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A smear slide online reference tool for novices and experts: TMI.
Myrbo, A., A. Morrison, R. McEwan, D. Ariztegui, A. Breckenridge, A. Cohen, T.C. Johnson, M. Rosen, R.G. Rothwell, J.
Russell, D. Schnurrenberger, M. Shapley, J. Smoot, B. Valero-Garcés
Key words (up to 6: need to cut some): Lithological
core description, Sediment classification, Smear slides,
Petrography, Lacustrine sedimentology, Marine
sedimentology, Limnogeology, Paleolimnology, Lake
sediments
ABSTRACT (<350 words)
Smear slides of unconsolidated sediment are a
powerful semiquantitative analytical tool. Simple to
prepare, low-tech, and virtually nondestructive, their
use in marine and especially lacustrine core description
has been hampered by the lack of a suitable reference
work. A new online database provides images of
lithological components and sedimentary facies to
assist both the novice and expert smear slide user. The
online resource, TMI (Tool for Microscopic
Identification; http://tmi.laccore.umn.edu), also
features tutorials on preparation and analysis of smear
slides and their use in lithological core description. TMI
makes the smear slide method more accessible to
researchers and also supports its use in classrooms and
informal educational settings.
“[Smear slide analysis] remains unrivalled as a cheap,
simple, and rapid investigative method.” –Rothwell
1989, p.24
“To the trained eye, all of the common rock-forming
minerals are familiar friends and can usually be
identified on sight.” – Zoltai and Stout 19XX, pYY
“it soon becomes possible to generate most
paleoenvironmental interpretations directly with the
initial microscopic study.” –Kelts 2003, p. 60
Introduction
LacCore announces the launch of an interactive web-
based tool, TMI (Tool for Microscopic Identification;
http://tmi.laccore.umn.edu), for the identification of
sedimentary components and facies in smear slide. The
smear slide technique (Mazzullo and Graham, 1988;
Rothwell, 1989; Kelts, 2003) is one of sedimentology’s
most powerful sources of information on past
depositional environments, geochemistry, and ecology.
Preparation of smear slides, using tiny amounts of
unconsolidated sediment, is cheap, fast, and low-tech,
and their analysis requires only a petrographic
microscope available in most geology departments.
Unfortunately, until now, no reference work has
existed for lacustrine sediments, and the marine
sedimentary textbook (Rothwell, 1989) is long out of
print. The method has thus remained difficult for
students and researchers to learn except under the
instruction of an experienced tutor. The result is that in
most paleolimnological studies, a large amount of very
useful information is not collecteddue to researchers’
lack of knowledge and comfort with smear slides and
lithological description.
Smear slide analysis is used to semiquantitatively
determine sediment mineralogy, grain size
distribution/sorting/rounding, abundance and type of
organic matter, biological assemblages, degree and
nature of diagenesis, and other characteristics that
provide the essential context for interpretation of the
geochemical, biological, and chronological data that
are generated from sediment subsamples. Used as a
part of initial core description, smear slides can –
virtually nondestructively – give a tremendous amount
of paleoenvironmental information before the first
analytical dollar is spent.
TMI features both an interactive key structure for
identification of sedimentary componentsby the novice
or in the classroom, and tag clouds/searchable
attributes that all analysts can use to confirm an
identification. The website is loaded with digital images
(usually several) of each sedimentary component, text
descriptions of distinguishing and diagnostic features,
and notes on “imposter” components. Minerals and
mineraloids are TMI’s primary focus, but the tool also
includes biological components found in both lakes and
oceans, and has an integrated link with the Diatoms of
the United States websiteof inland taxa
(http://westerndiatoms.colorado.edu). The resource is
thus valuable to workers inany continental or marine
sedimentary environment.
Why smear slides?
Sedimentary context for analytical data
Smear slides allow rapid characterization of
sedimentary component assemblages, complementing
macroscopic description of sedimentary features.
Lithological core description is recognized in the
marine (Mazzullo and Graham 1988) and lacustrine
(Schnurrenberger et al., 2003) core communities as not
only a crucial part of the documentation of cores but as
the basis for interpretation of all analytical data
generated from a sedimentary sequence.
