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Eric Miller

Publications and source records attributed to Eric Miller.

42 records · Page 3Linked to original sources

Fast algorithms for hyperspectral Diffuse Optical Tomography

The image reconstruction of chromophore concentrations using Diffuse Optical Tomography (DOT) data can be described mathematically as an ill-posed inverse problem. Recent work has shown that the use of hyperspectral DOT data, as opposed to data sets comprising of a single or, at most, a dozen wavelengths, has the potential for improving the quality of the reconstructions. The use of hyperspectral diffuse optical data in the formulation and solution of the inverse problem poses a significant computational burden. The forward operator is, in actuality, nonlinear. However, under certain assumptions, a linear approximation, called the Born approximation, provides a suitable surrogate for the forward operator, and we assume this to be true in the present work. Computation of the Born matrix requires the solution of thousands of large scale discrete PDEs and the reconstruction problem, requires matrix-vector products with the (dense) Born matrix. In this paper, we address both of these difficulties, thus making the Born approach a computational viable approach for hyDOT reconstruction. In this paper, we assume that the images we wish to reconstruct are anomalies of unknown shape and constant value, described using a parametric level set approach, (PaLS) on a constant background. Specifically, to address the issue of the PDE solves, we develop a novel recycling-based Krylov subspace approach that leverages certain system similarities across wavelengths. To address expense of using the Born operator in the inversion, we present a fast algorithm for compressing the Born operator that locally compresses across wavelengths for a given source-detector set and then recursively combines the low-rank factors to provide a global low-rank approximation. This low-rank approximation can be used implicitly to speed up the recovery of the shape parameters and the chromophore concentrations.

math.NA↗

Large-Scale Automatic Reconstruction of Neuronal Processes from Electron Microscopy Images

Automated sample preparation and electron microscopy enables acquisition of very large image data sets. These technical advances are of special importance to the field of neuroanatomy, as 3D reconstructions of neuronal processes at the nm scale can provide new insight into the fine grained structure of the brain. Segmentation of large-scale electron microscopy data is the main bottleneck in the analysis of these data sets. In this paper we present a pipeline that provides state-of-the art reconstruction performance while scaling to data sets in the GB-TB range. First, we train a random forest classifier on interactive sparse user annotations. The classifier output is combined with an anisotropic smoothing prior in a Conditional Random Field framework to generate multiple segmentation hypotheses per image. These segmentations are then combined into geometrically consistent 3D objects by segmentation fusion. We provide qualitative and quantitative evaluation of the automatic segmentation and demonstrate large-scale 3D reconstructions of neuronal processes from a $\mathbf{27,000}$ $\mathbf{μm^3}$ volume of brain tissue over a cube of $\mathbf{30 \; μm}$ in each dimension corresponding to 1000 consecutive image sections. We also introduce Mojo, a proofreading tool including semi-automated correction of merge errors based on sparse user scribbles.

q-bio.NC↗

New CTI Correction Method for the Spaced-Row Charge Injection of the Suzaku X-Ray Imaging Spectrometer

The charge transfer inefficiency (CTI) of the X-ray CCDs on board the Suzaku satellite (X-ray Imaging Spectrometers; XIS) has increased since the launch due to radiation damage, and the energy resolution has been degraded. To improve the CTI, we have applied a spaced-row charge injection (SCI) technique to the XIS in orbit; by injecting charges into CCD rows periodically, the CTI is actively decreased. The CTI in the SCI mode depends on the distance between a signal charge and a preceding injected row, and the pulse height shows periodic positional variations. Using in-flight data of onboard calibration sources and of the strong iron line from the Perseus cluster of galaxies, we studied the variation in detail. We developed a new method to correct the variation. By applying the new method, the energy resolution (FWHM) at 5.9 keV at March 2008 is ~155 eV for the front-illuminated CCDs and ~175 eV for the back-illuminated CCD.

astro-ph↗

Energy-Scale Calibration of the Suzaku X-Ray Imaging Spectrometer Using the Checker Flag Charge Injection Technique in Orbit

The X-ray Imaging Spectrometer (XIS) on board the Suzaku satellite is an X-ray CCD camera system that has superior performance such as a low background, high quantum efficiency, and good energy resolution in the 0.2-12 keV band. Because of the radiation damage in orbit, however, the charge transfer inefficiency (CTI) has increased, and hence the energy scale and resolution of the XIS has been degraded since the launch of July 2005. The CCD has a charge injection structure, and the CTI of each column and the pulse-height dependence of the CTI are precisely measured by a checker flag charge injection (CFCI) technique. Our precise CTI correction improved the energy resolution from 230 eV to 190 eV at 5.9 keV in December 2006. This paper reports the CTI measurements with the CFCI experiments in orbit. Using the CFCI results, we have implemented the time-dependent energy scale and resolution to the Suzaku calibration database.

astro-ph↗

Reproducibility of Non-X-ray Background for the X-ray Imaging Spectrometer aboard Suzaku

One of the advantages of the X-ray Imaging Spectrometer (XIS) system on board Suzaku is its low and stable non-X-ray background (NXB). In order to make the best use of this advantage, modeling the NXB spectra with high accuracy is important to subtract them from the spectra of on-source observations. We construct an NXB database by collecting XIS events when the dark Earth covers the XIS FOV. The total exposure time of the NXB data is about 785 ks for each XIS. It is found that the count rate of the NXB anti-correlates with the cut-off-rigidity and correlates with the count rate of the PIN upper discriminator (PIN-UD) in Hard X-ray Detector on board Suzaku. We thus model the NXB spectrum for a given on-source observation by employing either of these parameters and obtain a better reproducibility of the NXB for the model with PIN-UD than that with the cut-off-rigidity. The reproducibility of the NXB model with PIN-UD is 4.55-5.63% for each XIS NXB in the 1-7 keV band and 2.79-4.36% for each XIS NXB in the 5-12 keV band for each 5 ks exposure of the NXB data. This NXB reproducibility is much smaller than the spatial fluctuation of the cosmic X-ray background in the 1-7 keV band, and is almost comparable to that in the 5-12 keV band.

astro-ph↗

Suzaku Observations of the Local and Distant Hot ISM

Suzaku observed the molecular cloud MBM12 and a blank field less than 3 degrees away to separate the local and distant components of the diffuse soft X-ray background. Towards MBM12, a local (D< 275 pc) O VII emission line was clearly detected with an intensity of 3.5 ph cm^{-2} s^{-1} sr^{-1}$ (or line units, LU), and the O VIII flux was <0.34 LU. The origin of this O VII emission could be hot gas in the Local Hot Bubble (LHB), charge exchange between oxygen ions in the solar wind (SWCX) and geocoronal or interplanetary material, or a combination of the two. If entirely from the LHB, the implied temperature and emission measure would predict 1/4 keV emission in excess of observations. There is no evidence in the X-ray light curve or solar wind data for a significant contribution from geocoronal SWCX. In any case, the observed O VII flux represents an upper limit to both the LHB emission and interplanetary SWCX in this direction. The off-cloud observation was performed immediately following the on-cloud. The net off-cloud O VII and O VIII intensities were (respectively) 2.34\pm0.33 and 0.77\pm0.16 LU, after subtracting the on-cloud foreground emission. Assuming the LHB and SWCX components did not change, these increases can be attributed to more distant Galactic disk, halo, or extragalactic emission. If the distant O VII and O VIII emission is from a thermal plasma in collisional equilibrium beyond the Galactic disk, a temperature of (2.1\pm0.1)\times10^6 K with an emission measure of (4\pm0.6)\times10^-3} cm^{-6}pc is inferred.

astro-ph↗