A Smear Slide Online Reference Tool for Novices and Experts: TMI

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; 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.

~750 words/page; 2-4 pages (~1500-3000 words) including intro through conclusion

“[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; 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 ( 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 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 ( 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.

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 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 slip, and the cement will move between the plates of 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 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.