Non-Destructive 3D Imaging Method Using Muonic X-Rays and a CdTe Double-Sided Strip Detector

Elemental analysis based on muonic X-rays resulting from muon irradiation provides information about bulk material composition without causing damage, which is essential in the case of precious or otherwise unreachable samples, such as in archeology and planetary science. We developed a three-dimensional (3D) elemental analysis technique by combining the elemental analysis method based on negative muons with an imaging cadmium telluride double-sided strip detector (CdTe-DSD) designed for the hard X-ray and soft γ-ray observation. A muon irradiation experiment using spherical plastic samples was conducted at the Japan Proton Accelerator Research Complex (J-PARC); a set of projection images was taken by the CdTe-DSD, equipped with a pinhole collimator, for different sample rotation angles. The projection images measured by the CdTe-DSD were utilized to obtain a 3D volumetric phantom by using the maximum likelihood expectation maximization algorithm. The reconstructed phantom successfully revealed the 3D distribution of carbon in the bulk samples and the stopping depth of the muons. This result demonstrated the feasibility of the proposed non-destructive 3D elemental analysis method for bulk material analysis based on muonic X-rays.

Completion of Metal-Damaged Traces Based on Deep Learning in Sinogram Domain for Metal Artifacts Reduction in CT Images

In computed tomography (CT) images, the presence of metal artifacts leads to contaminated object structures. Theoretically, eliminating metal artifacts in the sinogram domain can correct projection deviation and provide reconstructed images that are more real. Contemporary methods that use deep networks for completing metal-damaged sinogram data are limited to discontinuity at the boundaries of traces, which, however, lead to secondary artifacts. This study modifies the traditional U-net and adds two sinogram feature losses of projection images—namely, continuity and consistency of projection data at each angle, improving the accuracy of the complemented sinogram data. Masking the metal traces also ensures the stability and reliability of the unaffected data during metal artifacts reduction. The projection and reconstruction results and various evaluation metrics reveal that the proposed method can accurately repair missing data and reduce metal artifacts in reconstructed CT images.

Impacts of Phantom Off-Center Positioning on CT Numbers and Dose Index CTDIv: An Evaluation of Two CT Scanners from GE

The purpose of this work is to evaluate the impacts of body off-center positioning on CT numbers and dose index CTDIv of two scanners from GE. HD750 and APEX scanners were used to acquire a PBU60 phantom of Kagaku and a 062M phantom of CIRS respectively. CT images were acquired at various off-center positions under automatic tube current modulation using various peak voltages. CTDIv were recorded for each of the acquisitions. An abdomen section of the PBU60 phantom was used for CT number analysis and tissue inserts of the 062M phantom were filled with water balloons to mimic the human abdomen. CT numbers of central regions of interests were averaged using the Fiji software. As phantoms were lifted above the iso-center, both CTDIv and CT numbers were increased for the HD750 scanner whilst they were approximately constant for the APEX scanner. The measured sizes of anterior-posterior projection images were also increased for both scanners whilst the sizes of lateral projection images were increased for the HD750 scanner but decreased for the APEX scanner. Off-center correction algorithms were implemented in the APEX scanner. Matching the X-ray projection center with the system’s iso-center could improve the accuracy of CT imaging.

A Fast Image Alignment Approach for 2D Classification of Cryo-EM Images Using Spectral Clustering

Three-dimensional (3D) reconstruction in single-particle cryo-electron microscopy (cryo-EM) is a significant technique for recovering the 3D structure of proteins or other biological macromolecules from their two-dimensional (2D) noisy projection images taken from unknown random directions. Class averaging in single-particle cryo-EM is an important procedure for producing high-quality initial 3D structures, where image alignment is a fundamental step. In this paper, an efficient image alignment algorithm using 2D interpolation in the frequency domain of images is proposed to improve the estimation accuracy of alignment parameters of rotation angles and translational shifts between the two projection images, which can obtain subpixel and subangle accuracy. The proposed algorithm firstly uses the Fourier transform of two projection images to calculate a discrete cross-correlation matrix and then performs the 2D interpolation around the maximum value in the cross-correlation matrix. The alignment parameters are directly determined according to the position of the maximum value in the cross-correlation matrix after interpolation. Furthermore, the proposed image alignment algorithm and a spectral clustering algorithm are used to compute class averages for single-particle 3D reconstruction. The proposed image alignment algorithm is firstly tested on a Lena image and two cryo-EM datasets. Results show that the proposed image alignment algorithm can estimate the alignment parameters accurately and efficiently. The proposed method is also used to reconstruct preliminary 3D structures from a simulated cryo-EM dataset and a real cryo-EM dataset and to compare them with RELION. Experimental results show that the proposed method can obtain more high-quality class averages than RELION and can obtain higher reconstruction resolution than RELION even without iteration.

Single-Shot Optical Projection tomography for high-speed volumetric imaging

We present a single-shot adaptation of Optical Projection Tomography (OPT) for high-speed volumetric snapshot imaging of dynamic mesoscopic samples. Conventional OPT has been applied to in vivo imaging of animal models such as D. rerio but the sequential acquisition of projection images required for volumetric reconstruction typically requires samples to be immobilised during the acquisition of an OPT data set. We present a proof-of-principle system capable of single-shot imaging of a 1 mm diameter volume, demonstrating camera-limited rates of up to 62.5 volumes/second, which we have applied to 3D imaging of a freely-swimming zebrafish embryo. This is achieved by recording 8 projection views simultaneously on 4 low-cost CMOS cameras. With no stage required to rotate the sample, this single-shot OPT system can be implemented with a component cost of under 5,000GBP. The system design can be adapted to different sized fields of view and may be applied to a broad range of dynamic samples, including fluid dynamics.

