JOURNAL OF Journal of Petrology, 2020, Vol. 61, No.

4: egaa047
doi: 10.1093/petrology/egaa047

PETROLOGY Advance Access Publication Date: 24 April 2020

Original Article

QEMSCAN as a Method of Semi-Automated

Crystal Size Distribution Analysis: Insights from
Apollo 15 Mare Basalts

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S. K. Bell *, K. H. Joy, J. F. Pernet-Fisher and M. E. Hartley
Department of Earth and Environmental Sciences, University of Manchester, Manchester M13 9PL, UK
*Corresponding author. Telephone: þ44 1612753406. E-mail: samantha.bell@manchester.ac.uk
Received March 27, 2019; Accepted April 6, 2020

ABSTRACT
Crystal size distribution analysis is a non-destructive, quantitative method providing insights into
the crystallization histories of magmas. Traditional crystal size distribution data collection requires
the manual tracing of crystal boundaries within a sample from a digital image. Although this man-
ual method requires minimal equipment to perform, the process is often time-intensive. In this
study we investigate the feasibility of using the Quantitative Evaluation of Minerals by SCANing
electron microscopy (QEMSCAN) software for semi-automated crystal size distribution analysis.
Four Apollo 15 mare basalt thin sections were analysed using both manual and QEMSCAN crystal
size distribution data collection methods. In most cases we observe an offset between the crystal
size distribution plots produced by QEMSCAN methods compared with the manual data, leading to
differences in calculated crystal residence times and nucleation densities. The source of the dis-
crepancy is two-fold: (1) the touching particles processor in the QEMSCAN software is prone to
segmenting overlapping elongate crystals into multiple smaller crystals; (2) this segmentation of
elongate crystals causes estimates of true 3D crystal habit to vary between QEMSCAN and manual
data. The reliability of the QESMCAN data appears to be a function of the crystal texture and aver-
age crystal shape, both of which influence the performance of the touching particles processor.
Despite these limitations, QEMSCAN is able to produce broadly similar overall trends in crystal
size distribution plots to the manual approach, in a considerably shorter time frame. If an accurate
crystal size distribution is required to calculate crystal residence time or nucleation density, we rec-
ommend that QEMSCAN should only be used after careful consideration of the suitability of the
sample texture and average crystal shape.

Key words: crystal size distribution; QEMSCAN; Apollo 15; mare basalt; quantitative petrology

INTRODUCTION from Hawaii, aim to address fundamental processes

Basaltic magmatism is a fundamental planetary-scale
process that occurs on terrestrial bodies throughout the
Solar System (e.g. Basaltic Volcanism Study Project,
1981; Cattermole, 1989; Wilson, 2009, 2014), and is re-
sponsible for the creation of ‘secondary’ crust (Taylor,
1989; Taylor & McLennan, 2009). The journey a basaltic
magma takes through the crust and during eruptive
processes has been extensively studied in terrestrial
magmatic systems (e.g. Watson & McKenzie, 1991;
Sisson & Layne, 1993; Walker, 1993; Hofmann, 1997).
Studies of terrestrial magmatic systems, such as those
such as magma differentiation, magma storage at
depth and timescales, and ascent rates and eruption
styles (Cashman & Marsh, 1988; Mangan, 1990; Vinet &
Higgins, 2010, 2011; Bradshaw et al., 2018). Whereas
unravelling complex magmatic histories is difficult in
terrestrial systems, understanding these processes on
other planetary bodies in the Solar System has add-
itional challenges. Extra-terrestrial rock samples are
often of limited size, with little to no field context as to
the origin of the sample. In some cases, owing to their
precious nature, analysis of extra-terrestrial samples is

C The Author(s) 2020. Published by Oxford University Press.

V
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits
unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. 1
2 Journal of Petrology, 2020, Vol. 61, No. 4

limited to non-destructive techniques. Therefore, non-
destructive petrological analyses of samples with lim-
ited sizes are incredibly important tools for the study of
magmatic processes on other planetary bodies.
Crystal size is considered a fundamental property in
igneous petrology, from which magmatic processes
such crystal fractionation, accumulation and magma
mixing can be inferred (Marsh, 1988). One of the most
commonly used theories of crystal size distribution
(CSD) analysis for geological applications was originally
developed by Randolph & Larson (1971) for use in the
Lentz & McSween, 2000, 2005; Day et al., 2006;
Sarbadhikari et al., 2009; Ennis & McSween, 2014) and
eucrite meteorites (Jaret et al., 2008) have also been
studied using CSD analysis.
Crystal size distribution analysis considers the popu-
lation density of a mineral phase within different crystal
size intervals, providing a measure of processes such
as fractionation, accumulation and magma mixing
(Fig. 1; Marsh, 1998). CSDs are conventionally plotted
as the natural logarithm of the population density
against corrected crystal length (Fig. 1). The population
density (mm–4) is the volumetric number density of

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chemical engineering industry. Since then, their theory
has been adapted and used as a non-destructive quanti-
tative method for determining the crystallization history
of a magma (Cashman & Marsh, 1988; Marsh, 1988,
1998). The technique has been used in many studies
investigating the magmatic histories of terrestrial mag-
matic systems (e.g. Cashman & Marsh, 1988; Higgins &
Chandrasekharam, 2007; Higgins & Roberge, 2007;
Jerram & Martin, 2008; Jerram et al., 2009; Neave et al.,
2013, 2014, 2017; Holness, 2014). It has also been
applied to lunar meteorites and Apollo samples to dis-
tinguish rocks that are the products of impact melts
from volcanic mare basalts (Fagan et al., 2013; Neal
et al., 2015), identify textural relationships between
samples in lava flows (Day & Taylor, 2007), and investi-
gate how magmatic processes may vary across differ-
ent regions of the Moon (Hui et al., 2011; Fagan et al.,
2013; Donohue & Neal, 2015; Donohue & Neal, 2018).
Other extra-terrestrial materials such as Martian (e.g.
crystals within a given crystal length bin width.
Corrected crystal length (mm) refers to measured crys-
tal lengths that have been converted from two-
dimensional (2D) to three-dimensional (3D) values.
Linear CSD trends (Fig. 1a) imply that the crystals
formed during steady-state crystallization (Marsh, 1988)
with a constant cooling rate (Higgins, 2000). The slope
of a CSD graph can be described as
CSD slope ¼ –1=ðGtÞ (1)
where G is the crystal growth rate (in mm s–1) and s is a
measure of the average crystal growth time (seconds),
more commonly referred to as the crystal residence
time. Such relationships are applicable to only straight
sections of a CSD graph and cannot be applied to
curved trend lines. The y-intercept of a CSD graph is
equal to the nucleation density of those crystals within
the system. Systems that underwent fractionation show

