3D reconstruction and comparison of shapes of DNA minicircles observed by cryo-electron microscopy.

We use cryo-electron microscopy to compare 3D shapes of 158 bp long DNA minicircles that differ only in the sequence within an 18 bp block containing either a TATA box or a catabolite activator protein binding site. We present a sorting algorithm that correlates the reconstructed shapes and groups them into distinct categories. We conclude that the presence of the TATA box sequence, which is believed to be easily bent, does not significantly affect the observed shapes.

3D dose reconstruction for narrow beams using ion chamber array measurements.

3D dose reconstruction is a verification of the delivered absorbed dose. Our aim was to describe and evaluate a 3D dose reconstruction method applied to phantoms in the context of narrow beams. A solid water phantom and a phantom containing a bone-equivalent material were irradiated on a 6 MV linac. The transmitted dose was measured by using one array of a 2D ion chamber detector. The dose reconstruction was obtained by an iterative algorithm. A phantom set-up error and organ interfraction motion were simulated to test the algorithm sensitivity. In all configurations convergence was obtained within three iterations. A local reconstructed dose agreement of at least 3% / 3mm with respect to the planned dose was obtained, except in a few points of the penumbra. The reconstructed primary fluences were consistent with the planned ones, which validates the whole reconstruction process. The results validate our method in a simple geometry and for narrow beams. The method is sensitive to a set-up error of a heterogeneous phantom and interfraction heterogeneous organ motion.

Free-breathing 3D steady-state free precession coronary MR angiography with radial k-space sampling: comparison with cartesian k-space sampling and cartesian gradient-echo coronary MR angiography--pilot study.

The authors compared radial steady-state free precession (SSFP) coronary magnetic resonance (MR) angiography, cartesian k-space sampling SSFP coronary MR angiography, and gradient-echo coronary MR angiography in 16 healthy adults and four pilot study patients. Standard gradient-echo MR imaging with a T2 preparatory pulse and cartesian k-space sampling was the reference technique. Image quality was compared by using subjective motion artifact level and objective contrast-to-noise ratio and vessel sharpness. Radial SSFP, compared with cartesian SSFP and gradient-echo MR angiography, resulted in reduced motion artifacts and superior vessel sharpness. Cartesian SSFP resulted in increased motion artifacts (P <.05). Contrast-to-noise ratio with radial SSFP was lower than that with cartesian SSFP and similar to that with the reference technique. Radial SSFP coronary MR angiography appears preferable because of improved definition of vessel borders.

Estimating the apparent transverse relaxation time (R2(*)) from images with different contrasts (ESTATICS) reduces motion artifacts.

Relaxation rates provide important information about tissue microstructure. Multi-parameter mapping (MPM) estimates multiple relaxation parameters from multi-echo FLASH acquisitions with different basic contrasts, i.e., proton density (PD), T1 or magnetization transfer (MT) weighting. Motion can particularly affect maps of the apparent transverse relaxation rate R2(*), which are derived from the signal of PD-weighted images acquired at different echo times. To address the motion artifacts, we introduce ESTATICS, which robustly estimates R2(*) from images even when acquired with different basic contrasts. ESTATICS extends the fitted signal model to account for inherent contrast differences in the PDw, T1w and MTw images. The fit was implemented as a conventional ordinary least squares optimization and as a robust fit with a small or large confidence interval. These three different implementations of ESTATICS were tested on data affected by severe motion artifacts and data with no prominent motion artifacts as determined by visual assessment or fast optical motion tracking. ESTATICS improved the quality of the R2(*) maps and reduced the coefficient of variation for both types of data-with average reductions of 30% when severe motion artifacts were present. ESTATICS can be applied to any protocol comprised of multiple 2D/3D multi-echo FLASH acquisitions as used in the general research and clinical setting.

Navigator-gated free-breathing 3D balanced FFE projection renal MRA: Comparison with contrast-enhanced breath-hold 3D MRA in a swine model.

