3D Data Cube Research Articles

Probability of correct reconstruction in compressive spectral imaging

Coded Aperture Snapshot Spectral Imaging (CASSI) systems capture the 3-dimensional (3D) spatio-spectral information of a scene using a set of 2-dimensional (2D) random coded Focal Plane Array (FPA) measurements. A compressed sensing reconstruction algorithm is then used to recover the underlying spatio-spectral 3D data cube. The quality of the reconstructed spectral images depends exclusively on the CASSI sensing matrix, which is determined by the statistical structure of the coded apertures. The Restricted Isometry Property (RIP) of the CASSI sensing matrix is used to determine the probability of correct image reconstruction and provides guidelines for the minimum number of FPA measurement shots needed for image reconstruction. Further, the RIP can be used to determine the optimal structure of the coded projections in CASSI. This article describes the CASSI optical architecture and develops the RIP for the sensing matrix in this system. Simulations show the higher quality of spectral image reconstructions when the RIP property is satisfied. Simulations also illustrate the higher performance of the optimal structured projections in CASSI.

Characteristic Contrast in Δfmin Maps of Organic Molecules Using Atomic Force Microscopy.

Scanning tunneling microscopy and atomic force microscopy can provide detailed information about the geometric and electronic structure of molecules with submolecular spatial resolution. However, an essential capability to realize the full potential of these techniques for chemical applications is missing from the scanning probe toolbox: chemical recognition of organic molecules. Here, we show that maps of the minima of frequency shift-distance curves extracted from 3D data cubes contain characteristic contrast. A detailed theoretical analysis based on density functional theory and molecular mechanics shows that these features are characteristic for the investigated species. Structurally similar but chemically distinct molecules yield significantly different features. We find that the van der Waals and Pauli interaction, together with the specific adsorption geometry of a given molecule on the surface, accounts for the observed contrast.

Characterization of Coal Micro-Pore Structure and Simulation on the Seepage Rules of Low-Pressure Water Based on CT Scanning Data

This paper used the X-ray three-dimensional (3D) microscope and acquired, through CT scanning, the 3D data of the long-frame coal sample from the Daliuta Coal Mine. Then, the 3D datacube reconstructed from the coal’s CT scanning data was visualized with the use of Avizo, an advanced visualization software (FEI, Hillsboro, OR, USA). By means of a gray-scale segmentation technique, the model of the coal’s micro-pore structure was extracted from the object region, and the precise characterization was then conducted. Finally, the numerical simulation on the water seepage characteristics in the coal micro-pores model under the pressure of 3 MPa was performed on the CFX platform. Results show that the seepage of low-pressure water exhibited preference to the channels with large pore radii, short paths, and short distance from the outlet. The seepage pressure of low-pressure water decreased gradually along the seepage direction, while the seepage velocity of low-pressure water decreased gradually along the direction from the pore center to the wall. Regarding the single-channel seepage behaviors, the seepage velocity and mass flow rate of water seepage in the X direction were the largest, followed by the values of the seepage in the Y direction, and the seepage velocity and mass flow rate of water seepage in the Z direction were the smallest. Compared with the results in single-channel seepage, the dual-channel seepage in the direction of (X + Y) and the multi-channel seepage in the direction of (X + Y + Z) exhibited significant increases in the overall seepage velocity. The present study extends the application of 3D CT scanning data and provides a new idea and approach for exploring the seepage rules in coal micro-pore structures.

Multispectral imaging using a single bucket detector.

Existing multispectral imagers mostly use available array sensors to separately measure 2D data slices in a 3D spatial-spectral data cube. Thus they suffer from low photon efficiency, limited spectrum range and high cost. To address these issues, we propose to conduct multispectral imaging using a single bucket detector, to take full advantage of its high sensitivity, wide spectrum range, low cost, small size and light weight. Technically, utilizing the detector’s fast response, a scene’s 3D spatial-spectral information is multiplexed into a dense 1D measurement sequence and then demultiplexed computationally under the single pixel imaging scheme. A proof-of-concept setup is built to capture multispectral data of 64 pixels × 64 pixels × 10 wavelength bands ranging from 450 nm to 650 nm, with the acquisition time being 1 minute. The imaging scheme holds great potentials for various low light and airborne applications, and can be easily manufactured as production-volume portable multispectral imagers.

