Spatio-temporal wavelet regularization for parallel MRI reconstruction: application to functional MRI

Parallel MRI is a fast imaging technique that enables the acquisition of highly resolved images in space or/and in time. The performance of parallel imaging strongly depends on the reconstruction algorithm, which can proceed either in the original k-space (GRAPPA, SMASH) or in the image domain (SENSE-like methods). To improve the performance of the widely used SENSE algorithm, 2D- or slice-specific regularization in the wavelet domain has been deeply investigated. In this paper, we extend this approach using 3D-wavelet representations in order to handle all slices together and address reconstruction artifacts which propagate across adjacent slices. The gain induced by such extension (3D-Unconstrained Wavelet Regularized -SENSE: 3D-UWR-SENSE) is validated on anatomical image reconstruction where no temporal acquisition is considered. Another important extension accounts for temporal correlations that exist between successive scans in functional MRI (fMRI). In addition to the case of 2D+t acquisition schemes addressed by some other methods like kt-FOCUSS, our approach allows us to deal with 3D+t acquisition schemes which are widely used in neuroimaging. The resulting 3D-UWR-SENSE and 4D-UWR-SENSE reconstruction schemes are fully unsupervised in the sense that all regularization parameters are estimated in the maximum likelihood sense on a reference scan. The gain induced by such extensions is illustrated on both anatomical and functional image reconstruction, and also measured in terms of statistical sensitivity for the 4D-UWR-SENSE approach during a fast event-related fMRI protocol. Our 4D-UWR-SENSE algorithm outperforms the SENSE reconstruction at the subject and group levels (15 subjects) for different contrasts of interest (eg, motor or computation tasks) and using different parallel acceleration factors (R=2 and R=4) on 2x2x3mm3 EPI images.Comment: arXiv admin note: substantial text overlap with arXiv:1103.353

In-situ acoustic-based analysis system for physical and chemical properties of the lower Martian atmosphere

The Environmental Acoustic Reconnaissance and Sounding experiment (EARS), is composed of two parts: the Environmental Acoustic Reconnaissance (EAR) instrument and the Environmental Acoustic Sounding Experiment (EASE). They are distinct, but have the common objective of characterizing the acoustic environment of Mars. The principal goal of the EAR instrument is "listening" to Mars. This could be a most significant experiment if one thinks of everyday life experience where hearing is possibly the most important sense after sight. Not only will this contribute to opening up this important area of planetary exploration, which has been essentially ignored up until now, but will also bring the general public closer in contact with our most proximate planet. EASE is directed at characterizing acoustic propagation parameters, specifically sound velocity and absorption, and will provide information regarding important physical and chemical parameters of the lower Martian atmosphere; in particular, water vapor content, specific heat capacity, heat conductivity and shear viscosity, which will provide specific constraints in determining its composition. This would enable one to gain a deeper understanding of Mars and its analogues on Earth. Furthermore, the knowledge of the physical and chemical parameters of the Martian atmosphere, which influence its circulation, will improve the comprehension of its climate now and in the past, so as to gain insight on the possibility of the past presence of life on Mars. These aspect are considered strategic in the contest of its exploration, as is clearly indicated in NASA's four main objectives on "Long Term Mars Exploration Program" (http://marsweb.jpl.nasa.gov/mer/science).Comment: 16 pages including figure

In and out of Madagascar : dispersal to peripheral islands, insular speciation and diversification of Indian Ocean daisy trees (Psiadia, Asteraceae)

This study was supported by the European Union’s HOTSPOTS Training Network (MEST-2005-020561)Madagascar is surrounded by archipelagos varying widely in origin, age and structure. Although small and geologically young, these archipelagos have accumulated disproportionate numbers of unique lineages in comparison to Madagascar, highlighting the role of waif-dispersal and rapid in situ diversification processes in generating endemic biodiversity. We reconstruct the evolutionary and biogeographical history of the genus Psiadia (Asteraceae), a plant genus with near equal numbers of species in Madagascar and surrounding islands. Analyzing patterns and processes of diversification, we explain species accumulation on peripheral islands and aim to offer new insights on the origin and potential causes for diversification in the Madagascar and Indian Ocean Islands biodiversity hotspot. Our results provide support for an African origin of the group, with strong support for non-monophyly. Colonization of the Mascarenes took place by two evolutionary distinct lineages from Madagascar, via two independent dispersal events, each unique for their spatial and temporal properties. Significant shifts in diversification rate followed regional expansion, resulting in co-occurring and phenotypically convergent species on high-elevation volcanic slopes. Like other endemic island lineages, Psiadia have been highly successful in dispersing to and radiating on isolated oceanic islands, typified by high habitat diversity and dynamic ecosystems fuelled by continued geological activity. Results stress the important biogeographical role for Rodrigues in serving as an outlying stepping stone from which regional colonization took place. We discuss how isolated volcanic islands contribute to regional diversity by generating substantial numbers of endemic species on short temporal scales. Factors pertaining to the mode and tempo of archipelago formation and its geographical isolation strongly govern evolutionary pathways available for species diversification, and the potential for successful diversification of dispersed lineages, therefore, appears highly dependent on the timing of arrival, as habitat and resource properties change dramatically over the course of oceanic island evolution.Publisher PDFPeer reviewe

