Characteristic Changes of the Stance-Phase Plantar Pressure Curve When Walking Uphill and Downhill: Cross-Sectional Study.

BACKGROUND: Monitoring of gait patterns by insoles is popular to study behavior and activity in the daily life of people and throughout the rehabilitation process of patients. Live data analyses may improve personalized prevention and treatment regimens, as well as rehabilitation. The M-shaped plantar pressure curve during the stance phase is mainly defined by the loading and unloading slope, 2 maxima, 1 minimum, as well as the force during defined periods. When monitoring gait continuously, walking uphill or downhill could affect this curve in characteristic ways. OBJECTIVE: For walking on a slope, typical changes in the stance phase curve measured by insoles were hypothesized. METHODS: In total, 40 healthy participants of both sexes were fitted with individually calibrated insoles with 16 pressure sensors each and a recording frequency of 100 Hz. Participants walked on a treadmill at 4 km/h for 1 minute in each of the following slopes: -20%, -15%, -10%, -5%, 0%, 5%, 10%, 15%, and 20%. Raw data were exported for analyses. A custom-developed data platform was used for data processing and parameter calculation, including step detection, data transformation, and normalization for time by natural cubic spline interpolation and force (proportion of body weight). To identify the time-axis positions of the desired maxima and minimum among the available extremum candidates in each step, a Gaussian filter was applied (σ=3, kernel size 7). Inconclusive extremum candidates were further processed by screening for time plausibility, maximum or minimum pool filtering, and monotony. Several parameters that describe the curve trajectory were computed for each step. The normal distribution of data was tested by the Kolmogorov-Smirnov and Shapiro-Wilk tests. RESULTS: Data were normally distributed. An analysis of variance with the gait parameters as dependent and slope as independent variables revealed significant changes related to the slope for the following parameters of the stance phase curve: the mean force during loading and unloading, the 2 maxima and the minimum, as well as the loading and unloading slope (all P<.001). A simultaneous increase in the loading slope, the first maximum and the mean loading force combined with a decrease in the mean unloading force, the second maximum, and the unloading slope is characteristic for downhill walking. The opposite represents uphill walking. The minimum had its peak at horizontal walking and values dropped when walking uphill and downhill alike. It is therefore not a suitable parameter to distinguish between uphill and downhill walking. CONCLUSIONS: While patient-related factors, such as anthropometrics, injury, or disease shape the stance phase curve on a longer-term scale, walking on slopes leads to temporary and characteristic short-term changes in the curve trajectory.

Spherically symmetric volume elements as basis functions for image reconstructions in computed laminography.

BACKGROUND: Laminography is a tomographic technique that allows three-dimensional imaging of flat and elongated objects that stretch beyond the extent of a reconstruction volume. Laminography images can be reconstructed using iterative algorithms based on the Kaczmarz method. OBJECTIVE: This study aims to develop and demonstrate a new reconstruction algorithm that may provide superior image reconstruction quality for this challenged imaging application. METHODS: The images are initially represented using the coefficients over basis functions, which are typically piecewise constant functions (voxels). By replacing voxels with spherically symmetric volume elements (blobs) based on the generalized Kaiser-Bessel window functions, the images are reconstructed using this new adapted version of the algebraic image reconstruction technique. RESULTS: Band-limiting properties of blob functions are beneficial particular in the case of noisy projections and with only a limited number of available projections. Study showed that using blob basis functions improved full-width-at-half-maximum resolution from 10.2±1.0 to 9.9±0.9 (p < 0.001). Signal-to-noise ratio also improved from 16.1 to 31.0. The increased computational demand per iteration was compensated by using a faster convergence rate, such that the overall performance is approximately identical for blobs and voxels. CONCLUSIONS: Despite the higher complexity, tomographic reconstruction from computed laminography data should be implemented using blob basis functions, especially if noisy data is expected.

Progressive Stochastic Reconstruction Technique (PSRT) for cryo electron tomography.

Cryo Electron Tomography (cryoET) plays an essential role in Structural Biology, as it is the only technique that allows to study the structure of large macromolecular complexes in their close to native environment in situ. The reconstruction methods currently in use, such as Weighted Back Projection (WBP) or Simultaneous Iterative Reconstruction Technique (SIRT), deliver noisy and low-contrast reconstructions, which complicates the application of high-resolution protocols, such as Subtomogram Averaging (SA). We propose a Progressive Stochastic Reconstruction Technique (PSRT) - a novel iterative approach to tomographic reconstruction in cryoET based on Monte Carlo random walks guided by Metropolis-Hastings sampling strategy. We design a progressive reconstruction scheme to suit the conditions present in cryoET and apply it successfully to reconstructions of macromolecular complexes from both synthetic and experimental datasets. We show how to integrate PSRT into SA, where it provides an elegant solution to the region-of-interest problem and delivers high-contrast reconstructions that significantly improve template-based localization without any loss of high-resolution structural information. Furthermore, the locality of SA is exploited to design an importance sampling scheme which significantly speeds up the otherwise slow Monte Carlo approach. Finally, we design a new memory efficient solution for the specimen-level interior problem of cryoET, removing all associated artifacts.