A cardiac-triggered, free-breathing, 3D balanced FFE projection renal MR angiography (MRA) technique with a 2D pencil beam aortic labeling pulse for selective aortic spin tagging was developed. For respiratory motion artifact suppression during free breathing, a prospective real-time navigator was implemented for renal MRA. Images obtained with the new approach were compared with standard contrast-enhanced (CE) 3D breath-hold MRA in seven swine. Signal properties and vessel visualization were analyzed. With the presented technique, high-resolution, high-contrast renal projection MRA with superior vessel length visualization (including a greater visible number of distal branches of the renal arteries) compared to standard breath-hold CE-MRA was obtained. The present results warrant clinical studies in patients with renal artery disease.

Impact of bulk cardiac motion on right coronary MR angiography and vessel wall imaging.

The purpose of this study was to investigate the impact of in-plane coronary artery motion on coronary magnetic resonance angiography (MRA) and coronary MR vessel wall imaging. Free-breathing, navigator-gated, 3D-segmented k-space turbo field echo ((TFE)/echo-planar imaging (EPI)) coronary MRA and 2D fast spin-echo coronary vessel wall imaging of the right coronary artery (RCA) were performed in 15 healthy adult subjects. Images were acquired at two different diastolic time periods in each subject: 1) during a subject-specific diastasis period (in-plane velocity <4 cm/second) identified from analysis of in-plane coronary artery motion, and 2) using a diastolic trigger delay based on a previously implemented heart-rate-dependent empirical formula. RCA vessel wall imaging was only feasible with subject-specific middiastolic acquisition, while the coronary wall could not be identified with the heart-rate-dependent formula. For coronary MRA, RCA border definition was improved by 13% (P < 0.001) with the use of subject-specific trigger delay (vs. heart-rate-dependent delay). Subject-specific middiastolic image acquisition improves 3D TFE/EPI coronary MRA, and is critical for RCA vessel wall imaging.

3D coronary vessel wall imaging utilizing a local inversion technique with spiral image acquisition.

Current 2D black blood coronary vessel wall imaging suffers from a relatively limited coverage of the coronary artery tree. Hence, a 3D approach facilitating more extensive coverage would be desirable. The straightforward combination of a 3D-acquisition technique together with a dual inversion prepulse can decrease the effectiveness of the black blood preparation. To minimize artifacts from insufficiently suppressed blood signal of the nearby blood pools, and to reduce residual respiratory motion artifacts from the chest wall, a novel local inversion technique was implemented. The combination of a nonselective inversion prepulse with a 2D selective local inversion prepulse allowed for suppression of unwanted signal outside a user-defined region of interest. Among 10 subjects evaluated using a 3D-spiral readout, the local inversion pulse effectively suppressed signal from ventricular blood, myocardium, and chest wall tissue in all cases. The coronary vessel wall could be visualized within the entire imaging volume.

Cardiac motion estimation by joint alignment of tagged MRI sequences

Image registration has been proposed as an automatic method for recovering cardiac displacement fields from Tagged Magnetic Resonance Imaging (tMRI) sequences. Initially performed as a set of pairwise registrations, these techniques have evolved to the use of 3D+t deformation models, requiring metrics of joint image alignment (JA). However, only linear combinations of cost functions defined with respect to the first frame have been used. In this paper, we have applied k-Nearest Neighbors Graphs (kNNG) estimators of the -entropy (H ) to measure the joint similarity between frames, and to combine the information provided by different cardiac views in an unified metric. Experiments performed on six subjects showed a significantly higher accuracy (p < 0.05) with respect to a standard pairwise alignment (PA) approach in terms of mean positional error and variance with respect to manually placed landmarks. The developed method was used to study strains in patients with myocardial infarction, showing a consistency between strain, infarction location, and coronary occlusion. This paper also presentsan interesting clinical application of graph-based metric estimators, showing their value for solving practical problems found in medical imaging.