Fig. 1. Schematic CSD graphs showing the trends associated with different magmatic processes (after Neal et al., 2015): (a) linear
cooling; (b) accumulation and fractionation; (c) multistage cooling history; (d) magma mixing. The gradient of a CSD plot is equal to
the negative reciprocal of Gs, where G is the growth rate and s is the crystal residence time.
Journal of Petrology, 2020, Vol. 61, No. 4
curved concave-down trends owing to the removal of
larger crystal sizes (Marsh, 1988, 1998). On the other
hand, systems that experienced crystal accumulation
display curved concave-up trends that reflect entrain-
ment of larger crystals (Marsh, 1988, 1998). Concave-up
CSD plots coupled with a lack of small crystals can also
be indicative of textural coarsening, a common process
in plutonic rocks and some volcanic systems whereby
larger crystals grow at the expense of smaller crystals
(e.g. Higgins, 2011). Kinked CSD plots (Fig. 1c and d)
can indicate that the system experienced two (or more)
different cooling rates, with macrocrysts forming under
a slower cooling rate than the smaller groundmass
crystals (e.g. Higgins, 2006). Magma mixing can also re-
sult in kinked CSD trends owing to differences in the
cooling rates that formed the two crystal populations
(e.g. Marsh, 1988, 1998; Higgins, 1996a, 1996b, 2006).
Traditional CSD data collection methods require the
manual tracing of crystal boundaries from digital
images of thin sections or polished rock samples, to de-
termine crystal sizes and shapes. An important aspect
of this method is distinguishing between touching crys-
tals of the same mineral. This is simple to achieve using
a polarizing microscope or by any other methods that
depend on crystal anisotropy, such as electron back-
scatter diffraction. The separation of touching crystals is
required to produce a crystal map as opposed to a
phase map (Higgins, 2015). Data collected in this man-
ner represent 2D measurements of 3D crystals, and,
therefore, require conversion to true 3D values (e.g.
Higgins, 1994, 2000). Morgan & Jerram (2006) sug-
gested that a minimum of 250 crystals should be used
for CSD analysis, to produce a reliable estimate of true
3D crystal shape. Consequently, the manual tracing of
many thousands of crystals boundaries is often
required to produce a reliable overview of a particular
thin section. This time-consuming process may take
many days or weeks to complete, depending on the size
of the sample and the number of crystals it contains.
For instance, Neal et al. (2015) conducted a large study
of more than 70 lunar thin sections requiring the man-
ual tracing of over 50 000 crystal boundaries. This study
represented 6 years of work by multiple team members
to develop a non-destructive method of distinguishing
impact melts from mare basalts within the Apollo sam-
ple collection using CSD analysis (see also Oshrin &
Neal, 2009; Hui et al., 2011; Fagan & Neal, 2012;
Donohue, 2013; Fagan et al., 2013; Donohue & Neal,
2018).
Quantitative Evaluation of Minerals by SCANing
electron microscopy (QEMSCAN) is a system of auto-
mated quantitative petrology originally developed for
use in the mining industry. Since then, the technique
has successfully been applied in the oil and gas indus-
try (Sølling et al., 2014), forensic science (Pirrie et al.,
2004), archaeological science (Knappett et al., 2011),
and geological research (Neave et al., 2014, 2017).
The QEMSCAN system combines energy-dispersive
spectroscopy (EDS) and backscattered electron (BSE)
3
intensity from a scanning electron microscope to iden-
tify the minerals present in the sample based on com-
parison with a pre-defined mineral database [see
Gottlieb et al. (2000) or Pirrie & Rollinson (2011) for a
general overview]. The images produced are particular-
ly useful because, as well as providing mineralogical in-
formation, textural relationships can also be observed.
Neave et al. (2017) used QEMSCAN for CSD analysis as
part of a study on plagioclase crystals in a basaltic lava
from Iceland, and concluded that QEMSCAN-derived
CSDs were able to capture the main features of a manu-
ally derived CSD.
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Here, we present the first study to explore the use of
QEMSCAN for CSD analysis of extra-terrestrial sam-
ples. We compare manual (i.e. human) and semi-
automated QEMSCAN methods of CSD data collection
on plagioclase, pyroxene and olivine crystals in four
Apollo 15 mare basalt thin sections, to explore whether
semi-automated processes of data collection may be
able to provide a more time-efficient alternative without
loss of information or accuracy. We show that the reli-
ability of QEMSCAN as a method of automated CSD
analysis is dependent on sample texture and crystal
habit, but that QEMSCAN offers an effective non-
destructive, rapid classification method for both Apollo
and other extra-terrestrial samples.
SAMPLES: THE APOLLO 15 BASALTS
The thin section samples considered in this study are
Apollo 15 mare basalts. Apollo samples are rare and
precious; therefore, being able to collect data via non-
destructive analytical methods is critical if these sam-
ples are to be preserved for future generations (Allen
et al., 2011).
The Apollo 15 landing site is located on the eastern
edge of Mare Imbrium (2613222 N, 363386 E) on the
lunar nearside. Two suites of mare basalts, with similar
eruption ages of 335–325 Ga, were collected at this
locality. Based on differences in whole-rock major elem-
ent abundances (FeO, SiO2 and TiO2), the Apollo 15
mare basalts are subdivided into the quartz-normative
(QN) and olivine-normative (ON) suites (Chappell &
Green, 1973; Rhodes & Hubbard, 1973). The quartz-
normative samples have bulk SiO2 contents of 47–
49 wt%, 19–20 wt% FeO and 10–20 wt% TiO2 (Rhodes &
Hubbard, 1973). The slightly younger olivine-normative
samples have lower SiO2 concentrations of 44–46 wt%
and comparatively higher bulk FeO (22–23 wt%) and
TiO2 (2–3 wt%) (Rhodes & Hubbard, 1973).
The Apollo 15 mare basalts display a wide range of
textures including vitrophyric, porphyritic and highly
vesicular samples, with the quartz-normative samples
showing a larger textural variability than olivine-
normative samples. Within the two suites, samples are
further defined as being either parent, cumulate or frac-
tionate. Parent samples are thought to be representa-
tive of the initial magma composition from which the
respective Apollo 15 mare basalt suites differentiated.
4 Journal of Petrology, 2020, Vol. 61, No. 4

Fractionate samples have chemical compositions that

can be linked to parent magma compositions via the
process of fractional crystallization (i.e. the removal of
crystals from a melt). Cumulate samples are related to
parent magmas via accumulation of crystals, either by
flotation or via crystal settling.
The petrogenetic relationships and eruption histories
of the quartz-normative and olivine-normative suites
remains controversial (Chappell & Green, 1973; Rhodes
& Hubbard, 1973; Lofgren et al., 1975; Ma et al., 1976,
1978; Lindstrom & Haskin, 1978; Ryder & Steele, 1988;
Vetter & Shervais, 1989). Recent major and trace elem-

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ent studies (Schnare et al., 2008) suggest that the two
suites may be related through crystal fractionation. In
this scenario, the quartz-normative suite experienced a
multi-stage cooling history, whereas the olivine-
normative suite predominantly crystallized in shallow
crustal sills and/or in lava flows on the lunar surface
(Ryder & Steele, 1988; Ryder & Schuraytz, 2001;
Schnare et al., 2008). For the purposes of our study, the
important distinction between the two suites is that of a
simple versus a complex magmatic history. If the
olivine-normative samples experienced relatively sim-
ple magmatic histories, then they are expected to ex- Fig. 2. A flowchart outlining the steps involved in CSD analysis
hibit near-linear CSD trends. If the quartz-normative via the manual method (left) compared with QEMSCAN (right).
(See text for details.)
samples underwent a more complex magmatic history,
their CSDs are expected to exhibit signatures of mag-
via the FEI MAPS software, using a single frame and a
matic processes such as fractionation and accumula-
dwell time of 10 ls at an accelerating voltage of 15 kV.
tion. To thoroughly compare manual and automated
Each sample map is a montage of 1 mm tiles mapped at
CSD methods, a range of samples were selected to in-
resolution of 1024  884 pixels, resulting in a 098 lm
corporate as many potential CSD trends as possible.
per pixel scale. The BSE maps were saved as .tif files
Our wider goal is to use CSD analysis to quantify proc-
and at no stage in the process were the images com-
esses of magma storage and transport in the Apollo 15
pressed or rotated. Instrument error was negated as
magmatic plumbing system and to understand the
much as possible by producing all BSE maps using the
petrogenesis of the olivine-normative and quartz-
same instrument under the same operating conditions.
normative suites.
Four Apollo 15 mare basalt thin sections were con- Each map was visually inspected to ensure individual
sidered in this study: 15597,18 (QN, parent); 15125,6 frames were adequately stitched together. If inconsis-
(QN, parent); 15475,15 (QN, fractionate); 15555,209 (ON, tencies were found with the stitching of the BSE map,
parent). These samples were selected to reflect the then the samples were re-imaged. Full-resolution BSE
range of crystal shapes, sizes and textures within the maps of each sample were uploaded to a data reposi-
Apollo 15 mare basalt collection. tory and can be accessed via the link doi:10.17632/
rh37cdm9hv.1.