Contemporary developments in core analysis

methodologies include numerous advanced techniques
for characterization of sediment organic and inorganic
chemistry, supplementing established techniques such
as isotopes, grain size, and X-ray diffractometry, and
paleoecological methods such as pollen, ostracode,
and diatom analysis. Each of these analytical methods
benefits from grounding in core lithological
description: smear slide analysis may guide
subsampling strategy (e.g., recognition of authigenic
vs. detrital calcite in sampling for stable isotope
analysis); may provide the basis for interpreting
instrumental data (e.g., whether high Fe in a portion of
core is due to a mineralogical or a redox change); and
provides evidence of changing depositional
environments (e.g., shallow vs. deep water facies) and
events (e.g., turbidites).
Smear slides are ideally suited to identifying not only
the major components of a sedimentary matrix, but
also the rare components (e.g., pyrite, vivianite, heavy
minerals), which have environmental significance.
Lithological description and classification based on
sediment composition (Schnurrenberger et al., 2003) is
essential to improving communication between lake
sediment researchers, who come from a wide variety
of disciplines. Some standardization is desirable to
ensure interoperability of core descriptions and
facilitate the use of archived cores (Schnurrenberger et
al. 2001).
Tool for Microscopic Identification
TMI is a free, web-based resource containing digital
photomicrographs of individual sedimentary
components and facies as seen in smear slide, using
mainly plane-polarized, cross-polarized, and reflected
light. The initial population of ~200 photos was
contributed by subject matter experts (SMEs; the
authors and others) in both lacustrine and marine
smear slide analysis during and following a workshop in
October 2011. Additional images are welcome and will
be evaluated for accuracy of component identification
by Myrbo and SMEs, and treated for consistency of
resolution, scale bar, etc. by LacCore staff.
Contributions may be made according to guidelines
provided on the website. A second workshop of
experts in identification of biological components is
planned for early 2012 (the initial workshop involved
mainly geoscientists). A formal link with the Diatoms of
the United States website provides high-quality diatom
identification tools, and will be further enhanced with
paleolimnology-related content (a review of diatom
preservation, diversity, abundance, and ecological
gradients as seen in cores) and guidance for what
aspects of diatom identification can be achieved with
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smear slides, at relatively low magnifications and in the
smear slide mounting medium rather than the diatom
standard Naphrax. The TMI application is easy for non-
technical LacCore staff to maintain, and will be
expanded and further developed as funding
allows.Integration with Corelyzer software (Conze et
al., 2010) will allow smear slide descriptions to be
associated with locations and intervals in core
description session files.
The advantages of TMI over past static resources
(Mazzullo and Graham 1988, Rothwell 1989, Kelts
2003) mainly result from its web format. The resource
can house many color images without the limitations of
space and cost faced by print media. In fact, the
number of images uploaded to TMI in its first day (180)
exceeded the total number of figures in Rothwell 1989
(150). Because the appearance of a sedimentary
mineral can be variable depending on its means of
formation, and because relatively few analysts have
training in optical mineralogy, presenting an array of
visual examples is critical to TMI’s utility to the
community.
Information in TMI can be accessed in three basic
ways. An interactive key (based on the key in Rothwell
1989, Appendix 4) provides a guide that is especially
useful to novice smear slide users, but that also
benefits experienced smear slide analysts confronted
with an unknown component. The key can be
expanded with additional nodes as components are
added to the site. A search feature indexes all text
associated with each image, and is valuable to both
novice and advanced users. Finally, a tag cloud feature
displays metadata keywords, size-weighted according
to the frequency of their appearance in text
descriptions of components and individual images. The
tag cloud gives a sense of relative rarity of certain
characteristics, as well as providing dozens of
suggested terms for analysts lacking the requisite
vocabulary to provide their own search terms. The TMI
website also features text and video tutorials on smear
slide preparation and analysis.
Photographic examples oflithologies or facies, and of
sediments of known composition, are provided in TMI
to help especially novice analysts develop their skills in
sediment classification and percentage estimation. This
part of TMI also emphasizes common associations
between components in a given lithology, for instance
highly calcareous sediments with partially dissolved
diatoms, or iron-bearing phases such as biotite with
diagenetic pyrite.