Spatially-resolved SFR in nearby disk galaxies using IFS data

AbstractExploring the spatial distribution of the star formation rate (SFR) in nearby galaxies is essential to understand their evolution through cosmic time. With this aim in mind, we use a representative sample that contains a variety of morphological types, the CALIFA Integral Field Spectroscopy (IFS) sample. Previous to this work, we have verified that our extinction-corrected Hα measurements successfully reproduce the values derived from other SFR tracers such as Hαobs + IR or UVobs + IR (Catalán-Torrecilla et al. 2015).Now, we go one step further applying 2-dimensional photometric decompositions (Méndez-Abreu et al. (2008), Méndez-Abreu et al. (2014)) over these datacubes. This method allows us to obtain the amount of SFR in the central part (bulge or nuclear source), the bar and the disk, separately. First, we determine the light coming from each component as the ratio between the luminosity in every component (bulge, bar or disk) and the total luminosity of the galaxy. Then, for each galaxy we multiply the IFS datacubes by these previous factors to recover the luminosity in each component. Finally, we derive the spectrum associated to each galaxy component integrating the spatial information in the weighted datacube using an elliptical aperture covering the whole galaxy.2D photometric decomposition applied over 3D datacubes will give us a more detailed understanding of the role that disks play in more massive galaxies. Knowing if the disks in more massive SF galaxies have on average a lower or higher level of star formation activity and how these results are affected by the presence of nuclear bars are still open questions that we can now solve. We describe the behavior of these components in the SFR vs. stellar mass diagram. In particular, we highlight the role of the disks and their contribution to both the integrated SFR for the whole galaxy and the SFR in the disk at different stellar masses in the SFR vs. stellar mass diagram together with their relative position to the star forming Main Sequence.

High-dynamic range compressive spectral imaging by grayscale coded aperture adaptive filtering

<p class="p1">The coded aperture snapshot spectral imaging system (CASSI) is an imaging architecture which senses the three dimensional informa-tion of a scene with two dimensional (2D) focal plane array (FPA) coded projection measurements. A reconstruction algorithm takes advantage of the compressive measurements sparsity to recover the underlying 3D data cube. Traditionally, CASSI uses block-un-block coded apertures (BCA) to spatially modulate the light. In CASSI the quality of the reconstructed images depends on the design of these coded apertures and the FPA dynamic range. This work presents a new CASSI architecture based on grayscaled coded apertu-res (GCA) which reduce the FPA saturation and increase the dynamic range of the reconstructed images. The set of GCA is calculated in a real-time adaptive manner exploiting the information from the FPA compressive measurements. Extensive simulations show the attained improvement in the quality of the reconstructed images when GCA are employed. In addition, a comparison between traditional coded apertures and GCA is realized with respect to noise tolerance.</p>

SFR bulge-to-disk ratios from the CALIFA IFS nearby galaxies survey

AbstractOur aim is to study the Star Formation Rate (SFR) by galaxy components such as bulges, bars and disks in a representative sample of nearby galaxies. A 2-dimensional (2D) photometric decomposition approach (GASP2D) is used to obtain these components. The availability of IFS data for the CALIFA galaxies makes possible to go one step further as we can apply the previous decompositions over 3D datacubes to disentangle the spatial distribution of the SFR over different components free from the limitations associated to narrow-band imaging.

SIMULATED PHOTOEVAPORATIVE MASS LOSS FROM HOT JUPITERS IN 3D

ABSTRACT Ionizing stellar photons heat the upper regions of planetary atmospheres, driving atmospheric mass loss. Gas escaping from several hot, hydrogen-rich planets has been detected using UV and X-ray transmission spectroscopy. Because these planets are tidally locked, and thus asymmetrically irradiated, escaping gas is unlikely to be spherically symmetric. In this paper, we focus on the effects of asymmetric heating on local outflow structure. We use the Athena code for hydrodynamics to produce 3D simulations of hot Jupiter mass loss that jointly model wind launching and stellar heating via photoionization. Our fiducial planet is an inflated, hot Jupiter with radius R p = 2.14 R Jup ?> and mass M p = 0.53 M Jup ?> . We irradiate the initially neutral, atomic hydrogen atmosphere with 13.6 eV photons and compute the outflow’s ionization structure. There are clear asymmetries in the atmospheric outflow, including a neutral shadow on the planet’s nightside. Given an incident ionizing UV flux comparable to that of the Sun, we find a steady-state mass loss rate of ∼ 2 × 10 10 ?> g s−1. The total mass loss rate and the outflow substructure along the substellar ray show good agreement with earlier 1D models, for two different fluxes. Our 3D data cube can be used to generate the outflow’s extinction spectrum during transit. As a proof of concept, we find absorption of stellar Lyα at Doppler-shifted velocities of up to ±50 km s−1. Our work provides a starting point for further 3D models that can be used to predict observable signatures of hot Jupiter mass loss.