METHODS Crystal tracing

All samples were analysed using the data reduction
processes summarized in Fig. 2. Thin sections were pre-
pared at the NASA Johnson Space Center Apollo
Curatorial labs, then imaged optically using plane- and
cross-polarized light at the University of Manchester be-
fore being carbon coated.
Manual CSD calculation
Image acquisition
Backscattered electron (BSE) maps of each sample
were collected using a FEI QUANTA 650 field emission
gun (FEG) scanning electron microscope (SEM) at the
University of Manchester. The BSE maps were collected
Each BSE map was imported into CorelDraw X6, at full
resolution. Crystal outlines of the mineral(s) in question
(i.e. plagioclase, olivine and pyroxene) were manually
traced from the BSE maps (Fig. 3). Optical images of the
thin sections, taken under plane- and cross-polarized
light, were used to determine the boundaries between
touching crystals of the same mineral. The smallest re-
solvable crystals were those with an area of four pixels
(4 lm2); crystals below this size could not be reliably
identified. Crystals that intersected the perimeter of the
thin section were not included in the analysis as they do
not represent true 2D crystal lengths. For the same rea-
son, crystals that were bisected (i.e. cut) by large cracks
Journal of Petrology, 2020, Vol. 61, No. 4
Fig. 3. An example of the manual tracing of crystals in sample 15555,209. (a) A BSE map and (b) traces (and coloured fill) of pyrox-
ene and olivine crystals. Black areas in (a) are voids within the sample.
or fractures were also excluded. In samples where
CSDs of more than one mineral could be produced, dif-
ferent layers were used to trace each mineral phase
separately. Each layer was saved as a separate .tif file
keeping the same resolution as the original BSE map.
Image processing in ImageJ
Images of the traced crystal boundaries were imported
into ImageJ version 1.51 for analysis (Abràmoff et al.,
2004). The Analyse Particles function was used to calcu-
late the following parameters: crystal coordinates
(X and Y), area (mm2), roundness (0–10), major and
minor axis length (mm). Data were exported as
Microsoft Excel worksheets (.xls), as well as using the
CSD output plugin to save data as .csd files for use in
CSDcorrections v1.50 (Higgins, 2000). Image data qual-
ity was ensured throughout the data handling process
by repeating exactly the same steps for each of the
samples in question.
CSD calculation
To produce a CSD plot, the 2D data collected from the
images must be converted into true 3D values. The first
step in the conversion process is to evaluate the 3D
habit of the crystals within the sample. Estimates of 3D
crystal habit were calculated using the Microsoft Excel
macro CSDslice (Morgan & Jerram, 2006). In CSDslice,
measured 2D minor and major crystal axis length data
from ImageJ are compared with a database of 2D crys-
tal shapes. Using a linear regression, CSDslice provides
a list of the top five best-fit estimates of the ratios be-
tween the short (x), intermediate (y) and long (z) crystal
dimensions, based on the input 2D data. Each crystal
habit ratio is also given an R2 value, a statistical meas-
ure of how close the 2D data lie to the fitted regression
line. Morgan & Jerram (2006) considered R2 values of
5
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>08 to be reliable representations of true 3D crystal
habits.
The 3D crystal shape parameters are important
when stereologically converting 2D crystal lengths into
3D lengths using the program CSDcorrections v1.50
(Higgins, 2000). Crystal habit estimates from CSDslice,
along with total measured area (mm2), roundness
(0–10) and measured major and minor crystal lengths
(mm) were input into CSDcorrections to calculate CSDs
using corrected 3D crystal sizes. Resulting CSD plots
show the natural logarithm of the population density
(mm–4) against corrected crystal length (mm).
Crystal lengths were sorted into size bins with five
bins per decade, which is the optimal number when
using CSDcorrections to avoid errors associated with
too few crystals in each bin (Higgins, 2000). The error
associated with population density is a combination of
three principal sources (Higgins, 2000). The first is a
statistical counting error, which is equal to the square
root of the number of crystals within a particular size
interval. The second is a systematic error that arises as
a result of the stereological conversion of 2D short and
intermediate axes to true 3D crystal lengths. Owing to
the often irregular shapes of natural crystals, the third
source of error is associated with shape probability
parameters that are calculated for idealized crystal
shapes. The overall influence of each error on the popu-
lation density is dependent on the magnitude of the size
interval and/or the number of crystals within it. For in-
stance, the counting error is more significant in large
size bins that contain a small number of crystals.
Uncertainties exist as to how to accurately quantify the
errors associated with the shape probability parameters
and the conversion to 3D crystal lengths (Higgins,
2000). Therefore, error bars calculated using CSD cor-
rections are considered to be minima, as they are calcu-
lated using the counting error only.
6 Journal of Petrology, 2020, Vol. 61, No. 4
From start to finish, the manual derivation of a crys-
tal size distribution took on average 30–70 h per thin
section, depending on the number of crystals within
the thin section (Supplementary Data Table S1;
supplementary data are available for downloading at
http://www.petrology.oxfordjournals.org). The process
is, thus, very labour-intensive.
QEMSCAN CSD calculation
Image acquisition
The FEI QEMSCAN at the University of Manchester
operates using the QUANTA 650 FEG SEM, equipped
with a single Bruker XFlash energy-dispersive X-ray
spectrometer (EDS), at an accelerating voltage of 25 kV
and a 10 nA beam current. This set-up was used to col-
lect data in field scan mode, which produces full images
of each field of the sample block to produce both quali-
tative major element chemical maps and a mineral map
of the full thin section. The QEMSCAN uses a combin-
ation of EDS and BSE brightness to identify the miner-
als present within the sample (Gottlieb et al., 2000;
Pirrie & Rollinson, 2011). Using BSE brightness, areas
of the sample that contain minerals as opposed to the
mounting material (i.e. epoxy) are initially identified.
Areas that contain only the mounting material are con-
sequently excluded from further analysis to reduce
scan times. To ensure minerals are correctly identified,
BSE brightness is calibrated using homogeneous
quartz, copper and gold standards. During sample ana-
lysis EDS spectra were acquired using 1000 counts per
pixel, measured at a point in the centre of the pixel. The
distance between each measurement is known as step
size, and is equivalent to the pixel size of the resulting
mineral phase map.
To assign a mineral based on the measured spec-
trum, the data are compared with the Species
Identification Protocol (SIP), a list of pre-defined mineral
definitions. SIP files include ‘optional’ and ‘must have’
elemental ranges, BSE brightness and X-ray count rate
thresholds. Element peaks from the EDS spectra at each
point are matched by comparing the relative heights of
the measured peaks against the standard peak heights
stored within the mineral SIP file. Element proportions
are reported in the software as a percentage out of a
total of 125 % to account for low counting statistics.
Each pixel is assigned to a mineral on a first match
basis when the all of the conditions outlined in a SIP file
have been met by the data. Customization of the SIP list
allows users to adjust the mineral database to be more
suitable for the samples being analysed. In this study
we created a SIP list tailored towards lunar samples,
referred to hereafter as the lunar SIP list. It excludes
many of the mineral SIP files stored in the master data-
base provided by FEI, such as hydrous minerals or
metalliferous ore minerals. This allows for a more effi-
cient mineral assignment process and accurate mineral
identification, based only on minerals commonly found
in lunar and extra-terrestrial samples.
Although every effort has been made to include as
many relevant minerals within the lunar SIP list as pos-
sible, this list is by no means exhaustive. Even major
phase minerals such as plagioclase, pyroxene and oliv-
ine have wide ranges of potential compositions, all of
which may not be present within the SIP list. Therefore,
the ability of QEMSCAN to correctly assign each pixel
to a mineral phase is dependent on the range of miner-
als included in the SIP list. As measurements are taken
from the centre of each pixel, it is also possible to hit
grain boundaries, which produce a mixed signal. Often
these pixels are designated as unclassified unless there
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is a SIP file corresponding to a mixture of the two min-
erals (e.g. 50:50 quartz:plagioclase). Problems with min-
eral identification can also arise if a sample has
undergone any form of alteration. This is not an issue in
this study as Apollo 15 mare basalts are pristine; how-
ever, alteration may be an important factor for other ter-
restrial and extra-terrestrial samples.
Mineral phase maps of each sample were acquired
using step sizes (i.e. pixel sizes) of 5, 10 and 20 lm to
understand the effect of resolution on the final CSD ana-
lysis. Full-resolution QEMSCAN phase maps of each
sample were uploaded to a data repository and can be
accessed via the link doi:10.17632/rh37cdm9hv.1. All
maps were classified in the iExplorer QEMSCAN soft-
ware using the full lunar SIP list, and then using a sim-
plified secondary SIP list. The secondary SIP list is
customized to group minerals together; for example,
augite and pigeonite are grouped as ‘pyroxene’. Owing
to the chemically zoned nature of crystals in the major-
ity of our samples, the implementation of a secondary
SIP list makes data processing faster for CSD analysis.
Mineral map analysis
After applying the secondary SIP list, all mineral phase
maps were analysed in the same way using functions
known as processors found in the QEMSCAN iExplorer
software. The granulator processor was used to extract
crystals of a specified mineral from a mineral map
(Fig. 4), dismissing particles of any other mineral spe-
cies. The granulator displays only occurrences of the
mineral specified by the user. The granulator will not,
however, separate two crystals of the same mineral that
are touching. To separate touching crystals, the touch-
ing particles processor is required. The algorithms used
in the touching particles processor look for abrupt
changes in the direction of the particle boundary,
known as cusps. An A* path algorithm is then used to
determine the path between two cusps with the lowest
cost, taking into account distance, mineral chemistry
and filters based on features such as particle roughness
and particle feature size (M. Owen, personal communi-
cation). A 3  3 erosion is then used to separate the par-
ticle composed of touching crystals into individual
crystals (M. Owen, personal communication).
When combined, the two processors allow individual
crystals of a particular mineral to be separated and
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Fig. 4. Example of the data processing using iExplorer: (a) field scan of sample 15125,6 at 5 lm step size, classified using the lunar
SIP list; (b) the same field scan reclassified using a simplified secondary SIP list; (c) data processing using the granulator tool; (d)
additional data processing using the touching particles tool; (e) an example of how touching particles are separated using the
touching particles processor.