In addition to the clear benefits of its use in research,
TMI and the smear slide technique are powerful
educationaltools.Smear slide analysis in the geoscience

classroom uses, reinforces, and expands
opticalmineralogy knowledge. Sediment analysis using
smear slides integrates geology, biology, chemistry,
and other (sub)disciplinary topics, thus engaging
students with a range of interests. TMI can help
introduce young students to the microscopic world,
and help all students, as well as the interested public
(e.g., museumgoers, lake associations), to ask and
understand “what is mud made of?” In classrooms
where microscopes are not available, TMI can be used
in a “virtual core description” lesson.
Technical design and implementation
TMI is designed as an database-driven web application
implemented using the open source Grails framework,
v.1.3.7 (http://grails.org).  Grails supported our
preference for iterative development and its rich plug-
in ecosystem supplied additional out-of-the-box
functionality for search (Searchable), tagging
(Taggable), and security (Spring Security).  This
approach facilitated creation of the project from a
funded idea to a deployed online resource in less than
four months of part-time effort.  The database backend
is MySQL 5.0.  Rothwell's identification key was
implemented as dichotomous graph of nodes and
edges loosely based on the ideas presented in Rocker
et al (2007) and  Gallagher (1999) where questions
posed to the user are nodes and possible choices are
edges.  Unique identification of a smear slide
component represents a terminal node in the graph.
Metadata (magnification, contributor, lake name,
location, depth, coring device used, etc) is captured for
each image.  Future extensions to TMI will utilize this
metadata to link to external resources such as the
LacCore data repository or core data in Corelyzer.   slip, and the cement will move between the plates of
Materials and methods
Smear slide preparation
Smear slides are prepared as modified from Rothwell
(1989) and Kelts (2003).A standard microscope slide is
first wiped thoroughly using alcohol to remove any
glass shards that might be confused with volcanic glass
when viewed under the microscope. The slide is then
labeled with the complete name of the lake, core,
section, depth in core, and reason the slide was made
(e.g., white layer, top of F.U. sequence, routine
sedimentation; these notes are essential to facilitate
relation of the smear slide analysis with the core face).
Use of a thermal transfer label printer with 1” square
labels is preferable to hand-writing, for archival
purposes. One drop of deionized water is placed in the
center of the slide. If evaporite minerals are expected
in the sample, alcohol should be used rather than
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water to avoid dissolving (and then reprecipitating) any
components. A weak solution of detergent (e.g., 0.5%
sodium hexametaphosphate) can be used to help
disperse clays if necessary. A very small quantity of
sediment, <0.5 mm3, is removed from the core using a
wooden toothpick or sampling spatula and thoroughly
dispersed in the water (or alcohol or detergent) using a
circular smearing motion with the tool held nearly flat
against the slide. Small clumps of sediment can be
gently broken up, although with the risk of breaking
microfossils. The resulting smear should be about the
diameter of a cover slip, and translucent. (The novice
preparer should view several finished slides before
preparing additional slides in order to ascertain that
the concentration of particles is low enough to see
individual components, while high enough to provide a
large number of particles to view.) The slide is placed
on a slide warmer or hot plate at about 60°C to dry
before embedding. When the water or alcohol has
completely evaporated, the mounting medium is
added, while the slide is still sitting on the warmer. The
standard medium is Norland 61 optical cement, which
has a refractive index of 1.55-1.56 and cures under
ultraviolet light of wavelengths between 320-400 nm,
typical of a fluorescent blacklight available at hardware
stores; sunlight can also be used. Without touching the
dropper dispenser to the slide, place two drops of
optical cement in the middle of the dried sediment.
Place a cover slip on the cement, allow the cement to
spread beneath the slip, and transfer the slide to a
position under UV light to cure for 2-3 minutes. If the
presence of large grains prevents the optical cement
from spreading to the edges of the cover slip, one or
more additional drops can be added at the edge of the
glass by capillary action. The smear can also be made
on the cover slip rather than on the slide, if it is
desirable that all components be in the same focal
plane.
How many slides?
The quantity and nature of smear slides to be prepared
from a given core section depends upon the sediment
character and the research questions being asked.
