Reliable automatic alignment of tomographic projection data by passive auto-focus

PURPOSE

The authors present a robust algorithm that removes the blurring and double-edge artifacts in high-resolution computed tomography (CT) images that are caused by misaligned scanner components. This alleviates the time-consuming process of physically aligning hardware, which is of particular benefit if components are moved or swapped frequently.

METHODS

The proposed method uses the experimental data itself for calibration. A parameterized model of the scanner geometry is constructed and the parameters are varied until the sharpest 3D reconstruction is found. The concept is similar to passive auto-focus algorithms of digital optical instruments. The parameters are used to remap the projection data from the physical detector to a virtual aligned detector. This is followed by a standard reconstruction algorithm, namely the Feldkamp algorithm. Feldkamp et al. [J. Opt. Soc. Am. A 1, 612-619 (1984)].

RESULTS

An example implementation is given for a rabbit liver specimen that was collected with a circular trajectory. The optimal parameters were determined in less computation time than that for a full reconstruction. The example serves to demonstrate that (a) sharpness is an appropriate measure for projection alignment, (b) our parameterization is sufficient to characterize misalignments for cone-beam CT, and (c) the procedure determines parameter values with sufficient precision to remove the associated artifacts.

CONCLUSIONS

The algorithm is fully tested and implemented for regular use at The Australian National University micro-CT facility for both circular and helical trajectories. It can in principle be applied to more general imaging geometries and modalities. It is as robust as manual alignment but more precise since we have quantified the effect of misalignment.

Refraction corrected transmission ultrasound computed tomography for application in breast imaging

PURPOSE

We present an iterative framework for CT reconstruction from transmission ultrasound data which accurately and efficiently models the strong refraction effects that occur in our target application: Imaging the female breast.

METHODS

Our refractive ray tracing framework has its foundation in the fast marching method (FNMM) and it allows an accurate as well as efficient modeling of curved rays. We also describe a novel regularization scheme that yields further significant reconstruction quality improvements. A final contribution is the development of a realistic anthropomorphic digital breast phantom based on the NIH Visible Female data set.

RESULTS

Our system is able to resolve very fine details even in the presence of significant noise, and it reconstructs both sound speed and attenuation data. Excellent correspondence with a traditional, but significantly more computationally expensive wave equation solver is achieved.

CONCLUSIONS

Apart from the accurate modeling of curved rays, decisive factors have also been our regularization scheme and the high-quality interpolation filter we have used. An added benefit of our framework is that it accelerates well on GPUs where we have shown that clinical 3D reconstruction speeds on the order of minutes are possible.

A bicontinuous mesophase geometry with hexagonal symmetry

We report that a specific realization of Schwarz's triply periodic hexagonal minimal surface is isotropic with respect to the Doi-Ohta interface tensor and simultaneously has minimal packing and stretching frustration similar to those of the commonly found cubic bicontinuous mesophases. This hexagonal surface, of symmetry P6(3)/mmc with a lattice ratio of c/a = 0.832, is therefore a likely candidate geometry for self-assembled lipid/surfactant or copolymer mesophases. Furthermore, both the peak position ratios in its powder diffraction pattern and the elastic moduli closely resemble those of the cubic bicontinuous phases. We therefore argue that a genuine possibility of experimental misidentification exists.

Fast Bilateral Filtering for Denoising Large 3D Images

A fast implementation of bilateral filtering is presented, which is based on an optimal expansion of the filter kernel into a sum of factorized terms. These terms are computed by minimizing the expansion error in the mean-square-error sense. This leads to a simple and elegant solution in terms of eigenvectors of a square matrix. In this way, the bilateral filter is applied through computing a few Gaussian convolutions, for which very efficient algorithms are readily available. Moreover, the expansion functions are optimized for the histogram of the input image, leading to improved accuracy. It is shown that this further optimization it made possible by removing the commonly deployed constrain of shiftability of the basis functions. Experimental validation is carried out in the context of digital rock imaging. Results on large 3D images of rock samples show the superiority of the proposed method with respect to other fast approximations of bilateral filtering.

Iteration of transmit-beam aberration correction in medical ultrasound imaging

Simulations of iterative transmit-beam aberration correction using a time-delay and amplitude filter have been performed to study the convergence of such a process. Aberration in medical ultrasonic imaging is usually modeled by arrival-time and amplitude fluctuations concentrated on the transducer array. This is an approximation of the physical aberration process, and may be applied to correct the transmitted signal using a time-delay and amplitude filter. Estimation of such a filter has proven difficult in the presence of severe aberration. Presented here is an iterative approach, whereby a filter estimate is applied to correct the transmit-beam. This beam induces acoustic backscatter better suited for arrival-time and amplitude estimation, thus facilitating an improved filter estimate. Two correlation-based methods for estimating arrival-time and amplitude fluctuations in received echoes from random scatterers were employed. Aberration was introduced using eight models emulating aberration produced by the human abdominal wall. Results show that only a few iterations are needed to obtain corrected transmit-beam profiles comparable to those of an ideal aberration correction filter. Furthermore, a previously developed focusing criterion is found to quantify the convergence accurately.