Evaluation of Iodine-123 and Iodine-131 SPECT activity quantification: a Monte Carlo study

Purpose The quantitative accuracy of Nuclear Medicine images, acquired for both planar and SPECT studies, is influenced by the isotope-collimator combination as well as image corrections incorporated in the iterative reconstruction process. These factors can be investigated and optimised using Monte Carlo simulations. This study aimed to evaluate SPECT quantification accuracy for 123I with both the low-energy high resolution (LEHR) and medium-energy (ME) collimators and 131I with the high-energy (HE) collimator. Methods Simulated SPECT projection images were reconstructed using the OS-EM iterative algorithm, which was optimised for the number of updates, with appropriate corrections for scatter, attenuation and collimator detector response (CDR), including septal scatter and penetration compensation. An appropriate calibration factor (CF) was determined from four different source geometries (activity-filled: water-filled cylindrical phantom, sphere in water-filled (cold) cylindrical phantom, sphere in air and point-like source), investigated with different volume of interest (VOI) diameters. Recovery curves were constructed from recovery coefficients to correct for partial volume effects (PVEs). The quantitative method was evaluated for spheres in voxel-based digital cylindrical and patient phantoms. Results The optimal number of OS-EM updates was 60 for all isotope-collimator combinations. The CFpoint with a VOI diameter equal to the physical size plus a 3.0-cm margin was selected, for all isotope-collimator geometries. The spheres’ quantification errors in the voxel-based digital cylindrical and patient phantoms were less than 3.2% and 5.4%, respectively, for all isotope-collimator combinations. Conclusion The study showed that quantification errors of less than 6.0% could be attained, for all isotope-collimator combinations, if corrections for; scatter, attenuation, CDR (including septal scatter and penetration) and PVEs are performed. 123I LEHR and 123I ME quantification accuracies compared well when appropriate corrections for septal scatter and penetration were applied. This can be useful in departments that perform 123I studies and may not have access to ME collimators.

Grid-free least-squares method for pressure evaluation from LPT data

Lagrangian particle tracking Shake-the-box (STB) method (Schanz et al., 2016) acquires the 3D positions of tracer particles from the temporal sequences of their 2D projection images even for rather high seeding densities. Approximation of tracks by analytical functions (Gesemann, 2015) provides an accurate evaluation of tracers’ local velocity and acceleration. This data, which is obtained on non-regular grid, can be used to estimate local pressure fluctuations based on the Navier–Stokes equation. The present paper describes a grid-free least-squares method for the gradients and pressure evaluation based on irregularly scattered LPT data with random noise minimization.

PatchPerPixMatch for Automated 3d Search of Neuronal Morphologies in Light Microscopy

Studies of individual neurons in the Drosophila nervous system are facilitated by transgenic lines that sparsely and repeatably label respective neurons of interest. Sparsity can be enhanced by means of intersectional approaches like the split-GAL4 system, which labels the positive intersection of the expression patterns of two (denser) GAL4 lines. To this end, two GAL4 lines have to be identified as labelling a neuron of interest. Current approaches to tackling this task include visual inspection, as well as automated search in 2d projection images, of single cell multi-color flip-out (MCFO) acquisitions of GAL4 expression patterns. There is to date no automated method available that performs full 3d search in MCFO imagery of GAL4 lines, nor one that leverages automated reconstructions of the labelled neuron morphologies. To close this gap, we propose PatchPerPixMatch, a fully automated approach for finding a given neuron morphology in MCFO acquisitions of Gen1 GAL4 lines. PatchPerPixMatch performs automated instance segmentation of MCFO acquisitions, and subsequently searches for a target neuron morphology by minimizing an objective that aims at covering the target with a set of well-fitting segmentation fragments. PatchPerPixMatch is computationally efficient albeit being full 3d, while also highly robust to inaccuracies in the automated neuron instance segmentation. We are releasing PatchPerPixMatch search results for ~30,000 neuron morphologies from the Drosophila hemibrain in ~20,000 MCFO acquisitions of ~3,500 Gen1 GAL4 lines.

Analysis of Distortion Based on 2D MEMS Micromirror Scanning Projection System

To analyze the distortion problem of two-dimensional micro-electromechanical system (MEMS) micromirror in-plane scanning, this paper makes a full theoretical analysis of the distortion causes from many aspects. Firstly, the mathematical relations among the deflection angle, laser incidence angle, and plane scanning distance of the micromirror are constructed, and the types of projection distortion of the micromirror scanning are discussed. Then the simulation results of reflection angle distribution and point cloud distribution are verified by MATLAB software under different working conditions. Finally, a two-dimensional MEMS micromirror scanning projection system is built. The predetermined waveform can be scanned and projected successfully. The distortion theory is proved to be correct by analyzing the distortion of the projection images, which lays a foundation for practical engineering application.