displayed (Fig. 4). The images of the separated crystals
were then exported at full spatial resolution (i.e. 5, 10
and 20 lm per pixel) as .tif files, which can then be dir-
ectly imported into ImageJ for processing (Fig. 2). For
reasons outlined in the discussion section, crystals less
than four pixels in area were removed from the
QEMSCAN datasets following ImageJ analysis, with the
exception of 15125,6 from which crystals with areas
less than 5 pixels were removed. The 2D QEMSCAN
data were then processed using CSDslice and
CSDcorrections following the same method as
described for the manually collected data (Fig. 2).
Processed data (i.e. with crystals <4 pixels in area
removed) collected at 5, 10 and 20 lm step sizes are
hereafter denoted as Q5, Q10 and Q20.
From start to finish, derivation of a crystal size
distribution using QEMSCAN, including processing
time in iExplorer, took on average 35–22 hrs, depending
on the size of the sample and the step size used
(Supplementary Data Table S1).
RESULTS
Backscattered electron images and QEMSCAN mineral
maps (secondary SIP list at 5 lm step size) of each thin
section are shown in Fig. 5 (doi:10.17632/rh37cdm9hv.1).
Sample 15597,18 (Fig. 5a and e) is vitrophyric, domi-
nated by acicular pyroxene crystals in a glassy matrix.
Pyroxene crystals in 15597,18 are up to 1 mm in length.
Whereas 15125,6 has a similar vitrophyric texture to
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Fig. 5. Backscattered electron maps (a–d) and QEMSCAN mineral maps (e–h) of samples: (a, e) 15597,18; (b, f) 15125,6; (c, g)
15475,15; (d, h) 15555,209. The scale is the same in all images. Black areas in (a)–(d) are voids within the sample. The QEMSCAN
mineral maps shown here are all field scans taken using a 5 lm step size and the simplified secondary SIP list. The legend shows
the main minerals present in these samples. QEMSCAN mineral maps using the full lunar SIP list at 5, 10 and 20 lm step sizes are
provided in Supplementary Data Fig S1–S4.

15597,18, it contains skeletal olivine crystals (3 %) plagioclase crystals (Fig. 5c and g). Minor amounts of
along with pyroxene phenocrysts (005–3 mm), set in a chromite can be found in both 15125,6 and 15597,18.
microcrystalline matrix of needle-like pyroxene and Sample 157475,15 has a porphyritic texture with
Journal of Petrology, 2020, Vol. 61, No. 4 9

Table 1: Crystal size distribution data for the Apollo 15 mare basalts

Sample Mineral Area (mm2) Method No. of crystals Crystal R2 CSD intercept Residence
shape (x:y:z) time (days)

15597,18 pyroxene 6168 Manual 6869 1:125:55 0810 906 53–343

Q5 5925 1:13:19 0854 1285 10–83
Q10 4228 1:125:19 0909 1008 41–296
Q20 3058 1:15:20 0887 880 42–83
15125,6 pyroxene 5912 Manual 1630 1:14:50 0863 743 64–397
Q5 19 332 1:15:28 0722 1487 10–304
Q10 4445 1:15:28 0846 1225 19–331
Q20 558 1:14:24 0883 898 41–136
15555,209 pyroxene 23528 Manual 1130 1:14:28 0784 542 65–336
Q5 5758 1:14:25 0833 1127 13–248

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Q10 3201 1:15:20 0884 808 47–373
Q20 2027 1:15:21 0872 767 58–546
15555,209 olivine 23528 Manual 1716 1:125:19 0888 671 37–131
Q5 17 827 1:14:22 0864 1298 6–66
Q10 6699 1:15:21 0869 1131 10–90
Q20 2735 1:15:20 0864 878 21–90
15475,15 plagioclase 8692 Manual 953 1:18:80 0808 705 62–2734
Q5 2587 1:16:36 0800 1020 33–368
Q10 1671 1:15:30 0888 848 66–324
Q20 1074 1:15:30 0864 703 112–342

subhedral pyroxene phenocrysts up to 45 mm in length
(Fig. 5c and g) in a matrix of sub-ophitic plagioclase and
smaller anhedral pyroxene. It also contains minor
amounts of ilmenite, chromite and silica. Sample
15555,209 is porphyritic with phenocrysts of pyroxene
up to 3 mm in length and olivine up to 15 mm in length,
set in a plagioclase matrix (Fig. 5d and h). It contains
minor chromite, ilmenite and silica. The crystal size of
15555,209 is the coarsest of the samples included in this
study.
Mineral maps using the full lunar SIP list for each
sample at 5, 10 and 20 lm step sizes can be found as
Supplementary Data Figs S1–S5. Examples of images
produced by the iExplorer software, after using the
granulator and touching particles processors, are
shown in Supplementary Data Fig. S5.
Crystal size distribution analysis data are presented
for each of the four samples in Table 1. The number of
crystals traced during manual data collection varies sig-
nificantly from the number of crystals identified by
QEMSCAN at each of the three step sizes. For 15597,18,
more crystals were identified by manual tracing than by
QEMSCAN, with about twice as many crystals in the
manually traced data compared with Q20. Conversely,
QEMSCAN identified more crystals of both pyroxene
and olivine in 15555,209 than the manual data, by up to a
factor of 10. Plagioclase in 15475,15 shows similar trends
in the number of crystals, with Q5 identifying double the
number of crystals compared with the manual datasets,
and the number of crystals identified at Q20 being clos-
est to the manual values. The largest variation in the
number of crystals identified is between the manual and
Q5 data for pyroxene in 15125,6. In every dataset the
number of crystals exceeds the recommended minimum
value of 250 crystals needed for both robust CSD ana-
lysis and crystal shape analysis from a 2D section (Mock
& Jerram, 2005; Morgan & Jerram, 2006).
Crystal habit estimates calculated using CSDslice
(Morgan & Jerram, 2006) differ between the manual
and QEMSCAN data. In the case of 15597,18, 15125,6
and 15475,15, the long axis (z) estimates are larger for
the manual data compared with Q5, Q10 and Q20
(Table 1). For example, the manual data for 15475,15 re-
turn a long axis ratio estimate of 80, compared with
30–36 for the QEMSCAN data. Less variation is seen in
the intermediate (y) value estimates calculated for the
manual and QEMSCAN data. In all but two cases
(15125,6 Q5 and 15555,209 manual pyroxene), the R2
values for crystal habit estimates are >08 and would be
considered to be reliable estimates of 3D crystal habits
according to Morgan & Jerram (2006).
The CSD plots produced via manual and QEMSCAN
data collection methods are shown in Fig. 6, where Q5,
Q10, and Q20 refer to QEMSCAN data collected at step
sizes of 5, 10 and 20 lm respectively. Pyroxene crystals
were measured in samples 15597,18 and 15125,6.
Although olivine is also present in 15125,6, there are
not enough crystals (n < 250) to produce a reliable CSD.
In 15475,15 only plagioclase crystals were measured,
and in 15555, 209 both olivine and pyroxene crystals
were measured. The manual data for 15597,18, 15125,6
and 15475,15 all show concave-up CSD trends. Olivine
and pyroxene crystals in 15555,209 show more pro-
nounced concave-up trends than the other samples,
with the change in gradient from steeper to shallower
occurring at a crystal length of 1 mm for pyroxene and
075 mm for olivine. In all samples apart from
15555,209, the manual CSD data trends extend to larger
crystal lengths than the QEMSCAN data. This is most
pronounced in 15475,15, where maximum crystal
lengths are <3 mm for Q5, Q10, and Q20, but the max-
imum corrected crystal length for the manual data is
9 mm (Fig. 6). Crystals up to 12 mm in length are
observed in the 15125,6 manual data; however, this size
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Fig. 6. Crystal size distributions for (a) pyroxene in 15597,18, (b) pyroxene in 15125,6, (c) plagioclase in 15475,15, (d) pyroxene in
15555,209 and (e) olivine in 15555,209. For each sample the plots show CSDs for data collected manually (Manual, black circles)
and using QEMSCAN at step sizes of 5 lm (Q5, blue diamonds), 10 lm (Q10, green triangles) and 20 lm (Q20, red squares). Crystals
<4 pixels in size were removed from the Q5, Q10 and Q20 datasets prior to processing. Error bars represent a minimum error as
calculated by CSDcorrections (see text for details) and in most cases the symbol is larger than the error bar. The x- and y-axes vary
in size frame to frame. Size bins containing fewer than three crystals were not used to derive the CSD trends but are plotted here as
grey symbols.