Marker Detection in Electron Tomography: A Comparative Study.

We conducted a comparative study of three widely used algorithms for the detection of fiducial markers in electron microscopy images. The algorithms were applied to four datasets from different sources. For the purpose of obtaining comparable results, we introduced figures of merit and implemented all three algorithms in a unified code base to exclude software-specific differences. The application of the algorithms revealed that none of the three algorithms is superior to the others in all cases. This leads to the conclusion that the choice of a marker detection algorithm highly depends on the properties of the dataset to be analyzed, even within the narrowed domain of electron tomography.

Matched Backprojection Operator for Combined Scanning Transmission Electron Microscopy Tilt- and Focal Series.

Combined tilt- and focal series scanning transmission electron microscopy is a recently developed method to obtain nanoscale three-dimensional (3D) information of thin specimens. In this study, we formulate the forward projection in this acquisition scheme as a linear operator and prove that it is a generalization of the Ray transform for parallel illumination. We analytically derive the corresponding backprojection operator as the adjoint of the forward projection. We further demonstrate that the matched backprojection operator drastically improves the convergence rate of iterative 3D reconstruction compared to the case where a backprojection based on heuristic weighting is used. In addition, we show that the 3D reconstruction is of better quality.

Combined scanning transmission electron microscopy tilt- and focal series.

In this study, a combined tilt- and focal series is proposed as a new recording scheme for high-angle annular dark-field scanning transmission electron microscopy (STEM) tomography. Three-dimensional (3D) data were acquired by mechanically tilting the specimen, and recording a through-focal series at each tilt direction. The sample was a whole-mount macrophage cell with embedded gold nanoparticles. The tilt-focal algebraic reconstruction technique (TF-ART) is introduced as a new algorithm to reconstruct tomograms from such combined tilt- and focal series. The feasibility of TF-ART was demonstrated by 3D reconstruction of the experimental 3D data. The results were compared with a conventional STEM tilt series of a similar sample. The combined tilt- and focal series led to smaller "missing wedge" artifacts, and a higher axial resolution than obtained for the STEM tilt series, thus improving on one of the main issues of tilt series-based electron tomography.

Effects of age, body height, body weight, body mass index and handgrip strength on the trajectory of the plantar pressure stance-phase curve of the gait cycle.

The analysis of gait patterns and plantar pressure distributions via insoles is increasingly used to monitor patients and treatment progress, such as recovery after surgeries. Despite the popularity of pedography, also known as baropodography, characteristic effects of anthropometric and other individual parameters on the trajectory of the stance phase curve of the gait cycle have not been previously reported. We hypothesized characteristic changes of age, body height, body weight, body mass index and handgrip strength on the plantar pressure curve trajectory during gait in healthy participants. Thirty-seven healthy women and men with an average age of 43.65 ± 17.59 years were fitted with Moticon OpenGO insoles equipped with 16 pressure sensors each. Data were recorded at a frequency of 100 Hz during walking at 4 km/h on a level treadmill for 1 minute. Data were processed via a custom-made step detection algorithm. The loading and unloading slopes as well as force extrema-based parameters were computed and characteristic correlations with the targeted parameters were identified via multiple linear regression analysis. Age showed a negative correlation with the mean loading slope. Body height correlated with Fmeanload and the loading slope. Body weight and the body mass index correlated with all analyzed parameters, except the loading slope. In addition, handgrip strength correlated with changes in the second half of the stance phase and did not affect the first half, which is likely due to stronger kick-off. However, only up to 46% of the variability can be explained by age, body weight, height, body mass index and hand grip strength. Thus, further factors must affect the trajectory of the gait cycle curve that were not considered in the present analysis. In conclusion, all analyzed measures affect the trajectory of the stance phase curve. When analyzing insole data, it might be useful to correct for the factors that were identified by using the regression coefficients presented in this paper.

Temporal Coherence-Based Distributed Ray Tracing of Massive Scenes.

