Fully Automatic Segmentation of Brain Tumor Images using Support Vector Machine Classiffication in Combination with Hierarchical Conditional Random Field Regularization

Delineating brain tumor boundaries from magnetic resonance images is an essential task for the analysis of brain cancer. We propose a fully automatic method for brain tissue segmentation, which combines Support Vector Machine classification using multispectral intensities and textures with subsequent hierarchical regularization based on Conditional Random Fields. The CRF regularization introduces spatial constraints to the powerful SVM classification, which assumes voxels to be independent from their neighbors. The approach first separates healthy and tumor tissue before both regions are subclassified into cerebrospinal fluid, white matter, gray matter and necrotic, active, edema region respectively in a novel hierarchical way. The hierarchical approach adds robustness and speed by allowing to apply different levels of regularization at different stages. The method is fast and tailored to standard clinical acquisition protocols. It was assessed on 10 multispectral patient datasets with results outperforming previous methods in terms of segmentation detail and computation times.

On the use of textural features for writer identification in old handwritten music scores

Writer identification consists in determining the writer of a piece of handwriting from a set of writers. In this paper we present a system for writer identification in old handwritten music scores which uses only music notation to determine the author. The steps of the proposed system are the following. First of all, the music sheet is preprocessed for obtaining a music score without the staff lines. Afterwards, four different methods for generating texture images from music symbols are applied. Every approach uses a different spatial variation when combining the music symbols to generate the textures. Finally, Gabor filters and Grey-scale Co-ocurrence matrices are used to obtain the features. The classification is performed using a k-NN classifier based on Euclidean distance. The proposed method has been tested on a database of old music scores from the 17th to 19th centuries, achieving encouraging identification rates.

Petrology and geochronology of "muscovite age standard" B4M

Muscovite B4M, distributed in 1961 as an age standard, was ground under ethanol. Five grain size fractions were obtained and characterized by X-ray diffraction. They display a mixing trend between a phengitic (enriched in the fraction <0.2 µm) and a muscovitic component (predominant in the fraction >20 µm). High-pressure phengite is preserved as a relict in retrograde muscovite. Electron microprobe analyses of the distributed mineral separate reveal at least four white mica populations based on Si, Al, Mg, Na, Fe and F. Rb/K ratios vary by one order of magnitude. Rb–Sr analyses link the mineralogical heterogeneity to variable Rb/Sr and 87Sr/86Sr ratios. The grain size fractions define no internal isochron. Relict fine-grained phengite gives older ages than coarse-grained retrograde greenschist facies muscovite. The inverse grain size–age relationship also characterizes 39Ar/40Ar analyses. Cl/K anticorrelates with step ages: Cl-rich coarse muscovite is younger than Cl-poor fine relict phengite. Sr and Ar preserve a similar isotopic inheritance despite peak metamorphism reaching 635±20 °C. A suitable mineral standard requires that its petrological equilibrium first be demonstrated. Relicts and retrograde reaction textures are a guarantee of isotopic disequilibrium and heterogeneous ages within single crystal at the micrometre scale.

Robust Denoising using Feature and Color Information

We propose a method that robustly combines color and feature buffers to denoise Monte Carlo renderings. On one hand, feature buffers, such as per pixel normals, textures, or depth, are effective in determining denoising filters because features are highly correlated with rendered images. Filters based solely on features, however, are prone to blurring image details that are not well represented by the features. On the other hand, color buffers represent all details, but they may be less effective to determine filters because they are contaminated by the noise that is supposed to be removed. We propose to obtain filters using a combination of color and feature buffers in an NL-means and cross-bilateral filtering framework. We determine a robust weighting of colors and features using a SURE-based error estimate. We show significant improvements in subjective and quantitative errors compared to the previous state-of-the-art. We also demonstrate adaptive sampling and space-time filtering for animations.

