Mayavi: 3D Visualization of Scientific Data

Ramachandran, Prabhu; Varoquaux, Gaël

doi:10.1109/mcse.2011.35

Cited by 603 publications

(411 citation statements)

References 4 publications

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“…Post hoc pairwise comparisons between groups were computed using the least squares means procedure with a Tukey's correction for multiple comparisons. Network results were rendered for display with custom software written using Mayavi (Ramachandran and Varoquaux, 2011).…”

Section: Image Analysis: Resting-state Functional Connectivitymentioning

confidence: 99%

Common and Dissociable Dysfunction of the Reward System in Bipolar and Unipolar Depression

Satterthwaite

Kable

Vandekar

et al. 2015

Neuropsychopharmacol

224

147

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Unipolar and bipolar depressive episodes have a similar clinical presentation that suggests common dysfunction of the brain's reward system. Here, we evaluated the relationship of both dimensional depression severity and diagnostic category to reward system function in both bipolar and unipolar depression. In total, 89 adults were included, including 27 with bipolar depression, 25 with unipolar depression, and 37 healthy comparison subjects. Subjects completed both a monetary reward task and a resting-state acquisition during 3T BOLD fMRI. Across disorders, depression severity was significantly associated with reduced activation for wins compared with losses in bilateral ventral striatum, anterior cingulate cortex, posterior cingulate cortex, and right anterior insula. Resting-state connectivity within this reward network was also diminished in proportion to depression severity, most notably connectivity strength in the left ventral striatum. In addition, there were categorical differences between patient groups: resting-state connectivity at multiple reward network nodes was higher in bipolar than in unipolar depression. Reduced reward system task activation and resting-state connectivity therefore appear to be a brain phenotype that is dimensionally related to depression severity in both bipolar and unipolar depression. In contrast, categorical differences in reward system resting connectivity between unipolar and bipolar depression may reflect differential risk of mania. Reward system dysfunction thus represents a common brain mechanism with relevance that spans categories of psychiatric diagnosis.

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Section: Image Analysis: Resting-state Functional Connectivitymentioning

confidence: 99%

Common and Dissociable Dysfunction of the Reward System in Bipolar and Unipolar Depression

Satterthwaite

Kable

Vandekar

et al. 2015

Neuropsychopharmacol

224

147

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“…2, we have attempted to capture the complete structure and shape of the bispectrum using a three-dimensional contour plot. We have made use of Mayavi and Python to create the three-dimensional plot [62]. We have plotted the parameter f NL for a wide range of the wavenumbers k 1 , k 2 and k 3 , over the allowed domain wherein the corresponding wavevectors satisfy the triangularity condition.…”

Section: F Nl For An Arbitrary Triangular Configuration Of the Wavenumentioning

confidence: 99%

On the scalar consistency relation away from slow roll

Vijayakumar

Hazra

Sriramkumar

2015

J. Cosmol. Astropart. Phys.

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Abstract. As is well known, the non-Gaussianity parameter f NL , which is often used to characterize the amplitude of the scalar bi-spectrum, can be expressed completely in terms of the scalar spectral index n s in the squeezed limit, a relation that is referred to as the consistency condition. This relation, while it is largely discussed in the context of slow roll inflation, is actually expected to hold in any single field model of inflation, irrespective of the dynamics of the underlying model, provided inflation occurs on the attractor at late times. In this work, we explicitly examine the validity of the consistency relation, analytically as well as numerically, away from slow roll. Analytically, we first arrive at the relation in the simple case of power law inflation. We also consider the non-trivial example of the Starobinsky model involving a linear potential with a sudden change in its slope (which leads to a brief period of fast roll), and establish the condition completely analytically. We then numerically examine the validity of the consistency relation in three inflationary models that lead to the following features in the scalar power spectrum due to departures from slow roll: (i) a sharp cut off at large scales, (ii) a burst of oscillations over an intermediate range of scales, and (iii) small, but repeated, modulations extending over a wide range of scales. It is important to note that it is exactly such spectra that have been found to lead to an improved fit to the CMB data, when compared to the more standard power law primordial spectra, by the Planck team. We evaluate the scalar bi-spectrum for an arbitrary triangular configuration of the wavenumbers in these inflationary models and explicitly illustrate that, in the squeezed limit, the consistency condition is indeed satisfied even in situations consisting of strong deviations from slow roll. We conclude with a brief discussion of the results.

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“…Iso-density contours are shown in grey scales in unit of cm −3 in logarithmic scale, while the magnetic field module is shown in colour scale in unit of μG. Field line plots are generated using the visualisation software package MAYAVI (Ramachandran & Varoquaux 2011). λ = 8.38 corresponds to the case of a "roundish" core, with a density distribution almost spherically symmetric; when λ = 1.63 the density is distributed in a disc-like configuration; finally, λ = 2.66 represents the intermediate case.…”

Section: Column-density Versus Magnetic-field Effects On Cosmic-ray Imentioning

confidence: 99%

Cosmic-ray ionisation in collapsing clouds

Padovani

Hennebelle

Galli

2013

A&A

104

118

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Context. Cosmic rays play an important role in dense molecular cores, affecting their thermal and dynamical evolution and initiating the chemistry. Several studies have shown that the formation of protostellar discs in collapsing clouds is severely hampered by the braking torque exerted by the entrained magnetic field on the infalling gas, as long as the field remains frozen to the gas. Aims. In this paper we examine the possibility that the concentration and twisting of the field lines in the inner region of collapse can produce a significant reduction of the ionisation fraction. Methods. To check whether the cosmic-ray ionisation rate can fall below the critical value required to maintain good coupling, we first study the propagation of cosmic rays in a model of a static magnetised cloud varying the relative strength of the toroidal/poloidal components and the mass-to-flux ratio. We then follow the path of cosmic rays using realistic magnetic field configurations generated by numerical simulations of a rotating collapsing core with different initial conditions. Results. We find that an increment of the toroidal component of the magnetic field, or, in general, a more twisted configuration of the field lines, results in a decrease in the cosmic-ray flux. This is mainly due to the magnetic mirroring effect that is stronger where larger variations in the field direction are present. In particular, we find a decrease of the cosmic-ray ionisation rate below 10 −18 s −1 in the central 300-400 AU, where density is higher than about 10 9 cm −3 . This very low value of the ionisation rate is attained in the cases of intermediate and low magnetisation (mass-to-flux ratio λ = 5 and 17, respectively) and for toroidal fields larger than about 40% of the total field. Conclusions. Magnetic field effects can significantly reduce the ionisation fraction in collapsing clouds. We provide a handy fitting formula to compute approximately the attenuation of the cosmic-ray ionisation rate in a molecular cloud as a function of the density and the magnetic configuration.

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Mayavi: 3D Visualization of Scientific Data

Cited by 603 publications

References 4 publications

Common and Dissociable Dysfunction of the Reward System in Bipolar and Unipolar Depression

Common and Dissociable Dysfunction of the Reward System in Bipolar and Unipolar Depression

On the scalar consistency relation away from slow roll

Cosmic-ray ionisation in collapsing clouds

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