bin is not considered during further processing as it
contains fewer than three crystals.
At 5, 10 and 20 lm step sizes, QEMSCAN-derived
CSDs generally plot within error of each other (Fig. 6),
but collectively they deviate from the trend of the man-
ual data in all samples except 15555,209. For the small-
est crystal size bins, the manual data plot closer to and
sometimes within error of the Q5, Q10 and Q20 data;
however, the QEMSCAN data deviate from the trend of
the manual data as crystal length increases, plotting at
lower population densities and maintaining a steeper
gradient. Sample 15555,209 is the only sample for
which the manual trends plot within error to the
QEMSCAN-derived trends, particularly Q5 for olivine
and Q10 for pyroxene.
The y-intercept of a CSD plot corresponds to the nu-
cleation density (mm–4) of the mineral of interest within
the magmatic system. The values for CSD y-intercept in
Table 1 are generally lower for the manual data com-
pared with the QEMSCAN data.
Residence times were calculated for each CSD plot
(Marsh, 1988) using growth rates for plagioclase
(1309  10–8 mm s–1), pyroxene (1797  10–8 mm s–1)
and olivine (3162  10–9 mm s–1) based on values that
have previously been used in CSD analysis of mare
basalts (Neal et al., 2015). These crystal growth rates
have been calculated using terrestrial basalts collected
from the Kilauea eruptions in Hawaii. Plagioclase and
pyroxene growth rates are an average of the experimen-
tally derived values of Burkhard (2005), conducted under
atmospheric conditions (see Electronic Appendix 1). The
olivine growth rate from Borell & Kilinc (2012) was
solved using CSD theory on basalts with known growth
rates and residence times for plagioclase, which crystal-
lized from the same melt as the olivine. We acknowledge
that growth rates based on terrestrial samples are not
able to completely replicate lunar conditions. However,
as crystal residence times can be used to interpret mag-
matic processes, the use of growth rates in this study is
merely to highlight any differences in calculated crystal
residence times calculated using manual versus
QEMSCAN-derived data.
Table 1 shows the range of calculated residence
times (in days) for each CSD plot. As residence times
can only be calculated using straight segments of a
CSD plot, gradients were measured across the shallow-
est and steepest portions of the CSD to give an estimate
of maximum and minimum residence times. Pyroxene
residence times (measured in 15597,18, 15125,6 and
15555,209) calculated using the manual data generally
return higher minimum and maximum residence time
estimates than the corresponding QEMSCAN data.
Journal of Petrology, 2020, Vol. 61, No. 4
Lower residence time estimates for pyroxene range
from 10 days (15597,18 Q5 and 15125,6 Q5) to 65 days
(15555,209 manual). Upper residence time estimates for
pyroxene vary from 83 days (15597,18 Q5 and Q20) to
546 days (15555,209 Q20). For plagioclase in 15475,15,
the upper residence time estimate using the manual
data is at least seven times greater than the largest
QEMSCAN-derived residence time. The lower residence
time estimate using the manual data falls within the
range of the lower estimates from QEMSCAN data. The
residence times of olivine in 15555,209 using the man-
ual data are in broad agreement with those calculated
from the QEMSCAN data. Lower estimates of olivine
residence times are all in the range of <40 days. The
upper estimates of olivine residence times for the man-
ual, Q5, Q10 and Q20 data are of the order of 66–
131 days.
DISCUSSION
The purpose of this study is to evaluate the use of
QEMSCAN for automated CSD data collection, with a
particular focus on precious samples for which there
are few, small thin sections available. The manual data
collection method for CSD analysis is a time-consuming
process requiring the tracing of hundreds of crystal
boundaries, whereas QEMSCAN offers the potential to
dramatically reduce the user input and hours required
to perform the analysis. In a broader sense, QEMSCAN
is a non-destructive method of analysis for the rare and
precious extra-terrestrial samples of limited mass.
Below we discuss some of the challenges inherent in
CSD data collection using QEMSCAN, and the potential
limitations these factors may have on the reliability of
this method.
Establishing a minimum crystal size
A proportion of crystals gathered and separated using
QEMSCAN are represented by a single pixel; that is, a
square crystal with dimensions equal to the step size.
Owing to the excitation volume of the QEMSCAN meas-
urement relative to the crystal size, they are not repre-
sentative of the true size or shape of the detected
crystal phase. As such, single pixel crystals could be
considered equivalent to noise within the image.
To determine at what size (total area in pixels) crys-
tals cease to be regarded as noise and start to represent
a true crystal population, raw data for each sample at 5,
10 and 20 lm step sizes were processed through
CSDslice while sequentially increasing the threshold for
the minimum crystal size (Electronic Appendix 2). For
all but one of the samples in this study we obtained
consistently reliable 3D crystal shapes (with R2 values
>08) when crystals smaller than four pixels in area
were excluded from the CSDslice calculation
(Supplementary Data Fig. S6). Therefore, we impose an
optimal minimum crystal area threshold of four pixels
for samples 15597,18, 15475,15 and 15555,209 at all
11
three step sizes. The exception to this was sample
15125,6, which has a fine-grained groundmass with a
feathery texture. In this case, we increased the min-
imum crystal area threshold to five pixels to obtain a
more reliable 3D crystal shape estimate.
We stress that the minimum crystal size in a
QEMSCAN CSD analysis should not simply be equal to
the step size at which the sample was scanned. We rec-
ommend, at minimum, that crystals smaller than four
pixels in area should be excluded from CSD analyses of
QEMSCAN datasets. An assessment should be made
on a sample-by-sample basis as to whether this min-
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imum should be increased based on the texture of the
sample.
Edge crystals
When gathering the manual CSD data, any crystals that
intersect the edge of the sample, hereafter referred to
as edge crystals, were not traced. This is because they
do not represent the true 2D length of a crystal, as they
have been randomly cut at the boundary of the thin sec-
tion. Whereas it is easy to distinguish and exclude these
from the manual data, it is not currently possible to
automatically exclude edge crystals from QEMSCAN
data using processors in iExplorer software. To explore
whether the inclusion of edge crystals in the QEMSCAN
data contributes to the disparities between the
QEMSCAN and manual CSD trends, edge crystals were
manually removed from 15597,18 Q5 in iExplorer and
the dataset was reprocessed through CSDslice and
CSDcorrections (referred to as Q5-E). Sample 15597,18
was selected for this comparison as the QEMSCAN data
showed the most variability from the manual results
(Fig. 6a). For a thorough comparison, edge crystals
from this sample that were originally excluded during
manual tracing were subsequently traced and added to
