Geological Thin Sections Research Articles

Unsupervised topological analysis of polarized light microscopy: application to quantitative birefringence imaging.

The determination of birefringence (magnitude and axis orientation) of optical materials is of significant interest in various fields. In the case of composite samples, this task becomes complicated and time-consuming; therefore, a partially automated procedure for reconstructing birefringence spatial distribution becomes valuable. Herein, we propose a procedure to reconstruct the spatial distributions of the retardance and optical axis orientation in a geological thin section from sparse quantitative birefringence measurements, using automatic boundary detection on cross-polarized light microscopy images. We examine two particular areas on the selected geological thin section: one that presents a uniaxial crystal with a circular cross-section of its refractive index ellipsoid and the other with grains of varying orientations. The measurement gives the orientation of the grain's optical axis both in and out of the plane of the thin section, which explains the qualitative observations with the cross-polarized light microscope. Future work will connect the measured orientation of the rock thin section with its 3D geological orientation in the field.

Development of scanning SQUID microscope system and its applications on geological samples: A case study on marine ferromanganese crust

We present developments and applications of a high resolution scanning superconducting quantum interference device (SQUID) microscope for imaging magnetic field of geological samples at room temperature. A directly coupled low-temperature SQUID with a 200 μm × 200 μm pickup loop was mounted on a sapphire rod and separated from room temperature by a sapphire window. The environmental noise of the SQUID was successfully reduced by subtracting the signal of an additional reference SQUID placed inside a cryostat. The resulting system noise level was estimated to be about 50 pT. A geological thin section could be placed on a non-magnetic sample holder with an XYZ stage for scanning in an area of 100 mm × 100 mm. The minimum achievable distance from the SQUID to the sample is measured as ∼200 µm. An application of the SSM to a marine ferromanganese crust successfully provided beautiful stripe patterns in the magnetic images. The patterns could be correlated to the history of geomagnetic field reversals. The boundaries of the magnetic polarity domains were useful guides for the estimation of the deposition age by correlation with the standard geomagnetic polarity timescale. The established age model gave an average growth rate of ∼2.7 mm/Ma, which is consistent with that obtained by radiometric dating using 10Be (∼2.6 mm/Ma).

Altered mineral segmentation in thin sections using an incremental-dynamic clustering algorithm

Intelligent mineral segmentation in thin section images of rocks still remains a challenging task in modern computational mineralogy. The objective of the paper is segmenting minerals in geological thin section’s images with special attention on altered mineral segmentation. In this paper, an efficient incremental-dynamic clustering algorithm is developed for segmentation of minerals in thin sections containing altered and non-altered minerals. In the clustering algorithm, there is no need for determining the number of clusters (minerals) existed in thin section images, and also it is able to deal with color changing and non-evident boundaries in altered minerals. We have solved two main existing limitations: segmentation of mineral pixels that are frequently labeled as background pixels, and segmentation of thin sections containing altered minerals. Moreover, we created an open database (Alborz Mineralogical Database), as a benchmark database in computational geosciences regarding image studies of mineral. The proposed method is validated based on the results provided by the segmentation maps, and experimental results indicate that the proposed method is very efficient and outperforms previous segmentation methods for altered minerals in thin section images. The proposed method can be applied in mining engineering, rock mechanics engineering, geotechnique engineering, mineralogy, petrography, and applications such as NASA’s Mars Rover Explorations (MRE).

Taphonomy of very ancient microfossils from the ∼3400 Ma Strelley Pool Formation and ∼1900 Ma Gunflint Formation: New insights using a focused ion beam