Direct shear mapping – a new weak lensing tool

We have developed a new technique called Direct Shear Mapping (DSM) to measure gravitational lensing shear directly from observations of a single background source. The technique assumes the velocity map of an un-lensed, stably-rotating galaxy will be rotationally symmetric. Lensing distorts the velocity map making it asymmetric. The degree of lensing can be inferred by determining the transformation required to restore axisymmetry. This technique is in contrast to traditional weak lensing methods, which require averaging an ensemble of background galaxy ellipticity measurements, to obtain a single shear measurement. We have tested the ecacy of our tting algorithm with a suite of systematic tests on simulated data. We demonstrate that we are in principle able to measure shears as small as 0.01. In practice, we have tted for the shear in very low redshift (and hence un-lensed) velocity maps, and have obtained null result with an error of 0:01. This high sensitivity results from analysing spatially resolved spectroscopic images (i.e. 3D data cubes), including not just shape information (as in traditional weak lensing measurements) but velocity information as well. Spirals and rotating ellipticals are ideal targets for this new technique. Data from any large IFU or radio telescope is suitable, or indeed any instrument with spatially resolved spectroscopy such as SAMI, ALMA, HETDEX and SKA.

Filamentary Structure of the Orion A Molecular Cloud

Interstellar filaments pervade molecular clouds on all scales providing a bridge between the gas with relatively low densities and the dense clumps. In this work, we characterize various physical properties of filaments in the Orion A molecular cloud using preliminary datasets from the CARMA Orion project. We use an automated filament finding algorithm, DisPerSE, on 3D datacubes, and custom characterization algorithms.

Deblurring and Sparse Unmixing of Hyperspectral Images Using Multiple Point Spread Functions

This paper is concerned with deblurring and spectral analysis of ground-based astronomical images of space objects. A numerical approach is provided for deblurring and sparse unmixing of ground-based hyperspectral images (HSIs) of objects taken through atmospheric turbulence. Hyperspectral imaging systems capture a three-dimensional (3D) datacube (tensor) containing two-dimensional (2D) spatial information and one-dimensional (1D) spectral information at each spatial location. Pixel intensities vary with wavelength bands, providing a spectral trace of intensity values and generating a spatial map of spectral variation (spectral signatures of materials). The deblurring and spectral unmixing problem is quite challenging since the point spread function (PSF) depends on the imaging system as well as the seeing conditions and is wavelength varying. We show how to efficiently construct an optimal Kronecker product--based preconditioner, and provide numerical methods for estimating the multiple PSFs using spectral data from an isolated (guide) star for joint deblurring and sparse unmixing of HSI datasets in order to spectrally analyze the image objects. The methods are illustrated with numerical experiments on a commonly used test example, a simulated HSI of the Hubble Space Telescope satellite.

Spectral resolution enhancement of hyperspectral imagery by a multiple-aperture compressive optical imaging system

The Coded Aperture Snapshot Spectral Imaging (CASSI) system captures the three-dimensional (3D) spatio-spectral information of a scene using a set of two-dimensional (2D) random-coded Focal Plane Array (FPA) measurements. A compressive sensing reconstruction algorithm is then used to recover the underlying spatio-spectral 3D data cube. The quality of the reconstructed spectral images depends exclusively on the CASSI sensing matrix, which is determined by the structure of a set of random coded apertures. In this paper, the CASSI system is generalized by developing a multiple-aperture optical imaging system such that spectral resolution enhancement is attainable. In the proposed system, a pair of high-resolution coded apertures is introduced into the CASSI system, allowing it to encode both spatial and spectral characteristics of the hyperspectral image. This approach allows the reconstruction of superresolved hyperspectral data cubes, where the number of spectral bands is significantly increased and the quality in the spatial domain is greatly improved. Extensively simulated experiments show a gain in the peak-signal-to-noise ratio (PSNR), along with a better fit of the reconstructed spectral signatures to the original spectral data.

Three-dimensional valency mapping in ceria nanocrystals.

