL MODELLING
for the mineral sphalerite, where the area with Iblue of
34 per cent and Ibright of 45 has the highest density of data
points (white colour); these two optical parameters enable
sphalerite characterisation. This library provides valuable
quantitative information for users of the DOM system that
can be used to set up automated mineral classification.
By linking DOM to automated XMOD many thousands of
reference points can be used for optical characterisation
and parameter variability which is beyond normal manual
approaches.
Image fusion
The approach to image fusion in the current study can be
illustrated using an example where identification and mapping
for sulfides and precious metal (electrum) was acquired using
the MLA SPL_Lite mode (Sparse Phase Liberation – Gu,
2003), gangue phase identification and mapping was acquired
using DOM transmitted light images, and the BSE image
acquired during MLA analysis was used to assist registration.
Table 3 shows the workflow for image fusion.
Figure 4 shows an example of a resulting classified integrated
mineral map after image processing and classification in
TABLE 3
Workflow for image fusion.
Loading registered images from two different microscopy systems
Segmenting the images into distinct objects using multiple-layer information
Classifying the mineral area relying on the strongest mineral discrimination
capabilities of both systems
Fused hybrid mineral map, eg gangue phases from DOM and sulfides from ASEM in
one classified hybrid mineral map
Exporting user-defined mineral data like modal mineralogy, grain size distribution
and mineral liberation
FIG 4 - Example of image fusion for a thin section.
THE FIRST AUSIMM INTERNATIONAL GEOMETALLURGY CONFERENCE / BRISBANE, QLD, 5 - 7 SEPTEMBER 2011
eCognition® (Trimble, 2011). Sulfides and electrum from the
MLA acquisition are combined with gangue classification
using DOM transmitted light (TL) and BSE grey level.
CONCLUSIONS
The following is a summary of new developments for
integration of optical and SEM-based microscopy for
automated mineralogical characterisation:
 Novel image registration techniques developed and
successfully demonstrated in this study facilitate pixel
by pixel coherence between DOM and ASEM images.
Registered congruent DOM and ASEM images can be
superimposed as an image stack and used in multi-layered
image analysis for further integrative image processing
like data integration and image fusion.
 Data integration takes the mineral phase boundaries from
DOM images and uses MLA classification to link identified
minerals with their key optical properties in multiple DOM
layers. This leads to a library showing optical property
variability for minerals, thus reducing the reliance on
skilled mineralogical identification and supplementing the
human interpretation. Many thousand reference points
can be used for optical characterisation and parameter
variability which is beyond normal manual approaches.
 Image fusion enables data extraction from multiple
image layers and creates hybrid integrated mineral
maps by applying user-defined mineral discrimination
capabilities of DOM along with ASEM microscopy
techniques. An example is given where the gangue phases
are characterised by DOM and the sulfides and electrum
identified and mapped by ASEM. This new approach
combines the advantages of both microscopy systems and
directly addresses their limitations.
 This methodology (for DOM and ASEM integration) can
be extended to for example, iron ore characterisation and
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R HARTNER, S G WALTERS AND R BERRY
coal analysis. It is not limited to DOM and ASEM but
could be used with other analytical mineralogy platforms
that would benefit from integrations such as infrared and
Raman spectroscopy for clay characterisation.
ACKNOWLEDGEMENTS
This research is part of a major collaborative geometallurgical
project being undertaken at CODES and SES (University of
Tasmania), JKMRC, BRC and CMLR (Sustainable Minerals
Institute, University of Queensland) and Parker Centre CRC
(CSIRO). The author acknowledges financial support and
permission to publish from industry sponsors of the AMIRA
International P843 and P843A GEMIII projects – Anglo Gold
Ashanti, Anglo American, ALS, Barrick, BHP Billiton, Boliden,
CAE Mining (Datamine), Codelco, Geotek, Gold Fields, Golder
Associates, ioGlobal, Metso Minerals, Minera San Cristobal,
Newcrest, Newmont, OZ Minerals, Penoles, Quantitative
Geoscience, Rio Tinto, Teck, Vale and Xstrata Copper (MIM).