the manual dataset (referred to as ManualþE), which
was then compared with the Q5 data.
The trend of the 15597,18 Q5 CSD plot shows min-
imal changes when edge crystals are removed (Fig. 7),
hereafter referred to as Q5-E. The Q5-E trend generally
falls within error of the Q5 trend and is marginally
closer to replicating the manual data. This suggests that
including edge crystals in the QEMSCAN data does not
make a substantial contribution to the offset between
Q5 and the manual data. This finding is in agreement
with Higgins (2006), who stated that edge effects can be
ignored in samples with a large number of crystals. In
addition, the minor difference between the trends of the
Q5 data and Q5-E data highlights that if QEMSCAN
could perfectly reproduce a manual CSD, the inclusion
of edge crystals should make very little difference to the
overall CSD trend.
CSDslice 3D crystal habit estimate
Obtaining a true 3D estimate of crystal habit from
CSDslice (Morgan & Jerram, 2006) is crucial, as this is
the basis from which stereological conversions are
12
Fig. 7. Crystal size distributions replotted to show the effect of
including or excluding edge crystals from both the manual and
processed Q5 data for pyroxene crystals in 15597,18. The plot
shows CSDs for data collected manually (Manual, black circles)
and using QEMSCAN at step size of 5 lm (Q5, black diamonds).
Crystals <5 pixels in size were removed from the Q5 dataset
prior to processing. The suffix ‘þE’ is used to denote that these
CSD plots were processed including edge crystals with the
manual data (ManualþE, purple circle). The suffix ‘-E’ is used
to denote that these CSD plots were processed excluding edge
crystals from the Q5 data (Q5-E, purple diamonds). It should be
noted that error bars represent a minimum error as calculated
by CSDcorrections (see text for details) and in most cases the
symbol is larger than the error bar.
made in CSDcorrections (Higgins, 2000). Manually col-
lected data often produce a larger estimate for the long
axis of crystal length than the QEMSCAN data (Table 1).
To explore the effect of crystal habit estimate on the
manual and QEMSCAN CSD trends (Fig. 6), all four
datasets for each sample (manual, Q5, Q10 and Q20)
were reprocessed using the same crystal habit esti-
mates (Fig. 8). By removing the variability in CSDslice
crystal habit estimates, we can more effectively com-
pare the raw QEMSCAN data with the manually col-
lected data.
We reprocessed each CSD using a calculated
weighted average of the CSDslice crystal habit esti-
mates for Q5, Q10, Q20 and manual data. Each crystal
shape estimate was weighted based on its correspond-
ing R2 value (Electronic Appendix 1); however, this
made very little difference as the R2 values in most
cases were similar and above 08. When CSDs are cal-
culated using a single crystal habit estimate, all of our
samples show manual and QEMSCAN CSDs within
error of each other. This suggests that the raw data col-
lected using QEMSCAN are broadly comparable with
the manual data. If the QEMSCAN data were vastly dif-
ferent from the manual data, this would be reflected in
the CSD plots even if calculated using the same crystal
habit estimate. Therefore, the differences between the
manual and QEMSCAN CSD plots in Fig. 6 must be
Journal of Petrology, 2020, Vol. 61, No. 4
derived from subtleties within the data which result in
CSDslice estimating different crystal habits. One possi-
bility is that the crystal shapes collected using
QEMSCAN are more rectangular and blocky because
they are collected at lower resolution than the manual
data. The more tabulate nature of these crystal shapes
would in turn make it easier for CSDslice to produce a
crystal habit estimate as opposed to the more acicular
shapes in the manual dataset.
To negate issues surrounding 3D crystal habit esti-
mates, some studies employ a method of CSD analysis
without using stereological conversions (e.g. Neave
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et al., 2014, 2017). Plots of our data using this non-
stereologically corrected CSD method are not
considered here, but can be found in Supplementary
Data Fig. S7.
Separation of crystals using QEMSCAN
processors
The granulator processor was used in the QEMSCAN
iExplorer software to separate each particular mineral
(i.e. plagioclase, pyroxene or olivine) from the rest of
the mineral map (Fig. 4c). The touching particles pro-
cessor was then used to separate crystals in contact
with each other, to produce an image of all the individ-
ual crystals of a particular mineral within the sample.
The ability of the touching particles processor to cor-
rectly identify and separate individual crystals is critical
if reasonable crystal habits are to be calculated in
CSDslice.
The lengths, areas and aspect ratios of the crystals in
the manual and QEMSCAN datasets show differences
suggestive of larger elongate crystals in the QEMSCAN
being segmented and split into multiple smaller crystals
by the touching particles processor. Figure 9 shows
variations in crystal length, area and aspect ratio for
pyroxene in 15125,6. The same graphs for the
remaining samples are shown in Supplementary Data
Figs S8–S11.
The percentage of pyroxene crystals in the manual
data with relatively long lengths (>03 mm) and large
areas (>005 mm) is consistently higher than in the Q5,
Q10 and Q20 data for 15597,12 (Fig. 9). Differences be-
tween the manual and QEMSCAN data are also shown
when plotting average aspect ratio against the square
root of the crystal area (Fig. 9). For both length and
area, the variation in total crystal percentage between
manual and QEMSCAN is small, at 1–3 %. However,
these results show a consistent discrepancy between
the raw manual and QEMSCAN datasets, which is not
influenced in any way by processing in CSDslice. In the
case of 15125,6, there are larger crystals with relatively
high average aspect ratios in the manual data, which
are missing from the QEMSCAN data (Fig. 9). For crys-
tals within a single size bin, the QEMSCAN data often
show lower average aspect ratios than the manual data,
and there is a systematic decrease in average aspect
ratio between the Q5, Q10 and Q20 datasets. This
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Fig. 8. Crystal size distributions replotted using the same crystal habit estimates for (a) pyroxene in 15597,18, (b) pyroxene in
15125,6, (c) plagioclase in 15475,15, (d) pyroxene in 15555,209 and (e) olivine in 15555,209. For each sample the plots show CSDs
for data collected manually (Manual_R, black circles) and using QEMSCAN at step sizes of 5 lm (Q5R, blue diamonds), 10 lm
(Q10R, green triangles) and 20 lm (Q20R, red squares). Crystals <4 pixels in size were removed from the Q5, Q10 and Q20 datasets
prior to processing. The suffix ‘R’ is used to denote that these CSD plots were processed using the same short, intermediate and
long axis ratios, the values for which are indicated on each graph. Error bars represent a minimum error as calculated by
CSDcorrections (see text for details) and in most cases the symbol is larger than the error bar. The x- and y-axes vary in size frame
to frame. Size bins containing fewer than three crystals were not used to derive the CSD trends but are plotted here as grey
symbols.