Aberration in nonlinear acoustic wave propagation

Theory and simulations are presented indicating that imaging at the second-harmonic frequency does not solve the problem of ultrasonic wave aberration. The nonlinearity of acoustic wave propagation in biological tissue is routinely exploited in medical imaging because the improved contrast resolution leads to better image quality in many applications. The major sources of acoustic noise in ultrasound images are aberration and multiple reflections between the transducer and tissue structures (reverberations), both of which are the result of spatial variations in the acoustic properties of the tissue. These variations mainly occur close to the body surface, i.e., the body wall. As a result, the nonlinearly generated, second harmonic is believed to alleviate both reverberation and aberration because it is assumed that the second harmonic is mainly generated after the body wall. However, in the case of aberration, the second harmonic is generated by an aberrated source. Thus the second harmonic experiences considerable aberration at all depths, originating from this source. The results in this paper show that the second harmonic experiences similar aberration as its generating source, the first harmonic.

Eigenfunction analysis of stochastic backscatter for characterization of acoustic aberration in medical ultrasound imaging

Presented here is a characterization of aberration in medical ultrasound imaging. The characterization is optimal in the sense of maximizing the expected energy in a modified beamformer output of the received acoustic backscatter. Aberration correction based on this characterization takes the form of an aberration correction filter. The situation considered is frequently found in applications when imaging organs through a body wall: aberration is introduced in a layer close to the transducer, and acoustic backscatter from a scattering region behind the body wall is measured at the transducer surface. The scattering region consists of scatterers randomly distributed with very short correlation length compared to the acoustic wavelength of the transmit pulse. The scatterer distribution is therefore assumed to be delta correlated. This paper shows how maximizing the expected energy in a modified beamformer output signal naturally leads to eigenfunctions of a Fredholm integral operator, where the associated kernel function is a spatial correlation function of the received stochastic signal. Aberration characterization and aberration correction are presented for simulated data constructed to mimic aberration introduced by the abdominal wall. The results compare well with what is obtainable using data from a simulated point source.

Estimation of ultrasound wave aberration with signals from random scatterers

A method for estimating waveform aberration from random scatterers in medical ultrasound imaging has been derived and its properties investigated using two-dimensional simulations. The method uses a weighted and modified cross-spectrum in order to estimate arrival time and amplitude fluctuations from received signals. The arrival time and amplitude fluctuations were used in a time delay, and a time delay and amplitude aberration correction filter, for evaluation of the retransmitted aberration corrected signal. Different types of aberration have been used in this study. First, aberration was concentrated on the plane of the transmitting/receiving array. Second, aberration was generated with a distributed aberrator. Both conditions emulated aberration from the human abdominal wall. Results show that for the concentrated aberrator, arrival time and amplitude fluctuations were estimated in close agreement with reference values. The reference values were obtained from simulations with a point source in the focal point of the array. Correction of the transmitted signal with a time delay, and a time delay and amplitude filter produced approximately equal correction as with point source estimates. For the distributed aberrator, the estimator performance degraded significantly. Arrival time and amplitude fluctuations deviated from reference values, leading to a limited correction of the retransmitted signal.

Spectral estimation for characterization of acoustic aberration

Spectral estimation based on acoustic backscatter from a motionless stochastic medium is described for characterization of aberration in ultrasonic imaging. The underlying assumptions for the estimation are: The correlation length of the medium is short compared to the length of the transmitted acoustic pulse, an isoplanatic region of sufficient size exists around the focal point, and the backscatter can be modeled as an ergodic stochastic process. The motivation for this work is ultrasonic imaging with aberration correction. Measurements were performed using a two-dimensional array system with 80 x 80 transducer elements and an element pitch of 0.6 mm. The f number for the measurements was 1.2 and the center frequency was 3.0 MHz with a 53% bandwidth. Relative phase of aberration was extracted from estimated cross spectra using a robust least-mean-square-error method based on an orthogonal expansion of the phase differences of neighboring wave forms as a function of frequency. Estimates of cross-spectrum phase from measurements of random scattering through a tissue-mimicking aberrator have confidence bands approximately +/- 5 degrees wide. Both phase and magnitude are in good agreement with a reference characterization obtained from a point scatterer.