Focused ion beam (FIB) milling permits the accurate extraction of ultrathin (c. 100nm) cross sectional lamellae from microfossils found in geological thin sections. Subsequent TEM analysis of these lamellae can provide unique insights into the ultrastructure, chemistry and taphonomy of Precambrian microfossils at the micrometer to nanometer scale. Combining serial FIB milling with SEM imaging extends this capability to three dimensional (3D) tomographic reconstruction and visualization of Precambrian microfossils, revealing information not available in light microscopy.Here we apply these techniques to two iconic silicified microfossil assemblages, from the ∼3400Ma Strelley Pool Formation of Western Australia and the ∼1900Ma Gunflint Formation of Canada. All the examined microfossils have carbonaceous walls surrounded by pure silica. Impregnation of microfossil walls by nano-grains of silica is common, together with variable degrees of wall displacement and replacement by silica. All microfossils are rigidly preserved in 3D and show little or no folding or compression. However, there are also notable differences in taphonomic preservation. Our examples of the spheroidal Gunflint microfossil Huroniospora showed the highest fidelity of preservation with a continuous carbonaceous wall fossilized by spheroidal nano-silica grains that resemble those found on bacterial surfaces in modern silicifying hot-spring environments. The nucleation of these silica nano-spheres on the microfossil walls has induced an artificial ‘saw-tooth-like’ ridged wall texture that may subsequently hinder species-level identification. The Strelley Pool microfossils in comparison show a lower fidelity of preservation with small parts of the microfossil walls completely replaced by silica, plus extensive recrystallization of spheroidal silica nano-grains to angular micro-quartz. Our examples of the sheath-like filamentous Gunflint microfossil Siphonophycus showed the lowest fidelity of preservation with many gaps in the carbonaceous walls and significant redistribution of carbon by recrystallizing silica grains. A model is presented to explain these observations.Criteria for distinguishing highly probable microfossils from non-cellular carbonaceous microstructures (e.g., botryoids and grain coatings) using FIB-based imaging are put forward for the first time here, using examples drawn from the Strelley Pool Formation and comparisons with younger Gunflint material.The combined in situ techniques of FIB–TEM and FIB–SEM nano-tomography potentially provide a wealth of new nano-scale information regarding the biogenicity, antiquity and taphonomy of Precambrian microfossils. However, the destructive nature of both techniques makes their application to unique palaeontological specimens problematical.

Paleointensity of the Earth's magnetic field using SQUID microscopy

Knowledge of the paleointensity of magnetic fields is valuable for our understanding of the origin and evolution of planetary dynamos and the history of planetary interiors. Until recently, quantitative paleomagnetic and paleointensity analyses were limited to magnetometry of bulk samples. The most sensitive of these moment magnetometers use superconducting quantum interference devices (SQUIDs), which measure the net moment of samples typically millimeters to centimeters in size with sensitivities of 10 − 9 Am 2. Recently, SQUIDs have been adapted to map the fine-scale magnetic fields of geological thin sections with unprecedented spatial resolutions of better than 100 μm and moment sensitivities better than 10 − 15 Am 2. Here we present a detailed study of the magnetization within basalts from the Hawaii Scientific Drilling Project using SQUID microscopy and moment magnetometry in combination with borehole magnetometry, petrographic and geologic data. We demonstrate how SQUID microscopy can be used to measure the paleointensity of the Earth's field which magnetized these basalts during the last 500 ky. These experiments are the first time alternating field demagnetization and paleointensity experiments have been conducted on natural remanent magnetization using submillimeter magnetic imaging techniques. Our high resolution field maps enable us to make thousands of paleointensity measurements on a single thin section which can be correlated with the minerals, petrologic textures, and alteration zones within the samples.

Analysis of bulk fabrics and microstructure variations using tesselations of autocorrelation functions

“Lazy ACF Tiles”, a macro written for the public domain program “NIH Image”, is presented. The macro permits the user to calculate local and bulk autocorrelation functions (ACFs) of halftone images such as photomicrographs of geological thin sections. Single ACFs, rows, or tessellations of ACFs can be calculated. ACF analysis is especially useful for the detection of subtle microstructures (weak anisotropies), and for the evaluation of large data sets. Segmentation of images (grain boundary contouring) is not necessary. Images do not have to be square. The macro is in the public domain, and a powerpoint manual is provided with it. As an example, the application of “Lazy ACF Tiles” to an experimentally deformed sample of quartzite is demonstrated. The ACF analysis reveals a periodic flattening intensity along the compressional axis of the sample, which cannot be detected with the unaided eye.