Comparison of Roadway Roughness Derived from LIDAR and SFM 3D Point Clouds, HR-3001, 2015

This report describes a short-term study undertaken to investigate the potential for using dense three-dimensional (3D) point clouds generated from light detection and ranging (LIDAR) and photogrammetry to assess roadway roughness. Spatially continuous roughness maps have potential for the identification of localized roughness features, which would be a significant improvement over traditional profiling methods. This report specifically illustrates the use of terrestrial laser scanning (TLS) and photogrammetry using a process known as structure from motion (SFM) to acquire point clouds and illustrates the use of these point clouds in evaluating road roughness. Five roadway sections were chosen for scanning and testing: three gravel road sections, one portland cement concrete (PCC) section, and one asphalt concrete (AC) section. To compare clouds obtained from terrestrial laser scanning and photogrammetry, the coordinates of the clouds for the same section on the same date were matched using open source computer code. The research indicates that the technologies described are very promising for evaluating road roughness. The major advantage of both technologies is the large amount of data collected, which allows the evaluation of the full surface. Additional research is needed to further develop the use of dense 3D point clouds for roadway assessment.

Free-breathing whole-heart coronary MRA with 3D radial SSFP and self-navigated image reconstruction.

Respiratory motion is a major source of artifacts in cardiac magnetic resonance imaging (MRI). Free-breathing techniques with pencil-beam navigators efficiently suppress respiratory motion and minimize the need for patient cooperation. However, the correlation between the measured navigator position and the actual position of the heart may be adversely affected by hysteretic effects, navigator position, and temporal delays between the navigators and the image acquisition. In addition, irregular breathing patterns during navigator-gated scanning may result in low scan efficiency and prolonged scan time. The purpose of this study was to develop and implement a self-navigated, free-breathing, whole-heart 3D coronary MRI technique that would overcome these shortcomings and improve the ease-of-use of coronary MRI. A signal synchronous with respiration was extracted directly from the echoes acquired for imaging, and the motion information was used for retrospective, rigid-body, through-plane motion correction. The images obtained from the self-navigated reconstruction were compared with the results from conventional, prospective, pencil-beam navigator tracking. Image quality was improved in phantom studies using self-navigation, while equivalent results were obtained with both techniques in preliminary in vivo studies.

Real-time MR imaging of myocardial regional function using strain-encoding (SENC) with tissue through-plane motion tracking.

PURPOSE: To implement real-time myocardial strain-encoding (SENC) imaging in combination with tracking the tissue displacement in the through-plane direction. MATERIALS AND METHODS: SENC imaging was combined with the slice-following technique by implementing three-dimensional (3D) selective excitation. Certain adjustments were implemented to reduce scan time to one heartbeat. A total of 10 volunteers and five pigs were scanned on a 3T MRI scanner. Spatial modulation of magnetization (SPAMM)-tagged images were acquired on planes orthogonal to the SENC planes for comparison. Myocardial infarction (MI) was induced in two pigs and the resulting SENC images were compared to standard delayed-enhancement (DE) images. RESULTS: The strain values computed from SENC imaging with slice-following showed significant difference from those acquired without slice-following, especially during systole (P < 0.01). The strain curves computed from the SENC images with and without slice-following were similar to those computed from the orthogonal SPAMM images, with and without, respectively, tracking the tag line displacement in the strain direction. The resulting SENC images showed good agreement with the DE images in identifying MI in infarcted pigs. CONCLUSION: Correction of through-plane motion in real-time cardiac functional imaging is feasible using slice-following. The strain measurements are more accurate than conventional SENC measurements in humans and animals, as validated with conventional MRI tagging.