suggests that the QEMSCAN datasets have more crys-
tals with smaller average aspect ratios, which could be
explained by segmentation of elongate (high aspect
ratio) crystals into smaller particles (low aspect ratio).
Evidence of the QEMSCAN segmentation issue is
shown in Fig. 10, where an example of a cluster contain-
ing a 09 mm long elongate crystal with an aspect ratio
of 96 is shown before and after processing with the
touching particles processor. The touching particles
processor separates this crystal into five crystals rang-
ing in size from 01 to 04 mm with an average aspect
ratio of 26.
The segmentation of touching elongate crystals is
able to explain why the 3D crystal habit estimates from
CSDslice have lower long axis values for the QEMSCAN
data than the manual data. If the touching particles pro-
cessor has incorrectly segmented elongate crystals in
the QEMSCAN mineral maps, this will reduce the num-
ber of elongate crystals within the dataset, resulting in
the 3D crystal habit ratios from CSDslice having smaller
estimates for the long axis value than the manual data.
Owing to the larger long axis estimates for the manual
data, their resulting CSD plots extend to larger cor-
rected crystals lengths. Conversely, because the
QEMSCAN data contain more small, low aspect ratio
crystals (owing to the segmentation of elongate crys-
tals) the long axis estimates from CSDslice are typically
smaller (Table 1), resulting in CSD trends with steeper
gradients that extend to shorter crystal lengths than the
manual data (Fig. 6).
Generally, the population of long elongate crystals in
any given sample is relatively small, often less than 1 %
of the total number of crystals (Fig. 9b). The effect of
segmentation of large elongate crystals is therefore
most apparent in the largest crystal size bins of a CSD
plot. In some circumstances, the incorrect segmentation
of elongate crystals can result in the complete removal
of a large size bin, as the standard practice with CSD
plots is not to consider size bins containing fewer than
three crystals (Higgins, 2000). The addition of several
segmented crystals to smaller size bins does not have a
pronounced effect, because these size bins already con-
tain large numbers of crystals. For example, if a large
size bin contains three 6 mm long crystals and two of
those crystals were segmented into 3  2 mm long crys-
tals, that large size bin would only have one crystal
remaining and consequently would not be included in
the CSD plot. The six new 2 mm long crystals are
14
Fig. 9. Histograms of pyroxene crystals in 15125,6 showing the
percentage of the total crystal population as a function of (a)
crystal area and (b) crystal length. Manual data (black) are com-
pared with Q5 (blue), Q10 (green) and Q20 (red) data. In each
case, the full extent of the graph is shown as an inset with a
box denoting the region that the scaled graph represents.
Aspect ratios of pyroxene crystals are shown in (c) for 15125,6
manual data (M, black circles) and QEMSCAN at step sizes of
Journal of Petrology, 2020, Vol. 61, No. 4
instead counted in a smaller crystal size bin, and the
addition of six crystals to a bin that already contains
some tens or possibly hundreds of crystals is relatively
small. The incorrect segmentation of elongate crystals
is the most probable explanation for higher total crys-
tals within some QEMSCAN datasets compared with
manual data (Table 1).
Inefficient segmentation of particles by QEMSCAN
was also noted by Neave et al. (2017), particularly in a
sample with an abundance of plagioclase agglomera-
tions; however, this study used manual segmentation
of crystals instead of the touching particles processor.
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Manual segmentation of touching crystals from
QEMSCAN mineral maps derived using the granulator
processor would remove the problems of incorrect seg-
mentation, but would increase the time required for
CSD analysis. We did not explore manual separation of
touching crystals from QEMSCAN maps in this study,
because our purpose was to explore the limitations of
the QEMSCAN software by allowing the CSD data col-
lection to be as automated as possible. However, given
the current limitations of the QEMSCAN processors,
manual segmentation of granulated QEMSCAN mineral
maps could improve accuracy whilst also providing a
faster method of CSD data collection than manual crys-
tal tracing.
How reliable are the QEMSCAN data?
Despite the inconsistences between the QEMSCAN and
manual CSD plots (e.g. Fig. 6), they both display broadly
similar CSD shapes. This suggests that QEMSCAN-
derived CSDs are still useful for correctly identifying the
signatures of crystallization processes in each of our
five samples. For example, the manual CSD for
15597,18 (Fig. 6b) shows a slight concave-up trend,
which is also apparent in the Q5, Q10 and Q20 CSDs.
Neave et al. (2017) likewise concluded that QEMSCAN
data are able to pick out the same primary features as
manually derived data, in their case identifying plagio-
clase microcryst and macrocryst populations in an
Icelandic basalt. However, they also noted that the crys-
tal number density (equivalent to nucleation density)
was higher for the QEMSCAN data compared with man-
ual data. This is also true in our study, with Q5 results
consistently returning higher nucleation densities than
the manual data, although nucleation density values for
Q10 and Q20 are much more similar to the manual val-
ues (Table 1).
Although QEMSCAN-derived CSD trends may show
similar shapes to manually derived CSDs, if the
iExplorer touching particles processor is wrongly seg-
menting elongate crystals into smaller crystals then this
5 lm (Q5, blue diamonds), 10 lm (Q10, green triangles) and
20 lm (Q20, red squares). In (c) the error bars shown are calcu-
lated as the standard deviation from the average crystal aspect
within each of the 01 mm size bins.
Journal of Petrology, 2020, Vol. 61, No. 4
Fig. 10. An example of a group of pyroxene crystals in 15597,18 (Q5) before (a) and after (b) processing with the touching particles
processor. Lines are used for reference to match the same points on the large central crystal in (a) and (b). It should be noted that
both (a) and (b) show an identical crystal area, but (b) appears to be elongated because the separation between segmented par-
ticles is exaggerated to highlight the effect of the touching particles processor. For reference, (c) shows a manual segmentation of
the same group of crystals.
raises questions as to what effect this may have on
interpretations of the CSD trends at the largest crystal
sizes. The large crystal size bins are often where charac-
teristic signatures of accumulation or fractionation may
be observed (Fig. 1), so if larger or elongate crystals are
effectively removed through segmentation into several
smaller crystals, this may result in signatures of import-
ant magmatic processes being masked or lost. For ex-
ample, the concave-up shape and pronounced kink in
the manual CSD trend for 15475,15 is completely miss-
ing in the QEMSCAN data. This is partly a function of
the differences in the CSDslice crystal shape estimate
between the manual (1:18:80) and QEMSCAN
(Q5 ¼ 1:15:30) datasets. However, the ultimate cause of
the differences in CSDslice crystal shape estimates is
related to the segmentation of large elongate crystals
by the QEMSCAN iExplorer processors.
One quantitative measure of the similarities between
CSD trends is to compare the residence times calcu-
lated using the gradient of the graph. Plotting character-
istic length (LC ¼ –1/slope) is an alternative way to
graphically consider the curvature of the CSD trends
(Higgins, 2009) (Supplementary Data Fig. S12).
However, because CSD analysis of other Apollo sam-
ples included calculations of crystal residence times
(e.g. Neal et al., 2015), the reliability of our QEMSCAN
data will be considered utilizing this method as
opposed to considering characteristic length.
Residence times can only be calculated using linear
portions of a CSD trend. The CSDs for our samples are
all curved to some extent; therefore, a residence time
range was produced for each dataset using minimum
and maximum linear regressions through the data. The
QEMSCAN data nearly always return a smaller and
shorter range for the residence time compared with the
manual data (Table 1). This could be caused by the seg-
mentation of larger crystal sizes from these samples, as
the larger crystal size bins typically have shallower CSD
gradients and hence longer residence times. However,
the QEMSCAN-derived residence times are generally of
the same order of magnitude as the manual data. For
example, the residence times of pyroxenes in 15597,12,
15
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15597,18, 15125,6 and 15555,209 are all of the order of
months (05–13 months) rather than years (with the
exception of the upper Q20 estimate for 15555,209).
QEMSCAN-derived residence times for olivine in
15555,209 have very small lower estimates of
<1 month, but overall the residence time estimates are
all <3 months. The only sample for which there is a sig-
nificant difference between the residence times calcu-
lated from the manual data compared with the
QEMSCAN data is for plagioclase in 15475,15. The
upper residence time estimate from the manual data
(2734 days) is seven times higher than the largest max-
imum estimate from the QEMSCAN data (368 days, Q5).
Such a difference means that the QEMSCAN data are
suggesting residence times of 1 year, whereas the
residence time from the manual data ranges up to
75 years.
Residence times of the order of months calculated in
this study using both manual and QEMSCAN-derived
data are comparable with the ranges calculated for
plagioclase, olivine and pyroxene in other Apollo mare
basalt samples (Donohue & Neal, 2015; Neal et al.,
2015). However, for sample 15475,15 the difference be-
tween manual and QEMSCAN data was of the order of
years. Regardless of whether both manual and
QEMSCAN-derived residence times for plagioclase in
15475,15 fall within the range of other mare basalts, this
result highlights the potential for significant differences
in interpretation of cooling rates depending on whether
these are derived from manual or QEMSCAN data.
To understand how the reliability of the QEMSCAN
data may influence interpretation of CSD trends with re-
spect to the magmatic processes that formed the Apollo
15 mare basalts, data from 15475,15 are used as an ex-
ample. The CSD derived from manual data (Fig. 6)
shows a slight convex-up trend between crystal lengths
of 25 and 575 mm, which could be interpreted as a sig-
nature of crystal fractionation. This would be consistent
with the chemical designation of this sample as a
quartz-normative fractionate. At a crystal length of
575 mm there is a sharp kink in the graph and a reduc-
tion in the CSD gradient. This may either reflect the
16 Journal of Petrology, 2020, Vol. 61, No. 4

