Drishti: a volume exploration and presentation tool

Limaye, Ajay

doi:10.1117/12.935640

Cited by 438 publications

(322 citation statements)

References 8 publications

(4 reference statements)

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“…These were converted to two image stacks that were cropped and then aligned in SPIERSalign (Sutton et al 2012), surfaced in SPIERSedit, rendered in Blender (cf. Garwood & Dunlop 2014) and volume rendered in Drishti (Limaye 2012).…”

Section: Methodsmentioning

confidence: 99%

Remarkable preservation of brain tissues in an Early Cretaceous iguanodontian dinosaur

Brasier

Norman

Liu

et al. 2016

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It has become accepted in recent years that the fossil record can preserve labile tissues. We report here the highly detailed mineralization of soft tissues associated with a naturally occurring brain endocast of an iguanodontian dinosaur found in c. 133 Ma fluvial sediments of the Wealden at Bexhill, Sussex, UK. Moulding of the braincase wall and the mineral replacement of the adjacent brain tissues by phosphates and carbonates allowed the direct examination of petrified brain tissues. Scanning electron microscopy (SEM) imaging and computed tomography (CT) scanning revealed preservation of the tough membranes (meninges) that enveloped and supported the brain proper. Collagen strands of the meningeal layers were preserved in collophane. The blood vessels, also preserved in collophane, were either lined by, or infilled with, microcrystalline siderite. The meninges were preserved in the hindbrain region and exhibit structural similarities with those of living archosaurs. Greater definition of the forebrain (cerebrum) than the hindbrain (cerebellar and medullary regions) is consistent with the anatomical and implied behavioural complexity previously described in iguanodontian-grade ornithopods. However, we caution that the observed proximity of probable cortical layers to the braincase walls probably resulted from the settling of brain tissues against the roof of the braincase after inversion of the skull during decay and burial.

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Section: Methodsmentioning

confidence: 99%

Remarkable preservation of brain tissues in an Early Cretaceous iguanodontian dinosaur

Brasier

Norman

Liu

et al. 2016

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“…These images were used to assess the difference of the imaged density of CASs between the soil close to macropores and the soil in the matrix of all natural soil samples. (Limaye, 2012).…”

Section: Spatial Distribution Of Cation Exchange Capacitymentioning

confidence: 99%

Quantitative imaging of the 3-D distribution of cation adsorption sites in undisturbed soil

Keck

Strobel

Gustafsson

et al. 2017

SOIL

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Abstract. Several studies have shown that the distribution of cation adsorption sites (CASs) is patchy at a millimetre to centimetre scale. Often, larger concentrations of CASs in biopores or aggregate coatings have been reported in the literature. This heterogeneity has implications on the accessibility of CASs and may influence the performance of soil system models that assume a spatially homogeneous distribution of CASs. In this study, we present a new method to quantify the abundance and 3-D distribution of CASs in undisturbed soil that allows for investigating CAS densities with distance to the soil macropores. We used X-ray imaging with Ba 2+ as a contrast agent. Ba 2+ has a high adsorption affinity to CASs and is widely used as an index cation to measure the cation exchange capacity (CEC). Eight soil cores (approx. 10 cm 3 ) were sampled from three locations with contrasting texture and organic matter contents. The CASs of our samples were saturated with Ba 2+ in the laboratory using BaCl 2 (0.3 mol L −1 ). Afterwards, KCl (0.1 mol L −1 ) was used to rinse out Ba 2+ ions that were not bound to CASs. Before and after this process the samples were scanned using an industrial X-ray scanner. Ba 2+ bound to CASs was then visualized in 3-D by the difference image technique. The resulting difference images were interpreted as depicting the Ba 2+ bound to CASs only. The X-ray image-derived CEC correlated significantly with results of the commonly used ammonium acetate method to determine CEC in well-mixed samples. The CEC of organic-matter-rich samples seemed to be systematically overestimated and in the case of the clay-rich samples with less organic matter the CEC seemed to be systematically underestimated. The results showed that the distribution of the CASs varied spatially within most of our samples down to a millimetre scale. There was no systematic relation between the location of CASs and the soil macropore structure. We are convinced that the approach proposed here will strongly aid the development of more realistic soil system models.

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“…Reconstruction and thermal drift correction was performed in NRecon v. 1.7.0.4 (Brucker microCT) and the images were converted to 8bit grayscale images via Fiji ImageJ v. 1.49k (Schindelin et al 2012). Volume rendering of the dataset for three-dimensional exploration and visualization was done in Drishti v. 2.6.3 (Limaye 2012). The tentorium and nebententorium were segmented automatically and corrected manually in ITK-SNAP v. 3.4.0 (Yushkevich et al 2006).…”

Section: Micro-ct Imagingmentioning

confidence: 99%

Integrative description of two new species of Malagasy chirping giant pill-millipedes, genus Sphaeromimus (Diplopoda: Sphaerotheriida: Arthrosphaeridae)

Moritz‍

Wesener‍

2017

EJT

774

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Abstract. The species-rich giant pill-millipedes (Sphaerotheriida) often represent a microendemic component of Madagascar's mega-invertebrate fauna. Of the chirping genus Sphaeromimus de Saussure & Zehntner, 1902, ten species have been described. Here, we describe two new species of Sphaeromimus integratively, combining light microscopy, scanning electron microscopy, DNA barcoding and micro-CT technology for the first time in a taxonomic description of a giant pillmillipede. S. kalambatritra sp. nov. and S. midongy sp. nov. are the first giant pill-millipedes collected and described from the mountainous rainforests of Kalambatritra and Midongy. Both species show island gigantism compared to their congeners. Our analysis of the mitochondrial COI gene shows that the two species are related to one another with a moderate genetic distance (9.4%), while they are more closely related to an undetermined specimen from the forest of Vevembe (6.3% and 8.4%). They stand in a basal position with S. ivohibe S. musicus (de Saussure & Zehntner, 1897). The four aforementioned species share a high number of stridulation ribs on the male harp. Our micro-CT analysis provides a look into the head of S. kalambatritra sp. nov. and shows that non-destructive CT methods are a useful tool for studying the inner morphology of giant pill-millipedes.

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Drishti: a volume exploration and presentation tool

Cited by 438 publications

References 8 publications

Remarkable preservation of brain tissues in an Early Cretaceous iguanodontian dinosaur

Remarkable preservation of brain tissues in an Early Cretaceous iguanodontian dinosaur

Quantitative imaging of the 3-D distribution of cation adsorption sites in undisturbed soil

Integrative description of two new species of Malagasy chirping giant pill-millipedes, genus Sphaeromimus (Diplopoda: Sphaerotheriida: Arthrosphaeridae)

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