Analysis of polygonal cracking patterns in chloride-bearing terrains on Mars: Indicators of ancient playa settings

The ancient southern highlands on Mars (~3.5 Gyr old) contain > 600 regions that display spectral evidence in the infrared for the presence of chloride-bearing materials. Many of these locations were previously reported to display polygonal cracking patterns. We studied more than 80 of the chloride-bearing terrains using high-resolution (0.25-0.5 m/pixel) images, as well as near-infrared spectral data, to characterize the surface textures and the associated cracking patterns and mineralogies. Our study indicates that ~75% of the studied locations display polygonal cracks that resemble desiccation cracks, while some resemble salt expansion/thrust polygons. Furthermore, we detect, spectrally, the presence of smectites in association with ~30% of the studied fractured terrains. We note that smectites are a special class of swelling clay minerals that can induce formation of large desiccation cracks. As such, we suggest that the cracking patterns are indicative of the presence of smectite phyllosilicates even in the absence of spectral confirmation. Our results suggest that many chloride-bearing terrains have a lacustrine origin and a geologic setting similar to playas on Earth. Such locations would have contained ephemeral lakes that may have undergone repeated cycles of desiccation and recharging by a near-surface fluctuating water table in order to account for the salt-phyllosilicates associations. These results have notable implications for the ancient hydrology of Mars. We propose that the morphologies and sizes of the polygonal cracks can be used as paleoenvironmental, as well as lithological, indicators that could be helpful in planning future missions.

Photometric properties of Mars soils analogs

We have measured the bidirectional reflectance of analogs of dry, wet, and frozen Martian soils over a wide range of phase angles in the visible spectral range. All samples were produced from two geologic samples: the standard JSC Mars-1 soil simulant and Hawaiian basaltic sand. In a first step, experiments were conducted with the dry samples to investigate the effects of surface texture. Comparisons with results independently obtained by different teams with similar samples showed a satisfying reproducibility of the photometric measurements as well as a noticeable influence of surface textures resulting from different sample preparation procedures. In a second step, water was introduced to produce wet and frozen samples and their photometry investigated. Optical microscope images of the samples provided information about their microtexture. Liquid water, even in relatively low amount, resulted in the disappearance of the backscattering peak and the appearance of a forward-scattering peak whose intensity increases with the amount of water. Specular reflections only appeared when water was present in an amount large enough to allow water to form a film at the surface of the sample. Icy samples showed a wide variability of photometric properties depending on the physical properties of the water ice. We discuss the implications of these measurements in terms of the expected photometric behavior of the Martian surface, from equatorial to circum-polar regions. In particular, we propose some simple photometric criteria to improve the identification of wet and/or icy soils from multiple observations under different geometries.

Seismic anisotropy in the Morcles nappe shear zone: Implications for seismic imaging of crustal scale shear zones

Microstructures and textures of calcite mylonites from the Morcles nappe large-scale shear zone in southwestern Switzerland develop principally as a function of 1) extrinsic physical parameters including temperature, stress, strain, strain rate and 2) intrinsic parameters, such as mineral composition. We collected rock samples at a single location from this shear zone, on which laboratory ultrasonic velocities, texture and microstructures were investigated and quantified. The samples had different concentration of secondary mineral phases (< 5 up to 40 vol.%). Measured seismic P wave anisotropy ranges from 6.5% for polyphase mylonites (~ 40 vol.%) to 18.4% in mylonites with < 5 vol.% secondary phases. Texture strength of calcite is the main factor governing the seismic P wave anisotropy. Measured S wave splitting is generally highest in the foliation plane, but its origin is more difficult to explain solely by calcite texture. Additional texture measurements were made on calcite mylonites with low concentration of secondary phases (≤ 10 vol.%) along the metamorphic gradient of the shear zone (15 km distance). A systematic increase in texture strength is observed moving from the frontal part of the shear zone (anchimetamorphism; 280 °C) to the higher temperature, basal part (greenschist facies; 350–400 °C). Calculated P wave velocities become increasingly anisotropic towards the high-strain part of the nappe, from an average of 5.8% in the frontal part to 13.2% in the root of the basal part. Secondary phases raise an additional complexity, and may act either to increase or decrease seismic anisotropy of shear zone mylonites. In light of our findings we reinterpret the origin of some seismically reflective layers in the Grône–Zweisimmen line in southwestern Switzerland (PNR20 Swiss National Research Program). We hypothesize that reflections originate in part from the lateral variation in textural and microstructural arrangement of calcite mylonites in shear zones.