Distributed ray tracing algorithms are widely used when rendering massive scenes, where data utilization and load balancing are the keys to improving performance. One essential observation is that rays are temporally coherent, which indicates that temporal information can be used to improve computational efficiency. In this paper, we use temporal coherence to optimize the performance of distributed ray tracing. First, we propose a temporal coherence-based scheduling algorithm to guide the task/data assignment and scheduling. Then, we propose a virtual portal structure to predict the radiance of rays based on the previous frame, and send the rays with low radiance to a precomputed simplified model for further tracing, which can dramatically reduce the traversal complexity and the overhead of network data transmission. The approach was validated on scenes of sizes up to 355 GB. Our algorithm can achieve a speedup of up to 81% compared to previous algorithms, with a very small mean squared error.

A GPU-based caching strategy for multi-material linear elastic FEM on regular grids.

In this study, we present a novel strategy to the method of finite elements (FEM) of linear elastic problems of very high resolution on graphic processing units (GPU). The approach exploits regularities in the system matrix that occur in regular hexahedral grids to achieve cache-friendly matrix-free FEM. The node-by-node method lies in the class of block-iterative Gauss-Seidel multigrid solvers. Our method significantly improves convergence times in cases where an ordered distribution of distinct materials is present in the dataset. The method was evaluated on three real world datasets: An aluminum-silicon (AlSi) alloy and a dual phase steel material sample, both captured by scanning electron tomography, and a clinical computed tomography (CT) scan of a tibia. The caching scheme leads to a speed-up factor of ×2-×4 compared to the same code without the caching scheme. Additionally, it facilitates the computation of high-resolution problems that cannot be computed otherwise due to memory consumption.

How should a fixed budget of dwell time be spent in scanning electron microscopy to optimize image quality?

In scanning electron microscopy, the achievable image quality is often limited by a maximum feasible acquisition time per dataset. Particularly with regard to three-dimensional or large field-of-view imaging, a compromise must be found between a high amount of shot noise, which leads to a low signal-to-noise ratio, and excessive acquisition times. Assuming a fixed acquisition time per frame, we compared three different strategies for algorithm-assisted image acquisition in scanning electron microscopy. We evaluated (1) raster scanning with a reduced dwell time per pixel followed by a state-of-the-art Denoising algorithm, (2) raster scanning with a decreased resolution in conjunction with a state-of-the-art Super Resolution algorithm, and (3) a sparse scanning approach where a fixed percentage of pixels is visited by the beam in combination with state-of-the-art inpainting algorithms. Additionally, we considered increased beam currents for each of the strategies. The experiments showed that sparse scanning using an appropriate reconstruction technique was superior to the other strategies.

Exemplar-based inpainting as a solution to the missing wedge problem in electron tomography.

A new method for dealing with incomplete projection sets in electron tomography is proposed. The approach is inspired by exemplar-based inpainting techniques in image processing and heuristically generates data for missing projection directions. The method has been extended to work on three dimensional data. In general, electron tomography reconstructions suffer from elongation artifacts along the beam direction. These artifacts can be seen in the corresponding Fourier domain as a missing wedge. The new method synthetically generates projections for these missing directions with the help of a dictionary based approach that is able to convey both structure and texture at the same time. It constitutes a preprocessing step that can be combined with any tomographic reconstruction algorithm. The new algorithm was applied to phantom data, to a real electron tomography data set taken from a catalyst, as well as to a real dataset containing solely colloidal gold particles. Visually, the synthetic projections, reconstructions, and corresponding Fourier power spectra showed a decrease of the typical missing wedge artifacts. Quantitatively, the inpainting method is capable to reduce missing wedge artifacts and improves tomogram quality with respect to full width half maximum measurements.

A Quality-Centered Analysis of Eye Tracking Data in Foveated Rendering.

This work presents the analysis of data recorded by an eye tracking device in the course of evaluating a foveated rendering approach for head-mounted displays (HMDs). Foveated rendering methods adapt the image synthesis process to the user's gaze and exploiting the human visual system's limitations to increase rendering performance. Especially, foveated rendering has great potential when certain requirements have to be fulfilled, like low-latency rendering to cope with high display refresh rates. This is crucial for virtual reality (VR), as a high level of immersion, which can only be achieved with high rendering performance and also helps to reduce nausea, is an important factor in this field. We put things in context by first providing basic information about our rendering system, followed by a description of the user study and the collected data. This data stems from fixation tasks that subjects had to perform while being shown fly-through sequences of virtual scenes on an HMD. These fixation tasks consisted of a combination of various scenes and fixation modes. Besides static fixation targets, moving targets on randomized paths as well as a free focus mode were tested. Using this data, we estimate the precision of the utilized eye tracker and analyze the participants' accuracy in focusing the displayed fixation targets. Here, we also take a look at eccentricity-dependent quality ratings. Comparing this information with the users' quality ratings given for the displayed sequences then reveals an interesting connection between fixation modes, fixation accuracy and quality ratings.