Petrofabric study using electron channeling patterns of quartzes and hematites in dual-phase banded iron formations

Research in deformation of rocks requires the understanding of structure-property relationship. The study of structure-property relationships requires knowledge of the crystallographic texture on a local scale. Electron Channeling in scanning microscope has been used to analyze textures of local features in a microstructure, misorientations between grains and the spatial arrangement of grains of individual crystallographic orientations can be determined. This information is critical for a mechanical understanding of microstructure evolution during the deformation of rocks. Petrofabric analysis using Electron Channeling Patterns can use normal geological thin sections and mounted sections, which allows relatively fast and easy interpretation and allows one to determine the relationship between a microstructural feature and the individual orientations of its grains. The most efficient and satisfactory way of accomplishing this task is by direct electronic detection and indexing of Kikuchi patterns, which requires modification of the microscope, at considerable cost. This study, however, has been undertaken using only an unmodified SEM with electron channeling capability.

A new procedure for relocating mineral grains for microprobe analysis

AbstractA new procedure is described for locating mineral grains in geological samples prepared for microprobe analysis. This procedure uses a digital image of the entire sample surface to select points of interest. These features of interest must be visible in this external image. Once the sample is mounted on the specimen stage of the microprobe, the digital image is used as a ‘map’ to relocate minerals for analysis. The image can be recorded using either a video camera, fitted with a macro zoom lens, or a flat-bed scanner. A calibration procedure has been developed in which two indexing points are used to calculate the instrument stage coordinates from the pixel coordinates of the digital image. Following this calibration, the stage coordinates of any feature visible in the digital image can be displayed to facilitate rapid relocation. The procedure was evaluated by relocating magnetite grains visible in an optical image of a geological thin section. The repositioning accuracy in relocating 28 magnetite grains distributed over an area of about 20 × 30 mm was found to be 157 ± 102 µm (one standard deviation) from the video camera image and 48 ± 28 µm from a flat bed scanner image. The former image was thought to suffer from some optical distortion. The procedure may be applied to any microprobe instrument fitted with a digital x-y specimen stage. Future applications in relocating features visible in autoradiographs are currently being evaluated.

High resolution magnetic susceptibility imaging of geological thin sections: Pilot study of a pyroclastic sample from the Bishop Tuff, California, U.S.A.

High resolution magnetic susceptibility imaging is a new technique for studying the magnetic properties of geological thin sections. The two‐dimensional distribution of both remanent and induced magnetization can be determined with a spatial resolution (< 1.0 mm) that is similar to the size of phenocrysts in the sample. Amongst many problems in rock magnetism to which it could be applied, the technique holds great potential for understanding the origin of the anisotropy of magnetic susceptibility in pyroclastic flows. Preliminary tests on a single sample of ignimbrite indicate that secondary iron‐titanium oxide particles deposited within vesicle walls prior to their collapse are responsible for the bulk susceptibility.

Geoman: A FORTRAN program for the management of geological thin section data

A program for treating large numbers of qualitative and/or quantitative geological thin section data has been developed. Data are coded, stored in a direct access data bank, and extracted selectively for treatment. The system is easy to handle and flexible, that is the user can choose descriptive attributes (variables) and select parameters for different computational operations. The codification and program can be applied to all rock types. The treatment includes: Loading of data bank, Updating of data bank, Selection of samples and variables, Edition of samples, Variable distribution in geological sections, Histograms, Scatter diagrams, Association analysis and Correspondence analysis.

Lost & Found: 111. Lomax, James (1857 - 1934)

A researcher wishes to establish the whereabouts of material supplied to museums and educational establishments by James Lomax. Lomax and his Palaeobotanical Laboratories supplied fossil plant and geological thin sections in the first instance. Later he also sold coal material which may have been supplied under the name of the Lancashire & Cheshire Coal Research Organization of which his laboratories became a part....