Quantification and Reconstruction in Photoacoustic Tomography

Optical absorption is closely associated with many physiological important parameters, such as the concentration and oxygen saturation of hemoglobin. Conventionally, accurate quantification in PAT requires knowledge of the optical fluence attenuation, acoustic pressure attenuation, and detection bandwidth. We circumvent this requirement by quantifying the optical absorption coefficients from the acoustic spectra of PA signals acquired at multiple optical wavelengths. We demonstrate the method using the optical-resolution photoacoustic microscopy: OR-PAM) and the acoustical-resolution photoacoustic microscopy: AR-PAM) in the optical ballistic regime and in the optical diffusive regime, respectively. The data acquisition speed in photoacoustic computed tomography: PACT) is limited by the laser repetition rate and the number of parallel ultrasound detecting channels. Reconstructing an image with fewer measurements can effectively accelerate the data acquisition and reduce the system cost. We adapted Compressed Sensing: CS) for the reconstruction in PACT. CS-based PACT was implemented as a non-linear conjugate gradient descent algorithm and tested with both phantom and in vivo experiments. Speckles have been considered ubiquitous in all scattering-based coherent imaging technologies. As a coherent imaging modality based on optical absorption, photoacoustic: PA) tomography: PAT) is generally devoid of speckles. PAT suppresses speckles by building up prominent boundary signals, via a mechanism similar to that of specular reflection. When imaging smooth boundary absorbing targets, the speckle visibility in PAT, which is defined as the ratio of the square root of the average power of speckles to that of boundaries, is inversely proportional to the square root of the absorber density. If the surfaces of the absorbing targets have uncorrelated height fluctuations, however, the boundary features may become fully developed speckles. The findings were validated by simulations and experiments. The first- and second-order statistics of PAT speckles were also studied experimentally. While the amplitude of the speckles follows a Gaussian distribution, the autocorrelation of the speckle patterns tracks that of the system point spread function

How to find real-world applications for compressive sensing

The potential of compressive sensing (CS) has spurred great interest in the research community and is a fast growing area of research. However, research translating CS theory into practical hardware and demonstrating clear and significant benefits with this hardware over current, conventional imaging techniques has been limited. This article helps researchers to find those niche applications where the CS approach provides substantial gain over conventional approaches by articulating lessons learned in finding one such application; sea skimming missile detection. As a proof of concept, it is demonstrated that a simplified CS missile detection architecture and algorithm provides comparable results to the conventional imaging approach but using a smaller FPA. The primary message is that all of the excitement surrounding CS is necessary and appropriate for encouraging our creativity but we all must also take off our "rose colored glasses" and critically judge our ideas, methods and results relative to conventional imaging approaches.Comment: 10 page

Maskless imaging of dense samples using pixel super-resolution based multi-height lensfree on-chip microscopy.

Lensfree in-line holographic microscopy offers sub-micron resolution over a large field-of-view (e.g., ~24 mm2) with a cost-effective and compact design suitable for field use. However, it is limited to relatively low-density samples. To mitigate this limitation, we demonstrate an on-chip imaging approach based on pixel super-resolution and phase recovery, which iterates among multiple lensfree intensity measurements, each having a slightly different sample-to-sensor distance. By digitally aligning and registering these lensfree intensity measurements, phase and amplitude images of dense and connected specimens can be iteratively reconstructed over a large field-of-view of ~24 mm2 without the use of any spatial masks. We demonstrate the success of this multi-height in-line holographic approach by imaging dense Papanicolaou smears (i.e., Pap smears) and blood samples

Effect of decorrelation on 3-D grating detection with static and dynamic random-dot stereograms

Three experiments examined the effects of image decorrelation on the stereoscopic detection of sinusoidal depth gratings in static anddynamic random-dot stereograms (RDS). Detection was found to tolerate greater levels of image decorrelation as: (i) density increasedfrom 23 to 676 dots/deg2; (ii) spatial frequency decreased from 0.88 to 0.22 cpd; (iii) amplitude increased above 0.5 arcmin; and (iv) dotlifetime decreased from 1.6 s (static RDS) to 80 ms (dynamic RDS). In each case, the specific pattern of tolerance to decorrelation couldbe explained by its consequences for image sampling, filtering, and the influence of depth noise