On geometric artifacts in cryo electron tomography.

Single-tilt scheme is nowadays the prevalent acquisition geometry in electron tomography and subtomogram averaging experiments. Being an incomplete scheme that induces ill-posedness in the sense of the X-ray or Radon transform inverse problem, it introduces a number of artifacts that directly influence the quality of tomographic reconstructions. Though individually described by different authors before, a systematic study of these acquisition geometry-related artifacts in one place and across representative set of reconstruction methods has not been, to our knowledge, performed before. Moreover, the effects of these artifacts on the reconstructed density are sometimes misinterpreted, attributing them to the wrong cause, especially if their effects accumulate. In this work, we systematically study the major artifacts of single-tilt geometry known as the missing wedge (incomplete projection set problem), the missing information and the specimen-level interior problem (long-object problem). First, we illustratively describe, using a unified terminology, how and why these artifacts arise and when they can be avoided. Next, we describe the effects of these artifacts on the reconstructions across all major classes of reconstruction methods, including newly-appeared methods like the Iterative Nonuniform fast Fourier transform based Reconstruction method (INFR) and the Progressive Stochastic Reconstruction Technique (PSRT). Finally, we draw conclusions and recommendations on numerous points, especially regarding the mutual influence of the geometric artifacts, ability of different reconstruction methods to suppress them as well as implications to the interpretation of both electron tomography and subtomogram averaging experiments.

Feature Adaptive Sampling for Scanning Electron Microscopy.

A new method for the image acquisition in scanning electron microscopy (SEM) was introduced. The method used adaptively increased pixel-dwell times to improve the signal-to-noise ratio (SNR) in areas of high detail. In areas of low detail, the electron dose was reduced on a per pixel basis, and a-posteriori image processing techniques were applied to remove the resulting noise. The technique was realized by scanning the sample twice. The first, quick scan used small pixel-dwell times to generate a first, noisy image using a low electron dose. This image was analyzed automatically, and a software algorithm generated a sparse pattern of regions of the image that require additional sampling. A second scan generated a sparse image of only these regions, but using a highly increased electron dose. By applying a selective low-pass filter and combining both datasets, a single image was generated. The resulting image exhibited a factor of ≈3 better SNR than an image acquired with uniform sampling on a Cartesian grid and the same total acquisition time. This result implies that the required electron dose (or acquisition time) for the adaptive scanning method is a factor of ten lower than for uniform scanning.

The Ettention software package.

We present a novel software package for the problem "reconstruction from projections" in electron microscopy. The Ettention framework consists of a set of modular building-blocks for tomographic reconstruction algorithms. The well-known block iterative reconstruction method based on Kaczmarz algorithm is implemented using these building-blocks, including adaptations specific to electron tomography. Ettention simultaneously features (1) a modular, object-oriented software design, (2) optimized access to high-performance computing (HPC) platforms such as graphic processing units (GPU) or many-core architectures like Xeon Phi, and (3) accessibility to microscopy end-users via integration in the IMOD package and eTomo user interface. We also provide developers with a clean and well-structured application programming interface (API) that allows for extending the software easily and thus makes it an ideal platform for algorithmic research while hiding most of the technical details of high-performance computing.

Faster isosurface ray tracing using implicit KD-trees.

The visualization of high-quality isosurfaces at interactive rates is an important tool in many simulation and visualization applications. Today, isosurfaces are most often visualized by extracting a polygonal approximation that is then rendered via graphics hardware or by using a special variant of preintegrated volume rendering. However, these approaches have a number of limitations in terms of the quality of the isosurface, lack of performance for complex data sets, or supported shading models. An alternative isosurface rendering method that does not suffer from these limitations is to directly ray trace the isosurface. However, this approach has been much too slow for interactive applications unless massively parallel shared-memory supercomputers have been used. In this paper, we implement interactive isosurface ray tracing on commodity desktop PCs by building on recent advances in real-time ray tracing of polygonal scenes and using those to improve isosurface ray tracing performance as well. The high performance and scalability of our approach will be demonstrated with several practical examples, including the visualization of highly complex isosurface data sets, the interactive rendering of hybrid polygonal/isosurface scenes, including high-quality ray traced shading effects, and even interactive global illumination on isosurfaces.

XML3D and Xflow: combining declarative 3D for the Web with generic data flows.

Researchers have combined XML3D, which provides declarative, interactive 3D scene descriptions based on HTML5, with Xflow, a language for declarative, high-performance data processing. The result lets Web developers combine a 3D scene graph with data flows for dynamic meshes, animations, image processing, and postprocessing.