accumulation of larger plagioclase crystals, or else indi-
cate that there were two stages of cooling. Overall, this
combination of CSD features is consistent with the
quartz-normative Apollo 15 mare basalts being proc-
essed in a complex magmatic system, as suggested by
Schnare et al. (2008). However, QEMSCAN-derived CSD
data for 15475,15 would lead to a somewhat different
interpretation: the QEMSCAN-derived CSDs all show
slightly concave-up trends, which could be interpreted
as accumulation of crystals or as the product of crystal
coarsening.
Another way to investigate the reliability of the
We observe some minor lateral offsets between the
manual traces of crystals and the same crystals in the
QEMSCAN mineral maps. This is mostly probably due
to minor differences in the calibration between the BSE
maps collected using FEI MAPS software and the
QEMSCAN mineral maps. The lateral offset between
manual crystal shapes and QEMSCAN crystal shapes
appears to make very little visual difference to the
length of crystals and instead adds to the width of the
crystal. The minor axis length has a much smaller effect
on the crystal habit estimate, and thus on the resulting
CSD plot, than the major axis (Morgan & Jerram, 2006).

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QEMSCAN data is to consider the raw, unprocessed Therefore, we are confident that minor lateral offsets
modal value of the phases in question, expressed as between the manual crystal traces and raw QEMSCAN
area percentage of the sample. The area percentages mineral maps has negligible effect on the resulting CSD
attained using manual data are smaller than those for plots.
the QEMSCAN-derived data (Table 2). The largest differ-
ence is seen in the pyroxene proportion in 15125,6. This Recommendations for using QEMSCAN for CSD
result is not surprising, because this sample contains analysis
numerous pyroxene crystals in the fine-grained ground- In this study, we have demonstrated the capabilities
mass, which would have been detected by QEMSCAN and limitations of QEMSCAN data processed through
but not traced manually. Manual and QEMSCAN- iExplorer software to reproduce the CSD plots of manu-
derived mineral area percentages are most similar for ally derived CSD data, for samples of different textures,
olivine in 15555,209. This is equally unsurprising, as grain sizes and average crystal shapes. For samples
there are very few olivine crystals intersecting the edge that are primarily composed of small (<1 mm) acicular
of the sample that are excluded in the manual data but crystals with overlapping touching crystals, such as
included in the QEMSCAN data. 15597,18, the principal limitation of the QEMSCAN
When masking the QEMSCAN mineral maps with method is the ability of the touching particles processor
the manually traced crystal outlines, the biggest differ- to correctly segment touching crystals. Samples with
ence is seen in the number of edge and fragmented similar textures are therefore not optimal for CSD ana-
crystals included in the QEMSCAN maps lysis with automated QEMSCAN methods. Samples
(Supplementary Data Fig. S13). The inclusion of edge with larger (>1 mm) euhedral or rounded crystals
crystals is not believed to be a major source of discrep- touching in only a few places, such as 15555,209, are
ancy between manual and QEMSCAN-derived CSDs. generally processed successfully by the touching par-
ticles processor and are therefore most suitable for
Table 2: Comparison of the area percentage of the sample rep- automated CSD (stereological and non-stereologically
resented by the crystals used in CSD analysis for manual and converted) analysis by QEMSCAN.
QEMSCAN methods
Although the examples above show how texture,
Sample Mineral Method Area % of sample grain size, and crystal habit all affect the CSDs produced
15597,18 pyroxene Manual 482 by QEMSCAN, it is important to understand which of
5 lm 546 these factors is the most detrimental. The grain size is
10 lm 535 likely to be a limiting factor for samples composed of
20 lm 536
very small crystals approaching the step size of the
15125,6 pyroxene Manual 367
5 lm 621 QEMSCAN mineral map. For our samples, the majority
10 lm 627 of the Q5, Q10 and Q20 QEMSCAN data plot within
20 lm 627 error of each other (Figs 6 and 7), suggesting that crys-
15555,209 pyroxene Manual 410
5 lm 495 tal size and effective resolution is not a limiting factor in
10 lm 497 this study. This leaves the effects of average crystal
20 lm 497 habit and sample texture, which are best evaluated by
15555,209 olivine Manual 122
5 lm 128 looking at 15125,6 and 15597,18. The pyroxene crystals
10 lm 129 in 15125,6 are most similar in shape to those found in
20 lm 129 15597,18 (Fig. 6a and b); however, there are fewer con-
15475,15 plagioclase Manual 258
tacts between pyroxene macrocrysts in sample 15125,6
5 lm 350
10 lm 351 than in 15597,18 and the samples have different types
20 lm 351 of groundmass (fine-grained in 15125,6 versus mafic
glass in 15597,18). If crystal habit was the most influen-
Calculations were made using the raw QEMSCAN data (5, 10
and 20 lm) rather than processed QEMSCAN data (i.e. Q5, Q10 tial factor, similar results would be expected for sam-
and Q20). ples 15125,6 and 15597,18. However, we saw
Journal of Petrology, 2020, Vol. 61, No. 4
differences between the two samples owing to the
increased number of touching pyroxene crystals in
15597,18 and the inclusion of fine-grained groundmass
crystals in 15125,6. Therefore, we conclude that the
sample texture is the most influential factor for
QEMSCAN-derived CSD analysis, as this determines
how well the touching particles processor is able to sep-
arate touching crystals correctly. However, we note that
crystal habit may affect the overall sample texture, so
these two factors must both be considered when
assessing whether a sample is suitable for CSD analysis
using QEMSCAN.
Effect of step size
Whereas the differences between the Q5, Q10 and Q20
CSD plots are minimal (Fig. 6), there is a significant
trade-off between scan resolution and analysis time.
Field scans taken at a step size of 5 lm took upwards of
6 h for a 1 inch round thin section, whereas a scan of the
same sample with a 10 lm step size completed in half
that time and scans at 20 lm step sizes took as little as
05 h (Supplementary Data Table S1). Although 20 lm
step size is the quickest scan time, it produces notice-
ably pixelated mineral maps compared with the high-
definition mineral maps generated using a 5 lm step
size (Supplementary Data Figs S1–S4). For samples
with similar areas and average crystal sizes to those
used in this study we suggest that, unless a high-
definition QEMSCAN mineral map is required for
another purpose, a 10 lm step size offers an optimal
compromise between analysis time and data quality.
Even using a 5 lm step size, it is up to 11 times faster
to collect the QEMSCAN data compared with manually
tracing crystals. Taking into account the fact that the
QEMSCAN system can be set up in around 1 h and left
to run unassisted, the actual user time required for
QEMSCAN data collection is up to 13 times faster than
that for the manual method. A significant initial time in-
vestment is required to develop the primary and sec-
ondary lunar SIP lists on the QEMSCAN iExplorer
system; however, once complete, these SIP lists are
then available for any future analyses and can be opti-
mized with only minor alterations.
Potential future uses of QEMSCAN for CSD
analysis
There is considerable potential for future use of
QEMSCAN methods for rapid identification and classifi-
cation of extra-terrestrial samples. Previous work on
CSD analysis of Apollo samples has focused on
whether this technique could be used to accurately dis-
tinguish mare basalts from lunar impact melts (i.e.
basalts produced as a result of melting during meteorite
impacts). Neal et al. (2015) showed that the CSD slopes
and intercepts of plagioclase and olivine could be used
to determine impact melts from mare basalt samples.
Differences between the two types of basalts could be
recognized by considering olivine crystals 04 mm and
17
plagioclase crystals 03 mm. In this study, manual and
QEMSCAN CSD data were most comparable at smaller
crystal sizes (generally <05 mm). Therefore, QEMSCAN
offers an exciting potential to rapidly classify mare
basalts from impact melts using olivine crystal popula-
tions. Further work is required to evaluate whether this
could also be reliably achieved using plagioclase crys-
tals 03 mm, as our study indicates that QEMSCAN-
derived data tend to deviate from manually derived
CSDs at larger crystal lengths.
The potential limitations of QEMSCAN for semi-
automated CSD analysis do not negate its exceptional
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capacity to provide a rapid overall view of the general
CSD trends within a sample. A second major advantage
of QEMSCAN, which should not be overlooked, is the
amount of data collected during a single scan. Not only
is using QEMSCAN much quicker (i.e. semi-automated)
for CSD analysis, at the same time it is also collecting
the data required to produce (qualitative) element con-
centration and distribution maps of the sample (EDS
maps of samples in this study are available via the link
doi:10.17632/rh37cdm9hv.1). Processors available in
the iExplorer software provide capacity for detailed ana-
lysis of modal mineralogy, particle size and mineral
associations. The analysis is also non-destructive and
requires only a carbon-coated thin section. This is a
major advantage when studying precious extra-
terrestrial samples such as Apollo mare basalts, and is
a capacity that can be exploited for non-destructive ana-
lysis of future meteorite falls and finds, and analysis of
returned samples.
CONCLUSIONS
In this study we have used four Apollo 15 mare basalt
thin sections to evaluate the effectiveness of QEMSCAN
as a semi-automated method for obtaining crystal size
distribution analyses. Crystal size distribution data col-
lected by QEMSCAN recover similar CSD trends to
those collected using manual tracing of crystal bounda-
ries from digital images. However, we find some sys-
tematic differences between the CSD plots generated
by the two approaches.
The principal limitation with our QEMSCAN-derived
data is the inefficient segmentation of elongate crystals
that are in contact with other crystals, via the iExplorer
touching particles processor. The separation of long
crystals into several smaller crystals principally affects
the sparsely populated large crystal size bins of a CSD
plot, and may even result in the complete removal of
these size bins.
The effect of inefficient segmentation of long crystals
is carried through to 3D crystal habit estimates calcu-
lated in CSDslice, where QEMSCAN-derived data typic-
ally return shorter z-axis (i.e. long axis) ratios than
manual data for the same sample. When incorporated
into the stereological calculations in CSDcorrections,
the difference in 3D crystal habits causes the
QEMSCAN-derived CSD plots to have a steeper
18
gradient and extend to shorter crystal lengths than the
manual data.
Although the main differences between the
QEMSCAN and manual data are restricted to the largest
few crystal size bins of the CSD plots, this is often where
the petrologically important signatures of crystal accu-
mulation and/or fractionation are observed. Estimates
of crystal residence time and nucleation density calcu-
lated using QEMSCAN-derived CSD plots therefore de-
viate from those calculated using manually derived
data. However, the overall trends of the CSD plots using
QEMSCAN data (e.g. concave-up) are the same as those
of the manual data plots.
The sample texture and crystal habit can significantly
affect the performance of the touching particles proces-
sor, which in turn affects the overall reliability of the
QEMSCAN data. QEMSCAN-derived CSDs for samples
with numerous touching acicular crystals are most like-
ly to be different from their manually derived counter-
parts. Until the iExplorer software is further developed
to improve the segmentation of large touching elongate
crystals, this issue will remain a hurdle for the blanket
use of QEMSCAN as a reliable semi-automated method
of CSD analysis. We recommend that, if an accurate
CSD analysis is required to evaluate petrological proc-
esses such as crystal fractionation and accumulation,
and/or to accurately calculate crystal residence time or
nucleation density, QEMSCAN should only be used
after careful consideration of the suitability of the sam-
ple texture and average crystal habit. However, if only a
general overview of the CSD trend is required, then in
most cases examined here and in suitably fresh terres-
trial samples, QEMSCAN (with the correct mineral data-
base SIP list available) may be utilized to its full
advantage as a time-effective alternative to manual
CSD analysis of geological thin sections.
SUPPLEMENTARY DATA
Supplementary data are available at Journal of
Petrology online and see also data repository at
doi:10.17632/rh37cdm9hv.1.
ACKNOWLEDGEMENTS
We thank Lewis Hughes and Heath Bagshaw for their
help during the QEMSCAN data collection, and Iris
Buisman for assisting with initial QEMSCAN training
and providing helpful advice on data processing. We
thank the NASA Johnson Space Center curatorial team
for helping with the provision of Apollo samples for this
study. We thank Tod Waight for editorial handling, and
Michael Higgins, Elsa Pupier, Dougal Jerram and an an-
onymous reviewer for their constructive and helpful
comments.
Journal of Petrology, 2020, Vol. 61, No. 4
FUNDING
This work was supported by a Science and Technology
Facilities Council studentship to S.B., and a Royal
Society University Research Fellowship (RS/UF140190)
and Science and Technology Facilities Council grant
(ST/R000751/1) to K.H.J.
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