A re-examination of petrogenesis and 40Ar/39Ar systematics in the the Chain of Ponds K-feldspar: "diffusion domain" archetype versus polyphase hygrochronology

K-feldspar (Kfs) from the Chain of Ponds Pluton (CPP) is the archetypal reference material, on which thermochronological modeling of Ar diffusion in discrete “domains” was founded. We re-examine the CPP Kfs using cathodoluminescence and back-scattered electron imaging, transmission electron microscopy, and electron probe microanalysis. 40Ar/39Ar stepwise heating experiments on different sieve fractions, and on handpicked and unpicked aliquots, are compared. Our results reproduce the staircase-shaped age spectrum and the Arrhenius trajectory of the literature sample, confirming that samples collected from the same locality have an identical Ar isotope record. Even the most pristine-looking Kfs from the CPP contains successive generations of secondary, metasomatic/retrograde mineral replacements that post-date magmatic crystallization. These chemically and chronologically distinct phases are responsible for its staircase-shaped age spectra, which are modified by handpicking. While genuine within-grain diffusion gradients are not ruled out by these data, this study demonstrates that the most important control on staircase-shaped age spectra is the simultaneous presence of heterochemical, diachronous post-magmatic mineral growth. At least five distinct mineral species were identified in the Kfs separate, three of which can be traced to external fluids interacting with the CPP in a chemically open system. Sieve fractions have size-shifted Arrhenius trajectories, negating the existence of the smallest “diffusion domains”. Heterochemical phases also play an important role in producing non-linear trajectories. In vacuo degassing rates recovered from Arrhenius plots are neither related to true Fick’s Law diffusion nor to the staircase shape of the age spectra. The CPP Kfs used to define the "diffusion domain" model demonstrates the predominance of metasomatic alteration by hydrothermal fluids and recrystallization in establishing the natural Ar distribution amongst different coexisting phases that gives rise to the staircase-shaped age spectrum. Microbeam imaging of textures is as essential for 40Ar-39Ar hygrochronology as it is for U-Pb geochronology.

The geomorphology and morphometry of the banded terrain in Hellas basin, Mars

Hellas basin is a large impact basin situated in the southern highlands of Mars. The north-western part of the basin has the lowest elevation (-7.5 km) on the planet and contains a possibly unique terrain type, which we informally call “banded terrain”. The banded terrain is made up of smooth-looking banded deposits that display signs of viscous behavior and a paucity of superimposed impact craters. In this study, we use newly acquired high spatial resolution images from the High Resolution Imaging Science Experiment (HiRISE) in addition to existing datasets to characterize the geomorphology, the morphometry and the architecture of the banded terrain. The banded terrain is generally confined to the NW edge of the Alpheus Colles plateau. The individual bands are ~3–15 km-long, ~0.3 km-wide and are separated by narrow inter-band depressions, which are ~65 m-wide and ~10 m-deep. The bands display several morphologies that vary from linear to concentric forms. Morphometric analysis reveals that the slopes along a given linear or lobate band ranges from 0.5° to 15° (average~6°), whereas the concentric bands are located on flatter terrain (average slope~2–3°). Crater-size frequency analysis yields an Amazonian-Hesperian boundary crater retention age for the terrain (~3 Gyr), which together, with the presence of very few degraded craters, either implies a recent emplacement, resurfacing, or intense erosion. The apparent sensitivity to local topography and preference for concentrating in localized depressions is compatible with deformation as a viscous fluid. In addition, the bands display clear signs of degradation and slumping at their margins along with a suite of other features that include fractured mounds, polygonal cracks at variable size-scales, and knobby/hummocky textures. Together, these features suggest an ice-rich composition for at least the upper layers of the terrain, which is currently being heavily modified through loss of ice and intense weathering, possibly by wind.