Using electron tomography combined with electron energy loss spectroscopy (EELS), we are able to map the valency of the Ce ions in CeO2-x nanocrystals in three dimensions. Our results show a clear facet-dependent reduction shell at the surface of ceria nanoparticles; {111} surface facets show a low surface reduction, whereas at {001} surface facets, the cerium ions are more likely to be reduced over a larger surface shell. Our generic tomographic technique allows a full 3D data cube to be reconstructed, containing an EELS spectrum in each voxel. This possibility enables a three-dimensional investigation of a plethora of material-specific physical properties such as valency, chemical composition, oxygen coordination, or bond lengths, triggering the synthesis of nanomaterials with improved properties.

RECONSTRUCTING THE SUBSURFACE THREE-DIMENSIONAL MAGNETIC STRUCTURE OF A SOLAR ACTIVE REGION USING SDO /HMI OBSERVATIONS

A solar active region (AR) is a three-dimensional (3D) magnetic structure formed in the convection zone, whose property is fundamentally important for determining the coronal structure and solar activity when emerged. However, our knowledge of the detailed 3D structure prior to its emergence is rather poor, largely limited by the low cadence and sensitivity of previous instruments. Here, using the 45?s high-cadence observations from the Helioseismic and Magnetic Imager on board the Solar Dynamics Observatory, we are able for the first time to reconstruct a 3D data cube and infer the detailed subsurface magnetic structure of NOAA AR 11158, and to characterize its magnetic connectivity and topology. This task is accomplished with the aid of the image-stacking method and advanced 3D visualization. We find that the AR consists of two major bipoles or four major polarities. Each polarity in 3D shows interesting tree-like structure, i.e., while the root of the polarity appears as a single tree-trunk-like tube, the top of the polarity has multiple branches consisting of smaller and thinner flux tubes which connect to the branches of the opposite polarity that is similarly fragmented. The roots of the four polarities align well along a straight line, while the top branches are slightly non-coplanar. Our observations suggest that an active region, even appearing highly complicated on the surface, may originate from a simple straight flux tube that undergoes both horizontal and vertical bifurcation processes during its rise through the convection zone.

Efficient video coding using optimal compression plane and background modelling

All existing video coding standards consider a video as a temporal (along T-axis) collection of two-dimensional (2D) pictures (formed by XY-axes) and compress them by exploiting spatial and temporal redundancy in the pictures. A recent optimal compression plane (OCP) determination technique shows that better compression can be achieved by relaxing the physical meaning of axes by exploring information redundancy in a fuller extent where a video is considered as a 3D data cube. Spatial and temporal dimensions are determined based on the statistical redundancy along each axis. Treating a video as a 3D data cube revolutionises the traditional video features such as background, motion, object, zooming, panning etc. In this study, the authors apply dynamic background modelling to the OCP plane to exploit the newly generated background in the video for further improving the coding performance. The experimental results reveal that the proposed approach outperforms the existing state-of-the-art OCP technique as well as the H.264 video coding standard.

Constant cross section of loops in the solar corona

The corona of the Sun is dominated by emission from loop-like structures. When observed in X-ray or extreme ultraviolet emission, these million K hot coronal loops show a more or less constant cross section. In this study we show how the interplay of heating, radiative cooling, and heat conduction in an expanding magnetic structure can explain the observed constant cross section. We employ a three-dimensional magnetohydrodynamics (3D MHD) model of the corona. The heating of the coronal plasma is the result of braiding of the magnetic field lines through footpoint motions and subsequent dissipation of the induced currents. From the model we synthesize the coronal emission, which is directly comparable to observations from, e.g., the Atmospheric Imaging Assembly on the Solar Dynamics Observatory (AIA/SDO). We find that the synthesized observation of a coronal loop seen in the 3D data cube does match actually observed loops in count rate and that the cross section is roughly constant, as observed. The magnetic field in the loop is expanding and the plasma density is concentrated in this expanding loop; however, the temperature is not constant perpendicular to the plasma loop. The higher temperature in the upper outer parts of the loop is so high that this part of the loop is outside the contribution function of the respective emission line(s). In effect, the upper part of the plasma loop is not bright and thus the loop actually seen in coronal emission appears to have a constant width. From this we can conclude that the underlying field-line-braiding heating mechanism provides the proper spatial and temporal distribution of the energy input into the corona --- at least on the observable scales.