Analyzing many slides made at a regular, arbitrary
interval (e.g., every 10 cm) can lead to fatigue with the
process, and is not recommended. In general we
suggest initially taking one or two slides of each routine
“background” sediment type or lithology per core
section, as well as a slide of any anomalous sediment
type. During core description, toothpicks can be lightly
inserted into the core to mark locations where smear
slides should be taken, and the toothpicks then used to

make the slides. The researcher should view the smear
slides while the core is also available for viewing
whenever possible (i.e., ideally when the core has just
been split and is being described), in order to mentally
relate the sediment composition (as determined from
the smear slide) with its expression in core face, and
regularly return to the core face to address questions
raised by the smear slide analysis. By this method the
researcher can learn to infer composition from the
core face alone, and can prepare fewer slides as she
continues analysis of the core. Slides of previously-
analyzed lithologies should be periodically prepared in
order to check the identification, and replicate slides
should be analyzed if semiquantitative analysis is a
goal. Core description conducted iteratively using
smear slides, core face, and (if available) analytical data
such as multisensor core logs provides the optimal
setting for the researcher to understand the
sedimentary matrix and its variations, recognize
important sedimentary features, and form hypotheses
about processes in the paleoenvironment to guide the
core sampling and analysis strategy.
Smear slide analysis
The casual analysis of smear slides provides insight into
the components that make up lacustrine or marine
sediments, but to fulfill their potential as a
semiquantitative analytical tool, smear slide
observations must be made systematically. Adherence
to a standard form (at) prompts the analyst to make
the same observations on each slide, allowing relative
changes in lithology to be recognized. Several
suggested formats are provided on the TMI website.
Analysis is made using a petrographic microscope; an
additional fiber-optic light source is useful for providing
the reflected light required to distinguish between
certain components, e.g., some opaques. The
distribution of material on the slide may be uneven, so
each analysis should begin with a scan of the entire
slide area at low magnification, e.g., 100x. Although
the variety of components viewed in smear slide may
appear overwhelming, the novice analyst should
remember that virtually all can be grouped into one of
four broad categories: clastics, organics, diatoms, and
carbonates (the latter of which may or may not be
present, depending on water chemistry). In addition to
these dominant parts of the sediment, there may be
components with minor or trace abundance but which
have paleoenvironmental significance, such as
diagenetic minerals and mineraloids (e.g., pyrite,
vivianite, hematite), volcanic glass, and anthropogenic
debris such as fly ash. Evaporite minerals (e.g.,
gypsum, halite) are common in some environments
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and can also occur as secondary precipitates from pore
water as the core desiccates over time. Observations
of the grain size distribution, sorting, and rounding of
clastic components (i.e., sediment texture) should be
made using alternating plane- and cross-polarized light,
and rotation of the stage, to illuminate all mineral
grains, including the fine silt- to clay-sized fraction that
may show very low relief. Percentage estimates of
each sedimentary component should be attempted,
and the eye can be “calibrated” by comparing visual
estimates with numerical compositional data from the
same sediments as analyzed at a later date. Partial
dissolution of components such as diatoms and
carbonate minerals should be noted, as their condition
provides information about saturation with respect to
these phases in the water column and pore waters.
Exceptional preservation, e.g., of algal pigments and
unstable minerals, can occur in environments with
rapid deposition, anoxic bottom waters, or both.
Smear slides and sediment classification
One of the primary goals in conducting smear slide
analysis is to generatecompositionally-based names for
sedimentary lithologies and facies, to be used in core
description and archived with the core data and
metadata. The lacustrine sediment classification
scheme outlined in Schnurrenberger et al. (2003)
provides a flexible terminology for continental
sediments, and sediment names can be readily
determined based on smear slide descriptions.
Acknowledgments
The development of TMI was funded by a University of
Minnesota (UMN) Interdisciplinary Informatics Seed
Grant to Myrbo. The resource is hosted at the
Minnesota Supercomputer Institute, UMN. TMI
benefits from the infrastructure provided by LacCore,
the National Lacustrine Core Facility, which is
supported by the National Science Foundation and
UMN. The lead author wishes to dedicate this effort to
the memory of Kerry Kelts, whose project we are
attempting to complete.
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