Manganiferous minerals of the epidote group from the Archaean basement of West Greenland

The chemical compositions and crystal structures of Mn3+-containing minerals from the epidote group in Greenland rocks are investigated and described in detail. They occur in hydrothermally altered Archaean mafic sequences within the gneissic complex of the North Atlantic craton of West Greenland. The Mn-containing minerals have a characteristic red to pink colour. A detailed microchemical study shows a significant inter- and intra-sample variation in Mn content. The samples from different parageneses can be classified as Mn-bearing epidote and Mn-bearing clinozoisite. The intra-sample variation in the content of Al, Fe and Mn is on a very fine scale, but still allows for identification of a negative correlation between Mn and Fe. Textures indicate different stages of growth. Crystal chemical data are compared with literature data and illustrate the basic systematic differences between the influence of Fe and Mn on the crystal structure of the epidote group minerals.

Regularizing Image Reconstruction for Gradient-Domain Rendering with Feature Patches

We present a novel algorithm to reconstruct high-quality images from sampled pixels and gradients in gradient-domain rendering. Our approach extends screened Poisson reconstruction by adding additional regularization constraints. Our key idea is to exploit local patches in feature images, which contain per-pixels normals, textures, position, etc., to formulate these constraints. We describe a GPU implementation of our approach that runs on the order of seconds on megapixel images. We demonstrate a significant improvement in image quality over screened Poisson reconstruction under the L1 norm. Because we adapt the regularization constraints to the noise level in the input, our algorithm is consistent and converges to the ground truth.

A systematic evaluation of the Zr-in-rutile thermometer in ultra-high temperature (UHT) rocks

The Zr-in-rutile geothermometer is potentially a widely applicable tool to estimate peak metamorphic temperatures in rocks from diverse geological settings. In order to evaluate its usefulness and reliability to record and preserve high temperatures in granulite facies rocks, rutile from UHT rocks was investigated to assess different mechanisms of Zr (re-)distribution following cooling from high temperature. Granulite facies paragneisses from the lowermost part of the Ivrea Zone, Italy, incorporated as thin sheets into the extensive basaltic body of the Mafic Complex were selected for this study. The results show that Zr-in-rutile thermometry, if properly applied, is well suited to identify and study UHT terranes as it preserves a record of temperatures up to 1190 °C, although the thermometer is susceptible to partial post-peak metamorphic resetting by Zr diffusion. Texturally homogeneous rutile grains preserve Zr concentrations corresponding to temperatures of prograde rutile growth. Diverse rutile textures and relationships between some rutile host grains and included or adjacent Zr-bearing phases bear testimony to varying mechanisms of partial redistribution and resetting of Zr in rutile during cooling and link Zr-in-rutile temperatures to different steps of the metamorphic evolution. Rutile grains that equilibrated their Zr concentrations at temperatures above 1070 °C (i.e. 1.1 wt% Zr) could not retain all Zr in the rutile structure during cooling and exsolved baddeleyite (ZrO2). By subsequent reaction of baddeleyite exsolution lamellae with SiO2, zircon needles formed before the system finally closed at 650–700 °C without significant net loss of Zr from the whole host rutile grain. By reintegration of zircon exsolution needles, peak metamorphic temperatures of up to 1190 °C are derived for the studied rocks, which demonstrates the suitability of this solution thermometer to record UHT conditions and also confirms the extraordinary geological setting of the lowermost part of the Ivrea Zone.

The morphological diversity of comet 67P/Churyumov-Gerasimenko

Images of comet 67P/Churyumov-Gerasimenko acquired by the OSIRIS (Optical, Spectroscopic and Infrared Remote Imaging System) imaging system onboard the European Space Agency's Rosetta spacecraft at scales of better than 0.8 meter per pixel show a wide variety of different structures and textures. The data show the importance of airfall, surface dust transport, mass wasting, and insolation weathering for cometary surface evolution, and they offer some support for subsurface fluidization models and mass loss through the ejection of large chunks of material.