Constructing hydrocarbon reservoir analogues of aeolian systems using ground penetrating radar

Abstract This paper presents a three-dimensional ground penetrating radar (GPR) case study of contemporary dunes from southern Libya that may serve as an analogue for oil and gas reservoirs in aeolian systems. A 30 MHz inline GPR system was used to image an undulating region 260 m wide × 480 m long in less than 4 h, with a line spacing of approximately 1 m at survey speeds of over 30 km/h. The internal aeolian architecture was imaged to a depth of about 40 m. Complex three-dimensional cross-stratification is evident within the resultant 3D data cube. A full range of dune heterogeneity is inferred: facies interaction between lake and dune environments, the course of ancient streams, dune field/sand sheet relationships, bounding surface geometry and primary strata type distribution. Different dune generations are perceived within the survey, with complex superimposed relationships apparent. Near-surface sand sheet and deeper linear dune/barchanoid ridge geometries are revealed. However, it is recognised that the complex pattern of contemporary dune formations in the area may indicate alternative interpretations. Finally, the distribution of appropriate reservoir properties is discussed.

DENOISING OF THREE-DIMENSIONAL DATA CUBE USING BIVARIATE WAVELET SHRINKING

The denoising of a natural signal/image corrupted by Gaussian white noise is a classical problem in signal/image processing. However, it is still in its infancy to denoise high dimensional data. In this paper, we extended Sendur and Selesnick's bivariate wavelet thresholding from two-dimensional (2D) image denoising to three-dimensional (3D) data cube denoising. Our study shows that bivariate wavelet thresholding is still valid for 3D data cubes. Experimental results show that bivariate wavelet thresholding on 3D data cube is better than performing 2D bivariate wavelet thresholding on every spectral band separately, VisuShrink, and Chen and Zhu's 3-scale denoising.

Real-Time Hyperspectral Imaging of Multiple Biosensors in Pancreatic Beta Cells

Spectral imaging techniques are important for many biological experiments, particularly live-cell quantitative imaging of multiple fluorescence probes. Existing hyperspectral imaging systems require sequential techniques, limiting the data acquisition rate. A newly-developed snapshot device, the Image Mapping Spectrometer (IMS), acquires full spectral information simultaneously from every pixel in the field with image acquisition rates up to 10 frames/second. The IMS maps adjacent pixels from the object to create space between them in the image, and then uses a grating to spread wavelength content from each pixel into this space. Direct image re-mapping provides the final 3D (x, y, lambda) data cube. Fluorescent protein (FP)-based biosensors are increasingly valuable tools for identifying subcellular dynamic processes in live cells. Many biosensors are based on FP-FRET, and measurements of the resultant small changes in FRET require high quality data. Tracking intracellular free Ca2+ levels is also crucial to elucidating signaling events, but the best Ca2+ indicator dyes overlap in the spectral emission range of the common FP-FRET biosensors. We have used the IMS system to simultaneously image multicolored FPs (i.e., CFP, GFP, YFP) in combination with extrinsic indicator dyes, such as Fluo-4. To demonstrate the speed and resolution of the IMS approach, we monitored both intracellular Ca2+ oscillations and caspase-3 activity during hydrogen peroxide-induced apoptosis. Ca2+ activity was measured with Fluo-4 (emission peak at 517 nm) and caspase-3 activity was measured with SCAT3.1, a FRET biosensor based on the ECFP (emission peak at 484 nm) and EYFP (emission peak at 527 nm) pair. Using the IMS, the three fluorophores were imaged with sub-second temporal resolution and spectrally unmixed in real-time. This permits direct correlation of Ca2+ activity with other apoptotic signaling events and demonstrates the power of the IMS for measuring dynamic physiological processes.

Native synthetic imaging of smoothed particle hydrodynamics density fields using gridless Monte Carlo radiative transfer

An algorithm for creating synthetic telescope images of Smoothed Particle Hydrodynamics (SPH) density fields is presented, which utilises the adaptive nature of the SPH formalism in full. The imaging process uses Monte Carlo Radiative Transfer (MCRT) methods to model the scattering and absorption of photon packets in the density field, which then exit the system and are captured on a pixelated image plane, creating a 2D image (or a 3D datacube, if the photons are also binned by their wavelength). The algorithm is implemented on the density field directly: no gridding of the field is required, allowing the density field to be described to an identical level of accuracy as the simulations that generated it. Some applications of the method to star and planet formation simulations are presented to illustrate the advantages of this new technique, and suggestions as to how this framework could support a Radiative Equilibrium algorithm are also given as an indication for future development.