The authors also wish to acknowledge financial support and
permission to publish from JKTech.
Financial support is also being provided by the Australian
government through the CODES ARC Centre of Excellence in
Ore Deposits and CRC ORE.
REFERENCES
Baatz, M and Schäpe, A, 2000. Multiresolution Segmentation –
An optimization approach for high quality multi-scale image
segmentation, in Strobl/Blaschke/Griesebner (eds), Angewandte
Geographische Informationsverarbeitung XII, pp 12-23
(Wichmann-Verlag: Heidelberg).
Berry, R, Walters, S G and McMahon, C, 2008. Automated
mineral identification by Optical Microscopy, in Proceedings
Ninth International Congress for Applied Mineralogy,
pp 91-94 (The Australasian Institute of Mining and Metallurgy:
Melbourne).
Criddle, A J and Stanley, C J, 1993. Quantitative Data File for Ore
Minerals, third edition (Chapman & Hall: London: UK).
Donskoi, E, Suthersa, S P, Fradda, S B, Younga, J M, Campbella, J J,
Raynlyna, T D and Clout, J M F, 2007. Utilization of optical image
analysis and automatic texture classification for iron ore particle
characterization, Minerals Engineering, (20/5):461-471
Gottlieb, P and Wilkie, G, 2000. Using quantitative electron
microscopy for process mineralogy applications, JOM Journal of
the Minerals, Metals and Materials Society, 52(4):24-25.
162 THE FIRST AUSIMM INTERNATIONAL GEOMETALLURGY CONFERENCE / BRISBANE, QLD, 5 - 7 SEPTEMBER 2011
Gu, Y, 2003. Automated scanning electron microscope based
mineral liberation analysis, Journal of Minerals and Materials
Characterization and Engineering, 2(1):33-41.
Gu, Y and Sugden, T, 1995. A highly integrated SEM-EDS-IP system
automated quantitative mineral analysis, in Proceedings of the
Third Biennial Symposium on SEM Imaging and Analysis:
Applications and Techniques, University of Melbourne.
Humphries, D W, 1967. The contribution of Henry Clifton Sorby
(1826-1908) to microscopy, Microscope, 15:351-362.
Ibáñez, L, Schroeder, W, Ng, L and Cates, J, 2005. The ITK Software
Guide [online], second edition, Clifton Park, NY. Available from:
<www.paraview.org/paraview/resources/software.html>
Ixer, R A, 1990. Atlas of Opaque and Ore Minerals in their
Associations (Open University Press: UK).
Jenkins, B M and Kwan, H A, 2003. Calibration of the MACE300™
System, in 55th Meeting of the International Committee for Coal
and Organic Petrology, B, Utrecht, The Netherlands.
Katz, E, Verleyen, W, Blackmore, C G, Edward, M, Smith, V A
and Harrison, D J, 2011. An analytical approach differentiates
between individual and collective cancer invasion, Analytical
Cellular Pathology, 34(1): 35-48.
Klein, S, Staring, M, Murphy, K, Viergever, M A and Pluim, J
P W, 2010. ELASTIX: a toolbox for intensity-based medical
image registration, IEEE Transactions on Medical Imaging,
29(1):196-205.
Lowe, D G, 2004. Distinctive image features from scale-invariant
keypoints, International Journal of Computer Vision,
60(2):91-110.
Pirard, E, 2004. Multispectral imaging of ore minerals in optical
microscopy, Mineralogical Magazine, 68:323-333.
Pirard, E, Lebichot, S and Krier, W, 2007. Particle texture
analysis using polarized light imaging and grey level intercepts,
International Journal of Mineral Processing, 84:299-309.
Ramdohr, P, 1980. The Ore Minerals and their Intergrowths,
second English edition (Pergamon: Oxford).
Schouten, C, 1962. Determination Tables for Ore Microscopy,
(Elsevier: Amsterdam, The Netherlands).
Trimble, 2011. Object-based image analysis (segmentation and
classification) [online], Available from: <http://www.ecognition.
com/>
Zitova, B and Flusser, J, 2003. Image registration methods:
A survey, Image and Vision Computing 21:977-1000.