Computer simulation of forward wave propagation in soft tissue

A method for simulating forward wavefront propagation in heterogeneous tissue is discussed. The intended application of this method is for the study of aberration produced when performing ultrasound imaging through a layer of soft tissue. A one-way wave equation that permits smooth variation in all acoustically important variables is derived. This equation also describes tissue exhibiting nonlinear elasticity and arbitrary frequency-dependent relaxation. A numerical solution to this equation is found by means of operator splitting and propagation along the spatial depth coordinate. The numerical solution is accurate when compared to analytical solutions for special cases, and when compared to numerical solutions of the full wave equation by other methods. The presented implementation provides a fast numerical method for studying the impact of aberration in medical ultrasound imaging through soft tissue--both on the transmitted beam and the nonlinearly generated harmonic beam.

Parakeet: a digital twin software pipeline to assess the impact of experimental parameters on tomographic reconstructions for cryo-electron tomography

In cryo-electron tomography (cryo-ET) of biological samples, the quality of tomographic reconstructions can vary depending on the transmission electron microscope (TEM) instrument and data acquisition parameters. In this paper, we present Parakeet, a 'digital twin' software pipeline for the assessment of the impact of various TEM experiment parameters on the quality of three-dimensional tomographic reconstructions. The Parakeet digital twin is a digital model that can be used to optimize the performance and utilization of a physical instrument to enable in silico optimization of sample geometries, data acquisition schemes and instrument parameters. The digital twin performs virtual sample generation, TEM image simulation, and tilt series reconstruction and analysis within a convenient software framework. As well as being able to produce physically realistic simulated cryo-ET datasets to aid the development of tomographic reconstruction and subtomogram averaging programs, Parakeet aims to enable convenient assessment of the effects of different microscope parameters and data acquisition parameters on reconstruction quality. To illustrate the use of the software, we present the example of a quantitative analysis of missing wedge artefacts on simulated planar and cylindrical biological samples and discuss how data collection parameters can be modified for cylindrical samples where a full 180° tilt range might be measured.

X-ray attenuation models to account for beam hardening in computed tomography

We introduce a beam-hardening correction method for lab-based X-ray computed tomography (CT) by modifying existing iterative tomographic reconstruction algorithms. Our method simplifies the standard Alvarez-Macovski X-ray attenuation model [Phys. Med. Biol.21, 733 (1976)] and is compatible with conventional (i.e., single-spectrum) CT scans. The sole modification involves a polychromatic projection operation, which is equivalent to applying a weighting that more closely matches the attenuation of polychromatic X-rays. Practicality is a priority, so we only require information about the X-ray spectrum and some constants relating to material properties. No other changes to the experimental setup or the iterative algorithms are necessary. Using reconstructions of simulations and several large experimental datasets, we show that this method is able to remove or reduce cupping, streaking, and other artefacts from X-ray beam hardening and improve the self-consistency of projected attenuation in CT. When the assumptions made in the simplifications are valid, the reconstructed tomogram can even be quantitative.

Pillar data-acquisition strategies for cryo-electron tomography of beam-sensitive biological samples

For cryo-electron tomography (cryo-ET) of beam-sensitive biological specimens, a planar sample geometry is typically used. As the sample is tilted, the effective thickness of the sample along the direction of the electron beam increases and the signal-to-noise ratio concomitantly decreases, limiting the transfer of information at high tilt angles. In addition, the tilt range where data can be collected is limited by a combination of various sample-environment constraints, including the limited space in the objective lens pole piece and the possible use of fixed conductive braids to cool the specimen. Consequently, most tilt series are limited to a maximum of ±70°, leading to the presence of a missing wedge in Fourier space. The acquisition of cryo-ET data without a missing wedge, for example using a cylindrical sample geometry, is hence attractive for volumetric analysis of low-symmetry structures such as organelles or vesicles, lysis events, pore formation or filaments for which the missing information cannot be compensated by averaging techniques. Irrespective of the geometry, electron-beam damage to the specimen is an issue and the first images acquired will transfer more high-resolution information than those acquired last. There is also an inherent trade-off between higher sampling in Fourier space and avoiding beam damage to the sample. Finally, the necessity of using a sufficient electron fluence to align the tilt images means that this fluence needs to be fractionated across a small number of images; therefore, the order of data acquisition is also a factor to consider. Here, an n-helix tilt scheme is described and simulated which uses overlapping and interleaved tilt series to maximize the use of a pillar geometry, allowing the entire pillar volume to be reconstructed as a single unit. Three related tilt schemes are also evaluated that extend the continuous and classic dose-symmetric tilt schemes for cryo-ET to pillar samples to enable the collection of isotropic information across all spatial frequencies. A fourfold dose-symmetric scheme is proposed which provides a practical compromise between uniform information transfer and complexity of data acquisition.