A minimal set of coordinates for describing humanoid shoulder motion

The kinematics of the anatomical shoulder are analysed and modelled as a parallel mechanism similar to a Stewart platform. A new method is proposed to describe the shoulder kinematics with minimal coordinates and solve the indeterminacy. The minimal coordinates are defined from bony landmarks and the scapulothoracic kinematic constraints. Independent from one another, they uniquely characterise the shoulder motion. A humanoid mechanism is then proposed with identical kinematic properties. It is then shown how minimal coordinates can be obtained for this mechanism and how the coordinates simplify both the motion-planning task and trajectory-tracking control. Lastly, the coordinates are also shown to have an application in the field of biomechanics where they can be used to model the scapulohumeral rhythm.

Apnea-like suppression of respiratory motion: First evaluation in radiotherapy.

BACKGROUND AND PURPOSE: Compensation for respiratory motion is needed while administering radiotherapy (RT) to tumors that are moving with respiration to reduce the amount of irradiated normal tissues and potentially decrease radiation-induced collateral damages. The purpose of this study was to test a new ventilation system designed to induce apnea-like suppression of respiratory motion and allow long enough breath hold durations to deliver complex RT. MATERIAL AND METHODS: The High Frequency Percussive Ventilation system was initially tested in a series of 10 volunteers and found to be well tolerated, allowing a median breath hold duration of 11.6min (range 3.9-16.5min). An evaluation of this system was subsequently performed in 4 patients eligible for adjuvant breast 3D conformal RT, for lung stereotactic body RT (SBRT), lung volumetric modulated arc therapy (VMAT), and VMAT for palliative pleural metastases. RESULTS: When compared to free breathing (FB) and maximal inspiration (MI) gating, this Percussion Assisted RT (PART) offered favorable dose distribution profiles in 3 out of the 4 patients tested. PART was applied in these 3 patients with good tolerance, without breaks during the "beam on time period" throughout the overall courses of RT. The mean duration of the apnea-like breath hold that was necessary for delivering all the RT fractions was 7.61min (SD=2.3). CONCLUSIONS: This first clinical implementation of PART was found to be feasible, tolerable and offers new opportunities in the field of RT for suppressing respiratory motion.

Strategies to evaluate the impact of rectal volume on prostate motion during three-dimensional conformal radiotherapy for prostate cancer

Abstract Objective: To evaluate the rectal volume influence on prostate motion during three-dimensional conformal radiotherapy (3D-CRT) for prostate cancer. Materials and Methods: Fifty-one patients with prostate cancer underwent a series of three computed tomography scans including an initial planning scan and two subsequent scans during 3D-CRT. The organs of interest were outlined. The prostate contour was compared with the initial CT images considering the anterior, posterior, superior, inferior and lateral edges of the organ. Variations in the anterior limits and volume of the rectum were assessed and correlated with prostate motion in the anteroposterior direction. Results: The maximum range of prostate motion was observed in the superoinferior direction, followed by the anteroposterior direction. A significant correlation was observed between prostate motion and rectal volume variation ( p = 0.037). A baseline rectal volume superior to 70 cm3 had a significant influence on the prostate motion in the anteroposterior direction ( p = 0.045). Conclusion: The present study showed a significant interfraction motion of the prostate during 3D-CRT with greatest variations in the superoinferior and anteroposterior directions, and that a large rectal volume influences the prostate motion with a cutoff value of 70 cm3. Therefore, the treatment of patients with a rectal volume > 70 cm3 should be re-planned with appropriate rectal preparation.

Visual SLAM for 3D large-scale seabed acquisition employing underwater vehicles

This paper presents a novel technique to align partial 3D reconstructions of the seabed acquired by a stereo camera mounted on an autonomous underwater vehicle. Vehicle localization and seabed mapping is performed simultaneously by means of an Extended Kalman Filter. Passive landmarks are detected on the images and characterized considering 2D and 3D features. Landmarks are re-observed while the robot is navigating and data association becomes easier but robust. Once the survey is completed, vehicle trajectory is smoothed by a Rauch-Tung-Striebel filter obtaining an even better alignment of the 3D views and yet a large-scale acquisition of the seabed